bioRxiv Channel: Stowers Institute for Medical Research
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Phylogenetic tree inference from local gene content
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https://biorxiv.org/content/10.1101/017699v1?rss=1
Galina GlazkoMichael GensheimerArcady Mushegian2015-04-08doi:10.1101/017699Cold Spring Harbor Laboratory Press2015-04-08
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Crucial Roles of the Arp2/3 Complex during Mammalian Corticogenesis
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https://biorxiv.org/content/10.1101/026161v1?rss=1
Pei-Shan WangFu-Sheng ChouFengli GuoPraveen SuraneniSheng XiaSree RamachandranRong Li2015-09-06doi:10.1101/026161Cold Spring Harbor Laboratory Press2015-09-06
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Drosophila poised enhancers are generated during tissue patterning with the help of repression
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https://biorxiv.org/content/10.1101/052142v1?rss=1
Nina KoeneckeJeff JohnstonQiye HeJulia Zeitlinger2016-05-07doi:10.1101/052142Cold Spring Harbor Laboratory Press2016-05-07
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Robust Gap Repair in the Contractile Ring Ensures Timely Completion of Cytokinesis
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https://biorxiv.org/content/10.1101/052704v1?rss=1
Ana Marta SilvaDaniel Sampaio OsorioAntonio Jose PereiraHelder MaiatoInes Mendes Mendes PintoBoris RubinsteinReto GassmannIvo Andreas A TelleyAna Xavier de Carvalho2016-05-21doi:10.1101/052704Cold Spring Harbor Laboratory Press2016-05-21
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Host Vesicle Fusion Proteins VAPB, Rab11b and Rab18 Contribute to HSV-1 Infectivity by Facilitating Egress through the Nuclear Membrane
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https://biorxiv.org/content/10.1101/088633v1?rss=1
Saiz-Ros, N.Czapiewski, R.Stevenson, A.Epifano, I.Swanson, S. K.McElwee, M.Vijayakrishnan, S.Richardson, C. A.Dixon, C.Pytowski, L.Goldberg, M. W.Florens, L.Graham, S. V.Schirmer, E. C.2016-11-19doi:10.1101/088633Cold Spring Harbor Laboratory Press2016-11-19
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A new coactivator complex required for retinoic acid-dependent regulation of embryonic symmetry
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https://biorxiv.org/content/10.1101/089201v1?rss=1
Vilhais-Neto, G. C.Fournier, M.Plassat, J.-L.Sardiu, M. E.Saraf, A.Garnier, J.-M.Maruhashi, M.Florens, L.Washburn, M. P.Pourquie, O.2016-11-22doi:10.1101/089201Cold Spring Harbor Laboratory Press2016-11-22
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Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets
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https://biorxiv.org/content/10.1101/092296v1?rss=1
De Kumar, B.Parker, H. J.Paulson, A.Parrish, M. E.Pushel, I.Slaughter, B. D.Unruh, J. R.Zeitlinger, J. B.Krumlauf, R.2016-12-07doi:10.1101/092296Cold Spring Harbor Laboratory Press2016-12-07
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PHRED-1 Is A Divergent Neurexin-1 Homolog That Organizes Muscle Fibers And Patterns Organs During Regeneration
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https://biorxiv.org/content/10.1101/131789v1?rss=1
Adler, C. E.Sanchez Alvarado, A.2017-04-28doi:10.1101/131789Cold Spring Harbor Laboratory Press2017-04-28
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The Human Cytoplasmic Dynein Interactome Reveals Novel Activators Of Motility
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https://biorxiv.org/content/10.1101/143743v1?rss=1
Redwine, W. B.DeSantis, M. E.Hollyer, I.Htet, Z. M.Tran, P. T.Swanson, S. K.Florens, L.Washburn, M. P.Reck-Peterson, S. L.2017-05-30doi:10.1101/143743Cold Spring Harbor Laboratory Press2017-05-30
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Insulin resistance in cavefish as an adaptation to a nutrient-limited environment
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https://biorxiv.org/content/10.1101/179069v1?rss=1
Aspiras, A.Riddle, M.Gaudenz, K.Peuss, R.Sung, J.Martineau, B.Peavey, M.Box, A.Tabin, J. A.McGaugh, S.Borowsky, R.Tabin, C. J.Rohner, N.2017-08-21doi:10.1101/179069Cold Spring Harbor Laboratory Press2017-08-21
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Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea
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https://biorxiv.org/content/10.1101/179986v1?rss=1
Cheng, L.-C.Tu, K. C.Seidel, C. W.Robb, S. M. C.Guo, F.Sanchez Alvarado, A.2017-08-24doi:10.1101/179986Cold Spring Harbor Laboratory Press2017-08-24
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NECAPs are negative regulators of the AP2 clathrin adaptor complex
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https://biorxiv.org/content/10.1101/192898v1?rss=1
Beacham, G. M.Partlow, E. A.Lange, J. J.Hollopeter, G.2017-09-22doi:10.1101/192898Cold Spring Harbor Laboratory Press2017-09-22
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A Holistic Analysis of the Intestinal Stem Cell Niche Network
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https://biorxiv.org/content/10.1101/2019.12.12.871756v1?rss=1
Hansen, D. M.Meneses Giles, P. I.He, X. C.Chen, S.Paulson, A.Dekaney, C. M.Wang, J.Hu, D.Venkatraman, A.Kim, W.Kaddis, J.Olack, B. J.Dunn, J. C. Y.Kuo, C.Henning, S.Hanash, A. M.Houchen, C. W.Lynch, J.Martin, M. G.Niland, J. C.Stelzner, M.Wong, M.Wang, T. C.Yu, J.Yan, K.Li, L.2019-12-12doi:10.1101/2019.12.12.871756Cold Spring Harbor Laboratory Press2019-12-12
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Diet-induced loss of adipose Hexokinase 2 triggers hyperglycemia
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https://biorxiv.org/content/10.1101/2019.12.28.887794v1?rss=1
Shimobayashi, M.Shetty, S.Frei, I. C.Wölnerhanssen, B. K.Weissenberger, D.Dietz, N.Thomas, A.Ritz, D.Meyer-Gerspach, A. C.Maier, T.Hay, N.Peterli, R.Rohner, N.Hall, M. N.2019-12-28doi:10.1101/2019.12.28.887794Cold Spring Harbor Laboratory Press2019-12-28
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CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos
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https://biorxiv.org/content/10.1101/2020.01.13.904763v1?rss=1
Kushawah, G.Abugattas-Nunez del Prado, J.Martinez-Morales, J. R.DeVore, M.Guelfo, J. R.Brannan, E. O.Wang, W.Corbin, T. J.Moran, A. M.Sanchez Alvarado, A.Malaga-Trillo, E.Takacs, C. M.Bazzini, A. A.Moreno-Mateos, M. A.2020-01-14doi:10.1101/2020.01.13.904763Cold Spring Harbor Laboratory Press2020-01-14
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Repeated evolution of circadian clock dysregulation in cavefish populations
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https://biorxiv.org/content/10.1101/2020.01.14.906628v1?rss=1
Mack, K. L.Jaggard, J. B.Persons, J. L.Passow, C. N.Stanhope, B. A.Ferrufino, E.Tsuchiya, D.Smith, S. E.Slaughter, B. D.Kowalko, J. E.Rohner, N.Keene, A. C.McGaugh, S. E.2020-01-15doi:10.1101/2020.01.14.906628Cold Spring Harbor Laboratory Press2020-01-15
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Hedgehog signaling is required for endomesodermal patterning and germ cell development in Nematostella vectensis
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https://biorxiv.org/content/10.1101/2020.01.15.907238v1?rss=1
Gibson, M. C.Chen, C.-Y.McKinney, S. A.Ellington, L. R.2020-01-15doi:10.1101/2020.01.15.907238Cold Spring Harbor Laboratory Press2020-01-15
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Acquisition of Innate Odor Preference Depends on Spontaneous and Experiential Activities During Critical Period
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https://biorxiv.org/content/10.1101/2020.01.28.923722v1?rss=1
Qiu, Q.Wu, Y.Ma, L.Yu, C. R.2020-01-29doi:10.1101/2020.01.28.923722Cold Spring Harbor Laboratory Press2020-01-29
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Encoding Innately Recognized Odors via a Generalized Population Code
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https://biorxiv.org/content/10.1101/2020.01.28.923748v1?rss=1
Qiu, Q.Wu, Y.Ma, L.Yu, C. R.2020-01-29doi:10.1101/2020.01.28.923748Cold Spring Harbor Laboratory Press2020-01-29
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The wtf4 meiotic driver utilizes controlled protein aggregation to generate selective cell death
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https://biorxiv.org/content/10.1101/2020.02.05.935874v1?rss=1
Nuckolls, N. L.Mok, A. C.Lange, J. J.Yi, K.Kandola, T. S.Hunn, A. M.McCroskey, S.Snyder, J. L.Bravo Nunez, M. A.McClain, M.McKinney, S. A.Wood, C.Halfmann, R.Zanders, S. E.2020-02-07doi:10.1101/2020.02.05.935874Cold Spring Harbor Laboratory Press2020-02-07
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Transcriptome profiling of the branchial arches reveals cell type composition and a conserved signature of neural crest cell invasion
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https://biorxiv.org/content/10.1101/2020.02.28.969915v1?rss=1
Morrison, J. A.McLennan, R.Teddy, J. M.Scott, A. R.Kasemeier-Kulesa, J. C.Gogol, M. M.Kulesa, P. M.2020-02-28doi:10.1101/2020.02.28.969915Cold Spring Harbor Laboratory Press2020-02-28
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Canonical Wnt signaling Is Involved in Anterior Regeneration of the Annelid Aeolosoma viride
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https://biorxiv.org/content/10.1101/2020.03.01.972448v1?rss=1
Chen, C.-Y.Yueh, W.-T.Chen, J.-H.2020-03-02doi:10.1101/2020.03.01.972448Cold Spring Harbor Laboratory Press2020-03-02
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Feeding-dependent tentacle development in the sea anemone Nematostella vectensis
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https://biorxiv.org/content/10.1101/2020.03.12.985168v1?rss=1
Ikmi, A.Steenbergen, P. J.Anzo, M.McMullen, M. R.Stokkermans, A.Ellington, L. R.Gibson, M. C.2020-03-12doi:10.1101/2020.03.12.985168Cold Spring Harbor Laboratory Press2020-03-12
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Identification of Stem Cells from Large Cell Populations with Topological Scoring
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https://biorxiv.org/content/10.1101/2020.04.08.032102v1?rss=1
Sardiu, M.Box, A.Haug, J.Washburn, M.2020-04-09doi:10.1101/2020.04.08.032102Cold Spring Harbor Laboratory Press2020-04-09
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Driving Integrative Structural Modeling with Serial Capture Affinity Purification
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https://biorxiv.org/content/10.1101/2020.04.08.032151v1?rss=1
Liu, X.Zhang, Y.Wen, Z.Hao, Y.Banks, C.Lange, J. J.Slaughter, B.Unruh, J.Florens, L.Abmayr, S.Workman, J.Washburn, M.2020-04-09doi:10.1101/2020.04.08.032151Cold Spring Harbor Laboratory Press2020-04-09
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Atypical meiosis can be adaptive in outcrossed S. pombe due to wtf meiotic drivers
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https://biorxiv.org/content/10.1101/2020.04.28.066035v1?rss=1
Bravo Nunez, M. A.Sabbarini, I. M.Eide, L. E.Unckless, R. L.Zanders, S. E.2020-05-01doi:10.1101/2020.04.28.066035Cold Spring Harbor Laboratory Press2020-05-01
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Preferred Conformations in the Intrinsically Disordered Region of Human CPEB3 Explain its Role in Memory Consolidation
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https://biorxiv.org/content/10.1101/2020.05.12.091587v1?rss=1
Ramirez de Mingo, D.Pantoja-Uceda, D.Hervas, R.Carrion-Vazquez, M.Laurents, D. V.2020-05-14doi:10.1101/2020.05.12.091587Cold Spring Harbor Laboratory Press2020-05-14
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Superior Colliculus-Projected GABAergic Retinal Ganglion Cells Mediate Looming-Evoked Flight Response
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https://biorxiv.org/content/10.1101/2020.05.14.090167v1?rss=1
Luo, X.Cai, D.Shen, K.Deng, Q.Lei, X.Jin, S.Zeng, W.-B.Li, H.Xu, F.Huang, L.Ren, C.Luo, M.-H.Xie, T.Shen, Y.2020-05-16doi:10.1101/2020.05.14.090167Cold Spring Harbor Laboratory Press2020-05-16
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Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold
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https://biorxiv.org/content/10.1101/2020.05.19.103804v1?rss=1
Hervas, R.Fernandez-Ramirez, M. d. C.Galera-Prat, A.Suzuki, M.Nagai, Y.Bruix, M.Menendez, M.Laurents, D. V.Carrion-Vazquez, M.2020-05-21doi:10.1101/2020.05.19.103804Cold Spring Harbor Laboratory Press2020-05-21
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Regulation of SETD2 stability by its intrinsically disordered regions maintains the fidelity of H3K36me3 deposition
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https://biorxiv.org/content/10.1101/2020.05.21.100552v1?rss=1
Bhattacharya, S.Zhang, N.Li, H.Workman, J.2020-05-22doi:10.1101/2020.05.21.100552Cold Spring Harbor Laboratory Press2020-05-22
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Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase
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https://biorxiv.org/content/10.1101/2020.05.22.110296v1?rss=1
Geymonat, M.Peng, Q.Guo, Z.Yu, Z.Unruh, J.Jaspersen, S.Segal, M.2020-05-22doi:10.1101/2020.05.22.110296Cold Spring Harbor Laboratory Press2020-05-22
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DNA methylation mediated downregulation of histone H3 variant H3.3 affects cell proliferation contributing to the development of HCC
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https://biorxiv.org/content/10.1101/2020.05.23.112516v1?rss=1
Gupta, S.Reddy, D.Bhattacharya, S.Shah, S.Rashid, M.2020-05-26doi:10.1101/2020.05.23.112516Cold Spring Harbor Laboratory Press2020-05-26
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Molecular determinants of liquid demixing and amyloidogenesis in human CPEB3
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https://biorxiv.org/content/10.1101/2020.06.02.129783v1?rss=1
Ramirez de Mingo, D.Lopez-Garcia, P.Hervas, R.Laurents, D. V.Carrion-Vazquez, M.2020-06-03doi:10.1101/2020.06.02.129783Cold Spring Harbor Laboratory Press2020-06-03
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The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity
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https://biorxiv.org/content/10.1101/2020.06.02.130369v1?rss=1
Lee, J.Oh, S.Bhattacharya, S.Zhang, Y.Florens, L.Washburn, M. P.Workman, J. L.2020-06-02doi:10.1101/2020.06.02.130369Cold Spring Harbor Laboratory Press2020-06-02
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Identification of rare transient somatic cell states induced by injury and required for whole-body regeneration
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https://biorxiv.org/content/10.1101/2020.06.04.132753v1?rss=1
Benham-Pyle, B. W.Brewster, C. E.Kent, A. M.Mann, F. G.Chen, S.Scott, A. R.Box, A. C.Sanchez Alvarado, A.2020-06-05doi:10.1101/2020.06.04.132753Cold Spring Harbor Laboratory Press2020-06-05
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The role of gene dosage in budding yeast centrosome scaling and spontaneous diploidization
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https://biorxiv.org/content/10.1101/2020.06.04.133975v1?rss=1
Chen, J.Xiong, Z.Miller, D.Yu, Z.McCroskey, S.Bradford, W.Cavanaugh, A.Jaspersen, S. L.2020-06-04doi:10.1101/2020.06.04.133975Cold Spring Harbor Laboratory Press2020-06-04
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The disordered regions of SETD2 govern H3K36me3 deposition by regulating its proteasome-mediated decay
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https://biorxiv.org/content/10.1101/2020.06.05.137232v1?rss=1
Bhattacharya, S.Zhang, N.Li, H.Workman, J.2020-06-10doi:10.1101/2020.06.05.137232Cold Spring Harbor Laboratory Press2020-06-10
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The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain
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https://biorxiv.org/content/10.1101/2020.06.06.138156v1?rss=1
Bhattacharya, S.Levy, M. J.Zhang, N.Li, H.Florens, L.Washburn, M.Workman, J.2020-06-06doi:10.1101/2020.06.06.138156Cold Spring Harbor Laboratory Press2020-06-06
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Plasticity in parental effects confers rapid larval thermal tolerance in Nematostella vectensis
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https://biorxiv.org/content/10.1101/2020.06.15.153148v1?rss=1
Rivera, H. E.Chen, C.-Y.Gibson, M.Tarrant, A. M.2020-06-16doi:10.1101/2020.06.15.153148Cold Spring Harbor Laboratory Press2020-06-16
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A physicochemical model of odor sampling
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https://biorxiv.org/content/10.1101/2020.06.16.154807v1?rss=1
Gronowitz, M. E.Liu, A.Cleland, T. A.2020-06-17doi:10.1101/2020.06.16.154807Cold Spring Harbor Laboratory Press2020-06-17
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Tau amyloidogenesis begins with a loss of its conformational polymorphism
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https://biorxiv.org/content/10.1101/2020.06.18.158923v1?rss=1
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]]>Fernandez-Ramirez, M. d. C.Hervas, R.Menendez, M.Laurents, D. V.Carrion-Vazquez, M.2020-06-20doi:10.1101/2020.06.18.158923Cold Spring Harbor Laboratory Press2020-06-20
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Germline gene de-silencing by a transposon insertion is triggered by an altered landscape of local piRNA biogenesis
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https://biorxiv.org/content/10.1101/2020.06.26.173187v1?rss=1
Miller, D.Van Vaerenberghe, K.Li, A.Grantham, E. K.Cummings, C.Barragan, M.Egidy, R.Scott, A. R.Hall, K.Perera, A.Gilliland, W. D.Blumenstiel, J. P.2020-06-26doi:10.1101/2020.06.26.173187Cold Spring Harbor Laboratory Press2020-06-26
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SWR1-independent association of H2A.Z to the LINC complex promotes meiotic chromosome motion
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https://biorxiv.org/content/10.1101/2020.06.30.181016v1?rss=1
Gonzalez-Arranz, S.Gardner, J. M.Yu, Z.Patel, N. J.Heldrich, J.Santos, B.Carballo, J. A.Jaspersen, S.Hochwagen, A.San-Segundo, P. A.2020-07-01doi:10.1101/2020.06.30.181016Cold Spring Harbor Laboratory Press2020-07-01
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A new species of planarian flatworm from Mexico: Girardia guanajuatiensis
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https://biorxiv.org/content/10.1101/2020.07.01.183442v1?rss=1
Duncan, E. M.Nowotarski, S. H.Guerrero-Hernandez, C.Ross, E. J.D'Orazio, J. A.Clubes de Ciencia Mexico Workshop for Developmental Biology,McKinney, S. A.Guo, L.Sanchez Alvarado, A.2020-07-02doi:10.1101/2020.07.01.183442Cold Spring Harbor Laboratory Press2020-07-02
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A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.
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https://biorxiv.org/content/10.1101/2020.07.06.189654v1?rss=1
Warren, W. C.Boggs, T. E.Borowsky, R.Carlson, B. M.Ferrufino, E.Gross, J. B.Hiller, L.Hu, Z.Keene, A. C.Kenzior, A.Kowalko, J. E.Tomlinson, C.Kremitzki, M.Lemieux, M. E.Graves-Lindsay, T.McGaugh, S. E.Miller, J. T.Mommersteeg, M.Moran, R. L.Peuss, R.Rice, E.Riddle, M. R.Sifuentes-Romero, I.Stanhope, B. A.Tabin, C. J.Thakur, S.Yoshiyuki, Y.Rohner, N.2020-07-06doi:10.1101/2020.07.06.189654Cold Spring Harbor Laboratory Press2020-07-06
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TATA and paused promoters active in differentiated tissues have distinct expression characteristics
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https://biorxiv.org/content/10.1101/2020.07.15.196493v1?rss=1
Ramalingam, V.Natarajan, M.Johnston, J.Zeitlinger, J.2020-07-16doi:10.1101/2020.07.15.196493Cold Spring Harbor Laboratory Press2020-07-16
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High-throughput identification of nuclear envelope protein interactions in Schizosaccharomyces pombe using an arrayed membrane yeast-two hybrid library
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https://biorxiv.org/content/10.1101/2020.07.29.227819v1?rss=1
Varberg, J. M.Gardner, J. M.McCroskey, S.Saravanan, S.Bradford, W. D.Jaspersen, S. L.2020-07-30doi:10.1101/2020.07.29.227819Cold Spring Harbor Laboratory Press2020-07-30
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The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms
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https://biorxiv.org/content/10.1101/2020.08.14.251579v1?rss=1
Sanchez Alvarado, A.Nowotarski, S.Davies, E.Robb, S.Ross, E.Matentzoglu, N.Doddihal, V.Mir, M.McClain, M.2020-08-14doi:10.1101/2020.08.14.251579Cold Spring Harbor Laboratory Press2020-08-14
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Genome-wide analysis of cis-regulatory changes in the metabolic adaptation of cavefish
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https://biorxiv.org/content/10.1101/2020.08.27.270371v1?rss=1
Krishnan, J.Seidel, C.Zhang, N.VanCampen, J.Peuss, R.Xiong, S.Kenzior, A.Li, H.Conaway, J. W.Rohner, N.2020-08-28doi:10.1101/2020.08.27.270371Cold Spring Harbor Laboratory Press2020-08-28
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Hmx gene conservation identifies the evolutionary origin of vertebrate cranial ganglia
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https://biorxiv.org/content/10.1101/2020.09.07.281501v1?rss=1
Papadogiannis, V.Parker, H. J.Pennati, A.Patthey, C.Bronner, M. E.Shimeld, S. M.2020-09-07doi:10.1101/2020.09.07.281501Cold Spring Harbor Laboratory Press2020-09-07
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The structure, function, and evolution of a complete human chromosome 8
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https://biorxiv.org/content/10.1101/2020.09.08.285395v1?rss=1
Logsdon, G. A.Vollger, M. R.Hsieh, P.Mao, Y.Liskovykh, M. A.Koren, S.Nurk, S.Mercuri, L.Dishuck, P. C.Rhie, A.de Lima, L. G.Porubsky, D.Bzikadze, A. V.Kremitzki, M.Graves-Lindsay, T. A.Jain, C.Hoekzema, K.Murali, S. C.Munson, K. M.Baker, C.Sorenson, M.Lewis, A. M.Surti, U.Gerton, J. L.Larionov, V.Ventura, M.Miga, K. H.Phillippy, A. M.Eichler, E. E.2020-09-08doi:10.1101/2020.09.08.285395Cold Spring Harbor Laboratory Press2020-09-08
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Decellularization enables functional analysis of ECM remodeling in planarian regeneration
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https://biorxiv.org/content/10.1101/2020.09.11.293936v1?rss=1
Sonpho, E.Mann, F. G.Levy, M.Ross, E. J.Guerrero-Hernandez, C.Florens, L.Saraf, A.Doddihal, V.Ounjai, P.Sanchez Alvarado, A.2020-09-11doi:10.1101/2020.09.11.293936Cold Spring Harbor Laboratory Press2020-09-11
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Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
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https://biorxiv.org/content/10.1101/2020.09.24.311530v1?rss=1
Jing, Y.Montano, J. L.Levy, M. J.Lopez, J.Kung, P.-P.Richardson, P.Krajewski, K.Florens, L.Washburn, M.Meier, J. L.2020-09-25doi:10.1101/2020.09.24.311530Cold Spring Harbor Laboratory Press2020-09-25
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Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish
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https://biorxiv.org/content/10.1101/2020.09.27.314278v1?rss=1
O'Gorman, M.Thakur, S.Imrie, G.Moran, R.Duboue, E. R.Rohner, N.McGaugh, S. E.Keene, A. C.Kowalko, J. E.2020-09-27doi:10.1101/2020.09.27.314278Cold Spring Harbor Laboratory Press2020-09-27
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Untargeted Metabolomics of the Cavefish Astyanax mexicanus Reveals the Basis of Metabolic Strategies in Adaptation to Extreme Conditions
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https://biorxiv.org/content/10.1101/2020.10.27.358077v1?rss=1
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org.highwire.dtl.DTLVardef@bcaff5org.highwire.dtl.DTLVardef@1c40b89org.highwire.dtl.DTLVardef@1d17d69org.highwire.dtl.DTLVardef@80a483_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Metabolic resilience survivability under a variety of extreme conditions. Certain populations of cavefish have adaptations that cause increased appetite (1) and increased fat accumulation (2) (in cases where nutrients are plentiful, such as in lab-raised populations). These same populations also exhibit robust health and longevity (2, 3) and do not suffer ill-effects due to high levels of visceral fat and hyper-glycemia, both of which are features of most cave populations. However, visceral fat accumulation in cave populations is highly dependent on nutrient availability and is not displayed in wild-caught specimens (4). Thus, cavefish paradoxically appear to tolerate both extremely low and extremely high levels of triglycerides, glucose, and other energy storage metabolites. We argue that these differences can be reconciled under a hypothesis whereby the cave environment selects not for resistance to nutrient deprivation per se, but rather resilience to a variety of nutrient availability states (such as seasonal floods). Survival under such challenging conditions ostensibly favors the ability to tolerate extreme metabolic states, including not only starvation but also high levels of potentially deleterious metabolites such as triglycerides and reactive oxygen species (ROS). We find evidence for elevated antioxidant levels and altered cholesterol / cholesteryl ester homeostasis in cavefish, suggesting that cavefish may use these mechanisms to offset potentially harmful metabolites and tolerate a broad range of metabolic conditions.
C_FIG
]]>Medley, J. K.Persons, J.Peuss, R.Olsen, L.Xiong, S.Rohner, N.2020-10-28doi:10.1101/2020.10.27.358077Cold Spring Harbor Laboratory Press2020-10-28
<![CDATA[
Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
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https://biorxiv.org/content/10.1101/2020.10.30.359448v1?rss=1
Zimmermann, B.Robb, S. M. C.Genikhovich, G.Fropf, W. J.Weilguny, L.He, S.Chen, S.Lovegrove-Walsh, J.Hill, E. M.Ragkousi, K.Praher, D.Fredman, D.Moran, Y.Gibson, M. C.Technau, U.2020-10-30doi:10.1101/2020.10.30.359448Cold Spring Harbor Laboratory Press2020-10-30
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Yeast Nuak1 phosphorylates histone H3 threonine 11 in low glucose stress conditions by the cooperation of AMPK and CK2 signaling
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https://biorxiv.org/content/10.1101/2020.11.03.367094v1?rss=1
Oh, S.Lee, J.Swanson, S. K.Florens, L.Washburn, M. P.Workman, J. L.2020-11-03doi:10.1101/2020.11.03.367094Cold Spring Harbor Laboratory Press2020-11-03
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Mechanistic inferences from analysis of measurements of protein phase transitions in live cells
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https://biorxiv.org/content/10.1101/2020.11.04.369017v1?rss=1
Posey, A. E.Ruff, K. M.Lalmansingh, J. M.Kandola, T. S.Lange, J. J.Halfmann, R.Pappu, R. V.2020-11-05doi:10.1101/2020.11.04.369017Cold Spring Harbor Laboratory Press2020-11-05
<![CDATA[
Predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning
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https://biorxiv.org/content/10.1101/2020.11.09.373878v1?rss=1
Quadir, F.Roy, R. S.Halfmann, R.Cheng, J.2020-11-10doi:10.1101/2020.11.09.373878Cold Spring Harbor Laboratory Press2020-11-10
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Adaptive cell invasion maintains organ homeostasis
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https://biorxiv.org/content/10.1101/2020.12.01.404954v1?rss=1
Peloggia, J.Münch, D.Meneses-Giles, P.Romero-Carvajal, A.McClain, M.Pan, Y. A.Piotrowski, T.2020-12-02doi:10.1101/2020.12.01.404954Cold Spring Harbor Laboratory Press2020-12-02
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Redistribution of centrosomal proteins by centromeres and Polo kinase controls nuclear envelope breakdown
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https://biorxiv.org/content/10.1101/2020.12.01.406553v1?rss=1
Bestul, A. J.Yu, Z.Unruh, J. R.Jaspersen, S. L.2020-12-01doi:10.1101/2020.12.01.406553Cold Spring Harbor Laboratory Press2020-12-01
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Highly contiguous assemblies of 101 drosophilid genomes
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https://biorxiv.org/content/10.1101/2020.12.14.422775v1?rss=1
Kim, B. Y.Wang, J.Miller, D. E.Barmina, O.Delaney, E. K.Thompson, A.Comeault, A. A.Peede, D.D'Agostino, E. R. R.Pelaez, J.Aguilar, J. M.Haji, D.Matsunaga, T.Armstrong, E. E.Zych, M.Ogawa, Y.Stamenkovic-Radak, M.Jelic, M.Veselinovic, M. S.Tanaskovic, M.Eric, P.Gao, J.-j.Katoh, T. K.Toda, M. J.Watabe, H.Watada, M.Davis, J. S.Moyle, L. C.Manoli, G.Bertolini, E.Kostal, V.Hawley, R. S.Takahashi, A.Jones, C. D.Price, D. K.Whiteman, N. K.Kopp, A.Matute, D. R.Petrov, D. A.2020-12-15doi:10.1101/2020.12.14.422775Cold Spring Harbor Laboratory Press2020-12-15
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Genome-wide binding analyses of HOXB1 revealed a novel DNA binding motif associated with gene repression
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Singh, N. P.De Kumar, B.Paulson, A.Parrish, M.Scott, C.Zhang, Y.Florens, L.Krumlauf, R.2020-12-29doi:10.1101/2020.12.29.424720Cold Spring Harbor Laboratory Press2020-12-29
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Ocular elongation and retraction in foveated reptiles
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Rasys, A. M.Pau, S. H.Irwin, K. E.Luo, S.Trainor, P. A.Menke, D. B.Lauderdale, J. D.2021-01-21doi:10.1101/2021.01.20.427408Cold Spring Harbor Laboratory Press2021-01-21
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Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals
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Arnold, C.Migueles-Lozano, A.Mann, F. G.Lange, J. J.Seidel, C.Sanchez Alvarado, A.2021-01-26doi:10.1101/2021.01.24.427972Cold Spring Harbor Laboratory Press2021-01-26
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Perturbation of BRMS1 interactome reveals pathways that impact cell migration
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Zimmermann, R. C.Sardiu, M. E.Manton, C. A.Miah, M. S.Banks, C. A.Adams, M. K.Koestler, D. C.Washburn, M. P.Welch, D. R.2021-02-04doi:10.1101/2021.02.04.429764Cold Spring Harbor Laboratory Press2021-02-04
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Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells
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Pushel, I.Trainor, P. A.Krumlauf, R.2021-02-09doi:10.1101/2021.02.09.430457Cold Spring Harbor Laboratory Press2021-02-09
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H3K36 methylation and DNA-binding are critical for Ioc4 recruitment and Isw1b remodeller function
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Li, J.Bergmann, L.Webb, K. M.Gogol, M. M.Voigt, P.Liu, Y.Liang, H.Smolle, M. M.2021-02-26doi:10.1101/2021.02.26.432832Cold Spring Harbor Laboratory Press2021-02-26
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The feedback regulator Nord controls Dpp/BMP signaling via extracellular interaction with Dally in the Drosophila wing
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Gibson, M. C.Akiyama, T.Seidel, C. W.2021-03-11doi:10.1101/2021.03.11.434947Cold Spring Harbor Laboratory Press2021-03-11
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Proteome plasticity in response to persistent environmental change
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Domnauer, M.Zheng, F.Li, L.Zhang, Y.Chang, C. E.Unruh, J.Conkright-Fincham, J.McCroskey, S.Florens, L.Zhang, Y.Seidel, C.Fong, B.Schilling, B.Sharma, R.Ramanathan, A.Si, K.Zhou, C.2021-03-22doi:10.1101/2021.03.22.436511Cold Spring Harbor Laboratory Press2021-03-22
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Heterologous reporter expression in the planarian Schmidtea mediterranea through somatic mRNA transfection
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Hall, R. N.Weill, U.Khariton, M.Leal-Ortiz, S.Drees, L.Chai, C.Xue, Y.Rosental, B.Quake, S. R.Sanchez Alvarado, A.Melosh, N. A.Fire, A.Rink, J. C.Wang, B.2021-04-20doi:10.1101/2021.04.20.440701Cold Spring Harbor Laboratory Press2021-04-20
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Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity.
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Xiong, S.Wang, W.Kenzior, A.Olsen, L.Krishnan, J.Persons, J.Medley, K.Peuss, R.Wang, Y.Chen, S.Zhang, N.Thomas, N.Miles, J.Sanchez Alvarado, A.Rohner, N.2021-04-28doi:10.1101/2021.04.27.441667Cold Spring Harbor Laboratory Press2021-04-28
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iCodon: ideal codon design for customized gene expression
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Medina-Munoz, S.Diez, M.Castellano, L.da Silva Pescador, G.Wu, Q.Bazzini, A. A.2021-05-07doi:10.1101/2021.05.06.442969Cold Spring Harbor Laboratory Press2021-05-07
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Hybridization underlies localized trait evolution in cavefish
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Moran, R. L.Jaggard, J. B.Roback, E. Y.Rohner, N.Kowalko, J. E.Ornelas-Garcia, P.McGaugh, S. E.Keene, A. C.2021-05-12doi:10.1101/2021.05.11.443489Cold Spring Harbor Laboratory Press2021-05-12
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BMP signaling underlies the craniofacial heterochrony in phyllostomid bats, a hyperdiverse mammal group
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https://biorxiv.org/content/10.1101/2021.05.17.444516v1?rss=1
Camacho, J.Lin, J. D.McCormack, M.Moon, R.Smith, S. K.Abzhanov, A.2021-05-17doi:10.1101/2021.05.17.444516Cold Spring Harbor Laboratory Press2021-05-17
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Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing
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https://biorxiv.org/content/10.1101/2021.05.22.445248v1?rss=1
Bhattacharya, S.Wang, S.Reddy, D.Shen, S.Zhang, Y.Zhang, N.Li, H.Washburn, M.Florens, L.Shi, Y.Li, F.Workman, J.2021-05-23doi:10.1101/2021.05.22.445248Cold Spring Harbor Laboratory Press2021-05-23
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Island-specific evolution of a sex-primed autosome in the planarian Schmidtea mediterranea
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https://biorxiv.org/content/10.1101/2021.05.24.445457v1?rss=1
Guo, L.Bloom, J. S.Serrate, D. D.David, E. B.Schubert, O. T.Kazuma, K.Ho, K.Wei, Y.Leighton, D.Boocock, J.Vergara, T. L.Riutort, M.Alvarado, A. S.Kruglyak, L.2021-05-24doi:10.1101/2021.05.24.445457Cold Spring Harbor Laboratory Press2021-05-24
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The complete sequence of a human genome
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https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1
Nurk, S.Koren, S.Rhie, A.Rautiainen, M.Bzikadze, A. V.Mikheenko, A.Vollger, M. R.Altemose, N.Uralsky, L.Gershman, A.Aganezov, S.Hoyt, S. J.Diekhans, M.Logsdon, G. A.Alonge, M.Antonarakis, S. E.Borchers, M.Bouffard, G. G.Brooks, S. Y.Caldas, G. V.Cheng, H.Chin, C.-S.Chow, W.de Lima, L. G.Dishuck, P. C.Durbin, R.Dvorkina, T.Fiddes, I. T.Formenti, G.Fulton, R. S.Fungtammasan, A.Garrison, E.Grady, P. G. S.Graves-Lindsay, T. A.Hall, I. M.Hansen, N. F.Hartley, G. A.Haukness, M.Howe, K.Hunkapiller, M. W.Jain, C.Jain, M.2021-05-27doi:10.1101/2021.05.26.445798Cold Spring Harbor Laboratory Press2021-05-27
<![CDATA[
Diverse mating phenotypes impact the spread of wtf meiotic drivers in S. pombe
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https://biorxiv.org/content/10.1101/2021.05.28.446231v1?rss=1
Zanders, S. E.Lopez Hernandez, J. F.Helston, R. M.Lange, J. J.Billmyre, R. B.Schaffner, S. H.Eickbush, M. T.McCroskey, S.2021-05-29doi:10.1101/2021.05.28.446231Cold Spring Harbor Laboratory Press2021-05-29
<![CDATA[
A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq
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https://biorxiv.org/content/10.1101/2021.06.10.447896v1?rss=1
Mudge, J. M.Ruiz-Orera, J.Prensner, J. R.Brunet, M. A.Gonzalez, J. M.Magrane, M.Martinez, T.Schulz, J. F.Yang, Y. T.Alba, M. M.Baranov, P. V.Bazzini, A.Bruford, E.Martin, M. J.Carvunis, A.-R.Chen, J.Couso, J. P.Flicek, P.Frankish, A.Gerstein, M.Hubner, N.Ingolia, N. T.Menschaert, G.Ohler, U.Roucou, X.Saghatelian, A.Weissman, J.van Heesch, S.2021-06-10doi:10.1101/2021.06.10.447896Cold Spring Harbor Laboratory Press2021-06-10
<![CDATA[
The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters
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https://biorxiv.org/content/10.1101/2021.06.18.448946v1?rss=1
Soffers, J. H.Garcia-Moreno Alcantara, S.Li, X.Shao, W.Seidel, C.Li, H.Zeitlinger, J.Abmayr, S.Workman, J.2021-06-18doi:10.1101/2021.06.18.448946Cold Spring Harbor Laboratory Press2021-06-18
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Stem cell-free therapy for glaucoma to preserve vision
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Kumar, A.Xiong, S.Zhou, M.Chen, W.Yang, E.Price, A.Le, L.Zhang, Y.Florens, L.Washburn, M.Kumar, A.Li, Y.Xu, Y.Lathrop, K. L.Davoli, K. A.Chen, Y.Schuman, J. S.Xie, T.Du, Y.2021-06-18doi:10.1101/2021.06.18.449038Cold Spring Harbor Laboratory Press2021-06-18
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Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis
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Bauerly, E.Akiyama, T.Yi, K.Gibson, M.2021-07-04doi:10.1101/2021.07.03.450990Cold Spring Harbor Laboratory Press2021-07-04
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From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
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https://biorxiv.org/content/10.1101/2021.07.12.451456v1?rss=1
Hoyt, S. J.Storer, J. M.Hartley, G. A.Grady, P. G. S.Gershman, A.de Lima, L. G.Limouse, C.Halabian, R.Wojenski, L.Rodriguez, M.Altemose, N.Core, L.Gerton, J. L.Makalowski, W.Olson, D.Rosen, J.Smit, A. F. A.Straight, A. F.Vollger, M. R.Wheeler, T.Schatz, M.Eichler, E.Phillippy, A. M.Timp, W.Miga, K. H.O'Neill, R. J.2021-07-12doi:10.1101/2021.07.12.451456Cold Spring Harbor Laboratory Press2021-07-12
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Complete genomic and epigenetic maps of human centromeres
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https://biorxiv.org/content/10.1101/2021.07.12.452052v1?rss=1
Altemose, N.Logsdon, G.Bzikadze, A. V.Sidhwani, P.Langley, S. A.Caldas, G. V.Hoyt, S. J.Uralsky, L.Ryabov, F. D.Shew, C.Sauria, M. E. G.Borchers, M.Gershman, A.Mikheenko, A.Shepelev, V. A.Dvorkina, T.Kunyavskaya, O.Vollger, M. R.Rhie, A.McCartney, A. M.Asri, M.Lorig-Roach, R.Shafin, K.Aganezov, S.Olson, D.Gomes de Lima, L.Potapova, T.Hartley, G. A.Haukness, M.Kerpedjiev, P.Gusev, F.Tigyi, K.Brooks, S. Y.Young, A.Nurk, S.Koren, S.Salama, S.Paten, B.Rogaev, E. I.Streets, A. M.Karpen, G. H.Dernburg, A.Sullivan, B.2021-07-13doi:10.1101/2021.07.12.452052Cold Spring Harbor Laboratory Press2021-07-13
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High-resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration
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Baek, S.Tran, N. T. T.Diaz, D. C.Tsai, Y.-Y.Piotrowski, T.2021-07-15doi:10.1101/2021.07.15.452338Cold Spring Harbor Laboratory Press2021-07-15
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Regulation of stem cell identity by miR-200a during spinal cord regeneration
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Walker, S.Sabin, K.Gearhart, M.Yamamoto, K.Echeverri, K.2021-07-21doi:10.1101/2021.07.21.453081Cold Spring Harbor Laboratory Press2021-07-21
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A distinct inner nuclear membrane proteome in Saccharomyces cerevisiae gametes
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Shelton, S. N.Smith, S. E.Unruh, J. R.Jaspersen, S. L.2021-08-02doi:10.1101/2021.08.02.454801Cold Spring Harbor Laboratory Press2021-08-02
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Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe
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Varberg, J. M.Unruh, J.Bestul, A. J.Khan, A. A.Jaspersen, S.2021-08-11doi:10.1101/2021.08.11.455278Cold Spring Harbor Laboratory Press2021-08-11
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The polyglutamine amyloid nucleus in living cells is monomeric and has competing dimensions of order
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Kandola, T.Zhang, J.Venkatesan, S.Lerbakken, B.Blanck, J. F.Wu, J.Unruh, J.Berry, P.Lange, J. L.Von Schulze, A.Box, A.Cook, M.Sagui, C.Halfmann, R.2021-08-31doi:10.1101/2021.08.29.458132Cold Spring Harbor Laboratory Press2021-08-31
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Genome-wide identification of sexual-reproduction genes in fission yeast via transposon-insertion sequencing
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Billmyre, R. B.Eickbush, M. T.Craig, C. J.Lange, J. J.Wood, C.Helston, R. M.Zanders, S. E.2021-09-01doi:10.1101/2021.08.31.458362Cold Spring Harbor Laboratory Press2021-09-01
<![CDATA[
The architecture and operating mechanism of a cnidarian stinging organelle
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https://biorxiv.org/content/10.1101/2021.09.09.459669v1?rss=1
Karabulut, A.McClain, M.Rubinstein, B.McKinney, S. A.Gibson, M.2021-09-10doi:10.1101/2021.09.09.459669Cold Spring Harbor Laboratory Press2021-09-10
<![CDATA[
Nucleolin loss-of-function leads to aberrant FGF signaling and craniofacial anomalies
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Dash, S.Trainor, P.2021-09-15doi:10.1101/2021.09.14.460382Cold Spring Harbor Laboratory Press2021-09-15
<![CDATA[
Dynamic regulation and requirement for ribosomal RNA transcription duringmammalian development
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https://biorxiv.org/content/10.1101/2021.09.22.461379v1?rss=1
Terrazas Falcon, K.Watt, K.Dash, S.Achilleos, A.Moore, E.Zhao, R.Fitriasari, S.Sakai, D.Childers, M.Sardiu, M.Swanson, S.Tsuchiya, D.Unruh, J.Bugarinovic, G.Li, L.Shiang, R.Dixon, J.Dixon, M.Trainor, P.2021-09-22doi:10.1101/2021.09.22.461379Cold Spring Harbor Laboratory Press2021-09-22
<![CDATA[
an anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury
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https://biorxiv.org/content/10.1101/2021.09.28.462132v1?rss=1
Denans, N.Tran, N. T. T.Swall, M. E.Diaz, D. C.Blanck, J.Piotrowski, T.2021-09-30doi:10.1101/2021.09.28.462132Cold Spring Harbor Laboratory Press2021-09-30
<![CDATA[
S. pombe wtf genes use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive
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https://biorxiv.org/content/10.1101/2021.09.30.462505v1?rss=1
Nuckolls, N. L.Nidamangala Srinivasa, A.Mok, A. C.Bravo Nunez, M. A.Lange, J. J.Gallagher, T. J.Seidel, C. W.Zanders, S.2021-10-01doi:10.1101/2021.09.30.462505Cold Spring Harbor Laboratory Press2021-10-01
<![CDATA[
Microglia remodel the synaptic signaling required for context-dependent cognitive performance
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https://biorxiv.org/content/10.1101/2021.10.18.464802v1?rss=1
Socodato, R.Almeida, T. O.Portugal, C. C.Santos, E. C. S.Tedim-Moreira, J.Canedo, T.Baptista, F.Magalhaes, A.Ambrosio, A. F.Brakebusch, C.Rubinstein, B.Moreira, I.Summavielle, T.Pinto, I. M.Relvas, J. B.2021-10-19doi:10.1101/2021.10.18.464802Cold Spring Harbor Laboratory Press2021-10-19
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Yn-situ: a robust single RNA molecule in situ detection method
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Wu, Y.Xu, W.Ma, L.Yu, Z.Wang, Y.Yu, R.2021-10-21doi:10.1101/2021.10.20.465061Cold Spring Harbor Laboratory Press2021-10-21
<![CDATA[
Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex
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https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1
Akey, C.Singh, D.Ouch, C.Echeverria, I.Nudelman, I.Varberg, J. M.Yu, Z.Fang, F.Shi, Y.Wang, J.Saltzberg, D.Song, K.Xu, C.Gumbart, J.Suslov, S.Unruh, J.Jaspersen, S. L.Chait, B.Sali, A.Menendez-Martinez, J.Ludke, S. J.Villa, E.Rout, M.2021-10-29doi:10.1101/2021.10.29.466335Cold Spring Harbor Laboratory Press2021-10-29
<![CDATA[
A powerful and versatile new fixation protocol for immunohistology and in situ hybridization that preserves delicate tissues in planaria
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https://biorxiv.org/content/10.1101/2021.11.01.466817v1?rss=1
Guerrero-Hernandez, C.Doddihal, V.Mann, F. G.Sanchez Alvarado, A.2021-11-03doi:10.1101/2021.11.01.466817Cold Spring Harbor Laboratory Press2021-11-03
<![CDATA[
A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis.
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https://biorxiv.org/content/10.1101/2021.12.15.472819v1?rss=1
Paez-Moscoso, D. J.Ho, D. V.Pan, L.Hildebrand, K.Jensen, K. L.Levy, M. J.Florens, L.Baumann, P.2021-12-16doi:10.1101/2021.12.15.472819Cold Spring Harbor Laboratory Press2021-12-16
<![CDATA[
Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation
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https://biorxiv.org/content/10.1101/2022.01.06.475101v1?rss=1
Krishnan, J.Wang, Y.Kenzior, O.Hassan, H.Olsen, L.Tsuchiya, D.Wang, Y.Zhao, C.Rohner, N.2022-01-06doi:10.1101/2022.01.06.475101Cold Spring Harbor Laboratory Press2022-01-06
<![CDATA[
A nucleation barrier spring-loads the CBM signalosome for binary activation
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https://biorxiv.org/content/10.1101/2022.01.28.477912v1?rss=1
Rodriguez Gama, A.Miller, T.Lange, J. J.Unruh, J.Halfmann, R.2022-01-29doi:10.1101/2022.01.28.477912Cold Spring Harbor Laboratory Press2022-01-29
<![CDATA[
Quinary structure kinetically controls protein function and dysfunction
]]>
https://biorxiv.org/content/10.1101/205690v1?rss=1
Khan, T.Kandola, T.Wu, J.Ketter, E.Venkatesan, S.Lange, J. J.Rodriguez Gama, A.Box, A.Unruh, J. R.Cook, M.Halfmann, R.2017-10-18doi:10.1101/205690Cold Spring Harbor Laboratory Press2017-10-18
<![CDATA[
Cohesin facilitates zygotic genome activation in zebrafish
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https://biorxiv.org/content/10.1101/214023v1?rss=1
Meier, M.Grant, J.Dowdle, A.Thomas, A.Gerton, J. E.Collas, P.O'Sullivan, J. M.Horsfield, J. A.2017-11-04doi:10.1101/214023Cold Spring Harbor Laboratory Press2017-11-04
<![CDATA[
Impaired Cu-Zn superoxide dismutase (SOD1) and calcineurin (Cn) interaction in ALS: A presumed consequence for TDP-43 and zinc aggregation in Tg SOD1G93A rodent spinal cord tissue.
]]>
https://biorxiv.org/content/10.1101/220210v1?rss=1
Kim, J. M.Billington, E.Reyes, A.Notarianni, T.Sage, J. M.Agbas, E.Taylor, M.Monast, I.Stanford, J. A.Agbas, A.2017-11-15doi:10.1101/220210Cold Spring Harbor Laboratory Press2017-11-15
<![CDATA[
An adaptable chromosome preparation methodology for use in invertebrate research organisms
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https://biorxiv.org/content/10.1101/226084v1?rss=1
Guo, L.Accorsi, A.He, S.Guerrero-Hernandez, C.Sivagnanam, S.McKinney, S.Gibson, M.Sanchez Alvarado, A.2017-11-29doi:10.1101/226084Cold Spring Harbor Laboratory Press2017-11-29
<![CDATA[
A conserved regulatory program drives emergence of the lateral plate mesoderm
]]>
https://biorxiv.org/content/10.1101/261115v1?rss=1
Hess, C.Prummel, K. D.Nieuwenhuize, S.Parker, H.Rogers, K. W.Kozmikova, I.Racioppi, C.Burger, S.Brombacher, E. C.Burger, A.Felker, A.Chiavacci, E.Shah, G.Huisken, J.Kozmik, Z.Christiaen, L.Mueller, P.Bronner, M.Krumlauf, R.Mosimann, C.2018-02-07doi:10.1101/261115Cold Spring Harbor Laboratory Press2018-02-07
<![CDATA[
High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing
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https://biorxiv.org/content/10.1101/267393v1?rss=1
Miller, D. E.Staber, C.Zeitlinger, J.Hawley, R. S.2018-02-18doi:10.1101/267393Cold Spring Harbor Laboratory Press2018-02-18
<![CDATA[
Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing
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https://biorxiv.org/content/10.1101/267401v1?rss=1
Solares, E. A.Chakraborty, M.Miller, D. E.Kalsow, S.Hall, K. E.Perera, A. G.Emerson, J. J.Hawley, R. S.2018-02-18doi:10.1101/267401Cold Spring Harbor Laboratory Press2018-02-18
<![CDATA[
CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts
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https://biorxiv.org/content/10.1101/269977v1?rss=1
Noe Gonzalez, M.Sato, S.Tomomori-Sato, C.Conaway, J. W.Conaway, R. C.2018-02-22doi:10.1101/269977Cold Spring Harbor Laboratory Press2018-02-22
<![CDATA[
Synaptonemal complex architecture facilitates the chromosome-specific regulation of recombination in Drosophila
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https://biorxiv.org/content/10.1101/277764v1?rss=1
Cahoon, C.Heenan, G. M.Yu, Z.Unruh, J. R.McKinney, S.Hawley, R. S.2018-03-06doi:10.1101/277764Cold Spring Harbor Laboratory Press2018-03-06
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A nuclear hormone receptor and lipid metabolism axis are required for the maintenance and regeneration of reproductive organs
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https://biorxiv.org/content/10.1101/279364v1?rss=1
Zhang, S.Guo, L.Guerrero-Hernandez, C.Ross, E. J.Gotting, K.McKinney, S. A.Wang, W.Xiang, Y.Hawley, R. S.Sanchez Alvarado, A.2018-03-09doi:10.1101/279364Cold Spring Harbor Laboratory Press2018-03-09
<![CDATA[
Histone H3 T11 phosphorylation by Sch9 and CK2 regulates lifespan by controlling the nutritional stress response
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https://biorxiv.org/content/10.1101/282384v1?rss=1
Workman, J. L.Oh, S.Gogol, M. M.Suganuma, T.2018-03-14doi:10.1101/282384Cold Spring Harbor Laboratory Press2018-03-14
<![CDATA[
A chemoproteomic portrait of the oncometabolite fumarate
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https://biorxiv.org/content/10.1101/285759v1?rss=1
Kulkarni, R. A.Bak, D. W.Wei, D.Bergholtz, S. E.Briney, C. A.Shrimp, J. H.Thorpe, A. L.Bavari, A.Alpsoy, A.Levy, M.Florens, L.Washburn, M. P.Dykhuizen, E. C.Frizzell, N.Weerapana, E.Linehan, W. M.Meier, J. L.2018-03-21doi:10.1101/285759Cold Spring Harbor Laboratory Press2018-03-21
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Ataxin-7 and non-stop coordinate SCAR protein levels, subcellular localization, and actin cytoskeleton organization
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https://biorxiv.org/content/10.1101/309476v1?rss=1
Cloud, V.Momtahan, E.Jack, J. L.Leiva, E.Rapp, S. R.Miller, S. A.Holsapple, D.Shelton, L. G.Pierce, R. A.Zhang, Y.Florens, L.Washburn, M. P.Mohan, R. D.2018-04-27doi:10.1101/309476Cold Spring Harbor Laboratory Press2018-04-27
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DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169
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https://biorxiv.org/content/10.1101/327510v1?rss=1
Menon, V. R.Ananthapadmanabhan, V.Swanson, S.Saini, S.Sesay, F.Yakovlev, V.Florens, L.DeCaprio, J. A.Washburn, M. P.Dozmorov, M.Litovchick, L.2018-05-21doi:10.1101/327510Cold Spring Harbor Laboratory Press2018-05-21
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Antimicrobial peptides modulate long-term memory
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https://biorxiv.org/content/10.1101/328286v1?rss=1
Si, K.Azpeleta, R. B.Wu, J.Gill, J.Welte, R.Seidel, C.2018-05-22doi:10.1101/328286Cold Spring Harbor Laboratory Press2018-05-22
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ClusterMap: Compare analysis across multiple Single Cell RNA-Seq profiling
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https://biorxiv.org/content/10.1101/331330v1?rss=1
Gao, X.Hu, D.Li, H.2018-05-30doi:10.1101/331330Cold Spring Harbor Laboratory Press2018-05-30
<![CDATA[
The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus
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https://biorxiv.org/content/10.1101/335182v1?rss=1
Herman, A.Brandvain, Y.Weagley, J.Jeffery, W. R.Keene, A. C.Kono, T. J. Y.Bilandzija, H.Borowsky, R.Espinasa, L.O'Quin, K.Ornelas-Garcia, C. P.Yoshizawa, M.Carlson, B.Maldonado, E.Gross, J. B.Cartwright, R. A.Rohner, N.Warren, W. C.McGaugh, S. E.2018-05-31doi:10.1101/335182Cold Spring Harbor Laboratory Press2018-05-31
<![CDATA[
Timed collinear activation of Hox genes during gastrulation controls the avian forelimb position
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https://biorxiv.org/content/10.1101/351106v1?rss=1
Moreau, C.Caldarelli, P.Rocancourt, D.Roussel, J.Denans, N.Pourquie, O.Gros, J.2018-06-20doi:10.1101/351106Cold Spring Harbor Laboratory Press2018-06-20
<![CDATA[
Molecular analysis of Drosophila melanogaster B chromosomes reveals their origin, composition, and structure
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https://biorxiv.org/content/10.1101/386995v1?rss=1
Hanlon, S. L.Miller, D. E.Eche, S.Hawley, R. S.2018-08-07doi:10.1101/386995Cold Spring Harbor Laboratory Press2018-08-07
<![CDATA[
Membrane insertion function for SUN-KASH complex revealed by high resolution analysis of yeast centrosomes
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https://biorxiv.org/content/10.1101/413799v1?rss=1
Chen, J.Gardner, J. M.Yu, Z.Smith, S. E.McKinney, S.Slaughter, B. D.Unruh, J. R.Jaspersen, S. L.2018-09-10doi:10.1101/413799Cold Spring Harbor Laboratory Press2018-09-10
<![CDATA[
Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis
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https://biorxiv.org/content/10.1101/422113v1?rss=1
Karabulut, A. C.He, S.Chen, C.-Y.McKinney, S. A.Gibson, M. C.2018-09-20doi:10.1101/422113Cold Spring Harbor Laboratory Press2018-09-20
<![CDATA[
RUNX proteins desensitize multiple myeloma to lenalidomide via protecting IKZFs from degradation
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https://biorxiv.org/content/10.1101/423350v1?rss=1
Zhou, N.Gutierrez Uzquiza, A.Zheng, X. Y.Vogl, D.Garfall, A. L.Bernabei, L.Saraf, A.Florens, L.Washburn, M. P.Illendula, A.Bushweller, J. H.Busino, L.2018-09-20doi:10.1101/423350Cold Spring Harbor Laboratory Press2018-09-20
<![CDATA[
Topological Scoring of Protein Interaction Networks
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https://biorxiv.org/content/10.1101/438408v1?rss=1
Sardiu, M.Gilmore, J.Groppe, B.Dutta, A.Florens, L.Washburn, M.2018-10-08doi:10.1101/438408Cold Spring Harbor Laboratory Press2018-10-08
<![CDATA[
The ULK1-FBXW5-SEC23B nexus controls autophagy
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https://biorxiv.org/content/10.1101/441923v1?rss=1
Pagano, M.Jeong, Y.-T.Simoneschi, D.Keegan, S.Melville, D.Adler, N.Saraf, A.Florens, L.Washburn, M. P.Cavasotto, C.Fenyö, D.Cuervo, A. M.Rossi, M.2018-10-12doi:10.1101/441923Cold Spring Harbor Laboratory Press2018-10-12
<![CDATA[
Asi1 regulates the distribution of proteins at the inner nuclear membrane in Saccharomyces cerevisiae
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https://biorxiv.org/content/10.1101/442970v1?rss=1
Smoyer, C. J.Smith, S. E.McCroskey, S.Unruh, J.Jaspersen, S. L.2018-10-14doi:10.1101/442970Cold Spring Harbor Laboratory Press2018-10-14
<![CDATA[
Rewiring of a SMAD4 Protein Interaction Network by Breast Tumor Kinase Mediated Phosphorylation
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https://biorxiv.org/content/10.1101/458190v1?rss=1
Miah, S.Banks, C.Ogunbolude, Y.Bagu, E.MacAusland-Berg, J.Saraf, A.Hattem, G.Kempf, C.Sardiu, M.Napper, S.Florens, L.Lukong, K. E.Washburn, M. P.2018-10-31doi:10.1101/458190Cold Spring Harbor Laboratory Press2018-10-31
<![CDATA[
Killer meiotic drive and dynamic evolution of the wtf gene family
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https://biorxiv.org/content/10.1101/461004v1?rss=1
Eickbush, M. T.Young, J. M.Zanders, S. E.2018-11-03doi:10.1101/461004Cold Spring Harbor Laboratory Press2018-11-03
<![CDATA[
Roles for stress response and cell wall biosynthesis pathways in caspofungin tolerance in Cryptococcus neoformans
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https://biorxiv.org/content/10.1101/465260v1?rss=1
Pianalto, K. M.Billmyre, R. B.Telzrow, C. L.Alspaugh, J. A.2018-11-07doi:10.1101/465260Cold Spring Harbor Laboratory Press2018-11-07
<![CDATA[
General characterization of regeneration in Aeolosoma viride
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https://biorxiv.org/content/10.1101/493304v1?rss=1
Chen, C.-P.Fok, S. K.-W.Hsieh, Y.-W.Chen, C.-Y.Hsu, F.-M.Chen, J.-H.2018-12-11doi:10.1101/493304Cold Spring Harbor Laboratory Press2018-12-11
<![CDATA[
Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling
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https://biorxiv.org/content/10.1101/496612v1?rss=1
Lush, M. E.Diaz, D. C.Koenecke, N.Baek, S.Boldt, H.St. Peter, M. K.Gaitan-Escudero, T.Romero-Carvajal, A.Busch-Nentwich, E.Perera, A.Hall, K.Peak, A.Haug, J. S.Piotrowski, T.2018-12-14doi:10.1101/496612Cold Spring Harbor Laboratory Press2018-12-14
<![CDATA[
HOOK3 is a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein and KIF1C
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https://biorxiv.org/content/10.1101/508887v1?rss=1
Kendrick, A. A.Redwine, W. B.Tran, P. T.Pontano Vaites, L.Dzieciatkowska, M.Harper, J. W.Reck-Peterson, S. L.2018-12-31doi:10.1101/508887Cold Spring Harbor Laboratory Press2018-12-31
<![CDATA[
Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides
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https://biorxiv.org/content/10.1101/526459v1?rss=1
Chang, Z.Billmyre, R. B.Lee, S. C.Heitman, J.2019-01-21doi:10.1101/526459Cold Spring Harbor Laboratory Press2019-01-21
<![CDATA[
Parallel control of mechanosensory hair cell orientation by the PCP and Wnt pathways
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https://biorxiv.org/content/10.1101/527937v1?rss=1
Navajas Acedo, J.Voas, M. G.Alexander, R. L.Woolley, T.Unruh, J.Li, H.Moens, C.Piotrowski, T.2019-01-23doi:10.1101/527937Cold Spring Harbor Laboratory Press2019-01-23
<![CDATA[
Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system.
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https://biorxiv.org/content/10.1101/535740v1?rss=1
Stahl, B. A.Peuss, R.McDole, B.Kenzior, A.Jaggard, J. B.Gaudenz, K.Krishnan, J.McGaugh, S. E.Duboue, E. R.Keene, A. C.Rohner, N.2019-01-30doi:10.1101/535740Cold Spring Harbor Laboratory Press2019-01-30
<![CDATA[
An atlas of anterior hox gene expression in the embryonic sea lamprey head: hox-code evolution in vertebrates
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https://biorxiv.org/content/10.1101/571448v1?rss=1
Parker, H. J.Bronner, M. E.Krumlauf, R.2019-03-09doi:10.1101/571448Cold Spring Harbor Laboratory Press2019-03-09
<![CDATA[
Cultured pluripotent planarian stem cells retain potency and express proteins from exogenously introduced mRNAs
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https://biorxiv.org/content/10.1101/573725v1?rss=1
Sanchez Alvarado, A.Lei, K.McKinney, S. A.Ross, E. J.Lee, H.-C.2019-03-12doi:10.1101/573725Cold Spring Harbor Laboratory Press2019-03-12
<![CDATA[
High-throughput, image-based flow cytometry and clustering method for phenotyping heterogeneous cell populations
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https://biorxiv.org/content/10.1101/603035v1?rss=1
Peuss, R.Box, A. C.Accorsi, A.Wood, C.Sanchez Alvarado, A.Rohner, N.2019-04-09doi:10.1101/603035Cold Spring Harbor Laboratory Press2019-04-09
<![CDATA[
Subcellular analyses of planarian meiosis implicates a novel, double-membraned vesiculation process in nuclear envelope breakdown
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https://biorxiv.org/content/10.1101/620609v1?rss=1
Guo, L.Guo, F.Zhang, S.Yi, K.McClain, M.Kuhn, C.-D.Parmely, T.Sanchez Alvarado, A.2019-05-05doi:10.1101/620609Cold Spring Harbor Laboratory Press2019-05-05
<![CDATA[
Single cell analysis reveals modified hematopoietic cell composition affecting inflammatory and immunopathological responses in Astyanax mexicanus
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https://biorxiv.org/content/10.1101/647255v1?rss=1
Peuss, R.Box, A. C.Wang, Y.Chen, S.Krishnan, J.Tsuchiya, D.Slaughter, B.Rohner, N.2019-05-23doi:10.1101/647255Cold Spring Harbor Laboratory Press2019-05-23
<![CDATA[
An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish
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https://biorxiv.org/content/10.1101/648188v1?rss=1
Loomis, C.Peuss, R.Jaggard, J. B.Wang, Y.McKinney, S.Raftopoulos, A.Raftopoulos, S.Whu, D.Green, M.McGaugh, S. E.Rohner, N. E.Keene, A. C.Duboue, E. R.2019-05-27doi:10.1101/648188Cold Spring Harbor Laboratory Press2019-05-27
<![CDATA[
Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome
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https://biorxiv.org/content/10.1101/650028v1?rss=1
Dayebgadoh, G.Sardiu, M.Florens, L.Washburn, M.2019-05-24doi:10.1101/650028Cold Spring Harbor Laboratory Press2019-05-24
<![CDATA[
A Dependency Capturing Code for Robust Object Representation
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https://biorxiv.org/content/10.1101/662130v1?rss=1
Raj, R.Dahlen, D.Duyck, K.Yu, C. R.2019-06-05doi:10.1101/662130Cold Spring Harbor Laboratory Press2019-06-05
<![CDATA[
A systems chemoproteomic analysis of acyl-CoA signaling networks
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https://biorxiv.org/content/10.1101/665281v1?rss=1
Levy, M. J.Montgomery, D. C.Sardiu, M. E.Thorpe, A. L.Fox, S. D.Lin, Q.Andresson, T.Florens, L.Washburn, M. P.Meier, J. L.2019-06-10doi:10.1101/665281Cold Spring Harbor Laboratory Press2019-06-10
<![CDATA[
Wampa is a dynein subunit required for axonemal assembly and male fertility in Drosophila
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https://biorxiv.org/content/10.1101/668012v1?rss=1
Bauerly, E.Yi, K.Gibson, M. C.2019-06-11doi:10.1101/668012Cold Spring Harbor Laboratory Press2019-06-11
<![CDATA[
Efficient depletion of ribosomal RNA for RNA sequencing in planarians
]]>
https://biorxiv.org/content/10.1101/670604v1?rss=1
Kim, I. V.Ross, E. J.Dietrich, S.Döring, K.Sanchez Alvarado, A.Kuhn, C. D.2019-06-13doi:10.1101/670604Cold Spring Harbor Laboratory Press2019-06-13
<![CDATA[
An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia
]]>
https://biorxiv.org/content/10.1101/677260v1?rss=1
Vincent, B. J.Rice, G. R.Wong, G. M.Glassford, W. J.Downs, K. I.Shastay, J. L.Charles-Obi, K.Natarajan, M.Gogol, M. M.Zeitlinger, J.Rebeiz, M.2019-06-26doi:10.1101/677260Cold Spring Harbor Laboratory Press2019-06-26
<![CDATA[
Neural crest cells bulldoze through the microenvironment using Aquaporin-1 to stabilize filopodia
]]>
https://biorxiv.org/content/10.1101/719666v1?rss=1
McLennan, R.McKinney, M. C.Teddy, J. M.Morrison, J. A.Kasemeier-Kulesa, J. C.Ridenour, D. A.Manthe, C. A.Giniunaite, R.Robinson, M.Baker, R. E.Maini, P. K.Kulesa, P. M.2019-07-30doi:10.1101/719666Cold Spring Harbor Laboratory Press2019-07-30
<![CDATA[
Dramatically diverse S. pombe wtf meiotic drivers all display high gamete-killing efficiency
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https://biorxiv.org/content/10.1101/728535v1?rss=1
85% gametes when heterozygous. We also find three new wtf genes that suppress drive, including two that also act as autonomous drivers. Additionally, we find that wtf genes do not underlie a weak (64%) transmission bias caused by a locus or loci on chromosome 1. Finally, we find that some Wtf proteins have expression or localization patterns that are distinct from the poison and antidote proteins encoded by drivers and suppressors, suggesting some wtf genes may have non-meiotic drive functions. Overall, this work expands our understanding of the wtf gene family and the burden selfish driver genes impose on S. pombe.nnArticle SummaryDuring gametogenesis, the two gene copies at a given locus, known as alleles, are each transmitted to 50% of the gametes (e.g. sperm). However, some alleles cheat so that they are found in more than the expected 50% of gametes, often at the expense of fertility. This selfish behavior is known as meiotic drive. Some members of the wtf gene family in the fission yeast, Schizosaccharomyces pombe, kill the gametes (spores) that do not inherit them, resulting in meiotic drive favoring the wtf allele. Other wtf genes act as suppressors of drive. However, the wtf gene family is diverse and only a small subset of the genes has been characterized. Here we analyze the functions of other members of this gene family and found eight new drivers as well as three new suppressors of drive. Surprisingly, we find that drive is relatively insensitive to changes in wtf gene sequence as highly diverged wtf genes execute gamete killing with similar efficiency. Finally, we also find that the expression and localization of some Wtf proteins are distinct from those of known drivers and suppressors, suggesting that these proteins may have non-meiotic drive functions.
]]>Bravo Nunez, M. A.Sabbarini, I. M.Eickbush, M. T.Liang, Y.Lange, J. J.Kent, A. M.Zanders, S.2019-08-07doi:10.1101/728535Cold Spring Harbor Laboratory Press2019-08-07
<![CDATA[
Telomere-to-telomere assembly of a complete human X chromosome
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https://biorxiv.org/content/10.1101/735928v1?rss=1
Miga, K. H.Koren, S.Rhie, A.Vollger, M. R.Gershman, A.Bzikadze, A.Brooks, S.Howe, E.Porubsky, D.Logsdon, G. A.Schneider, V. A.Potapova, T.Wood, J.Chow, W.Armstrong, J.Fredrickson, J.Pak, E.Tigyi, K.Kremitzki, M.Markovic, C.Maduro, V.Dutra, A.Bouffard, G. G.Chang, A. M.Hansen, N. F.Thibaud-Nissen, F.Schmitt, A. D.Belton, J.-M.Selvaraj, S.Dennis, M. Y.Soto, D. C.Sahasrabudhe, R.Kaya, G.Quick, J.Loman, N. J.Holmes, N.Loose, M.Surti, U.Risques, R. a.Lindsay, T. A. G.Fulton, R.Hall, I.Paten, B.Howe, K.Timp, W.2019-08-16doi:10.1101/735928Cold Spring Harbor Laboratory Press2019-08-16
<![CDATA[
Deep learning at base-resolution reveals motif syntax of the cis-regulatory code
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https://biorxiv.org/content/10.1101/737981v1?rss=1
Avsec, Z.Weilert, M.Shrikumar, A.Alexandari, A.Krueger, S.Dalal, K.Fropf, R.McAnany, C.Gagneur, J.Kundaje, A.Zeitlinger, J.2019-08-21doi:10.1101/737981Cold Spring Harbor Laboratory Press2019-08-21
<![CDATA[
Head Mesoderm Tissue Growth, Dynamics and Neural Crest Cell Migration
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https://biorxiv.org/content/10.1101/738542v1?rss=1
McKinney, M. C.McLennan, R.Giniunaite, R.Baker, R. E.Maini, P. K.Othmer, H. G.Kulesa, P.2019-08-16doi:10.1101/738542Cold Spring Harbor Laboratory Press2019-08-16
<![CDATA[
Integrative Modeling of a Sin3/HDAC Complex Sub-structure
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https://biorxiv.org/content/10.1101/810911v1?rss=1
Banks, C. A. S.Zhang, Y.Miah, S.Hao, Y.Adams, M. K.Wen, Z.Thornton, J. L.Florens, L.Washburn, M.2019-10-18doi:10.1101/810911Cold Spring Harbor Laboratory Press2019-10-18
<![CDATA[
STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation
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https://biorxiv.org/content/10.1101/823096v1?rss=1
Hahn, W. C.Kim, J. W.Berrios, C.Kim, M.Schade, A. E.Adelmant, G.Yeerna, H.Damato, E.Iniguez, A. B.Swanson, S. K.Florens, L.Washburn, M. P.Stegmaier, K.Gray, N. S.Tamayo, P.Gjoerup, O.Marto, J. A.DeCaprio, J.2019-10-29doi:10.1101/823096Cold Spring Harbor Laboratory Press2019-10-29
<![CDATA[
Differential complex formation via paralogs in the human Sin3 protein interaction network.
]]>
https://biorxiv.org/content/10.1101/830828v1?rss=1
Adams, M. K.Banks, C.Thornton, J. L.Sardiu, M.Killer, M.Kempf, C.Florens, L.Washburn, M.2019-11-04doi:10.1101/830828Cold Spring Harbor Laboratory Press2019-11-04
<![CDATA[
Hypoxic response is driven by the BAF form of SWI/SNF
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https://biorxiv.org/content/10.1101/2022.02.16.480689v1?rss=1
Tran, K. D.Chakravarty, T.Garzon, J.Saraf, A.Florens, L.Washburn, M.Dutta, A.2022-02-16doi:10.1101/2022.02.16.480689Cold Spring Harbor Laboratory Press2022-02-16
<![CDATA[
The C. elegans ASPP homolog APE-1 is a junctional protein phosphatase 1 modulator
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https://biorxiv.org/content/10.1101/2022.02.15.480428v1?rss=1
Beacham, G. M.Wei, D. T.Beyrent, E.Zhang, Y.Zheng, J.Camacho, M. M. K.Florens, L.Hollopeter, G.2022-02-18doi:10.1101/2022.02.15.480428Cold Spring Harbor Laboratory Press2022-02-18
<![CDATA[
Identification of protein aggregates in the aging vertebrate brain with prion-like andphase separation properties
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https://biorxiv.org/content/10.1101/2022.02.26.482115v1?rss=1
Harel, I.Chen, Y. R.Ziv, I.Singh, P. P.Navarro Negredo, P.Goshtchevsky, U.Wang, W.Astre, G.Moses, E.McKay, A.Machado, B. E.Hebestreit, K.Yin, S.Sanchez Alvarado, A.Jarosz, D. F.Brunet, A.2022-03-01doi:10.1101/2022.02.26.482115Cold Spring Harbor Laboratory Press2022-03-01
<![CDATA[
Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility
]]>
https://biorxiv.org/content/10.1101/2022.03.12.484091v1?rss=1
Olsen, L.Levy, M.Medley, J. K.Hassan, H.Alexander, R.Wilcock, E.Yi, K.Florens, L.McKinney, S.Peuss, R.Persons, J.Kenzior, A.Maldonado, E.Gluesenkamp, A.Mager, E.Coughlin, D.Rohner, N.2022-03-14doi:10.1101/2022.03.12.484091Cold Spring Harbor Laboratory Press2022-03-14
<![CDATA[
Syrah, a Slide-seqV2 pipeline augmentation
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https://biorxiv.org/content/10.1101/2022.03.20.485023v1?rss=1
Brewster, C. E.Mann, F. G.Benham-Pyle, B. W.Sanchez Alvarado, A.2022-03-21doi:10.1101/2022.03.20.485023Cold Spring Harbor Laboratory Press2022-03-21
<![CDATA[
Stem cells partner with matrix remodeling cells during regeneration
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https://biorxiv.org/content/10.1101/2022.03.20.485025v1?rss=1
Benham-Pyle, B. W.Mann, F. G.Brewster, C. E.Dewars, E. R.Nowotarski, S. H.Guerrero-Hernandez, C.Malloy, S.Hall, K. E.Maddera, L. E.Chen, S.Morrison, J. A.Slaughter, B. D.Perera, A.Alvarado, A. S.2022-03-21doi:10.1101/2022.03.20.485025Cold Spring Harbor Laboratory Press2022-03-21
<![CDATA[
Nr6a1 controls axially-restricted body elongation, segmentation, patterning and lineage allocation
]]>
https://biorxiv.org/content/10.1101/2022.03.21.485239v1?rss=1
McGlinn, E.Chang, Y.-C.Wong, S. F. L.Schroeder, J.Hauswirth, G. M.Shylo, N. A.Moore, E. L.Achilleos, A.Garside, V.Polo, J. M.Manent, J.Trainor, P.2022-03-22doi:10.1101/2022.03.21.485239Cold Spring Harbor Laboratory Press2022-03-22
<![CDATA[
Molecular Control of Circuit Plasticity and the Permanence of Imprinted Odor Memory
]]>
https://biorxiv.org/content/10.1101/2022.03.29.486284v1?rss=1
Wu, Y.Ma, L.Qiu, Q.Xu, W.Misra, A.Duyck, K.Blanck, J.Scott, A. R.Chen, S.Hassan, H.Corbin, T. J.Moran, A.Hall, K.Li, H.Perera, A.Yu, R.2022-03-29doi:10.1101/2022.03.29.486284Cold Spring Harbor Laboratory Press2022-03-29
<![CDATA[
Targeting N-Myc in Neuroblastoma with Selective Aurora Kinase A Degraders
]]>
https://biorxiv.org/content/10.1101/2022.04.09.487756v1?rss=1
Tang, J.Moorthy, R.Demir, O.Baker, Z. D.Naumann, J. A.Jones, K. F. M.Grillo, M. J.Haefner, E. S.Shi, K.Levy, M. J.Aihara, H.Harris, R. S.Amaro, R. E.Levinson, N. M.Harki, D. A.2022-04-10doi:10.1101/2022.04.09.487756Cold Spring Harbor Laboratory Press2022-04-10
<![CDATA[
Meiotic Nuclear Pore Complex Remodeling Provides Key Insights into Nuclear Basket Organization
]]>
https://biorxiv.org/content/10.1101/2022.04.14.488376v1?rss=1
King, G. A.Wettstein, R.Varberg, J. M.Chetlapalli, K.Walsh, M. E.Gillet, L.Hernandez-Armenta, C.Beltrao, P.Aebersold, R.Jaspersen, S. L.Matos, J.Unal, E.2022-04-15doi:10.1101/2022.04.14.488376Cold Spring Harbor Laboratory Press2022-04-15
<![CDATA[
Lola-I is a developmentally regulated promoter pioneer factor
]]>
https://biorxiv.org/content/10.1101/2022.04.25.489272v1?rss=1
Ramalingam, V.Yu, X.Slaughter, B. D.Unruh, J. R.Brennan, K. J.Onyshchenko, A.Lange, J. J.Natarajan, M.Buck, M.Zeitlinger, J.2022-04-27doi:10.1101/2022.04.25.489272Cold Spring Harbor Laboratory Press2022-04-27
<![CDATA[
Isthmal stem cells sustain intestinal homeostasis and regeneration
]]>
https://biorxiv.org/content/10.1101/2022.04.26.489611v1?rss=1
Malagola, E.Vasciaveo, A.Ochiai, Y.Kim, W.Middelhoff, M.Nienhuser, H.Belin, B.LaBella, J.Zamechek, L.Wong, M.Li, L.Guha, C.Yan, K.Califano, A.Wang, T.2022-04-28doi:10.1101/2022.04.26.489611Cold Spring Harbor Laboratory Press2022-04-28
<![CDATA[
Stem Cell Secretome Promotes Scarless Corneal Wound Healing and Rescues Corneal Sensory Nerves
]]>
https://biorxiv.org/content/10.1101/2022.05.07.490347v1?rss=1
Kumar, A.Li, Y.Mallick, S.Yang, E.Dhaliwal, D. K.Price, A.Xie, T.Du, Y.2022-05-07doi:10.1101/2022.05.07.490347Cold Spring Harbor Laboratory Press2022-05-07
<![CDATA[
An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii
]]>
https://biorxiv.org/content/10.1101/2022.05.20.492694v1?rss=1
Lopez, J. M.Tengganu, I. F.Liu, J.Murray, J. M.Arias Padilla, L. F.Zhang, Y.Florens, L.Hu, K.2022-05-20doi:10.1101/2022.05.20.492694Cold Spring Harbor Laboratory Press2022-05-20
<![CDATA[
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
]]>
https://biorxiv.org/content/10.1101/2022.05.24.493321v1?rss=1
Horton, C. A.Alexandari, A. M.Hayes, M. G. B.Marklund, E.Schaepe, J. M.Aditham, A. K.Shah, N.Shrikumar, A. A.Afek, A.Greenleaf, W. J.Gordan, R.Zeitlinger, J.Kundaje, A.Fordyce, P. M.2022-05-25doi:10.1101/2022.05.24.493321Cold Spring Harbor Laboratory Press2022-05-25
<![CDATA[
The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years
]]>
https://biorxiv.org/content/10.1101/2022.06.24.497463v1?rss=1
De Carvalho, M.Jia, G.-S.Nidamangala Srinivasa, A.Billmyre, R. B.Xu, Y.-H.Lange, J. J.Sabbarini, I. M.Du, L.-L.Zanders, S. E.2022-06-26doi:10.1101/2022.06.24.497463Cold Spring Harbor Laboratory Press2022-06-26
<![CDATA[
A PAK kinase family member and the Hippo/Yorkie pathway modulate WNT signaling to functionally integrate body axes during regeneration
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https://biorxiv.org/content/10.1101/2022.07.14.500084v1?rss=1
Doddihal, V.Mann, F. G.Ross, E. J.McKinney, S. A.Alvarado, A. S.2022-07-14doi:10.1101/2022.07.14.500084Cold Spring Harbor Laboratory Press2022-07-14
<![CDATA[
linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
]]>
https://biorxiv.org/content/10.1101/2022.07.21.501032v1?rss=1
Tornini, V. A.Lee, H.-J.Miao, L.Tang, Y.Dube, S. E.Gerson, T.Schmidt, V. J.Du, K.Kuchroo, M.Kroll, F.Vejnar, C. E.Bazzini, A. A.Krishnaswamy, S.Rihel, J.Giraldez, A.2022-07-22doi:10.1101/2022.07.21.501032Cold Spring Harbor Laboratory Press2022-07-22
<![CDATA[
Recombination between heterologous human acrocentric chromosomes
]]>
https://biorxiv.org/content/10.1101/2022.08.15.504037v1?rss=1
Guarracino, A.Buonaiuto, S.Potapova, T.Rhie, A.Koren, S.Rubinstein, B.Fischer, C.Human Pangenome Reference Consortium,Gerton, J. L.Phillippy, A. M.Colonna, V.Garrison, E.2022-08-15doi:10.1101/2022.08.15.504037Cold Spring Harbor Laboratory Press2022-08-15
<![CDATA[
A Local Hebbian Rule Based Model of Invariant Object Representation and Classification.
]]>
https://biorxiv.org/content/10.1101/2022.10.14.511519v1?rss=1
Raj, R.Yu, R.2022-10-18doi:10.1101/2022.10.14.511519Cold Spring Harbor Laboratory Press2022-10-18
<![CDATA[
Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors
]]>
https://biorxiv.org/content/10.1101/2022.11.03.515045v1?rss=1
Williams, R.Taylor, G.Ling, I. T. C.Candido-Ferreira, I.Mayes, S.Bozhilov, Y.Tyser, R. C. V.Srinivas, S.Hughes, J. R.Sauka-Spengler, T.2022-11-04doi:10.1101/2022.11.03.515045Cold Spring Harbor Laboratory Press2022-11-04
<![CDATA[
rRNA transcription is integral to liquid-liquid phase separation and maintenance of nucleolar structure
]]>
https://biorxiv.org/content/10.1101/2022.11.14.516489v1?rss=1
Dash, S.Lamb, M. C.Lange, J. J.McKinney, M. C.Tsuchiya, D.Guo, F.Zhao, X.Corbin, T. J.Kirkman, M.Delventhal, K.Moore, E. L.McKinney, S. A.Shiang, R.Trainor, P.2022-11-15doi:10.1101/2022.11.14.516489Cold Spring Harbor Laboratory Press2022-11-15
<![CDATA[
Distinct states of nucleolar stress induced by anti-cancer drugs
]]>
https://biorxiv.org/content/10.1101/2022.11.18.517150v1?rss=1
View larger version (80K):
org.highwire.dtl.DTLVardef@18724b6org.highwire.dtl.DTLVardef@17b60e7org.highwire.dtl.DTLVardef@117004dorg.highwire.dtl.DTLVardef@114ecec_HPS_FORMAT_FIGEXP M_FIG (1) DNA intercalators and RNA Pol inhibitors induced canonical nucleolar stress manifested by partial dispersion of granular component (GC) and segregation of rDNA and fibrillar center (FC) components UBF, Treacle, and POLR1A within nucleolar stress caps. (2) Inhibition of mTOR and PI3K growth pathways induced a metabolic suppression of function accompanied by the decrease in nucleolar normality score, size, and rRNA production, without dramatic re-organization of nucleolar anatomy. (3) Inhibitors targeting HSP90 and proteasome induced proteotoxicity, resulting in the disruption of protein homeostasis and the accumulation of misfolded and/or undegraded proteins. These effects were accompanied by a decrease in nucleolar normality score, rRNA output, and in some cases formation of protein aggregates (aggresomes) inside the nucleolus. (4) Inhibition of transcriptional CDK activity led to the disruption of interactions between rDNA, RNA Pol I, and GC proteins. This resulted in almost complete nucleolar dissolution, leaving behind an extended bare rDNA scaffold with only a few associated FC proteins remaining. UBF and PolI-recruiting protein Treacle remained associated with the rDNA, while POLR1A and GC dispersed in the nucleoplasm. rRNA production ceased and the nucleolar normality score was greatly reduced.
C_FIG
]]>Potapova, T. A.Unruh, J. R.Conkright-Fincham, J. J.Banks, C. A. S.Florens, L.Schneider, D. A.Gerton, J. L.2022-11-19doi:10.1101/2022.11.18.517150Cold Spring Harbor Laboratory Press2022-11-19
<![CDATA[
Selection-driven trait loss in independently evolved cavefish populations
]]>
https://biorxiv.org/content/10.1101/2022.11.28.518185v1?rss=1
Moran, R. L.Richards, E. J.Ornelas-Garcia, C. P.Gross, J. B.Donny, A.Wiese, J.Keene, A. C.Kowalko, J. E.Rohner, N.McGaugh, S. E.2022-11-28doi:10.1101/2022.11.28.518185Cold Spring Harbor Laboratory Press2022-11-28
<![CDATA[
Convergent deployment of ancestral programs during the evolution of mammalian flight membranes
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https://biorxiv.org/content/10.1101/2022.12.06.518272v1?rss=1
Feigin, C. Y.Moreno, J. A.Ramos, R.Mereby, S. A.Alivisatos, A.Wang, W.van Amerongen, R.Camacho, J.Rasweiler, J. J.Behringer, R.Ostrow, B.Plikus, M. V.Mallarino, R.2022-12-07doi:10.1101/2022.12.06.518272Cold Spring Harbor Laboratory Press2022-12-07
<![CDATA[
Next-generation plasmids for transgenesis in zebrafish and beyond
]]>
https://biorxiv.org/content/10.1101/2022.12.13.520107v1?rss=1
Kemmler, C. L.Moran, H. R.Murray, B. F.Scoresby, A.Klem, J. R.Eckert, R. L.Lepovsky, E.Bertho, S.Nieuwenhuize, S.Burger, S.D'Agati, G.Betz, C.Puller, A.-C.Felker, A.Ditrychova, K.Boetschi, S.Affolter, M.Rohner, N.Lovely, C. B.Kwan, K. M.Burger, A.Mosimann, C.2022-12-14doi:10.1101/2022.12.13.520107Cold Spring Harbor Laboratory Press2022-12-14
<![CDATA[
Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation
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https://biorxiv.org/content/10.1101/2022.12.20.520743v1?rss=1
Brennan, K. J.Weilert, M.Krueger, S.Pampari, A.Liu, H.-Y.Yang, A. W. H.Hughes, T. R.Rushlow, C. A.Kundaje, A.Zeitlinger, J.2022-12-20doi:10.1101/2022.12.20.520743Cold Spring Harbor Laboratory Press2022-12-20
<![CDATA[
A Borrelia burgdorferi LptD Homolog Facilitates Flipping of Surface Lipoproteins Through the Spirochetal Outer Membrane
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https://biorxiv.org/content/10.1101/2022.12.21.521298v1?rss=1
He, H.Pramanik, A. S.Swanson, S. K.Johnson, D. K.Florens, L.Zueckert, W. R.2022-12-22doi:10.1101/2022.12.21.521298Cold Spring Harbor Laboratory Press2022-12-22
<![CDATA[
Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis
]]>
https://biorxiv.org/content/10.1101/2023.01.09.523347v1?rss=1
He, S.Shao, W.Chen, S.Wang, T.Gibson, M.2023-01-10doi:10.1101/2023.01.09.523347Cold Spring Harbor Laboratory Press2023-01-10
<![CDATA[
DYRK1A interacts with Tuberous Sclerosis complex and promotes mTORC1 activity
]]>
https://biorxiv.org/content/10.1101/2023.01.18.524493v1?rss=1
Wang, P.Sarkar, S.Zhang, M.Zhang, Z.Datta, S.Jayaram, N.Datta, S.He, R.Wu, P.Chao, P.Zhang, Y.Washburn, M. P.Florens, L.Nagarkar, S.Jaiswal, M.Mohan, M.2023-01-18doi:10.1101/2023.01.18.524493Cold Spring Harbor Laboratory Press2023-01-18
<![CDATA[
Morphological changes and two Nodal paralogs drive left-right asymmetry in the squamate veiled chameleon (C. calyptratus).
]]>
https://biorxiv.org/content/10.1101/2023.01.18.524635v1?rss=1
Shylo, N.Smith, S. E.Price, A.Guo, F.McClain, M.Trainor, P.2023-01-18doi:10.1101/2023.01.18.524635Cold Spring Harbor Laboratory Press2023-01-18
<![CDATA[
Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish
]]>
https://biorxiv.org/content/10.1101/2023.01.25.525368v1?rss=1
Olsen, L.Krishnan, J.Hassan, H.Banks, C.Rohner, N.2023-01-25doi:10.1101/2023.01.25.525368Cold Spring Harbor Laboratory Press2023-01-25
<![CDATA[
Environmental and molecular regulation of asexual reproduction in the sea anemone Nematostella vectensis
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https://biorxiv.org/content/10.1101/2023.01.27.525773v1?rss=1
Al-Shaer, L.Leach, W.Baban, N.Yagodich, M.Gibson, M. C.Layden, M. J.2023-01-27doi:10.1101/2023.01.27.525773Cold Spring Harbor Laboratory Press2023-01-27
<![CDATA[
Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex
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https://biorxiv.org/content/10.1101/2023.01.31.526478v1?rss=1
Liu, X.Zhang, Y.Wen, Z.Hao, Y.Banks, C.Lange, J. J.Cesare, J.Bhattacharya, S.Slaughter, B.Unruh, J.Florens, L.Workman, J.Washburn, M.2023-02-03doi:10.1101/2023.01.31.526478Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
The Mexican Cavefish Mount a Rapid and Sustained Regenerative Response Following Skeletal Muscle Injury
]]>
https://biorxiv.org/content/10.1101/2023.02.05.527207v1?rss=1
Olsen, L.Hassan, H.Keaton, S.Rohner, N.2023-02-05doi:10.1101/2023.02.05.527207Cold Spring Harbor Laboratory Press2023-02-05
<![CDATA[
Gene coexpression analysis identifies genes associated with chlorophyll content and relative water content in pearl millet
]]>
https://biorxiv.org/content/10.1101/2023.03.16.532967v1?rss=1
Shinde, H.Dudhate, A.Sathe, A.Paserkar, N.Wagh, S. G.Kadam, U. S.2023-03-20doi:10.1101/2023.03.16.532967Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal
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https://biorxiv.org/content/10.1101/2023.03.20.533418v1?rss=1
Kandola, T.Venkatesan, S.Zhang, J.Lerbakken, B. T.Von Schulze, A.Blanck, J. F.Wu, J.Unruh, J. R.Berry, P.Lange, J. J.Box, A. C.Cook, M.Sagui, C.Halfmann, R.2023-03-21doi:10.1101/2023.03.20.533418Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
Protein supersaturation powers innate immune signaling
]]>
https://biorxiv.org/content/10.1101/2023.03.20.533581v1?rss=1
Rodriguez Gama, A.Miller, T.Lange, J. J.Wu, J.Song, X.Venkatesan, S.Unruh, J.Bradford, W.Halfmann, R.2023-03-21doi:10.1101/2023.03.20.533581Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding
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https://biorxiv.org/content/10.1101/2023.05.11.540401v1?rss=1
Alexandari, A. M.Horton, C. A.Shrikumar, A.Shah, N.Li, E.Weilert, M.Pufall, M. A.Zeitlinger, J.Fordyce, P. M.Kundaje, A.2023-05-11doi:10.1101/2023.05.11.540401Cold Spring Harbor Laboratory Press2023-05-11
<![CDATA[
Defining a core configuration for human centromeres during mitosis
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https://biorxiv.org/content/10.1101/2023.05.10.539634v1?rss=1
Gupta, A. S.Seidel, C.Tsuchiya, D.McKinney, S. A.Yu, Z.Smith, S. E.Unruh, J.Gerton, J.2023-05-12doi:10.1101/2023.05.10.539634Cold Spring Harbor Laboratory Press2023-05-12
<![CDATA[
Host-parasite interactions in perpetual darkness: macroparasite diversity in the cavefish Astyanax mexicanus
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https://biorxiv.org/content/10.1101/2023.05.16.540976v1?rss=1
Santacruz, A.Hernandez-Mena, D.Miranda-Gamboa, R.Perez-Ponce de Leon, G.Ornelas-Garcla, C. P.2023-05-18doi:10.1101/2023.05.16.540976Cold Spring Harbor Laboratory Press2023-05-18
<![CDATA[
The variation and evolution of complete human centromeres
]]>
https://biorxiv.org/content/10.1101/2023.05.30.542849v1?rss=1
Logsdon, G. A.Rozanski, A. N.Ryabov, F.Potapova, T.Shepelev, V. A.Mao, Y.Rautiainen, M.Koren, S.Nurk, S.Porubsky, D.Lucas, J. K.Hoekzema, K.Munson, K. M.Gerton, J. L.Phillippy, A. M.Alexandrov, I. A.Eichler, E. E.2023-05-31doi:10.1101/2023.05.30.542849Cold Spring Harbor Laboratory Press2023-05-31
<![CDATA[
Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemone Nematostella vectensis
]]>
https://biorxiv.org/content/10.1101/2023.06.07.544043v1?rss=1
Sabin, K. Z.Chen, S.Hill, E. M.Weaver, K. J.Yonker, J.Kirkman, M.Redwine, B.Klompen, A. M. L.Zhao, X.Guo, F.McKinney, M. C.Dewey, J. L.Gibson, M. C.2023-06-07doi:10.1101/2023.06.07.544043Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment.
]]>
https://biorxiv.org/content/10.1101/2023.06.09.544423v1?rss=1
Biswas, T.Rajendran, N.Hassan, H.Zhao, C.Rohner, N.2023-06-10doi:10.1101/2023.06.09.544423Cold Spring Harbor Laboratory Press2023-06-10
<![CDATA[
Sugar assimilation underlying dietary evolution of Neotropical bats
]]>
https://biorxiv.org/content/10.1101/2023.07.02.547432v1?rss=1
View larger version (39K):
org.highwire.dtl.DTLVardef@744e5dorg.highwire.dtl.DTLVardef@1c4e6fcorg.highwire.dtl.DTLVardef@18baaforg.highwire.dtl.DTLVardef@18853ee_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISugar assimilation differences emphasize metabolic adaptations to diet
C_LIO_LIGlucose tolerance tests provide a quick and practical assessment of dietary ecology
C_LIO_LIBat genomes exhibit positive selection on digestive enzymes and glucose transporters
C_LIO_LIStructural comparisons of proteins suggest altered activity of glucose transporters
C_LIO_LIGlucose absorption differences can be explained by gut anatomy
C_LIO_LIIntestinal villus diversity and novel microanatomy in bats
C_LIO_LIExtreme blood glucose (above 600 and 750 mg/dL) coincides with constitutive expression of apical Slc2a2
C_LIO_LIThe regulation of apical Slc2a2 highlights differences in blood glucose levels
C_LI
]]>Camacho, J.Bernal-Rivera, A.Robb, S.Russell, J.Yi, K.Tsuchiya, D.Wang, Y.Murillo-Garcia, O. E.Rohner, N.2023-07-03doi:10.1101/2023.07.02.547432Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation
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https://biorxiv.org/content/10.1101/2023.07.07.548143v1?rss=1
Bedois, A.Parker, H. J.Bronner, M. E.Krumlauf, R.2023-07-07doi:10.1101/2023.07.07.548143Cold Spring Harbor Laboratory Press2023-07-07
<![CDATA[
PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum.
]]>
https://biorxiv.org/content/10.1101/2023.09.11.557253v1?rss=1
Chahine, Z. M.Gupta, M.Lenz, T.Hollin, T.Abel, S.Banks, C.Saraf, A.Prudhomme, J.Florens, L.Le Roch, K. G.2023-09-11doi:10.1101/2023.09.11.557253Cold Spring Harbor Laboratory Press2023-09-11
<![CDATA[
Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species.
]]>
https://biorxiv.org/content/10.1101/2023.09.21.558237v1?rss=1
Ho, D. V.Tormey, D.Odell, A.Newton, A. A.Schnittker, R. R.Baumann, D. P.Neaves, W. B.Schroeder, M. R.Sigauke, R. F.Barley, A. J.Baumann, P.2023-09-22doi:10.1101/2023.09.21.558237Cold Spring Harbor Laboratory Press2023-09-22
<![CDATA[
Modeling the Evolution of Populations with Multiple Killer Meiotic Drivers
]]>
https://biorxiv.org/content/10.1101/2023.09.28.560003v1?rss=1
Hernandez, J. F. L.Rubinstein, B. Y.Unckless, R. L.Zanders, S. E.2023-10-01doi:10.1101/2023.09.28.560003Cold Spring Harbor Laboratory Press2023-10-01
<![CDATA[
Identification and characterization of intermediate states in mammalian neural crest cell epithelial to mesenchymal transition and delamination
]]>
https://biorxiv.org/content/10.1101/2023.10.26.564204v1?rss=1
Zhao, R.Moore, E. L.Gogol, M. M.Unruh, J. R.Yu, Z.Peak, A.Wang, Y.Rajendran, N. K.Trainor, P. A.2023-10-26doi:10.1101/2023.10.26.564204Cold Spring Harbor Laboratory Press2023-10-26
<![CDATA[
The prevalence of copy number increase at multiallelic CNVs associated with cave colonization
]]>
https://biorxiv.org/content/10.1101/2023.11.10.566513v1?rss=1
Pokrovac, I.Rohner, N.Warren, W. C.Pezer, Z.2023-11-14doi:10.1101/2023.11.10.566513Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery
]]>
https://biorxiv.org/content/10.1101/2023.11.16.567450v1?rss=1
Warren, W. C.Carroll, R. A.Haggerty, L.Keene, A. C.McGaugh, S. E.Ogeh, D.Rice, E. S.Roback, E.Rohner, N.Smith, F.X, M.2023-11-17doi:10.1101/2023.11.16.567450Cold Spring Harbor Laboratory Press2023-11-17
<![CDATA[
A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria.
]]>
https://biorxiv.org/content/10.1101/2023.11.21.568162v1?rss=1
Chahine, Z. M.Abel, S.Hollin, T.Chung, J. H.Barnes, G. L.Daub, M. E.Renard, I.Choi, J. Y.Vydyam, P.Chattopadhyay Pal, A.Argomaniz, M.Banks, C.kirkwood, J.Saraf, A.Camino Diaz, I.Castaneda-Casado, P.Cuevas-Martin, M.De Mercado-Arnanz, J.Fernandez Alvaro, E.Garcia-Perez, A.Ibarz-Ferrer, N.Viera-Morilla, S.Prudhomme, J.Joyner, C. J.Bei, A.Florens, L.Ben Mamoun, C.Vanderwal, C.Le Roch, K. G.2023-11-22doi:10.1101/2023.11.21.568162Cold Spring Harbor Laboratory Press2023-11-22
<![CDATA[
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
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https://biorxiv.org/content/10.1101/2023.11.30.569198v1?rss=1
100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species.
]]>Makova, K. D.Pickett, B. D.Harris, R. S.Hartley, G. A.Cechova, M.Pal, K.Nurk, S.Yoo, D.Li, Q.Hebbar, P.McGrath, B. C.Antonacci, F.Aubel, M.Biddanda, A.Borchers, M.Bornberg, E.Bouffard, G. G.Brooks, S. Y.Carbone, L.Carrel, L.Carroll, A.Chang, P.-C.Chin, C.-S.Cook, D. E.Craig, S. J. C.de Gennaro, L.Diekhans, M.Dutra, A.Garcia, G. H.Grady, P. G. S.Green, R. E.Haddad, D.Hallast, P.Harvey, W. T.Hickey, G.Hillis, D. A.Hoyt, S. J.Jeong, H.Kamali, K.Pond, S. L. K.LaPolice, T. M.Lee, C.Lewis, A. P.Loh, Y.-H. E.Maste2023-12-01doi:10.1101/2023.11.30.569198Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
A new genetically tractable non-vertebrate system to study complete camera-type eye regeneration
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https://biorxiv.org/content/10.1101/2024.01.26.577494v1?rss=1
Accorsi, A.Pardo, B.Ross, E.Corbin, T. J.McClain, M.Weaver, K.Delventhal, K.Morrison, J. A.McKinney, M. C.McKinney, S. A.Sanchez Alvarado, A.2024-01-27doi:10.1101/2024.01.26.577494Cold Spring Harbor Laboratory Press2024-01-27
<![CDATA[
Potential role of microRNAs in regulating transcriptional profile, and sculpting development and metabolism in cavefish.
]]>
https://biorxiv.org/content/10.1101/2024.01.30.578051v1?rss=1
Biswas, T.Hassan, H.Rohner, N.2024-02-02doi:10.1101/2024.01.30.578051Cold Spring Harbor Laboratory Press2024-02-02
<![CDATA[
Interpretable deep learning reveals the sequence rules of Hippo signaling
]]>
https://biorxiv.org/content/10.1101/2024.02.22.580842v1?rss=1
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org.highwire.dtl.DTLVardef@1ee22e9org.highwire.dtl.DTLVardef@1362c82org.highwire.dtl.DTLVardef@1a42512org.highwire.dtl.DTLVardef@17dd619_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Dalal, K.McAnany, C.Weilert, M.McKinney, M. C.Krueger, S.Zeitlinger, J.2024-02-23doi:10.1101/2024.02.22.580842Cold Spring Harbor Laboratory Press2024-02-23
<![CDATA[
Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex
]]>
https://biorxiv.org/content/10.1101/2024.03.05.583553v1?rss=1
Goswami, P.Banks, C.Thornton, J.Bengs, B.Sardiu, M. E.Florens, L.Washburn, M.2024-03-08doi:10.1101/2024.03.05.583553Cold Spring Harbor Laboratory Press2024-03-08
<![CDATA[
Identification of Neural Crest and Neural Crest-Derived Cancer Cell Invasion and Migration Genes Using High-throughput Screening and Deep Attention Networks
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https://biorxiv.org/content/10.1101/2024.03.07.583913v1?rss=1
Kasemeier-Kulesa, J. C.Martina Perez, S.Baker, r. E.Kulesa, P. M.2024-03-10doi:10.1101/2024.03.07.583913Cold Spring Harbor Laboratory Press2024-03-10
<![CDATA[
Gene regulatory network co-option is sufficient to induce a morphological novelty in Drosophila
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https://biorxiv.org/content/10.1101/2024.03.22.584840v1?rss=1
Rice, G. R.Gaitan-Escudero, T.Charles-Obi, K.Zeitlinger, J.Rebeiz, M.2024-03-27doi:10.1101/2024.03.22.584840Cold Spring Harbor Laboratory Press2024-03-27
<![CDATA[
Establishing Primary and Stable Cell Lines from Frozen Wing Biopsies for Cellular, Physiological, and Genetic Studies in Bats
]]>
https://biorxiv.org/content/10.1101/2024.03.22.586286v1?rss=1
Zhao, C.Camacho, J.Rohner, N.Deng, F.Morales-Sosa, P.Bernal-Rivera, A.Wang, Y.Tsuchiya, D.Javier, J.2024-03-27doi:10.1101/2024.03.22.586286Cold Spring Harbor Laboratory Press2024-03-27
<![CDATA[
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS
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https://biorxiv.org/content/10.1101/2024.03.24.586442v1?rss=1
Hintermann, A.Bolt, C. C.Hawkins, M. B.Valentin, G.Lopez-Delisle, L.Gitto, S.Gomez, P. B.Mascrez, B.Mansour, T. A.Nakamura, T.Harris, M. P.Shubin, N. H.Duboule, D.2024-03-27doi:10.1101/2024.03.24.586442Cold Spring Harbor Laboratory Press2024-03-27
<![CDATA[
Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration.
]]>
https://biorxiv.org/content/10.1101/2024.03.28.587250v1?rss=1
Ortega Granillo, A.Zamora, D.Schnittker, R. R.Scott, A. R.Russell, J.Brewster, C. E.Ross, E. J.Acheampong, D. A.Ferro, K.Morrison, J. A.Rubinstein, B. Y.Perera, A. G.Wei, W.Sanchez Alvarado, A.2024-03-31doi:10.1101/2024.03.28.587250Cold Spring Harbor Laboratory Press2024-03-31
<![CDATA[
Poly (A) Binding Protein 2 is critical for stem-progenitor differentiation during regeneration in the planarian Schmidtea mediterranea.
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https://biorxiv.org/content/10.1101/2024.04.11.588998v1?rss=1
Mukundan, N.Hariharan, N.Sasidharan, V.Lakshmanan, V.Palakodeti, D.Jamora, C.2024-04-15doi:10.1101/2024.04.11.588998Cold Spring Harbor Laboratory Press2024-04-15
<![CDATA[
foxg1a is required for hair cell development and regeneration in the zebrafish lateral line
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https://biorxiv.org/content/10.1101/2024.04.12.589268v1?rss=1
Bell, J. M.Biesemeyer, C.Turner, E.Vanderback, M.McGraw, H. F.2024-04-16doi:10.1101/2024.04.12.589268Cold Spring Harbor Laboratory Press2024-04-16
<![CDATA[
Elevated DNA Damage without signs of aging in the short-sleeping Mexican Cavefish
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https://biorxiv.org/content/10.1101/2024.04.18.590174v1?rss=1
Lloyd, E.Xia, F.Moore, K.Zertuche, C.Rastogo, A.Kozol, R.Kenzior, O.Warren, W. C.Appelbaum, L.Moran, R. L.Zhao, C.Duboue, E. R.Rohner, N. R.Keene, A. C.2024-04-21doi:10.1101/2024.04.18.590174Cold Spring Harbor Laboratory Press2024-04-21
<![CDATA[
CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts
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https://biorxiv.org/content/10.1101/2024.05.22.595167v1?rss=1
Hernandez-Huertas, L.Moreno-Sanchez, I.Crespo-Cuadrado, J.Vargas-Baco, A.da Silva-Pescador, G.Santos-Pereira, J. M.Bazzini, A. A.Moreno-Mateos, M. A.2024-05-23doi:10.1101/2024.05.22.595167Cold Spring Harbor Laboratory Press2024-05-23
<![CDATA[
Chromatin remodeling protein BPTF regulates transcriptional stability in planarian stem cells
]]>
https://biorxiv.org/content/10.1101/2024.05.24.595819v1?rss=1
Verma, P.Sanchez Alvarado, A.Duncan, E. M.2024-05-26doi:10.1101/2024.05.24.595819Cold Spring Harbor Laboratory Press2024-05-26
<![CDATA[
Characterization of Multicellular Niches Supporting Hematopoietic Stem Cells Within Distinct Zones
]]>
https://biorxiv.org/content/10.1101/2024.06.28.601225v1?rss=1
Dong, R.Li, H.He, X. C.Wang, C.Perera, A.Malloy, S.Russell, J.Li, W.Petentler, K.Mao, X.Yang, Z.Epp, M.Hall, K.Scott, A.Smith, S.Hembree, M.Wang, Y.McKinney, S.Haug, J.Unruh, J.Slaughter, B.Kang, X.Li, L.2024-07-02doi:10.1101/2024.06.28.601225Cold Spring Harbor Laboratory Press2024-07-02
<![CDATA[
Dynamic Localization of Leukemia Stem Cells via CXCL12 Regulates Leukemia Progression
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https://biorxiv.org/content/10.1101/2024.06.29.601323v1?rss=1
Wang, C.Pan, Y.Dong, R.Zhou, W.Meng, X.Shi, Y.Nistala, R.Hammer, R.Li, L.Kang, X.2024-07-02doi:10.1101/2024.06.29.601323Cold Spring Harbor Laboratory Press2024-07-02
<![CDATA[
Saturation transposon mutagenesis enables genome-wide identification of genes required for growth and fluconazole resistance in the human fungal pathogen Cryptococcus neoformans
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https://biorxiv.org/content/10.1101/2024.07.28.605507v1?rss=1
Billmyre, R. B.Craig, C.Lyon, J. W.Reichardt, C.Eickbush, M. T.Zanders, S. E.2024-07-29doi:10.1101/2024.07.28.605507Cold Spring Harbor Laboratory Press2024-07-29
<![CDATA[
Complete sequencing of ape genomes
]]>
https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1
Yoo, D.Rhie, A.Hebbar, P.Antonacci, F.Logsdon, G. A.Solar, S. J.Antipov, D.Pickett, B. D.Safonova, Y.Montinaro, F.Luo, Y.Malukiewicz, J.Storer, J. M.Lin, J.Sequeira, A. N.Mangan, R. J.Hickey, G.Anez, G. M.Balachandran, P.Bankevich, A.Beck, C. R.Biddanda, A.Borchers, M.Bouffard, G. G.Brannan, E.Brooks, S. Y.Carbone, L.Carrel, L.Chan, A. P.Crawford, J.Diekhans, M.Engelbrecht, E.Feschotte, C.Formenti, G.Garcia, G. H.Gennaro, L. d.Gilbert, D.Green, R. E.Guarracino, A.Gupta, I.Haddad, D.Han, J.Harris, R. S.Hartley2024-07-31doi:10.1101/2024.07.31.605654Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2
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https://biorxiv.org/content/10.1101/2024.08.01.606065v1?rss=1
Smaruj, P. N.Kamulegeya, F.Kelley, D. R.Fudenberg, G.2024-08-04doi:10.1101/2024.08.01.606065Cold Spring Harbor Laboratory Press2024-08-04
<![CDATA[
Borrelia burgdorferi BB0346 is an Essential, Structurally Variant LolA Homolog that is Primarily Required for Homeostatic Localization of Periplasmic Lipoproteins
]]>
https://biorxiv.org/content/10.1101/2024.08.06.606844v1?rss=1
Murphy, B. T.Wiepen, J. J.Graham, D. E.Swanson, S.Kashipathy, M. M.Cooper, A.Battaile, K. P.Johnson, D. K.Florens, L.Blevins, J. S.Lovell, S.Zückert, W. R.2024-08-07doi:10.1101/2024.08.06.606844Cold Spring Harbor Laboratory Press2024-08-07
<![CDATA[
Chamaeleo calyptratus (veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms.
]]>
https://biorxiv.org/content/10.1101/2024.09.03.611012v1?rss=1
Shylo, N.Price, A.Robb, S.Kupronis, R.Guzman Mendez, I. A.DeGraffenreid, D.Gamble, T.Trainor, P.2024-09-07doi:10.1101/2024.09.03.611012Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins
]]>
https://biorxiv.org/content/10.1101/2024.09.09.612016v1?rss=1
Deutsch, E. W.Kok, L. W.Mudge, J. M.Ruiz-Orera, J.Fierro-Monti, I.Sun, Z.Abelin, J. G.Alba, M. M.Aspden, J. L.Bazzini, A. A.Bruford, E.Brunet, M. A.Calviello, L.Carr, S. A.Carvunis, A.-R.Chothani, S.Clauwaert, J.Dean, K.Faridi, P.Frankish, A.Hubner, N.Ingolia, N.Magrane, M.Martin, M. J.Martinez, T. F.Menschaert, G.Ohler, U.Orchard, S.Rackham, O.Roucou, X.Slavoff, S. A.Valen, E.Wacholder, A. C.Weissman, J. S.Wu, W.Xie, Z.Choudhary, J.Bassani-Sternberg, M.Vizcaino, J. A.Ternette, N.Moritz, R. L.Prensner, J.van He2024-09-09doi:10.1101/2024.09.09.612016Cold Spring Harbor Laboratory Press2024-09-09
<![CDATA[
Epigenetic control and inheritance of rDNA arrays
]]>
https://biorxiv.org/content/10.1101/2024.09.13.612795v1?rss=1
Potapova, T. A.Kostos, P.McKinney, S. A.Borchers, M.Haug, J. S.Guarracino, A.Solar, S.Gogol, M. M.Monfort Anez, G.Gomes de Lima, L.Wang, Y.Hall, K. E.Hoffman, S.Garrison, E.Phillippy, A. M.Gerton, J. L.2024-09-16doi:10.1101/2024.09.13.612795Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions
]]>
https://biorxiv.org/content/10.1101/2024.09.17.613303v1?rss=1
Hu, Z.Mayes, S.Wang, W.Santos-Pereira, J. M.Theis, F.Sauka-Spengler, T.2024-09-17doi:10.1101/2024.09.17.613303Cold Spring Harbor Laboratory Press2024-09-17
<![CDATA[
Robust CRISPR/dCas13 RNA blockers specifically perturb miRNA-target interactions and rescue type 1 myotonic dystrophy pathology
]]>
https://biorxiv.org/content/10.1101/2024.09.16.612263v1?rss=1
Hanifi, M.Ates-Kalkan, P. S.Wen, W. X.Fischer, M.Kroesen, A.Yu, Z.Wood, M.Thongjuea, S.Mead, A.Fulga, T. A.Rinaldi, C.Sauka-Spengler, T.2024-09-19doi:10.1101/2024.09.16.612263Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
]]>
https://biorxiv.org/content/10.1101/2024.09.18.613276v1?rss=1
Matentzoglu, N.Bello, S. M.Stefancsik, R.Alghamdi, S. M.Anagnostopoulos, A. V.Balhoff, J. P.Balk, M. A.Bradford, Y. M.Bridges, Y.Callahan, T. J.Caufield, H.Cuzick, A.Carmody, L. C.Caron, A. R.de Souza, V.Engel, S. R.Fey, P.Fisher, M.Gehrke, S.Grove, C.Hansen, P.Harris, N. L.Harris, M. A.Harris, L.Ibrahim, A.Jacobsen, J. O. B.Köhler, S.McMurry, J. A.Munoz-Fuentes, V.Munoz-Torres, M. C.Parkinson, H.Pendlington, Z. M.Pilgrim, C.Robb, S. M. C.Robinson, P. N.Seager, J.Segerdell, E.Smedley, D.Sollis, E.Toro, S.Vasilevsk2024-09-22doi:10.1101/2024.09.18.613276Cold Spring Harbor Laboratory Press2024-09-22
<![CDATA[
A repeatedly evolved mutation in Cryptochrome-1 of subterranean animals alters behavioral and molecular circadian rhythms
]]>
https://biorxiv.org/content/10.1101/2024.09.19.613894v1?rss=1
Swaminathan, A.Kenzior, A.McCoin, C.Price, A.Weaver, K.Hintermann, A.Morris, N.Keene, A. C.Rohner, N.2024-09-23doi:10.1101/2024.09.19.613894Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Quorum sensing orchestrates parallel cell death pathways in Vibrio cholerae via Type 6 secretion dependent and independent mechanisms
]]>
https://biorxiv.org/content/10.1101/2024.09.23.614608v1?rss=1
Mashruwala, A. A.Bassler, B. L.2024-09-23doi:10.1101/2024.09.23.614608Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Real time imaging reveals a role for macrophage protrusive motility in melanoma invasion
]]>
https://biorxiv.org/content/10.1101/2024.09.25.614908v1?rss=1
Ramakrishnan, G.Miskolci, V.Hunter, M.Giese, M. A.Muench, D.Hou, Y.Eliceiri, K. W.Lasarev, M. R.White, R. M.Huttenlocher, A.2024-09-26doi:10.1101/2024.09.25.614908Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
Cave Adaptation Favors Aging Resilience in the Mexican Tetra
]]>
https://biorxiv.org/content/10.1101/2024.09.26.615235v1?rss=1
Cobham, A. E.Kenzior, A.Morales-Sosa, P.Javier, J.Swanson, S.Wood, C.Rohner, N.2024-09-29doi:10.1101/2024.09.26.615235Cold Spring Harbor Laboratory Press2024-09-29
<![CDATA[
An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata
]]>
https://biorxiv.org/content/10.1101/2024.09.29.615694v1?rss=1
He, S.Rangel-Huerta, E.Hill, E.Ellington, L.Chen, S.Robb, S.Majerov, E.Drury, C.Gibson, M.2024-09-30doi:10.1101/2024.09.29.615694Cold Spring Harbor Laboratory Press2024-09-30
<![CDATA[
3D genome organization under extreme metabolic adaptation shows variations in genome compartmentalization and looping
]]>
https://biorxiv.org/content/10.1101/2024.09.30.615929v1?rss=1
Biswas, T.Li, H.Rohner, N.2024-10-02doi:10.1101/2024.09.30.615929Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Enhanced RNA-targeting CRISPR-Cas technology in zebrafish
]]>
https://biorxiv.org/content/10.1101/2024.10.08.617220v1?rss=1
Moreno-Sanchez, I.Hernandez-Huertas, L.Nahon-Cano, D.Gomez-Marin, C.Martinez-Garcia, P. M.Tomas-Gallardo, L.da Silva Pescador, G.Kushawah, G.Diaz-Moscoso, A.Cano-Ruiz, A.Walker, J. A.Munoz, M. J.Holden, K.Galceran, J.Nieto, M. A.Bazzini, A.Moreno-Mateos, M. A.2024-10-10doi:10.1101/2024.10.08.617220Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
Stem and progenitor cell proliferation are independently regulated by cell type-specific cyclinD genes
]]>
https://biorxiv.org/content/10.1101/2024.10.21.619490v1?rss=1
Lush, M. E.Tsai, Y.-Y.Chen, S.Muench, D.Peloggia, J.Sandler, J. E.Piotrowski, T.2024-10-22doi:10.1101/2024.10.21.619490Cold Spring Harbor Laboratory Press2024-10-22
<![CDATA[
Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms
]]>
https://biorxiv.org/content/10.1101/2024.10.22.616524v1?rss=1
Franklin, J. M.Dubocanin, D.Chittenden, C.Barillas, A. G.Lee, R. J.Ghosh, R. P.Gerton, J. L.Guan, K.-L.Altemose, N.2024-10-23doi:10.1101/2024.10.22.616524Cold Spring Harbor Laboratory Press2024-10-23
<![CDATA[
Long-term hybridization in a karst window reveals the genetic basis of eye loss in cavefish
]]>
https://biorxiv.org/content/10.1101/2024.10.25.620266v1?rss=1
Kellermeyer, R.Seidel, C.Redwine, W. B.Moran, R. L.Bertho, S.Ornelas-Garcia, C. P.Alegre, D.Weaver, K. J.Unruh, J.Troutwine, B.Wang, Y.Collins, E.Rutkowski, J.McGaugh, S. E.Espinasa, L.Rohner, N.2024-10-28doi:10.1101/2024.10.25.620266Cold Spring Harbor Laboratory Press2024-10-28
<![CDATA[
Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis
]]>
https://biorxiv.org/content/10.1101/2024.11.07.622483v1?rss=1
Kushawah, G.Amaral, D. B.Hassan, H.Gogol, M. M.Nowotarski, S. H.Bazzini, A. A.2024-11-08doi:10.1101/2024.11.07.622483Cold Spring Harbor Laboratory Press2024-11-08
<![CDATA[
Paired and solitary ionocytes in the zebrafish olfactory epithelium
]]>
https://biorxiv.org/content/10.1101/2024.11.08.620918v1?rss=1
Peloggia, J.Cheung, K. Y.Whitfield, T. T.Petkova, M.Schalek, R.Boulanger-Weill, J.Wu, Y.Wang, S.van Hateren, N. J.Januszewski, M.Jain, V.Lichtman, J. W.Engert, F.Piotrowski, T.Jesuthasan, S.2024-11-08doi:10.1101/2024.11.08.620918Cold Spring Harbor Laboratory Press2024-11-08
<![CDATA[
Patterns of crossover distribution in Drosophila mauritiana necessitate a re-thinking of the centromere effect on crossing over
]]>
https://biorxiv.org/content/10.1101/2024.11.11.623017v1?rss=1
Hawley, R. S.Price, A.Li, H.Jagannathan, M.Staber, C.Hughes, S. E.Williams, S.Perera, A.Egidy, R. R.Lawlor, A.Blumenstiel, J. P.2024-11-11doi:10.1101/2024.11.11.623017Cold Spring Harbor Laboratory Press2024-11-11
<![CDATA[
Common AAV gene therapy vectors show indiscriminate transduction of living human brain cell types
]]>
https://biorxiv.org/content/10.1101/2024.11.14.623624v1?rss=1
McGinnis, J.Ortiz-Guzman, J.Guevara, M. C.Mallannagari, S.Belfort, B. D.Bao, S.Srivastava, S.Morkas, M.Ji, E.Addison, A.Tantry, E.Chen, S.Wang, Y.Chen, Z.Katlowitz, K. A.Lange, J. J.Blessing, M.Mohila, C.Ljungberg, M. C.Aldave, G.Jalali, A.Patel, A.Sheth, S.Weiner, H. L.Gopinath, S.Rao, G.Serin-Harmanci, A.Curry, D.Arenkiel, B.2024-11-15doi:10.1101/2024.11.14.623624Cold Spring Harbor Laboratory Press2024-11-15
<![CDATA[
Drone-Based Identification of Flood-Tolerant Maize via Multispectral Imaging: A Real-World Case Study
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https://biorxiv.org/content/10.1101/2024.11.26.625493v1?rss=1
Mitchell, M. N.Sidberry, G.Mathison, M.DeSalvio, A. J.Kick, D. R.Washburn, J. D.2024-11-28doi:10.1101/2024.11.26.625493Cold Spring Harbor Laboratory Press2024-11-28
<![CDATA[
Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures
]]>
https://biorxiv.org/content/10.1101/2024.12.03.626649v1?rss=1
Converse, A.Perry, M. J.Dipali, S. S.Isola, J. V.Kelley, E. B.Varberg, J. M.Zelinkski, M. B.Gerton, J. L.Stout, M.Pritchard, M. T.Duncan, F.2024-12-04doi:10.1101/2024.12.03.626649Cold Spring Harbor Laboratory Press2024-12-04
<![CDATA[
A tool to dissect heterotypic determinants of homotypic protein phase behavior
]]>
https://biorxiv.org/content/10.1101/2025.01.01.631016v1?rss=1
Kimbrough, H.Jensen, J.Weber, C.Miller, T.Maddera, L. E.Babu, V.Redwine, W. B.Halfmann, R.2025-01-02doi:10.1101/2025.01.01.631016Cold Spring Harbor Laboratory Press2025-01-02
<![CDATA[
NR6A1 is essential for neural crest cell specification, formation and survival
]]>
https://biorxiv.org/content/10.1101/2025.01.02.630962v1?rss=1
Moore, E. L.Munoz, W.Bhatt, S.Sakai, D.Achilleos, A.Zhao, R.Lamb, M.Price, A.Seidel, C.Tiana, M.Barral, A.Clawson, D.Manzanares, M.Trainor, P.2025-01-03doi:10.1101/2025.01.02.630962Cold Spring Harbor Laboratory Press2025-01-03
<![CDATA[
An unexpected mode of whole-body regeneration from reaggregated cell suspension in Hydractinia (Cnidaria, Hydrozoa)
]]>
https://biorxiv.org/content/10.1101/2025.01.06.631080v1?rss=1
Curantz, C.Krasovec, G.Horkan, H. R.Ryan, L. M.Varley, A.Frank, U.2025-01-06doi:10.1101/2025.01.06.631080Cold Spring Harbor Laboratory Press2025-01-06
<![CDATA[
Rdh10-mediated Retinoic Acid Signaling Regulates the Neural Crest Cell Microenvironment During ENS Formation
]]>
https://biorxiv.org/content/10.1101/2025.01.23.634504v1?rss=1
Butler Tjaden, N. E.Shannon, S. R.Seidel, C. W.Childers, M.Aoto, K.Sandell, L. L.Trainor, P.2025-01-23doi:10.1101/2025.01.23.634504Cold Spring Harbor Laboratory Press2025-01-23
<![CDATA[
Precise engineering of chimeric antigen receptor expression levels defines T cell identity and function
]]>
https://biorxiv.org/content/10.1101/2025.02.10.637482v1?rss=1
Ramos, A. S.Simon, S.Siller-Farfan, J.Rajan, A.Revale, S.Zanchini di Castiglionchio, E.Pelea, O.Fulga, T. A.Riddell, S.Dushek, O.Michaels, Y. S.Sauka-Spengler, T.2025-02-11doi:10.1101/2025.02.10.637482Cold Spring Harbor Laboratory Press2025-02-11
<![CDATA[
Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation
]]>
https://biorxiv.org/content/10.1101/2025.02.13.638191v1?rss=1
Xia, F.Santacruz, A.Wu, D.Bertho, S.Fritz, E.Morales-Sosa, P.McKinney, S.Nowotarski, S. H.Rohner, N.2025-02-17doi:10.1101/2025.02.13.638191Cold Spring Harbor Laboratory Press2025-02-17
<![CDATA[
PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data
]]>
https://biorxiv.org/content/10.1101/2025.04.07.647613v1?rss=1
Zeitlinger, J.McAnany, C. E.Weilert, M.Kamulegeya, F.Mehta, G.Gardner, J. M.Kundaje, A.2025-04-08doi:10.1101/2025.04.07.647613Cold Spring Harbor Laboratory Press2025-04-08
<![CDATA[
Clonal effects of the Ras oncogene revealed by somatic mutagenesis in a Drosophila cancer model
]]>
https://biorxiv.org/content/10.1101/2025.05.08.652841v1?rss=1
Akiyama, T.Gibson, M. C.2025-05-10doi:10.1101/2025.05.08.652841Cold Spring Harbor Laboratory Press2025-05-10
<![CDATA[
ASPPs multimerize protein phosphatase 1
]]>
https://biorxiv.org/content/10.1101/2025.05.16.654433v1?rss=1
Wei, D. T.Morrison, K. N.Beacham, G. M.Beyrent, E.Zhang, Y.Florens, L.Hollopeter, G.2025-05-19doi:10.1101/2025.05.16.654433Cold Spring Harbor Laboratory Press2025-05-19
<![CDATA[
Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images
]]>
https://biorxiv.org/content/10.1101/2025.05.20.654789v1?rss=1
Brence, B.Brummer, J.Dercksen, V. J.Ozel, M. N.Kulkarni, A.Wolterhoff, N.Prohaska, S.Hiesinger, P. R.Baum, D.2025-05-21doi:10.1101/2025.05.20.654789Cold Spring Harbor Laboratory Press2025-05-21
<![CDATA[
Impacts of stress and aging on spore health in Schizosaccharomyces pombe
]]>
https://biorxiv.org/content/10.1101/2025.05.29.656811v1?rss=1
Nuckolls, N. L.Eickbush, M. T.Lange, J. J.Wood, C. J.Nowotarski, S. H.Zanders, S. E.2025-05-30doi:10.1101/2025.05.29.656811Cold Spring Harbor Laboratory Press2025-05-30
<![CDATA[
prdm1a drives a fate switch between hair cells of different mechanosensory organs
]]>
https://biorxiv.org/content/10.1101/2025.06.01.657251v1?rss=1
Sandler, J.Tsai, Y.-Y.Chen, S.Sabin, L.Lush, M.Sur, A.Ellis, E.Tran, N. T. T.Cook, M.Scott, A. R.Kniss, J. S.Farrell, J. A.Piotrowski, T.2025-06-03doi:10.1101/2025.06.01.657251Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
Using evolution as a tool: Replacing corolla in Drosophila melanogaster with its Drosophila mauritiana ortholog creates a novel hypomorphic allele
]]>
https://biorxiv.org/content/10.1101/2025.06.11.659179v1?rss=1
Williams, S.McKown, G.Yu, Z.Staber, C.Gibson, M.Hawley, R. S.2025-06-13doi:10.1101/2025.06.11.659179Cold Spring Harbor Laboratory Press2025-06-13
<![CDATA[
From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines
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https://biorxiv.org/content/10.1101/2025.07.01.662643v1?rss=1
View larger version (30K):
org.highwire.dtl.DTLVardef@490f49org.highwire.dtl.DTLVardef@8ab615org.highwire.dtl.DTLVardef@b840e1org.highwire.dtl.DTLVardef@ab92eb_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Deng, F.Pena, V.Morales-Sosa, P.Bernal-Rivera, A.Yang, B.Ghosh, S.Castellano, L.Katt, M.Huang, S.Maddera, C.Yu, Z.Rohner, N.zhao, c.Camacho, J.2025-07-03doi:10.1101/2025.07.01.662643Cold Spring Harbor Laboratory Press2025-07-03
<![CDATA[
An expanded reference catalog of translated open reading frames for biomedical research
]]>
https://biorxiv.org/content/10.1101/2025.07.03.662928v1?rss=1
Chothani, S.Ruiz-Orera, J.Tierney, J. A. S.Clauwaert, J.Deutsch, E. W.Alba, M. M.Aspden, J. L.Baranov, P. V.Bazzini, A. A.Bruford, E. A.Brunet, M. A.Cardon, T.Carvunis, A.-R.Casola, C.Choudhary, J. S.Dean, K.Faridi, P.Fierro-Monti, I.Fournier, I.Frankish, A.Gerstein, M.Hubner, N.Jiang, Y.Kellis, M.Kok, L. W.Martinez, T. F.Menschaert, G.Ni, P.Orchard, S.Roucou, X.Rozowsky, J.Salzet, M.Siragusa, M.Slavoff, S.Swirski, M. I.Valen, E.Vizcaino, J. A.Wacholder, A.Wu, W.Xie, Z.Yang, Y. T.Moritz, R. L.Mudge, J.van Hee2025-07-07doi:10.1101/2025.07.03.662928Cold Spring Harbor Laboratory Press2025-07-07
<![CDATA[
GAME: Genomic API for Model Evaluation
]]>
https://biorxiv.org/content/10.1101/2025.07.04.663250v1?rss=1
Luthra, I.Priyadarshi, S.Guo, R.Mahieu, L.Kempynck, N.Dooley, D.Penzar, D.Vorontsov, I.Sheng, Y.Tu, X.Klie, A.Drusinsky, S.Floren, A.Armand, E.Alasoo, K.Seelig, G.Tewhey, R.Koo, P.Agarwal, V.Gosai, S.Pinello, L.White, M. A.Lal, A.Zeitlinger, J.Pollard, K. S.Libbrecht, M.Carter, H.Mostafavi, S.Kulakovskiy, I.Hsiao, W.Aerts, S.Zhou, J.de Boer, C. G.2025-07-08doi:10.1101/2025.07.04.663250Cold Spring Harbor Laboratory Press2025-07-08
<![CDATA[
Basal Cell-Contact Dynamics Influence Tissue Packing in a Proliferating Mammalian Epithelium
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https://biorxiv.org/content/10.1101/2025.07.30.665610v1?rss=1
Ramanathan, S. P.Sarkar, T.Krajnc, M.Mwithiga, R.Cerci, A.Zhao, C.Gibson, M. C.2025-07-31doi:10.1101/2025.07.30.665610Cold Spring Harbor Laboratory Press2025-07-31
<![CDATA[
Programmed meiotic errors facilitate dichotomous sperm production in the silkworm, Bombyx mori
]]>
https://biorxiv.org/content/10.1101/2025.08.03.667510v1?rss=1
Benner, L.Richmond, M.Xiang, Y.Lee, L.Li, T.Yu, Z.Tsuchiya, D.Huang, S.Hockens, C. B.Tromer, E. C.Hawley, R. S.Rosin, L. F.2025-08-03doi:10.1101/2025.08.03.667510Cold Spring Harbor Laboratory Press2025-08-03
<![CDATA[
Epiblast Lumenogenesis is not a mammalian-specific trait
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https://biorxiv.org/content/10.1101/2025.08.06.669009v1?rss=1
Weberling, A.Shylo, N. A.Wilson, H.McClain, M.Kupronis, R.Muensch, A.Williams, S. A.Hollfelder, F.Trainor, P. A.2025-08-09doi:10.1101/2025.08.06.669009Cold Spring Harbor Laboratory Press2025-08-09
<![CDATA[
Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex
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https://biorxiv.org/content/10.1101/2025.08.08.669391v1?rss=1
Nde, J.Kempf, C.Zimmermann, R.Cesare, J.Zhang, Y.Workman, J.Florens, L.Washburn, M.2025-08-09doi:10.1101/2025.08.08.669391Cold Spring Harbor Laboratory Press2025-08-09
<![CDATA[
Regulatory logic of neuronal identity specification in Drosophila
]]>
https://biorxiv.org/content/10.1101/2025.09.01.673531v1?rss=1
Coyne, R.Treese, M.Chen, Y.-C.Lake, C.Tabi, O. B.Rajesh, R.Hassan, H.Li, H.Desplan, C.Ozel, M. N.2025-09-03doi:10.1101/2025.09.01.673531Cold Spring Harbor Laboratory Press2025-09-03
<![CDATA[
Biophysical mechanisms of morphogenesis in lizard lungs
]]>
https://biorxiv.org/content/10.1101/2025.09.01.673487v1?rss=1
Hill, K.Griffing, A. H.Palmer, M. A.Lemma, B.Lupo, A.Gamble, T.Shylo, N. A.Kosmrlj, A.Trainor, P.Nelson, C. M.2025-09-04doi:10.1101/2025.09.01.673487Cold Spring Harbor Laboratory Press2025-09-04
<![CDATA[
Neurodegeneration emerges at a cellular tipping point between protein accumulation and removal.
]]>
https://biorxiv.org/content/10.1101/2025.09.08.674880v1?rss=1
Cotton, M. W.Venkatesan, S.Beckwith, J. S.Böken, D.Xu, C. K.Breiter, J. C.Berkowicz, L. E.Salazar, L. S.Von Schulze, A.Andrzejewska, E. A.Brock, E. E.Han, H. L.Schneider, M. M.Sahtoe, D. D.Baker, D.Rowe, J. B.Goriely, A.McEwan, W. A.Knowles, T. P. J.Lee, S. F.Halfmann, R.Klenerman, D.Meisl, G.2025-09-12doi:10.1101/2025.09.08.674880Cold Spring Harbor Laboratory Press2025-09-12
<![CDATA[
Structure-based phylogenetic analysis reveals multiple events of convergent evolution of cysteine-rich antimicrobial peptides in legume-rhizobium symbiosis
]]>
https://biorxiv.org/content/10.1101/2025.09.09.675119v1?rss=1
View larger version (50K):
org.highwire.dtl.DTLVardef@8d1698org.highwire.dtl.DTLVardef@c65b98org.highwire.dtl.DTLVardef@a75994org.highwire.dtl.DTLVardef@ea1a73_HPS_FORMAT_FIGEXP M_FIG Overview of the experimental and computational workflow for NCR peptide detection, characterization, and structural analysis.
Nodule and root samples from Indigofera argentea (8 weeks post-inoculation) were collected and subjected to RNA extraction, library preparation, and Illumina PE150 sequencing. Raw RNA-seq reads from two Lupinus species were also included (Lupinus luteus and Lupinus mariae-josephae). Bacteroid differentiation of I. argentea was assessed by flow cytometry and confocal microscopy. Transcriptomes were assembled de novo and analyzed for differential gene expression between root and nodule tissues. NCR peptides were identified from them and other legume genomes and transcriptomes using the SPADA pipeline and HMM profiles from NCR clusters of the known NCR peptides. The putative NCR peptides were filtered based on conserved cysteine motifs, length, and nodule expression to build an exhaustive NCR peptide database. 3D structural predictions of NCR clusters were performed using AlphaFold2 (pLDDT >70), followed by structural clustering (Foldseek) and phylogenetic analysis (Foldtree). Functional validation involved flow cytometry and antimicrobial assays (against Eschericha coli, Sinorhizobium meliloti, and Bacillus subtilis), enabling structural and evolutionary characterization of NCR peptides. The green box at the top represents the experimental analysis, the blue box represents the sequence-based computational pipeline, the red box represents the structure-based computational pipeline, and the grey box at the bottom left represents the functional validation and interpretation of the results.
C_FIG
]]>Boukherissa, A.Sankari, S.Timchenko, T.Bourge, M.Mergaert, P.diCenzo, G. C.Shykoff, J. A.Alunni, B.Rodriguez de la Vega, R. C.2025-09-14doi:10.1101/2025.09.09.675119Cold Spring Harbor Laboratory Press2025-09-14
<![CDATA[
Oogenesis and germinal bed morphology of the brown anole (A. sagrei)
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https://biorxiv.org/content/10.1101/2025.09.11.675729v1?rss=1
Kircher, B. K.Weberling, A.Vance, E. J.Shylo, N. A.Starr, K.Griffin, Z. B.Wilson, H.McClain, M.Hollfelder, F.Williams, S. A.Sanger, T. J.Behringer, R.Trainor, P.2025-09-17doi:10.1101/2025.09.11.675729Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Vascular Patterning affects Intramembranous Ossification through HIF1α-Vegf Signaling
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https://biorxiv.org/content/10.1101/2025.09.13.676037v1?rss=1
Dash, S.Rettig, J. R.Gogol, M. M.Trainor, P.2025-09-17doi:10.1101/2025.09.13.676037Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
The BacA(SbmA) Importer of Symbiotically Important Legume Nodule Cysteine-Rich Peptides: Insights into Protein Architecture, Function, and Evolutionary Implications
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https://biorxiv.org/content/10.1101/2025.09.17.676847v1?rss=1
Arnold, M. F. F.Sankari, S.Deutsch, M.Gruber, C. C.Guerra-Garcia, F. J.Beis, K.Walker, G. C.2025-09-20doi:10.1101/2025.09.17.676847Cold Spring Harbor Laboratory Press2025-09-20
<![CDATA[
A CRISPR Interference System for Inducible Gene Knockdown in soil bacterium Sinorhizobium meliloti
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https://biorxiv.org/content/10.1101/2025.09.23.678109v1?rss=1
Guerra-Garcia, F. J.Sankari, S.2025-09-25doi:10.1101/2025.09.23.678109Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
A proximity labeling approach to identify proteins that associate with synaptonemal complex components in Drosophila melanogaster females
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https://biorxiv.org/content/10.1101/2025.10.14.682398v1?rss=1
Hughes, S. E.Viermann, C.James, M.Banks, C. S.Hawley, R. S. E.2025-10-15doi:10.1101/2025.10.14.682398Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
Major cell type differences between larval and adult hemichordate body plans
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https://biorxiv.org/content/10.1101/2025.10.31.685866v1?rss=1
Bump, P.Brewster, C.Formery, L.Lubeck, L.Campbell, C.Morri, M.Sit, R.Rokhsar, D.Benham-Pyle, B.Lowe, C.2025-11-03doi:10.1101/2025.10.31.685866Cold Spring Harbor Laboratory Press2025-11-03
<![CDATA[
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
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https://biorxiv.org/content/10.1101/2025.11.18.685822v1?rss=1
Weilert, M.Brennan, K.Dalal, K.Krueger, S.Jiang, H.Martinez-Corral, R.Zeitlinger, J.2025-11-19doi:10.1101/2025.11.18.685822Cold Spring Harbor Laboratory Press2025-11-19
<![CDATA[
Loss of SPECC1L in cranial neural crest cells results in increased hedgehog signaling and frontonasal dysplasia
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https://biorxiv.org/content/10.1101/2025.11.21.689834v1?rss=1
Tran, A. J.Hufft-Martinez, B. M.Thalman, D. N.Maili, L.McKinney, S.Goering, J. P.Trainor, P. A.Saadi, I.2025-11-24doi:10.1101/2025.11.21.689834Cold Spring Harbor Laboratory Press2025-11-24
<![CDATA[
High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo
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https://biorxiv.org/content/10.64898/2025.12.22.691305v1?rss=1
Garcia-Moreno Alcantara, S.Bourdareau, S.Weilert, M.Zeitlinger, J.2025-12-23doi:10.64898/2025.12.22.691305Cold Spring Harbor Laboratory Press2025-12-23
<![CDATA[
Origin and evolution of acrocentric chromosomes in human and great apes
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https://biorxiv.org/content/10.64898/2025.12.22.696095v1?rss=1
Solar, S. J.Hebbar, P.de Lima, L. G.Sweeten, A. P.Rhie, A.Potapova, T. A.de Gennaro, L.Guarracino, A.Kim, J.Pickett, B. D.Paten, B.Wilson, M. A.Koren, S.Garrison, E.Eichler, E. E.Ventura, M.Gerton, J. L.Phillippy, A. M.2025-12-23doi:10.64898/2025.12.22.696095Cold Spring Harbor Laboratory Press2025-12-23
<![CDATA[
The Nematostella synaptonemal complex mediates divergent and sex-specific meiotic programs
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https://biorxiv.org/content/10.64898/2026.01.18.699972v1?rss=1
Williams, S.Gardner, J.Nowotarski, S. H.Gibson, M. C.2026-01-21doi:10.64898/2026.01.18.699972Cold Spring Harbor Laboratory Press2026-01-21
<![CDATA[
Morphological, molecular, and functional evidence for a CNS-like oral nerve ring in the sea anemone Nematostella vectensis
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https://biorxiv.org/content/10.64898/2026.01.28.701697v1?rss=1
Zhong, R.Seidel, C. W.Klompen, A. M.Gibson, M. C.2026-01-29doi:10.64898/2026.01.28.701697Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
Intracellular TDP-43 amyloid nucleates from arrested nascent condensates
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https://biorxiv.org/content/10.64898/2026.02.10.705006v1?rss=1
Wu, J.Venkatesan, S.Jensen, J.Miller, T.Lange, J. J.McKinney, S. A.Halldorsson, E.Yu, Z.Babu, V. M.Sancho Salazar, L.Haug, J.Unruh, J.Halfmann, R.2026-02-11doi:10.64898/2026.02.10.705006Cold Spring Harbor Laboratory Press2026-02-11
<![CDATA[
Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes
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https://biorxiv.org/content/10.64898/2026.02.23.707519v1?rss=1
Lu, Y.Podobnik, M.Ando, K.Pan, M.Locop, J.Guo, A.Mourrain, P.Kikuchi, K.Ruparelia, A. A.Currie, P. D.2026-02-25doi:10.64898/2026.02.23.707519Cold Spring Harbor Laboratory Press2026-02-25
<![CDATA[
The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling
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https://biorxiv.org/content/10.64898/2026.02.26.708310v1?rss=1
Yoo, S.Vannur, L.Li, L.Young, C.Liu, Q.Wen, Z.Zhang, Y.Florens, L.Si, K.Zhuang, J.Zheng, F.Zhou, C.2026-03-01doi:10.64898/2026.02.26.708310Cold Spring Harbor Laboratory Press2026-03-01
<![CDATA[
The human parasite, Toxoplasma gondii, is paralyzed without two components of the apical polar ring
]]>
https://biorxiv.org/content/10.64898/2026.03.07.707822v1?rss=1
Lopez, J. M.Arias Padilla, L. F.Tengganu, I. F.Hao, Y.Zhang, Y.Florens, L.Murray, J. M.Hu, K.2026-03-09doi:10.64898/2026.03.07.707822Cold Spring Harbor Laboratory Press2026-03-09
<![CDATA[
Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes
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https://biorxiv.org/content/10.64898/2026.03.08.710242v1?rss=1
Rhie, A.Kim, J.Rodriguez-Algarra, F.Solar, S.Koren, S.Antipov, D.Wilczewski, C. M.Maxwell, G. L.Gerton, J.Paschall, J.Potapova, T.Wolfsberg, T. G.Singh, S.del Castillo del Rio, S. O.Human Pangenome Reference Consortium,Turner, C.Rakyan, V. K.Phillippy, A. M.2026-03-10doi:10.64898/2026.03.08.710242Cold Spring Harbor Laboratory Press2026-03-10
<![CDATA[
Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome
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https://biorxiv.org/content/10.64898/2026.03.16.712198v1?rss=1
Nde, J.Majila, K.Zimmermann, R.Kempf, C.Zhang, Y.Cesare, J.Thornton, J.Workman, J.Florens, L.Viswanath, S.Washburn, M.2026-03-17doi:10.64898/2026.03.16.712198Cold Spring Harbor Laboratory Press2026-03-17
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Rapidly evolving aphid gall effector proteins exhibit saposin-like folds
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https://biorxiv.org/content/10.64898/2026.03.27.712717v1?rss=1
Bhoinderwala, F.Korgaonkar, A.Gopalakrishna, K.Mathers, T. C.Shigenobu, S.Bazan, F. J.Hogenhout, S. A.Gronenborn, A.Stern, D.2026-03-28doi:10.64898/2026.03.27.712717Cold Spring Harbor Laboratory Press2026-03-28
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fishROI: A specialized workflow for semi-automated muscle morphometry analysis in teleosts
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https://biorxiv.org/content/10.64898/2026.03.27.714781v1?rss=1
Lu, Y.Pan, M.Jamwal, V.Locop, J.Ruparelia, A. A.Currie, P. D.2026-03-30doi:10.64898/2026.03.27.714781Cold Spring Harbor Laboratory Press2026-03-30
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Haplotype-resolved centromeric chromatin organization from a complete diploid human genome
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https://biorxiv.org/content/10.64898/2026.03.27.714900v1?rss=1
Xu, Y.Loucks, H.Menendez, J.Ryabov, F.Lucas, J. K.Cechova, M.Morina, L.Xu, E.Dubocanin, D.Chittenden, C.Asri, M.Violich, I.Ortiz, C.Gardner, J. M. V.Hillaker, T.O'Rourke, S.McNulty, B.Potapova, T. A.Mitchell, M. W.Schwartz, J. P.Straight, A. F.Gerton, J. L.Timp, W.Alexandrov, I. A.Altemose, N.Miga, K. H.2026-03-31doi:10.64898/2026.03.27.714900Cold Spring Harbor Laboratory Press2026-03-31
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A versatile cryopreservation method for peri-gastrulation squamate embryos optimised using the veiled chameleon (C. calyptratus)
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https://biorxiv.org/content/10.64898/2026.04.01.715795v1?rss=1
Weberling, A.Durnin, M.Shylo, N. A.McKinney, M. C.Wilson, H.Kupronis, R.Williams, S. A.Trainor, P.2026-04-02doi:10.64898/2026.04.01.715795Cold Spring Harbor Laboratory Press2026-04-02