bioRxiv Channel: Morgridge Institute https://biorxiv.org This feed contains articles for bioRxiv Channel "Morgridge Institute" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Evaluation of de novo transcriptome assemblies from RNA-Seq data ]]> https://biorxiv.org/content/10.1101/006338v1?rss=1 Bo Li Nathanael Fillmore Yongsheng Bai Mike Collins James A Thomson Ron Stewart Colin Dewey 2014-06-13 doi:10.1101/006338 Cold Spring Harbor Laboratory Press 2014-06-13 <![CDATA[ OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/025437v1?rss=1 Ning Leng Jeea Choi Li-Fang Chu James Thomson Christina Kendziorski Ron Stewart 2015-08-25 doi:10.1101/025437 Cold Spring Harbor Laboratory Press 2015-08-25 <![CDATA[ scDD: A statistical approach for identifying differential distributions in single-cell RNA-seq experiments ]]> https://biorxiv.org/content/10.1101/035501v1?rss=1 Keegan D. Korthauer Li-Fang Chu Michael A. Newton Yuan Li James Thomson Ron Stewart Christina Kendziorski 2015-12-29 doi:10.1101/035501 Cold Spring Harbor Laboratory Press 2015-12-29 <![CDATA[ SCPattern: A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions ]]> https://biorxiv.org/content/10.1101/046110v1?rss=1 Ning Leng Li-Fang Chu Jeea Choi Christina Kendziorski James Thomson Ron Stewart 2016-03-29 doi:10.1101/046110 Cold Spring Harbor Laboratory Press 2016-03-29 <![CDATA[ SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/090167v1?rss=1 Bacher, R. Chu, L.-F. Leng, N. Gasch, A. P. Thomson, J. A. Stewart, R. M. Newton, M. Kendziorski, C. 2016-11-28 doi:10.1101/090167 Cold Spring Harbor Laboratory Press 2016-11-28 <![CDATA[ Opportunities And Obstacles For Deep Learning In Biology And Medicine ]]> https://biorxiv.org/content/10.1101/142760v1?rss=1 Ching, T. Himmelstein, D. S. Beaulieu-Jones, B. K. Kalinin, A. A. Do, B. T. Way, G. P. Ferrero, E. Agapow, P.-M. Xie, W. Rosen, G. L. Lengerich, B. J. Israeli, J. Lanchantin, J. Woloszynek, S. Carpenter, A. E. Shrikumar, A. Xu, J. Cofer, E. M. Harris, D. J. DeCaprio, D. Qi, Y. Kundaje, A. Peng, Y. Wiley, L. K. Segler, M. H. S. Gitter, A. Greene, C. S. 2017-05-28 doi:10.1101/142760 Cold Spring Harbor Laboratory Press 2017-05-28 <![CDATA[ Cell-Accurate Optical Mapping Across The Entire Developing Heart ]]> https://biorxiv.org/content/10.1101/143057v1?rss=1 Weber, M. Scherf, N. Kohl, P. Huisken, J. 2017-05-27 doi:10.1101/143057 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ Post-Transcriptional Control of Coenzyme Q Biosynthesis Revealed by Transomic Analysis of the RNA-Binding Protein Puf3p ]]> https://biorxiv.org/content/10.1101/146985v1?rss=1 Lapointe, C. P. Stefely, J. A. Jochem, A. Hutchins, P. D. Wilson, G. M. Kwiecien, N. W. Coon, J. J. Wickens, M. Pagliarini, D. J. 2017-06-07 doi:10.1101/146985 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient UbiB family ]]> https://biorxiv.org/content/10.1101/149823v1?rss=1 Reidenbach, A. Kemmerer, Z. Aydin, D. Jochem, A. McDevitt, M. Hutchins, P. Wilkerson, E. Stark, J. Stefely, J. Johnson, I. Bingman, C. Markley, J. Coon, J. Dal Peraro, M. Pagliarini, D. 2017-06-13 doi:10.1101/149823 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Multi-omic mitoprotease profiling defines a role for Oct1p in coenzyme Q production ]]> https://biorxiv.org/content/10.1101/155044v1?rss=1 Veling, M. Reidenbach, A. Freiberger, E. Kwiecien, N. Hutchins, P. Drahnak, M. Jochem, A. Ulbrich, A. Rush, M. Coon, J. Pagliarini, D. 2017-06-24 doi:10.1101/155044 Cold Spring Harbor Laboratory Press 2017-06-24 <![CDATA[ Pan-embryo cell dynamics of germlayer formation in zebrafish ]]> https://biorxiv.org/content/10.1101/173583v1?rss=1 Shah, G. Thierbach, K. Schmid, B. Reade, A. Roeder, I. Scherf, N. Huisken, J. 2017-08-08 doi:10.1101/173583 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments ]]> https://biorxiv.org/content/10.1101/185413v1?rss=1 Bacher, R. Leng, N. Chu, L.-F. Thomson, J. Kendziorski, C. Stewart, R. 2017-09-07 doi:10.1101/185413 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease ]]> https://biorxiv.org/content/10.1101/2020.02.25.963967v1?rss=1 Overmyer, K. A. Rhoads, T. Merrill, A. E. Ye, Z. Westphall, M. S. Acharya, A. Shukla, S. Coon, J. J. 2020-02-26 doi:10.1101/2020.02.25.963967 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Autofluorescence imaging of 3D tumor-macrophage microscale cultures resolves spatial and temporal dynamics of macrophage metabolism ]]> https://biorxiv.org/content/10.1101/2020.03.12.989301v1?rss=1 Heaster, T. Humayun, M. Yu, J. Beebe, D. J. Skala, M. 2020-03-12 doi:10.1101/2020.03.12.989301 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Adaptable pulsatile flow generated by quantitative imaging of stem-cell derived cardiomyocytes for disease modeling ]]> https://biorxiv.org/content/10.1101/2020.03.20.000752v1?rss=1 Qian, T. Gil, D. A. Contreras Guzman, E. Gastfriend, B. D. Tweed, K. E. Palecek, S. P. Skala, M. C. 2020-03-24 doi:10.1101/2020.03.20.000752 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ linus: Conveniently explore, share and present large-scale biological trajectory data from a web browser. ]]> https://biorxiv.org/content/10.1101/2020.04.17.043323v1?rss=1 Waschke, J. Hlawitschka, M. Anlas, K. Trivedi, V. Roeder, I. Huisken, J. Scherf, N. 2020-04-18 doi:10.1101/2020.04.17.043323 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Reference genome and demographic history of the most endangered marine mammal, the vaquita ]]> https://biorxiv.org/content/10.1101/2020.05.27.098582v1?rss=1 Morin, P. A. Archer, F. I. Avila, C. D. Balacco, J. R. Bukhman, Y. V. Chow, W. Fedrigo, O. Formenti, G. Fronczek, J. A. Fungtammasan, A. Gulland, F. M. D. Haase, B. Heide-Jorgensen, M. P. Houck, M. Howe, K. Misuraca, A. C. Mountcastle, J. Musser, W. Paez, S. Pelan, S. Phillippy, A. M. Rhie, A. Robinson, J. A. Rojas-Bracho, L. Rowles, T. K. Ryder, O. A. Smith, C. R. Stevenson, S. Taylor, B. L. Teilmann, J. Torrance, J. Wells, R. S. Westgate, A. Jarvis, E. 2020-05-28 doi:10.1101/2020.05.27.098582 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ In vivo fluorescence lifetime imaging captures metabolic changes in macrophages during wound responses in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.06.16.153361v1?rss=1 Miskolci, V. Tweed, K. Lasarev, M. Britt, E. C. McDougal, C. E. Walsh, A. J. Fan, J. Sauer, J.-D. Skala, M. Huttenlocher, A. 2020-06-16 doi:10.1101/2020.06.16.153361 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Dynamic regulatory module networks for inference of cell type specific transcriptional networks ]]> https://biorxiv.org/content/10.1101/2020.07.18.210328v1?rss=1 Fotuhi Siahpirani, A. Chasman, D. Seirup, M. Knaack, S. Sridharan, R. Stewart, R. Thomson, J. Roy, S. 2020-07-19 doi:10.1101/2020.07.18.210328 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Consensus-based somatic variant-calling method correlates FBXW7 mutations with poor prognosis in canine B-cell lymphoma ]]> https://biorxiv.org/content/10.1101/2020.08.16.250100v1?rss=1 White, M. E. Hayward, J. J. E. Hertafeld, S. R. Castelhano, M. G. Leung, W. Dave, S. Bhinder, B. H. Elemento, O. L. Richards, K. L. Suter, S. E. 2020-08-17 doi:10.1101/2020.08.16.250100 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ CRISPR screens in physiologic medium reveal conditionally essential genes in human cells ]]> https://biorxiv.org/content/10.1101/2020.08.31.275107v1?rss=1 Rossiter, N. J. Huggler, K. S. Adelmann, C. H. Keys, H. R. Soens, R. W. Sabatini, D. M. Cantor, J. R. 2020-08-31 doi:10.1101/2020.08.31.275107 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Interspecies Chimeric Conditions Affect the Developmental Rate of Human Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.09.12.293357v1?rss=1 Brown, J. Barry, C. Schmitz, M. Argus, C. Bolin, J. Schwartz, M. Van Aartsen, A. Steill, J. Swanson, S. Stewart, R. Thomson, J. Kendziorski, C. 2020-09-12 doi:10.1101/2020.09.12.293357 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.21.307363v1?rss=1 Seirup, M. Sengupta, S. Swanson, S. McIntosh, B. E. Collins, M. Chu, L.-F. Cheng, Z. Gorkin, D. Duffin, B. Bolin, J. M. Argus, C. Stewart, R. Thomson, J. A. 2020-09-22 doi:10.1101/2020.09.21.307363 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ CHARTS: A web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq datasets ]]> https://biorxiv.org/content/10.1101/2020.09.23.310441v1?rss=1 Bernstein, M. N. Ni, Z. Collins, M. Burkard, M. E. Kendziorski, C. Stewart, R. 2020-09-25 doi:10.1101/2020.09.23.310441 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Maternal high fiber diet protects offspring on diabetogenic diet in the Nile rat ]]> https://biorxiv.org/content/10.1101/2020.09.26.315069v1?rss=1 Toh, H. Thomson, J. Jiang, P. 2020-09-28 doi:10.1101/2020.09.26.315069 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization ]]> https://biorxiv.org/content/10.1101/2020.10.05.326553v1?rss=1 Bacher, R. Chu, L.-F. Argus, C. Bolin, J. M. Knight, P. Thomson, J. A. Stewart, R. Kendziorski, C. 2020-10-05 doi:10.1101/2020.10.05.326553 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ SKiM - A generalized literature-based discovery system for uncovering novel biomedical knowledge from PubMed ]]> https://biorxiv.org/content/10.1101/2020.10.16.343012v1?rss=1 Raja, K. Steill, J. Ross, I. Tsoi, L. C. Kuusisto, F. Ni, Z. Livny, M. Thomson, J. Stewart, R. 2020-10-17 doi:10.1101/2020.10.16.343012 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Interactions with stromal cells promote a more oxidized cancer cell redox state in pancreatic tumors ]]> https://biorxiv.org/content/10.1101/2020.10.20.347658v1?rss=1 Datta, R. Lau, A. N. Sivanand, S. Florek, L. Wyckoff, J. Skala, M. C. Vander Heiden, M. G. 2020-10-21 doi:10.1101/2020.10.20.347658 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Neural networks to learn protein sequence-function relationships from deep mutational scanning data ]]> https://biorxiv.org/content/10.1101/2020.10.25.353946v1?rss=1 Gelman, S. Romero, P. A. Gitter, A. 2020-10-25 doi:10.1101/2020.10.25.353946 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus ]]> https://biorxiv.org/content/10.1101/2020.11.09.355982v1?rss=1 Baker, S. F. Meistermann, H. Tzouros, M. Baker, A. Golling, S. Polster, J. S. Ledwith, M. P. Gitter, A. Augustin, A. Javanbakht, H. Mehle, A. 2020-11-10 doi:10.1101/2020.11.09.355982 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Reversed upper glycolysis and rapid activation of oxidative pentose phosphate pathway supports the oxidative burst in neutrophils ]]> https://biorxiv.org/content/10.1101/2020.11.25.396838v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@11f9509org.highwire.dtl.DTLVardef@71bffforg.highwire.dtl.DTLVardef@1f402adorg.highwire.dtl.DTLVardef@dbdf1f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Britt, E. C. Fan, J. 2020-11-26 doi:10.1101/2020.11.25.396838 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ UbiB proteins regulate cellular CoQ distribution ]]> https://biorxiv.org/content/10.1101/2020.12.09.418202v1?rss=1 Kemmerer, Z. A. Robinson, K. P. Schmitz, J. M. Paulson, B. R. Jochem, A. Hutchins, P. D. Coon, J. J. Pagliarini, D. J. 2020-12-09 doi:10.1101/2020.12.09.418202 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Patient-derived cancer organoid tracking with widefield one-photon redox imaging to assess treatment response ]]> https://biorxiv.org/content/10.1101/2020.12.19.423617v1?rss=1 Gil, D. A. Deming, D. Skala, M. C. 2020-12-21 doi:10.1101/2020.12.19.423617 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM ]]> https://biorxiv.org/content/10.1101/2021.04.20.440648v1?rss=1 Lucas, B. A. Himes, B. A. Xue, L. Grant, T. Mahamid, J. Grigorieff, N. 2021-04-21 doi:10.1101/2021.04.20.440648 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Generation of SIV resistant T cells and Macrophages from Nonhuman Primate Induced Pluripotent Stem Cells with Edited CCR5 locus ]]> https://biorxiv.org/content/10.1101/2021.05.03.442446v1?rss=1 D'Souza, S. S. Kumar, A. Weinfurter, J. Park, M. A. Maufort, J. Tao, L. Kang, H. Golos, T. Thomson, J. A. Reynolds, M. Slukvin, I. I. 2021-05-04 doi:10.1101/2021.05.03.442446 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Label-free imaging for quality control of cardiomyocyte differentiation ]]> https://biorxiv.org/content/10.1101/2021.06.01.446615v1?rss=1 Qian, T. Heaster, T. Houghtaling, A. Sun, K. Samimi, K. Skala, M. 2021-06-02 doi:10.1101/2021.06.01.446615 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Multi-layered transcriptomic analyses reveal an immunological overlap between COVID-19 and hemophagocytic lymphohistiocytosis associated with disease severity ]]> https://biorxiv.org/content/10.1101/2021.07.30.454529v1?rss=1 Schimke, L. F. Marques, A. H. Baiocchi, G. C. Prado, C. A. Fonseca, D. L. Freire, P. P. Placa, D. R. Filgueira, I. S. Salgado, R. C. Jansen-Marques, G. Oliveira, A. E. Peron, J. P. S. Barbuto, J. A. M. Camara, N. O. S. Calich, V. L. Ochs, H. D. Condino-Neto, A. Overmyer, K. A. Coon, J. J. Balnis, J. Jaitovich, A. Schulte-Schrepping, J. Ulas, T. Schultze, J. L. Nakaya, H. I. Jurisica, I. Marques, O. C. 2021-08-01 doi:10.1101/2021.07.30.454529 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Clinically-relevant T cell expansion protocols activate distinct cellular metabolic programs and phenotypes ]]> https://biorxiv.org/content/10.1101/2021.08.24.457536v1?rss=1 MacPherson, S. Keyes, S. Kilgour, M. K. Smazynski, J. Sudderth, J. Turcotte, T. Devlieger, A. Yu, J. Huggler, K. S. Cantor, J. R. DeBerardinis, R. J. Siatskas, C. Lum, J. J. 2021-08-26 doi:10.1101/2021.08.24.457536 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ 3D Structure Determination of Protein Complexes using Matrix-Landing Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2021.10.13.464253v1?rss=1 Westphall, M. S. Lee, K. W. Salome, A. Z. Lodge, J. Grant, T. Coon, J. 2021-10-13 doi:10.1101/2021.10.13.464253 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Krüppel-like factor 4 is required for development and regeneration of germline and yolk cells from somatic stem cells in planarians ]]> https://biorxiv.org/content/10.1101/2021.11.08.467675v1?rss=1 Issigonis, M. Redkar, A. Rozario, T. Khan, U. Mejia-Sanchez, R. Lapan, S. Reddien, P. Newmark, P. A. 2021-11-08 doi:10.1101/2021.11.08.467675 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Structure and functionality of a multimeric human COQ7:COQ9 complex ]]> https://biorxiv.org/content/10.1101/2021.11.15.468694v1?rss=1 Manicki, M. Aydin, H. Abriata, L. A. Overmyer, K. A. Guerra, R. M. Coon, J. J. Dal Peraro, M. Frost, A. S. Pagliarini, D. J. 2021-11-15 doi:10.1101/2021.11.15.468694 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Somatic regulation of female germ cell regeneration and development in planarians ]]> https://biorxiv.org/content/10.1101/2021.11.22.469583v1?rss=1 Khan, U. W. Newmark, P. A. 2021-11-23 doi:10.1101/2021.11.22.469583 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Label-free imaging to track reprogramming of human somatic cells ]]> https://biorxiv.org/content/10.1101/2021.12.08.471827v1?rss=1 Saha, K. Skala, M. C. Molugu, K. Battistini, G. A. Heaster, T. Rouw, J. Guzman, E. C. 2021-12-10 doi:10.1101/2021.12.08.471827 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.08.471837v1?rss=1 Toh, H. Yang, C. Formenti, G. Raja, K. Yan, L. Tracey, A. Chow, W. Howe, K. Bergeron, L. A. Zhang, G. Haase, B. Mountcastle, J. Fedrigo, O. Fogg, J. Kirilenko, B. Munegowda, C. Hiller, M. Jain, A. Kihara, D. Rhie, A. Phillippy, A. M. Swanson, S. A. Jiang, P. Clegg, D. O. Jarvis, E. D. Thomson, J. A. Stewart, R. Chaisson, M. J. P. Bukhman, Y. V. 2021-12-10 doi:10.1101/2021.12.08.471837 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Differentiation of a CD4+/CD8αβ+ Double Positive T Cell Population From The CD8 Pool Is Sufficient To Mediate Graft-vs-Host Disease but not Graft-vs-Leukemia Effects ]]> https://biorxiv.org/content/10.1101/2022.01.11.475845v1?rss=1 Hess, N. J. Turicek, D. P. Nadiminti, K. Hudson, A. Hematti, P. Gumperz, J. E. Capitini, C. M. 2022-01-12 doi:10.1101/2022.01.11.475845 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Modifications of lipoic arm by reactive nitrogen species regulate α-ketoacid dehydrogenases ]]> https://biorxiv.org/content/10.1101/2022.01.31.478543v1?rss=1 Seim, G. L. Fang, Z. Pagliarini, D. Fan, J. 2022-01-31 doi:10.1101/2022.01.31.478543 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ An approachable, flexible, and practical machine learning workshop for biologists ]]> https://biorxiv.org/content/10.1101/2022.02.03.479008v1?rss=1 Magnano, C. S. Mu, F. Russ, R. S. Cvetkovic, M. Treu, D. Gitter, A. 2022-02-04 doi:10.1101/2022.02.03.479008 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ SpatialCorr: Identifying Gene Sets with Spatially Varying Correlation Structure ]]> https://biorxiv.org/content/10.1101/2022.02.04.479191v1?rss=1 Bernstein, M. N. Ni, Z. Prasad, A. Brown, J. Mohanty, C. Stewart, R. Newton, M. A. Kendziorski, C. 2022-02-08 doi:10.1101/2022.02.04.479191 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ CRSP: Comparative RNA-seq pipeline for species lacking both of sequenced genomes and reference transcripts ]]> https://biorxiv.org/content/10.1101/2022.02.04.479193v1?rss=1 Bagheri, A. Dewey, C. Stewart, R. Jiang, P. 2022-02-08 doi:10.1101/2022.02.04.479193 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ A versatile pattern-forming cortical circuit based on Rho, F-actin, Ect2 and RGA-3/4 ]]> https://biorxiv.org/content/10.1101/2022.03.08.483353v1?rss=1 Michaud, A. Leda, M. Swider, Z. T. Kim, S. He, J. Landino, J. Valley, J. R. Huisken, J. Goryachev, A. B. von Dassow, G. Bement, W. 2022-03-08 doi:10.1101/2022.03.08.483353 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases ]]> https://biorxiv.org/content/10.1101/2022.03.31.486371v1?rss=1 Park, H. Yu, Q. Hundley, F. V. Overmyer, K. Serrano, L. Paulo, J. A. Paoli, J. C. Swarup, S. Coon, J. Gygi, S. Harper, W. 2022-03-31 doi:10.1101/2022.03.31.486371 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Asparagine starvation suppresses histone demethylation through iron depletion ]]> https://biorxiv.org/content/10.1101/2022.08.14.503884v1?rss=1 Zhang, J. Jiang, J. Srivastava, S. Liu, S. Seim, G. Zhong, M. Cao, S. Dave, U. Kapur, R. Mosley, A. L. Zhang, C. Wan, J. Fan, J. 2022-08-15 doi:10.1101/2022.08.14.503884 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Image restoration of degraded time-lapse microscopy data mediated by infrared-imaging. ]]> https://biorxiv.org/content/10.1101/2022.11.10.515910v1?rss=1 Gritti, N. Power, R. M. Graves, A. Huisken, J. 2022-11-10 doi:10.1101/2022.11.10.515910 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Differential metabolic adaptations define responses of winner and loser oncogenic mutant stem cells in skin epidermis in vivo ]]> https://biorxiv.org/content/10.1101/2022.11.21.517380v1?rss=1 Hemalatha, A. Li, Z. Tai, K. Gonzalez, D. G. Lathrop, E. Gil, D. Matte-Martone, C. Ganesan, S. Yun, S. Gonzalez, L. E. Skala, M. C. Perry, R. J. Greco, V. 2022-11-23 doi:10.1101/2022.11.21.517380 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Nodavirus RNA Replication Crown Architecture Reveals Proto-Crown Precursor and Viral Protein A Conformational Switching ]]> https://biorxiv.org/content/10.1101/2022.12.16.520638v1?rss=1 Zhan, H. Unchwaniwala, N. Rebolledo-Viveros, A. Pennington, J. Horswill, M. Broadberry, R. Myers, J. den Boon, J. A. Grant, T. Ahlquist, P. 2022-12-17 doi:10.1101/2022.12.16.520638 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue ]]> https://biorxiv.org/content/10.1101/2023.01.09.523303v1?rss=1 Dhavale, D. D. Barclay, A. M. Borcik, C. G. Basore, K. Gordon, I. R. Liu, J. Milchberg, M. H. O'Shea, J. Y. Rau, M. J. Smith, Z. Sen, S. Summers, B. Smith, J. W. Warmuth, O. A. Chen, Q. Fitzpatrick, J. A. J. Schwieters, C. D. Tajkhorshid, E. Rienstra, C. M. Kotzbauer, P. T. 2023-01-10 doi:10.1101/2023.01.09.523303 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Autofluorescence lifetime imaging classifies human lymphocyte activation and subtype ]]> https://biorxiv.org/content/10.1101/2023.01.23.525260v1?rss=1 Schmitz, R. L. Tweed, K. E. Rehani, P. Samimi, K. Riendeau, J. Jones, I. Maly, E. M. Guzman, E. C. Forsberg, M. H. Shahi, A. Capitini, C. M. Walsh, A. J. Skala, M. C. 2023-01-23 doi:10.1101/2023.01.23.525260 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Light sheet autofluorescence lifetime imaging with a single photon avalanche diode array ]]> https://biorxiv.org/content/10.1101/2023.02.01.526695v1?rss=1 Samimi, K. Desa, D. E. Lin, W. Weiss, K. Li, J. Huisken, J. Miskolci, V. Huttenlocher, A. Chacko, J. V. Velten, A. Rogers, J. D. Eliceiri, K. W. Skala, M. C. 2023-02-03 doi:10.1101/2023.02.01.526695 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ cell-analysis-tools: an open-source library for single-cell analysis of multi-dimensional microscopy images ]]> https://biorxiv.org/content/10.1101/2023.03.08.531732v1?rss=1 Contreras, E. Rehani, P. R. Skala, M. C. 2023-03-10 doi:10.1101/2023.03.08.531732 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Optical coherence tomography of human fetal membrane sub-layers during dynamic loading ]]> https://biorxiv.org/content/10.1101/2023.03.09.531932v1?rss=1 0.8). Intact amniochorion bilayer and separated amnion and chorion were individually loaded, and the amnion layer was identified as the load-bearing layer within intact fetal membranes for both labored and C-section samples, consistent with prior work. Additionally, the rupture pressure and thickness of the amniochorion bilayer from the near-placental region were greater than those of the near-cervical region for labored samples. This location-dependent change in fetal membrane thickness was not attributable to the load-bearing amnion layer. Finally, the initial phase of the loading curve indicates that amniochorion bilayer from the near-cervical region is strain-hardened compared to the near-placental region in labored samples. Overall, these studies fill a gap in our understanding of the structural and mechanical properties of human fetal membranes at high resolution under dynamic loading events. ]]> Samimi, K. Contreras Guzman, E. Wu, M. Carlson, L. Feltovich, H. Hall, T. J. Myers, K. M. Oyen, M. L. Skala, M. C. 2023-03-12 doi:10.1101/2023.03.09.531932 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository ]]> https://biorxiv.org/content/10.1101/2023.03.09.531970v1?rss=1 Weiss, K. Huisken, J. Bakalov, V. Engle, M. Gridley, L. Krzyzanowski, M. Madden, T. Maiese, D. Waterfield, J. Williams, D. Wu, X. Hamilton, C. M. Huggins, W. 2023-03-12 doi:10.1101/2023.03.09.531970 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Hem25p is a mitochondrial IPP transporter ]]> https://biorxiv.org/content/10.1101/2023.03.14.532620v1?rss=1 Tai, J. Guerra, R. M. Rogers, S. W. Fang, Z. Muehlbauer, L. K. Shishkova, E. Overmyer, K. A. Coon, J. J. Pagliarini, D. J. 2023-03-14 doi:10.1101/2023.03.14.532620 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ A role for cytoglobin in regulating intracellular hydrogen peroxide and redox signals in the vasculature ]]> https://biorxiv.org/content/10.1101/2023.03.31.535146v1?rss=1 Mathai, C. Jourd'heuil, F. L. Pham, L. G. C. Gilliard, K. Balnis, J. Jen, A. Overmyer, K. A. Coon, J. J. Jaitovich, A. Boivin, B. Jourd'heuil, D. 2023-04-01 doi:10.1101/2023.03.31.535146 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer Models ]]> https://biorxiv.org/content/10.1101/2023.05.30.542911v1?rss=1 Millikin, R. Raja, K. Steill, J. Lock, C. Tu, X. Ross, I. Tsoi, L. C. Kuusisto, F. Ni, Z. Livny, M. Bockelman, B. Thomson, J. Stewart, R. 2023-06-01 doi:10.1101/2023.05.30.542911 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Conditional lethality profiling reveals anticancer mechanisms of action and drug-nutrient interactions ]]> https://biorxiv.org/content/10.1101/2023.06.04.543621v1?rss=1 Flickinger, K. M. Wilson, K. M. Rossiter, N. J. Hunger, A. L. Lee, T. D. Hall, M. D. Cantor, J. R. 2023-06-06 doi:10.1101/2023.06.04.543621 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ The microenvironment dictates glycocalyx construction and immune surveillance ]]> https://biorxiv.org/content/10.1101/2023.06.23.546317v1?rss=1 Tharp, K. Park, S. Timblin, G. A. Richards, A. Berg, J. Twells, N. Riley, N. M. Peltan, E. Shon, D. J. Stevenson, E. Tsui, C. K. Palomba, F. Lefebvre, A. E. Soens, R. Ayad, N. ten Hoeve-Scott, J. Healy, K. Digman, M. Dillin, A. Bertozzi, C. Mahal, L. K. Swaney, D. Cantor, J. R. Paszek, M. Weaver, V. 2023-06-25 doi:10.1101/2023.06.23.546317 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Reactive nitrogen species inhibit branched chain alpha-ketoacid dehydrogenasecomplex and impact muscle cell metabolism ]]> https://biorxiv.org/content/10.1101/2023.07.31.551364v1?rss=1 Arp, N. L. Seim, G. Josephson, J. Fan, J. 2023-07-31 doi:10.1101/2023.07.31.551364 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Metabolic changes to host cells with Toxoplasma gondii infection ]]> https://biorxiv.org/content/10.1101/2023.08.10.552811v1?rss=1 Gallego-Lopez, G. M. Contreras Guzman, E. Knoll, L. Skala, M. C. 2023-08-10 doi:10.1101/2023.08.10.552811 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Naive primary neutrophils play a dual role in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2023.09.15.557892v1?rss=1 Babatunde, K. A. Datta, R. Ayuso, J. M. Huttenlocher, A. Skala, M. C. Beebe, D. J. Kerr, S. C. 2023-09-15 doi:10.1101/2023.09.15.557892 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Activation-induced shift in nutrient preference and function-specific nutrient dependence in human neutrophils ]]> https://biorxiv.org/content/10.1101/2023.09.25.559385v1?rss=1 Britt, E. C. Qing, X. Votava, J. A. Lika, J. Wagner, A. Shen, S. Arp, N. L. Khan, H. Schieke, S. M. Fletcher, C. D. Huttenlocher, A. Fan, J. 2023-09-26 doi:10.1101/2023.09.25.559385 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ SCD1 and monounsaturated lipids are required for autophagy and survival of adipocytes ]]> https://biorxiv.org/content/10.1101/2023.10.27.564376v1?rss=1 Mori, H. Peterson, S. K. Simmermon, R. Overmyer, K. Nishii, A. Paulsson, E. Ziru, L. Jen, A. Uranga, R. M. Maung, J. Yacawych, W. T. Lewis, K. T. Schill, R. L. Hetrick, T. Seino, R. Inoki, K. Coon, J. MacDougald, O. A. 2023-10-27 doi:10.1101/2023.10.27.564376 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Quantifying in vivo collagen reorganization during immunotherapy in murine melanoma with second harmonic generation imaging ]]> https://biorxiv.org/content/10.1101/2023.11.09.566407v1?rss=1 Heaton, A. R. Burkard, N. J. Sondel, P. M. Skala, M. C. 2023-11-13 doi:10.1101/2023.11.09.566407 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ One-Hour Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer ]]> https://biorxiv.org/content/10.1101/2023.11.21.568149v1?rss=1 Lancaster, N. M. Sinitcyn, P. Forny, P. Peters-Clarke, T. M. Fecher, C. Smith, A. J. Shishkova, E. Arrey, T. N. Pashkova, A. Robinson, M. L. Arp, N. Fan, J. Hansen, J. Galmozzi, A. Serrano, L. R. Westphall, M. S. Stewart, H. Hock, C. Damoc, E. Pagliarini, D. J. Zabrouskov, V. Coon, J. J. 2023-11-21 doi:10.1101/2023.11.21.568149 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Heme biosynthesis regulates BCAA catabolism and thermogenesis in brown adipose tissue ]]> https://biorxiv.org/content/10.1101/2023.11.28.568893v1?rss=1 Duerre, D. J. Hansen, J. K. John, S. Jen, A. Carrillo, N. Bui, H. Bao, Y. Fabregat, M. Overmyer, K. Shishkova, E. Keller, M. P. Anderson, R. A. Cryns, V. L. Attie, A. D. Coon, J. Fan, J. Galmozzi, A. 2023-11-28 doi:10.1101/2023.11.28.568893 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A niche-derived non-ribosomal peptide triggers planarian sexual development ]]> https://biorxiv.org/content/10.1101/2023.12.06.570471v1?rss=1 Issigonis, M. Browder, K. L. Chen, R. Collins, J. J. Newmark, P. A. 2023-12-07 doi:10.1101/2023.12.06.570471 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Macrophages undergo functionally significant reprograming of nucleotide metabolism upon classical activation ]]> https://biorxiv.org/content/10.1101/2023.12.27.573447v1?rss=1 John, S. V. Seim, G. L. Erazo-Flores, B. J. Steill, J. Freeman, J. Votava, J. A. Arp, N. L. Qing, X. Stewart, R. Knoll, L. J. Fan, J. 2023-12-27 doi:10.1101/2023.12.27.573447 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism ]]> https://biorxiv.org/content/10.1101/2024.01.09.574893v1?rss=1 Rashan, E. H. Bartlett, A. K. Khana, D. B. Zhang, J. Jain, R. Smith, A. J. Baker, Z. N. Cook, T. Caldwell, A. Chevalier, A. R. Pfleger, B. F. Yuan, P. Amador-Noguez, D. Simcox, J. A. Pagliarini, D. J. 2024-01-09 doi:10.1101/2024.01.09.574893 Cold Spring Harbor Laboratory Press 2024-01-09 <![CDATA[ High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan ]]> https://biorxiv.org/content/10.1101/2024.01.15.575638v1?rss=1 Gao, A. W. El Alam, G. W. Zhu, Y. Li, W. Katsyuba, E. Sulc, J. Li, T. Li, X. Overmyer, K. A. Lalou, A. Mouchiroud, L. Bou Sleiman, M. Cornaglia, M. Morel, J.-D. Houtkooper, R. Coon, J. Auwerx, J. 2024-01-16 doi:10.1101/2024.01.15.575638 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Metabolic priming of GD2 TRAC-CAR T cellsduring manufacturing promotes memory phenotypes while enhancing persistence ]]> https://biorxiv.org/content/10.1101/2024.01.31.575774v1?rss=1 Cappabianca, D. Pham, D. Forsberg, M. H. Bugel, M. Tommasi, A. Lauer, A. Vidugiriene, J. Hrdlicka, B. McHale, A. Sodji, Q. Skala, M. C. Capitini, C. M. Saha, K. 2024-02-02 doi:10.1101/2024.01.31.575774 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Label free metabolic imaging to enhance the efficacy of Chimeric Antigen Receptor T cell therapy ]]> https://biorxiv.org/content/10.1101/2024.02.20.581240v1?rss=1 Pham, D. L. Cappabianca, D. Forsberg, M. Weaver, C. Mueller, K. P. Tommasi, A. Vidugiriene, J. Lauer, A. Sylvester, K. Bugel, M. Capitini, C. M. Saha, K. Skala, M. C. 2024-02-23 doi:10.1101/2024.02.20.581240 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Biophysics-based protein language models for protein engineering ]]> https://biorxiv.org/content/10.1101/2024.03.15.585128v1?rss=1 Gelman, S. Johnson, B. Freschlin, C. D'Costa, S. Gitter, A. Romero, P. A. 2024-03-17 doi:10.1101/2024.03.15.585128 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2 ]]> https://biorxiv.org/content/10.1101/2024.03.26.586828v1?rss=1 Harper, J. W. Kraus, F. He, Y. Swarup, S. Overmyer, K. A. Brenner, J. Capitanio, C. Bieber, A. Jen, A. Nightingale, N. M. Anderson, B. J. Lee, C. Paulo, J. A. Smith, I. R. Plitzko, J. M. Schulman, B. A. Wilfling, F. Coon, J. J. 2024-03-27 doi:10.1101/2024.03.26.586828 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Autofluorescence lifetime flow cytometry with time-correlated single photon counting ]]> https://biorxiv.org/content/10.1101/2024.05.15.594394v1?rss=1 Samimi, K. Pasachhe, O. Guzman, E. C. Riendeau, J. Gillette, A. A. Pham, D. L. Wiech, K. J. Moore, D. L. Skala, M. C. 2024-05-18 doi:10.1101/2024.05.15.594394 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Piximi - An Images to Discovery web tool for bioimages and beyond ]]> https://biorxiv.org/content/10.1101/2024.06.03.597232v1?rss=1 Moser, L. M. Gogoberidze, N. Papaleo, A. Lucas, A. Dao, D. Friedrich, C. A. Paavolainen, L. Molnar, C. Stirling, D. R. Hung, J. Wang, R. Tromans-Coia, C. Li, B. Evans, E. L. Eliceiri, K. W. Horvath, P. Carpenter, A. E. Cimini, B. A. 2024-06-04 doi:10.1101/2024.06.03.597232 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Diminished Immune Cell Adhesion in Hypoimmune ICAM-1 Knockout Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.06.07.597791v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@890b56org.highwire.dtl.DTLVardef@147449borg.highwire.dtl.DTLVardef@1e94f08org.highwire.dtl.DTLVardef@43c55c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO ICAM-1 Knock-out in Transendothelial Migration and at the Immune Synapse. Abbreviations: PSC-EC - pluripotent stem cell-derived endothelial cells; KO - knock-out; dSMAC - distal supramolecular activation complex; pSMAC - peripheral supramolecular activation complex; cSMAC - central supramolecular activation complex. C_FIG ]]> Saha, S. Haynes, W. J. Del Rio, N. Young, E. E. Zhang, J. Seo, J. Huang, L. Holm, A. M. Blashka, W. Murphy, L. Scholz, M. Henrichs, A. Suresh Babu, J. Steill, J. Stewart, R. E. Kamp, T. J. Brown, M. E. 2024-06-09 doi:10.1101/2024.06.07.597791 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images ]]> https://biorxiv.org/content/10.1101/2024.06.07.597994v1?rss=1 0.9) between Cellpose and manually segmented masks for the ORR, mean NAD(P)H lifetime, and mean FAD lifetime across 2D and 3D cell culture treatment conditions. Masks generated from Cellpose and manual segmentation also maintain similar means, variances, and effect sizes between treatments for the ORR and FLIM parameters. Overall, Cellpose provides a fast, reliable, reproducible, and accurate method to segment single cells in autofluorescence microscopy images such that functional changes in cells are accurately captured in both 2D and 3D culture. ]]> Riendeau, J. M. Gillette, A. Contreras Guzman, E. Costa Cruz, M. Kralovec, A. Udgata, S. Schmitz, A. Deming, D. A. Cimini, B. A. Skala, M. C. 2024-06-10 doi:10.1101/2024.06.07.597994 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ MPAC: a computational framework for inferring cancer pathway activities from multi-omic data ]]> https://biorxiv.org/content/10.1101/2024.06.15.599113v1?rss=1 Liu, P. Page, D. Ahlquist, P. Ong, I. M. Gitter, A. 2024-06-17 doi:10.1101/2024.06.15.599113 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Single cell autofluorescence imaging reveals immediate metabolic shifts of neutrophils with activation across biological systems ]]> https://biorxiv.org/content/10.1101/2024.07.26.605362v1?rss=1 Datta, R. Miskolci, V. Gallego Lopez, G. M. Britt, E. Gillette, A. Kralovec, A. Giese, M. A. Qian, T. Fan, J. Huttenlocher, A. Skala, M. C. 2024-07-29 doi:10.1101/2024.07.26.605362 Cold Spring Harbor Laboratory Press 2024-07-29 <![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. 2024-09-26 doi:10.1101/2024.09.25.614908 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ GATA1-deficient human pluripotent stem cells generate neutrophils with improved antifungal immunity that is mediated by the integrin CD18 ]]> https://biorxiv.org/content/10.1101/2024.10.11.617742v1?rss=1 Wagner, A. S. Smith, F. M. Bennin, D. A. Votava, J. A. Datta, R. Giese, M. A. Zhao, W. Skala, M. Fan, J. Keller, N. P. Huttenlocher, A. 2024-10-11 doi:10.1101/2024.10.11.617742 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases ]]> https://biorxiv.org/content/10.1101/2024.11.11.622451v1?rss=1 Chernigovskaya, M. Le Quy, K. Stensland, M. Singh, S. Nelson, R. Yilmaz, M. Kalogeropoulos, K. Sinitcyn, P. Patel, A. Castellana, N. Bonissone, S. Foss, S. Andersen, J. T. Sandve, G. K. Jenkins, T. P. Noble, W. S. Nyman, T. A. Snapkow, I. Greiff, V. 2024-11-12 doi:10.1101/2024.11.11.622451 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Schistosome esophageal gland factor MEG-8.2 drives host cell lysis and interacts with host immune proteins ]]> https://biorxiv.org/content/10.1101/2024.11.15.623777v1?rss=1 Yadav, P. Simbassa, S. B. Sloan, R. Newmark, P. A. Lee, J. 2024-11-15 doi:10.1101/2024.11.15.623777 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ SPE-CZE-MS quantifies zeptomole concentrations ofphosphorylated peptides ]]> https://biorxiv.org/content/10.1101/2024.12.07.627347v1?rss=1 Serrano, L. R. Mellors, J. S. Thompson, J. W. Lancaster, N. M. Robinson, M. L. Overmyer, K. A. Quarmby, S. T. Coon, J. J. 2024-12-12 doi:10.1101/2024.12.07.627347 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Wide-field optical redox imaging with leading-edge detection for assessment of patient-derived cancer organoids ]]> https://biorxiv.org/content/10.1101/2024.12.23.630148v1?rss=1 Gillette, A. A. Udgata, S. Schmitz, A. E. Stoecker, J. E. Deming, D. A. Skala, M. C. 2024-12-23 doi:10.1101/2024.12.23.630148 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ A Technical Evaluation of Plasma Proteomics Technologies ]]> https://biorxiv.org/content/10.1101/2025.01.08.632035v1?rss=1 Beimers, W. F. Overmyer, K. A. Sinitcyn, P. Lancaster, N. M. Coon, J. J. 2025-01-13 doi:10.1101/2025.01.08.632035 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates ]]> https://biorxiv.org/content/10.1101/2025.01.10.632484v1?rss=1 Barten, L. M. Crandall, J. G. Xie, D. Serate, J. Handowski, E. Jen, A. Overmyer, K. A. Coon, J. J. Hittinger, C. T. Landick, R. Zhang, Y. Sato, T. K. 2025-01-12 doi:10.1101/2025.01.10.632484 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration ]]> https://biorxiv.org/content/10.1101/2025.01.23.634576v1?rss=1 Rich, A. Li, Z. De Simone, A. Garcia, L. Janssen, J. Ando, K. Ou, J. Vergassola, M. Poss, K. D. Di Talia, S. 2025-01-23 doi:10.1101/2025.01.23.634576 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response ]]> https://biorxiv.org/content/10.1101/2025.02.03.636312v1?rss=1 Lika, J. Votava, J. A. A. Datta, R. Kralovec, A. M. Smith, F. M. Huttenlocher, A. Skala, M. C. Fan, J. 2025-02-08 doi:10.1101/2025.02.03.636312 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production ]]> https://biorxiv.org/content/10.1101/2025.02.07.637120v1?rss=1 Huggler, K. S. Mellado Fritz, C. A. Flickinger, K. M. Chang, G. R. McGuire, M. F. Cantor, J. R. 2025-02-08 doi:10.1101/2025.02.07.637120 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue ]]> https://biorxiv.org/content/10.1101/2025.02.21.639411v1?rss=1 Aakhte, M. Mueller, G. F. Li, J. Weiss, K. R. Roos, L. Diniz, A. M. Wenzel, J. Schwaninger, M. Moser, T. Huisken, J. 2025-02-21 doi:10.1101/2025.02.21.639411 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition ]]> https://biorxiv.org/content/10.1101/2025.04.17.648362v1?rss=1 Cotet, T.-S. Krawczuk, I. Pacesa, M. Nickel, L. Correia, B. E. Haas, N. Qamar, A. Challacombe, C. A. Kidger, P. Ferragu, C. Naka, A. Castorina, L. V. Subr, K. Kluonis, T. Stam, M. J. Unal, S. M. Wood, C. W. Stocco, F. Ferruz, N. Kurumida, Y. Calia, C. N. Paesani, F. Machado, L. d. A. Belot, E. Gitter, A. Campbell, M. J. Hallee, L. Adaptyv Competition Organizers, 2025-04-23 doi:10.1101/2025.04.17.648362 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Human Plasma-Like Medium Promotes Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2025.04.24.650456v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@a169eforg.highwire.dtl.DTLVardef@131e6f4org.highwire.dtl.DTLVardef@131d52dorg.highwire.dtl.DTLVardef@a2b248_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhange, X. Simmons, A. D. Huggler, K. S. Feeney, A. K. Cantor, J. R. Skala, M. C. Palecek, S. P. 2025-04-26 doi:10.1101/2025.04.24.650456 Cold Spring Harbor Laboratory Press 2025-04-26 <![CDATA[ Spatial and longitudinal tracking of enhancer-AAV vectors that target transgene expression to injured mouse myocardium ]]> https://biorxiv.org/content/10.1101/2025.04.28.651096v1?rss=1 Wolfson, D. Hull, J. Li, Y. Gonzalez, T. Jayaram, M. Devlin, G. Cigliola, V. Oonk, K. Rosales, A. Bursac, N. Asokan, A. Poss, K. D. 2025-05-01 doi:10.1101/2025.04.28.651096 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Top-Down Scoring of Spectral Fitness by Image Analysis for Protein Structure Validation ]]> https://biorxiv.org/content/10.1101/2025.05.05.652267v1?rss=1 Harding, B. D. DeZonia, B. Garg, R. Hu, Z. Delaglio, F. Grant, T. Rienstra, C. M. 2025-05-06 doi:10.1101/2025.05.05.652267 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ NMR Spectral Alignment Utilizing a CryoEM Motion Correction Algorithm ]]> https://biorxiv.org/content/10.1101/2025.05.05.652277v1?rss=1 Hemme, C. Warmuth, O. Wang, S. Williams, C. Thome, A. Mueller, L. J. Rienstra, C. M. Grant, T. 2025-05-06 doi:10.1101/2025.05.05.652277 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Epicardial Tcf21 facilitates cardiomyocyte dedifferentiation and heart regeneration in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.05.15.654216v1?rss=1 Balciunas, D. Kalvaityte-Repecke, M. Gabrilaviciute, S. Kvederaviciute, K. Bakunaite, E. Burg, L. Poss, K. D. 2025-05-17 doi:10.1101/2025.05.15.654216 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Genetic mapping of lifespan and mitochondrial stress response in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.06.26.661693v1?rss=1 Li, X. Li, W. Gao, A. W. Zhu, Y. Katsyuba, E. Overmyer, K. A. Li, T. Wang, Z. Legon, L. Plantade, L. Mouchiroud, L. Cornaglia, M. Li, H. Houtkooper, R. Auwerx, J. 2025-06-26 doi:10.1101/2025.06.26.661693 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ SKiM-GPT: Combining Biomedical Literature-Based Discovery with Large Language Model Hypothesis Evaluation ]]> https://biorxiv.org/content/10.1101/2025.07.28.664797v1?rss=1 Freeman, J. Millikin, R. J. Xu, L. Sharma, I. Moore, B. M. Lock, C. George, K. S. Bal, A. Stewart, R. 2025-07-31 doi:10.1101/2025.07.28.664797 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data ]]> https://biorxiv.org/content/10.1101/209676v1?rss=1 Köksal, A. S. Beck, K. Cronin, D. R. McKenna, A. Camp, N. D. Srivastava, S. MacGilvray, M. E. Bodik, R. Wolf-Yadlin, A. Fraenkel, E. Fisher, J. Gitter, A. 2017-10-26 doi:10.1101/209676 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Continuous high-resolution in vivo imaging reveals tumor-specific dissemination in an embryonic zebrafish xenograft model ]]> https://biorxiv.org/content/10.1101/215921v1?rss=1 Asokan, N. Daetwyler, S. Bernas, S. N. Schmied, C. Volger, S. Lambert, K. Wobus, M. Wermke, M. Kempermann, G. Huisken, J. Brand, M. Bornhaeuser, M. 2017-11-08 doi:10.1101/215921 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Continuous addition of progenitors forms the cardiac ventricle in zebrafish ]]> https://biorxiv.org/content/10.1101/230649v1?rss=1 Felker, A. Prummel, K. D. Merks, A. M. Mickoleit, M. Brombacher, E. C. Huisken, J. Panakova, D. Mosimann, C. 2017-12-07 doi:10.1101/230649 Cold Spring Harbor Laboratory Press 2017-12-07 <![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. 2018-02-07 doi:10.1101/261115 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Neuromesodermal Progenitors are a Conserved Source of Spinal Cord with Divergent Growth Dynamics ]]> https://biorxiv.org/content/10.1101/304543v1?rss=1 Attardi, A. Fulton, T. Florescu, M. Shah, G. Muresan, L. Huisken, J. van Oudenaarden, A. Steventon, B. 2018-04-19 doi:10.1101/304543 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Practical model selection for prospective virtual screening ]]> https://biorxiv.org/content/10.1101/337956v1?rss=1 Liu, S. Alnammi, M. Ericksen, S. S. Voter, A. F. Keck, J. L. Hoffmann, F. M. Wildman, S. A. Gitter, A. 2018-06-04 doi:10.1101/337956 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Endothelial cells form transient Notch-dependent NO-containing cystic structures during zebrafish cerebrovascular development ]]> https://biorxiv.org/content/10.1101/416206v1?rss=1 Chico, T. J. Kugler, E. Chhabria, K. Daetwyler, S. Huisken, J. Plant, K. Savage, A. Wilkinson, R. N. Armitage, P. 2018-09-13 doi:10.1101/416206 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis ]]> https://biorxiv.org/content/10.1101/426247v1?rss=1 Niemi, N. M. Wilson, G. M. Overmyer, K. A. Vogtle, F.- N. Lohman, D. C. Schueler, K. L. Attie, A. D. Meisinger, C. Coon, J. J. Pagliarini, D. J. 2018-09-25 doi:10.1101/426247 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ A novel rotifer-derived alkaloid paralyzes schistosome larvae and prevents infection ]]> https://biorxiv.org/content/10.1101/426999v1?rss=1 Gao, J. Yang, N. Lewis, F. A. Yau, P. Collins, J. J. Sweedler, J. V. Newmark, P. A. 2018-09-27 doi:10.1101/426999 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Quantifying dynamic protein acetylation using quantitative stoichiometry ]]> https://biorxiv.org/content/10.1101/472530v1?rss=1 Baeza, J. Lawton, A. J. Fan, J. Smallegan, M. J. Leinert, I. Gandhi, T. Bernhardt, O. M. Reiter, L. Denu, J. M. 2018-11-18 doi:10.1101/472530 Cold Spring Harbor Laboratory Press 2018-11-18 <![CDATA[ Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish ]]> https://biorxiv.org/content/10.1101/478149v1?rss=1 Daetwyler, S. Günther, U. Modes, C. D. Harrington, K. Huisken, J. 2018-11-24 doi:10.1101/478149 Cold Spring Harbor Laboratory Press 2018-11-24 <![CDATA[ Region-specific regulation of stem cell-driven regeneration in tapeworms ]]> https://biorxiv.org/content/10.1101/495234v1?rss=1 Rozario, T. Quinn, E. B. Wang, J. Davis, R. A. Newmark, P. A. 2018-12-13 doi:10.1101/495234 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Predicting kinase inhibitors using bioactivity matrix derived informer sets ]]> https://biorxiv.org/content/10.1101/532762v1?rss=1 Zhang, H. Ericksen, S. S. Lee, C.-p. Ananiev, G. E. Wlodarchak, N. Mitchell, J. C. Gitter, A. Wright, S. J. Hoffmann, F. M. Wildman, S. A. Newton, M. A. 2019-01-28 doi:10.1101/532762 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data ]]> https://biorxiv.org/content/10.1101/534834v1?rss=1 Deshpande, A. Chu, L.-F. Stewart, R. Gitter, A. 2019-01-30 doi:10.1101/534834 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Label-free Method for Classification of T cell Activation ]]> https://biorxiv.org/content/10.1101/536813v1?rss=1 Walsh, A. Mueller, K. Jones, I. Walsh, C. M. Piscopo, N. Niemi, N. N. Pagliarini, D. J. Saha, K. Skala, M. C. 2019-01-31 doi:10.1101/536813 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Optical Metabolic Imaging of Heterogeneous Drug Response in Pancreatic Cancer Patient Organoids ]]> https://biorxiv.org/content/10.1101/542167v1?rss=1 Sharick, J. T. Walsh, C. M. Sprackling, C. M. Pasch, C. A. Parikh, A. A. Matkowskyj, K. A. Deming, D. A. Skala, M. C. 2019-02-06 doi:10.1101/542167 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Hierarchical cell type classification using mass, heterogeneous RNA-seq data from human primary cells ]]> https://biorxiv.org/content/10.1101/634097v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@208aeeorg.highwire.dtl.DTLVardef@814bd8org.highwire.dtl.DTLVardef@9a7c39org.highwire.dtl.DTLVardef@5195fb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bernstein, M. N. Dewey, C. N. 2019-05-10 doi:10.1101/634097 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ In vivo lineage conversion of vertebrate muscle into early endoderm-like cells ]]> https://biorxiv.org/content/10.1101/722967v1?rss=1 Campbell, C. Lancman, J. J. Espin-Palazon, R. Matalonga, J. He, J. Graves, A. Zeng, X.-X. I. Huisken, J. Traver, D. Dong, P. D. S. 2019-08-09 doi:10.1101/722967 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Classifying T cell activity in autofluorescence intensity images with convolutional neural networks ]]> https://biorxiv.org/content/10.1101/737346v1?rss=1 Wang, Z. J. Walsh, A. J. Skala, M. C. Gitter, A. 2019-08-15 doi:10.1101/737346 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Human plasma-like medium improves T lymphocyte activation ]]> https://biorxiv.org/content/10.1101/740845v1?rss=1 Leney-Greene, M. A. Boddapati, A. K. Su, H. Cantor, J. Lenardo, M. J. 2019-08-21 doi:10.1101/740845 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni ]]> https://biorxiv.org/content/10.1101/754713v1?rss=1 Diaz Soria, C. L. Lee, J. Chong, T. Coghlan, A. Tracey, A. Young, M. D. Andrews, T. Hall, C. Ng, B. L. Rawlinson, K. Doyle, S. R. Leonard, S. Lu, Z. Bennett, H. M. Rinaldi, G. Newmark, P. A. Berriman, M. 2019-09-11 doi:10.1101/754713 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Cell-type diversity and regionalized gene expression in the planarian intestine revealed by laser-capture microdissection transcriptome profiling ]]> https://biorxiv.org/content/10.1101/756924v1?rss=1 Forsthoefel, D. J. Cejda, N. I. Khan, U. W. Newmark, P. A. 2019-09-05 doi:10.1101/756924 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule ]]> https://biorxiv.org/content/10.1101/764191v1?rss=1 Seirup, M. Chu, L.-F. Sengupta, S. Leng, N. Shafer, C. M. Duffin, B. Elwell, A. L. Bolin, J. M. Swanson, S. Stewart, R. Kendziorski, C. Thomson, J. A. Bacher, R. 2019-09-11 doi:10.1101/764191 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Insights from a survey-based analysis of the academic job market ]]> https://biorxiv.org/content/10.1101/796466v1?rss=1 Fernandes, J. D. Sarabipour, S. Smith, C. T. Niemi, N. M. Jadavji, N. M. Kozik, A. J. Holehouse, A. S. Pejaver, V. Symmons, O. Bisson Filho, A. W. Haage, A. 2019-10-09 doi:10.1101/796466 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Automating parameter selection to avoid implausible biological pathway models ]]> https://biorxiv.org/content/10.1101/845834v1?rss=1 Magnano, C. S. Gitter, A. 2019-11-17 doi:10.1101/845834 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Atovaquone-induced therapeutic rewiring of melanoma metabolism ]]> https://biorxiv.org/content/10.1101/2025.09.08.674005v1?rss=1 Ponce, M. B. Heaton, A. R. Burkard, S. D'Amato, A. Boonpattrawong, N. Skala, M. C. Patankar, M. S. Barroilhet, L. 2025-09-12 doi:10.1101/2025.09.08.674005 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Non-invasive longitudinal imaging reveals aging-associated changes in neuroimmune cells in adult zebrafish ]]> https://biorxiv.org/content/10.1101/2025.09.23.676912v1?rss=1 Haynes, E. M. Steinhauser, C. Swader, R. Petry, G. Ulland, T. K. Eliceiri, K. W. 2025-09-25 doi:10.1101/2025.09.23.676912 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single-cell fluorescence lifetime data ]]> https://biorxiv.org/content/10.1101/2025.09.30.679625v1?rss=1 Zhao, W. Samimi, K. Skala, M. C. Datta, R. 2025-10-02 doi:10.1101/2025.09.30.679625 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Segmentation-guided photon pooling enables robust single cell analysis and fast fluorescence lifetime imaging microscopy ]]> https://biorxiv.org/content/10.1101/2025.09.30.679660v1?rss=1 Samimi, K. Desa, D. E. Zhang, X. Pham, D. L. Datta, R. Skala, M. C. 2025-10-02 doi:10.1101/2025.09.30.679660 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Divergent role of CD8 T cells with distinct metabolic phenotypes during curative radio-immunotherapy in hot versus cold tumors ]]> https://biorxiv.org/content/10.1101/2025.10.24.684274v1?rss=1 Heaton, A. R. Burkard, N. J. Gao, A. Hoefges, A. Feils, A. S. Burkard, S. K. Felder, M. A. Tsarovsky, N. W. Spiegelman, D. V. Lublin, G. M. Hampton, A. A. D'Amato, A. Dinh, H. Q. Rakhmilevich, A. L. Erbe, A. K. Sondel, P. M. Skala, M. C. 2025-10-26 doi:10.1101/2025.10.24.684274 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Buffering of genetic defects in animal development by regeneration programs ]]> https://biorxiv.org/content/10.1101/2025.10.25.684558v1?rss=1 Ando, K. Bangru, S. Welsby, J. Thompson, J. D. Poss, K. D. 2025-10-26 doi:10.1101/2025.10.25.684558 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Leonardo: a toolset to correct sample-induced artifacts in light sheet microscopy images ]]> https://biorxiv.org/content/10.1101/2025.10.26.684661v1?rss=1 Liu, Y. Mueller, G. F. Kowitz, L. Chobola, T. Weiss, K. Maier, P. Luo, J. Roessing, M. Stenzel, M. Grueneboom, A. Paetzold, J. Erturk, A. Navab, N. Marr, C. Chen, J. Huisken, J. Peng, T. 2025-10-27 doi:10.1101/2025.10.26.684661 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ An automated image analysis pipeline for wide-field optical redox imaging of patient-derived cancer organoids ]]> https://biorxiv.org/content/10.1101/2025.10.29.685427v1?rss=1 0.8 across systems, indicating high reproducibility. Automated single-PDCO tracking was compared to manual tracking and the accuracy of the tracking algorithm exceeded 94% by two metrics, recall and Jaccard index. For background correction, the automated pipeline uses the full field-of-view to reduce sampling bias. Compared to the manual analysis pipeline, the automated pipeline resolves single-PDCO responses with comparable sensitivity to drug treatment but with over 127x faster processing time. This novel automated image analysis pipeline improves throughput and robustness in PDCO image analysis, which increases the accessibility and scalability of wide-field optical redox imaging for PDCO drug screening. ]]> Hsu, A. Samimi, K. Gillette, A. Udgata, S. Schmitz, A. E. Zhao, W. Deming, D. A. Skala, M. C. 2025-10-31 doi:10.1101/2025.10.29.685427 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Live visualization of extracellular matrix dynamics during development and regeneration in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.11.02.686082v1?rss=1 Shen, J. Jayadev, R. Ou, J. Rich, A. Ando, K. Di Talia, S. Sherwood, D. R. Poss, K. D. 2025-11-03 doi:10.1101/2025.11.02.686082 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Autofluorescence imaging reveals the impact of cryopreservation on T cell metabolism and activation response ]]> https://biorxiv.org/content/10.1101/2025.11.14.688556v1?rss=1 Pham, D. L. Kalluri, M. Weaver, C. Hsu, A. Gillette, A. Zhao, W. Kearl, T. Hematti, P. Shah, N. Skala, M. C. 2025-11-16 doi:10.1101/2025.11.14.688556 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Enhancer-directed gene delivery for digit regeneration based on conserved epidermal factors ]]> https://biorxiv.org/content/10.64898/2025.12.01.691633v1?rss=1 Brown, D. A. Koll, K. Brush, E. Darner, G. Curtis, T. Dvergsten, T. Tran, M. Milligan, C. Wolfson, D. Gonzalez, T. J. Jeffs, S. Ehrhardt, A. Bitolas, R. Landau, M. Reitz, K. Salven, D. S. Slota-Burtt, L. A. Snee, I. Singer-Freeman, E. Bhatia, S. Ou, J. Asokan, A. Currie, J. D. Poss, K. D. 2025-12-02 doi:10.64898/2025.12.01.691633 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Genetic complementation reveals structure-function links in nodavirus RNA replication complex crowns ]]> https://biorxiv.org/content/10.64898/2025.12.10.693615v1?rss=1 den Boon, J. A. Jaramillo Mesa, H. Horswill, M. Jochem, A. Bracken, M. Zhan, H. Ahlquist, P. 2025-12-11 doi:10.64898/2025.12.10.693615 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Immune-mediated Engagement of T Regulatory Cells with Tumor Cells Results in Trogocytosis and Tumor Cell Killing. ]]> https://biorxiv.org/content/10.64898/2025.12.11.693807v1?rss=1 50% of patients with advanced melanoma are unresponsive to current therapies. Using the B78-D14 melanoma model (GD2+/MHC-I-/MHC-II+), we can cure mice with a regimen that includes radiation therapy (RT) in combination with immunocytokine (IC; anti-GD2 monoclonal antibody linked to IL-2) while establishing immunological memory. We interrogated the role of T cells in the antitumor and memory responses following RT+IC. We show a requirement for CD4, but not CD8 T cells, to achieve both the initial and memory responses. Upon IC-induced cell-cell contact, subsets of CD4 T cells, including Foxp3 T regulatory cells, trogocytose GD2 from tumor cells, acquire cytotoxic granules, and kill tumor cells. These results were confirmed using human tumor cell lines. These findings reveal that CD4 T regulatory cells, upon immunologically-induced binding to tumor cells, can trogocytose tumor antigens and directly kill tumor cells, redefining their potential role in antitumor immunity. ]]> Erbe, A. K. Feils, A. S. Gao, A. VandenHeuvel, S. Boyenga, S. Hampton, A. Heck, M. Zaborek, J. Spiegelman, D. Tsarovsky, N. Hoefges, A. Pieper, A. A. Carlson, P. M. Felder, M. Patel, R. B. Gillies, S. D. Heaton, A. Morris, Z. Dinh, H. Q. Rakhmilevich, A. L. Sondel, P. M. 2025-12-15 doi:10.64898/2025.12.11.693807 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Regarding Emitter Positioning for Nanoflow Electrospray Ionization ]]> https://biorxiv.org/content/10.64898/2025.12.18.695161v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@1a976ccorg.highwire.dtl.DTLVardef@b6627forg.highwire.dtl.DTLVardef@1fca93eorg.highwire.dtl.DTLVardef@cb61f6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lancaster, N. M. Quarmby, S. T. Overmyer, K. Coon, J. 2025-12-20 doi:10.64898/2025.12.18.695161 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Image-Based Profiling of Induced Trophoblast Stem Cells Identifies Signatures Associated with Sex, Schizophrenia Genomic Risk and Placental Stress ]]> https://biorxiv.org/content/10.64898/2025.12.23.695254v1?rss=1 Piscotta, F. J. Kim, J. Ha, J. Sheehan, B. Johnston, J. Peters, J. Hyde, T. M. Maher, B. J. Caicedo, J. Weinberger, D. R. Shlevkov, E. Ursini, G. 2025-12-25 doi:10.64898/2025.12.23.695254 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1 ]]> https://biorxiv.org/content/10.64898/2025.12.31.697202v1?rss=1 Arp, N. L. Urquiza, U. S. Morgenstern, M. Schrope, J. H. Votava, J. A. John, S. V. Stevens, J. J. Huttenlocher, A. Coon, J. J. Fan, J. 2026-01-01 doi:10.64898/2025.12.31.697202 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Atlas of lysine acetylation in the mouse ]]> https://biorxiv.org/content/10.64898/2026.01.09.698739v1?rss=1 Soens, R. W. Anderson, B. J. Lancaster, N. M. Kumar, M. Hansen, J. K. Galmozzi, A. Grant, T. Overmyer, K. A. Coon, J. J. 2026-01-10 doi:10.64898/2026.01.09.698739 Cold Spring Harbor Laboratory Press 2026-01-10 <![CDATA[ Visualization of the complete primosome reveals the structural mechanisms governing DNA replication restart ]]> https://biorxiv.org/content/10.64898/2026.01.13.699284v1?rss=1 Ducos, P. L. Duckworth, A. T. Satyshur, K. A. Keck, J. L. Grant, T. 2026-01-13 doi:10.64898/2026.01.13.699284 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Acetyl-CoA availability regulates neuronal metabolism, growth, and synaptic activity ]]> https://biorxiv.org/content/10.64898/2026.01.20.700435v1?rss=1 McGregor, E. R. McGill, C. J. Arp, N. L. Clark, J. P. Baldwin, D. A. Kuang, D. Fernandez-Fuente, G. Choi, Y. H. Pearson, K. S. Nagorski, J. K. Simcox, J. A. Fan, J. Puglielli, L. Anderson, R. M. 2026-01-20 doi:10.64898/2026.01.20.700435 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Proteotyping reactivant toxoplasmic encephalitis reveals virulence-associated dense granule protein GRA5 polymorphisms ]]> https://biorxiv.org/content/10.64898/2026.02.01.702898v1?rss=1 Montoro, R. A. Chadwick, B. Su, C. Overmyer, K. Coon, J. Knoll, L. Striker, R. 2026-02-02 doi:10.64898/2026.02.01.702898 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Autofluorescence lifetime imaging resolves cell heterogeneity within peripheral blood mononuclear cells ]]> https://biorxiv.org/content/10.64898/2026.03.06.710224v1?rss=1 Riendeau, J. M. Hockerman, L. Maly, E. Samimi, K. M. Skala, M. C. 2026-03-08 doi:10.64898/2026.03.06.710224 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ mnDINO: Accurate and robust segmentation of micronuclei with vision transformer networks ]]> https://biorxiv.org/content/10.64898/2026.03.09.710648v1?rss=1 Ren, Y. Morlot, L. Andrews, J. O. Thrane Hertz, E. P. Mailand, N. Caicedo, J. C. 2026-03-12 doi:10.64898/2026.03.09.710648 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ The pyruvate branch point controls lymphoid cancer cell dissemination ]]> https://biorxiv.org/content/10.64898/2026.03.16.712182v1?rss=1 Khan, H. John, S. Roy, S. Farhan, M. Hoang, N. M. Buethe, P. Prasad, A. Nihal, A. Yang, D. T. Rui, L. Fan, J. Schieke, S. M. 2026-03-18 doi:10.64898/2026.03.16.712182 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Discovery of metabolites produced by reactions between central carbon metabolites and cysteine that mark inflammatory macrophages ]]> https://biorxiv.org/content/10.64898/2026.03.18.712640v1?rss=1 Arp, N. L. Deng, F. Lika, J. Seim, G. L. Falco Cobra, P. Mellado Fritz, C. John, S. V. Rathinaraj, S. Shields, B. E. Amador-Noguez, D. Henzler-Wildman, K. Fan, J. 2026-03-20 doi:10.64898/2026.03.18.712640 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Dynamic UFMylation governs cellular fitness by coordinating multi-organelle proteostasis ]]> https://biorxiv.org/content/10.64898/2026.03.27.714830v1?rss=1 Kunzmann, G. B. Leiter, W. E. Durn, S. E. Weeks, A. M. Cantor, J. R. 2026-03-28 doi:10.64898/2026.03.27.714830 Cold Spring Harbor Laboratory Press 2026-03-28