bioRxiv Channel: Harvard Program in Therapeutic Sciences
https://biorxiv.org
This feed contains articles for bioRxiv Channel "Harvard Program in Therapeutic Sciences"
bioRxivbioRxiv
https://biorxiv.org
<![CDATA[
Cheminformatics tools for analyzing and designing optimized small molecule libraries
]]>
https://biorxiv.org/cgi/content/short/358978v1?rss=1"
Moret, N.Clark, N.Hafner, M.Wang, Y.Lounkine, E.Medvedovic, M.Wang, J.Gray, N.Jenkins, J.Sorger, P.2018-06-29doi:10.1101/358978Cold Spring Harbor Laboratory Press2018-06-29
<![CDATA[
Maintaining the provenance of microscopy metadata using OMERO.forms software
]]>
https://biorxiv.org/cgi/content/short/109199v1?rss=1"
Russell, D. P.Sorger, P. K.2017-02-16doi:10.1101/109199Cold Spring Harbor Laboratory Press2017-02-16
<![CDATA[
From word models to executable models of signaling networks using automated assembly
]]>
https://biorxiv.org/cgi/content/short/119834v1?rss=1"
Gyori, B. M.Bachman, J. A.Subramanian, K.Muhlich, J. L.Galescu, L.Sorger, P. K.2017-03-23doi:10.1101/119834Cold Spring Harbor Laboratory Press2017-03-23
<![CDATA[
A simple open-source method for highly multiplexed imaging of single cells in tissues and tumours
]]>
https://biorxiv.org/cgi/content/short/151738v1?rss=1"
Lin, J.-R.Izar, B.Mei, S.Wang, S.Shah, P.Sorger, P.2017-06-19doi:10.1101/151738Cold Spring Harbor Laboratory Press2017-06-19
<![CDATA[
Therapeutically advantageous secondary targets of abemaciclib identified by multi-omics profiling of CDK4/6 inhibitors
]]>
https://biorxiv.org/cgi/content/short/211680v1?rss=1"
Hafner, M.Mills, C. E.Subramanian, K.Chen, C.Chung, M.Boswell, S. A.Everley, R. A.Walmsley, C. S.Juric, D.Sorger, P.2017-11-07doi:10.1101/211680Cold Spring Harbor Laboratory Press2017-11-07
<![CDATA[
A multi-center study on factors influencing the reproducibility of in vitro drug-response studies
]]>
https://biorxiv.org/cgi/content/short/213553v1?rss=1"
Niepel, M.Hafner, M.Williams, E. H.Chung, M.Barrette, A. M.Stern, A. D.Hu, B.LINCS Consortium,Gray, J. W.Birtwistle, M. R.Heiser, L. M.Sorger, P. K.2017-11-03doi:10.1101/213553Cold Spring Harbor Laboratory Press2017-11-03
<![CDATA[
Bioentities: a resource for entity recognition and relationship resolution in biomedical text mining
]]>
https://biorxiv.org/cgi/content/short/225698v1?rss=1"
Bachman, J. A.Gyori, B. M.Sorger, P.2017-11-27doi:10.1101/225698Cold Spring Harbor Laboratory Press2017-11-27
<![CDATA[
Genome-encoded Cytoplasmic Double-Stranded RNAs, Found in C9ORF72 ALS-FTD Brain, Provoke Propagated Neuronal Death
]]>
https://biorxiv.org/cgi/content/short/248328v1?rss=1"
Rodriguez, S.Schrank, B. R.Sahin, A.Al-Lawati, H.Constantino, I.Benz, E.Fard, D.Albers, A. D.Cao, L.Gomez, A. C.Ratti, E.Cudkowicz, M.Frosch, M. P.Talkowski, M.Sorger, P. K.Hyman, B. T.Albers, M. W.2018-01-19doi:10.1101/248328Cold Spring Harbor Laboratory Press2018-01-19
<![CDATA[
Drug adaptation influences cardiotoxicity caused by tyrosine kinase inhibitors in iPSC-derived human cardiomyocytes
]]>
https://biorxiv.org/cgi/content/short/365841v1?rss=1"
Wang, H.Sheehan, R. P.Palmer, A. C.Everley, R. A.Boswell, S. A.Ron-Harel, N.Holton, K. M.Jacobson, C. A.Erickson, A.Maliszewski, L.Haigis, M. C.Sorger, P. K.2018-07-30doi:10.1101/365841Cold Spring Harbor Laboratory Press2018-07-30
<![CDATA[
Comparing the efficacy of cancer therapies between subgroups in basket trials
]]>
https://biorxiv.org/cgi/content/short/401620v1?rss=1"
Palmer, A. C.Plana, D.Sorger, P.2018-08-28doi:10.1101/401620Cold Spring Harbor Laboratory Press2018-08-28
<![CDATA[
Machine characterization of rat toxin responses identifies disease states, tolerance mechanisms and organ to whole-body communication
]]>
https://biorxiv.org/cgi/content/short/322446v1?rss=1"
Shimada, K.Mitchison, T.2018-05-28doi:10.1101/322446Cold Spring Harbor Laboratory Press2018-05-28
<![CDATA[
Mammalian Cells Engineered to Produce Novel Steroids
]]>
https://biorxiv.org/cgi/content/short/261362v1?rss=1"
Spady, E. S.Wyche, T. P.Rollins, N. J.Clardy, J.Way, J. C.Silver, P. A.2018-02-07doi:10.1101/261362Cold Spring Harbor Laboratory Press2018-02-07
<![CDATA[
Drugs in a curative combination therapy for lymphoma exhibit low cross-resistance but not pharmacological synergy
]]>
https://biorxiv.org/cgi/content/short/462184v1?rss=1"
Palmer, A. C.Chidley, C.Sorger, P. K.2018-11-05doi:10.1101/462184Cold Spring Harbor Laboratory Press2018-11-05
<![CDATA[
End-to-end differentiable learning of protein structure
]]>
https://biorxiv.org/cgi/content/short/265231v1?rss=1"
AlQuraishi, M.2018-02-14doi:10.1101/265231Cold Spring Harbor Laboratory Press2018-02-14
<![CDATA[
pNeRF: Parallelized Conversion from Internal to Cartesian Coordinates
]]>
https://biorxiv.org/cgi/content/short/385450v1?rss=1"
AlQuraishi, M.2018-08-06doi:10.1101/385450Cold Spring Harbor Laboratory Press2018-08-06
<![CDATA[
Systemic Lymphoid Architecture Response Assessment (SYLARAS): An approach to multi-organ, discovery-based immunophenotyping implicates a role for CD45R/B220+ CD8T cells in glioblastoma immunology
]]>
https://biorxiv.org/cgi/content/short/555854v1?rss=1"
Baker, G. J.Palaniappan, S. K.Moore, J. K.Davis, S. H.Santagata, S.Sorger, P. K.2019-02-20doi:10.1101/555854Cold Spring Harbor Laboratory Press2019-02-20
<![CDATA[
Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells
]]>
https://biorxiv.org/cgi/content/short/700625v1?rss=1"
Chopra, S. S.Jenney, A.Palmer, A.Niepel, M.Chung, M.Mills, C.Sivakumaren, S. C.Liu, Q.Chen, J.-Y.Yapp, C.Asara, J.Gray, N. S.Sorger, P. K.2019-07-12doi:10.1101/700625Cold Spring Harbor Laboratory Press2019-07-12
<![CDATA[
Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells
]]>
https://biorxiv.org/cgi/content/short/762294v1?rss=1"
Gerosa, L.Chidley, C.Froehlich, F.Sanchez, G.Lim, S. K.Muhlich, J.Chen, J.-Y.Baker, G. J.Schapiro, D.Shi, T.Yi, L.Nicora, C. D.Claas, A.Lauffenburger, D. A.Qian, W.-J.Wiley, H. S.Sorger, P. K.2019-09-08doi:10.1101/762294Cold Spring Harbor Laboratory Press2019-09-08
<![CDATA[
A tool for browsing the Cancer Dependency Map reveals functional connections between genes and helps predict the efficacy and selectivity of candidate cancer drugs
]]>
https://biorxiv.org/cgi/content/short/2019.12.13.874776v1?rss=1"
Shimada, K.Muchlich, J. L.Mitchison, T. J.2019-12-18doi:10.1101/2019.12.13.874776Cold Spring Harbor Laboratory Press2019-12-18
<![CDATA[
Channel Embedding for Informative Protein Identification from Highly Multiplexed Images
]]>
https://biorxiv.org/cgi/content/short/2020.03.24.004085v1?rss=1"
Magid, S. A.Jang, W.-D.Schapiro, D.Wei, D.Tompkin, J.Sorger, P. K.Pfister, H.2020-03-25doi:10.1101/2020.03.24.004085Cold Spring Harbor Laboratory Press2020-03-25
<![CDATA[
Interpretative guides for interacting with tissue atlas and digital pathology data using the Minerva browser
]]>
https://biorxiv.org/cgi/content/short/2020.03.27.001834v1?rss=1"
Rashid, R.Chen, Y.-A.Hoffer, J.Muhlich, J. L.Lin, J.-R.Krueger, R.Pfister, H.Mitchell, R.Santagata, S.Sorger, P.2020-03-30doi:10.1101/2020.03.27.001834Cold Spring Harbor Laboratory Press2020-03-30
<![CDATA[
Exploring the understudied human kinome for research and therapeutic opportunities
]]>
https://biorxiv.org/cgi/content/short/2020.04.02.022277v1?rss=1"
The NIH Understudied Kinome Consortium,Moret, N.Liu, C.Gyori, B. M.Bachman, J. A.Steppi, A.Taujale, R.Huang, L.-C.Hug, C.Berginski, M.Gomez, S. M.Kannan, N.Sorger, P.2020-04-02doi:10.1101/2020.04.02.022277Cold Spring Harbor Laboratory Press2020-04-02
<![CDATA[
Machine Learning Identifies Novel Candidates for DrugRepurposing in Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2020.05.15.098749v1?rss=1"
Rodriguez, S.Hug, C.Todorov, P.Moret, N.Boswell, S. A.Evans, K.Zhou, G.Johnson, N. T.Hyman, B.Sorger, P.Albers, M. W.Sokolov, A.2020-05-16doi:10.1101/2020.05.15.098749Cold Spring Harbor Laboratory Press2020-05-16
<![CDATA[
Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining
]]>
https://biorxiv.org/cgi/content/short/822668v1?rss=1"
Bachman, J. A.Gyori, B. M.Sorger, P. K.2019-10-29doi:10.1101/822668Cold Spring Harbor Laboratory Press2019-10-29
<![CDATA[
Micro-region transcriptomics of fixed human tissue using Pick-Seq
]]>
https://biorxiv.org/cgi/content/short/2021.03.18.431004v1?rss=1"
Maliga, Z.Nirmal, A. J.Ericson, N. G.Boswell, S. A.U'Ren, L.Podyminogin, R.Chow, J.Chen, Y.-A.Chen, A. A.Weinstock, D. M.Lian, C. G.Murphy, G. F.Kaldjian, E. P.Santagata, S.Sorger, P. K.2021-03-19doi:10.1101/2021.03.18.431004Cold Spring Harbor Laboratory Press2021-03-19
<![CDATA[
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging
]]>
https://biorxiv.org/cgi/content/short/2021.03.15.435473v1?rss=1"
Schapiro, D.Sokolov, A.Yapp, C.Muhlich, J. L.Hess, J.Lin, J.-R.Chen, Y.-A.Nariya, M. K.Baker, G. J.Ruokonen, J.Maliga, Z.Jacobson, C. A.Farhi, S. L.Abbondanza, D.McKinley, E. T.Betts, C.Regev, A.Coffey, R. J.Coussens, L. M.Santagata, S.Sorger, P. K.2021-03-16doi:10.1101/2021.03.15.435473Cold Spring Harbor Laboratory Press2021-03-16
<![CDATA[
Proteomic profiling of breast cancer cell lines and models
]]>
https://biorxiv.org/cgi/content/short/2020.12.15.422823v1?rss=1"
Kalocsay, M.Berberich, M.Everley, R.Nariya, M.Chung, M.Gaudio, B.Victor, C.Bradshaw, G.Hafner, M.Sorger, P. K.Mills, C.Subramanian, K.2020-12-15doi:10.1101/2020.12.15.422823Cold Spring Harbor Laboratory Press2020-12-15
<![CDATA[
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung
]]>
https://biorxiv.org/cgi/content/short/2020.10.14.339952v1?rss=1"
Kalocsay, M.Maliga, Z.Nirmal, A. J.Eisert, R. J.Bradshaw, G. A.Solomon, I. H.Chen, Y.-A.Pelletier, R. J.Jacobson, C. A.Mintseris, J.Padera, R. F.Martinot, A. J.Barouch, D. H.Santagata, S.Sorger, P.2020-10-15doi:10.1101/2020.10.14.339952Cold Spring Harbor Laboratory Press2020-10-15
<![CDATA[
Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma
]]>
https://biorxiv.org/cgi/content/short/724302v1?rss=1"
Jerby, L.Neftel, C.Shore, M. E.McBride, M. J.Haas, B.Izar, B.Weissman, H. R.Volorio, A.Boulay, G.Cironi, L.Richman, A. R.Broye, L. C.Gurski, J. M.Luo, C. C.Mylvaganam, R.Nguyen, L.Mei, S.Melms, J. c.Georgescu, C.Cohen, O.Buendia-Buendia, J. E.Cuoco, M. S.Labes, D.Zollinger, D. R.Beechem, J. M.Nielsen, P.Chebib, I.Cote, G.Choy, E.Letovanec, I.Cherix, S.Wagle, N.Sorger, P. K.Haynes, A. B.Mullen, J. T.Stamenkovic, I.Rivera, M. N.Kadoch, C.Rozenblatt-Rosen, O.Suva, M. L.Riggi, N.Regev, A.2019-08-04doi:10.1101/724302Cold Spring Harbor Laboratory Press2019-08-04
<![CDATA[
Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer
]]>
https://biorxiv.org/cgi/content/short/2021.03.31.437984v1?rss=1"
Lin, J.-R.Wang, S.Coy, S.Tyler, M. A.Yapp, C.Chen, Y.-A.Heiser, C. N.Lau, K.Santagata, S.Sorger, P. K.2021-04-02doi:10.1101/2021.03.31.437984Cold Spring Harbor Laboratory Press2021-04-02
<![CDATA[
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues
]]>
https://biorxiv.org/cgi/content/short/2021.04.02.438285v1?rss=1"
Yapp, C.Novikov, E.Jang, W.-D.Chen, Y.-A.Cicconet, M.Maliga, Z.Jacobson, C. A.Wei, D.Santagata, S.Pfister, H.Sorger, P. K.2021-04-04doi:10.1101/2021.04.02.438285Cold Spring Harbor Laboratory Press2021-04-04
<![CDATA[
Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus
]]>
https://biorxiv.org/cgi/content/short/2020.02.10.942748v1?rss=1"
Patino-Galindo, J. A.Filip, I.AlQuraishi, M.Rabadan, R.2020-02-18doi:10.1101/2020.02.10.942748Cold Spring Harbor Laboratory Press2020-02-18
<![CDATA[
Three-dimensional spatial transcriptomics uncovers cell type dynamics in the rheumatoid arthritis synovium
]]>
https://biorxiv.org/cgi/content/short/2020.12.10.420463v1?rss=1"
Vickovic, S.Schapiro, D.Carlberg, K.Loetstedt, B.Larsson, L.Korotkova, M.Hensvold, A. H.Catrina, A. I.Sorger, P. K.Malmstroem, V.Regev, A.Stahl, P. L.2020-12-11doi:10.1101/2020.12.10.420463Cold Spring Harbor Laboratory Press2020-12-11
<![CDATA[
Biomarker-guided treatment strategies for ovarian cancer identified from a heterogeneous panel of patient-derived tumor xenografts
]]>
https://biorxiv.org/cgi/content/short/2020.01.08.898734v1?rss=1"
Palmer, A. C.Plana, D.Gao, H.Korn, J. M.Yang, G.Green, J.Zhang, X.Velazquez, R.McLaughlin, M. E.Ruddy, D. A.Kowal, C.Goldovitz, J.Bullock, C.Rivera, S.Rakiec, D.Elliott, G.Fordjour, P.Meyer, R.Loo, A.Kurth, E.Engelman, J. A.Bitter, H.Sellers, W. R.Sorger, P. K.Williams, J. A.2020-01-13doi:10.1101/2020.01.08.898734Cold Spring Harbor Laboratory Press2020-01-13
<![CDATA[
GeneWalk identifies relevant gene functions for a biological context using network representation learning
]]>
https://biorxiv.org/cgi/content/short/755579v1?rss=1"
Ietswaart, R.Gyori, B. M.Bachman, J. A.Sorger, P. K.Churchman, L. S.2019-09-05doi:10.1101/755579Cold Spring Harbor Laboratory Press2019-09-05
<![CDATA[
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
]]>
https://biorxiv.org/cgi/content/short/731018v1?rss=1"
Wang, S.Lin, J.-r.Sontag, E. D.Sorger, P. K.2019-08-09doi:10.1101/731018Cold Spring Harbor Laboratory Press2019-08-09
<![CDATA[
Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software
]]>
https://biorxiv.org/cgi/content/short/2021.04.20.440625v1?rss=1"
Muhlich, J. L.Chen, Y.-A.Russell, D. P. W.Sorger, P. K.2021-04-21doi:10.1101/2021.04.20.440625Cold Spring Harbor Laboratory Press2021-04-21
<![CDATA[
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution
]]>
https://biorxiv.org/cgi/content/short/2021.05.23.445310v1?rss=1"
Nirmal, A. J.Maliga, Z.Vallius, T.Quattrochi, B.Chen, A. A.Jacobson, C. A.Pelletier, R. J.Yapp, C.Arias-Camison, R.Chen, Y.-A.Lian, C. G.Murphy, G. F.Santagata, S.Sorger, P. K.2021-05-23doi:10.1101/2021.05.23.445310Cold Spring Harbor Laboratory Press2021-05-23
<![CDATA[
Fides: Reliable Trust-Region Optimization for Parameter Estimation of Ordinary Differential Equation Models
]]>
https://biorxiv.org/cgi/content/short/2021.05.20.445065v1?rss=1"
Froehlich, F.Sorger, P. K.2021-05-22doi:10.1101/2021.05.20.445065Cold Spring Harbor Laboratory Press2021-05-22
<![CDATA[
Cancer patient survival can be accurately parameterized, revealing time-dependent therapeutic effects and doubling the precision of small trials
]]>
https://biorxiv.org/cgi/content/short/2021.05.14.442837v1?rss=1"
Plana, D.Fell, G.Alexander, B. M.Palmer, A. C.Sorger, P. K.2021-05-17doi:10.1101/2021.05.14.442837Cold Spring Harbor Laboratory Press2021-05-17
<![CDATA[
Temporal and spatial topography of cell proliferation in cancer
]]>
https://biorxiv.org/cgi/content/short/2021.05.16.443704v1?rss=1"
Gaglia, G.Kabraji, S.Argyropoulou, D.Dai, Y.Wang, S.Bergholz, J.Coy, S.Lin, J.-R.Jeselsohn, R.Metzger, O.Winer, E. P.Dillon, D. A.Zhao, J. J.Sorger, P. K.Santagata, S.2021-05-17doi:10.1101/2021.05.16.443704Cold Spring Harbor Laboratory Press2021-05-17
<![CDATA[
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes
]]>
https://biorxiv.org/cgi/content/short/2021.08.06.455458v1?rss=1"
Doherty, L. M.Mills, C. E.Boswell, S. A.Liu, X.Hoyt, C. T.Gyori, B. M.Buhrlage, S. J.Sorger, P. K.2021-08-09doi:10.1101/2021.08.06.455458Cold Spring Harbor Laboratory Press2021-08-09
<![CDATA[
Single-sequence protein structure prediction using language models from deep learning
]]>
https://biorxiv.org/cgi/content/short/2021.08.02.454840v1?rss=1"
Chowdhury, R.Bouatta, N.Biswas, S.Rochereau, C.Church, G. M.Sorger, P. K.AlQuraishi, M. N.2021-08-04doi:10.1101/2021.08.02.454840Cold Spring Harbor Laboratory Press2021-08-04
<![CDATA[
A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses
]]>
https://biorxiv.org/cgi/content/short/2021.08.06.455429v1?rss=1"
Gross, S. M.Dane, M. A.Smith, R. L.Devlin, K.Mclean, I.Derrick, D.Mills, C.Subramanian, K.London, A.Torre, D.Erdem, C.Lyons, N.Natoli, T.Pessa, S.Lu, X.Mullahoo, J.Li, J.Adam, M.Wassie, B.Liu, M.Kilburn, D. F.Liby, T.Bucher, E.Sanchez-Aguila, C.Daily, K.Omberg, L.Wang, Y.Jacobson, C.Yapp, C.Chung, M.Vidovic, D.Lu, Y.Schurer, S.Lee, A.Pillai, A.Subramanian, A.Papanastasiou, M.Fraenkel, E.Feiler, H.Mills, G. B.Jaffe, J.Ma'ayan, A.Birtwistle, M. R.Sorger, P. K.Korkola, J. E.Gray, J. W.Heiser, L. M.2021-08-09doi:10.1101/2021.08.06.455429Cold Spring Harbor Laboratory Press2021-08-09
<![CDATA[
Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method
]]>
https://biorxiv.org/cgi/content/short/2021.08.27.457854v1?rss=1"
Mills, C. E.Subramanian, K.Hafner, M.Niepel, M.Gerosa, L.Chung, M.Victor, C.Gaudio, B.Yapp, C.Sorger, P. K.2021-08-28doi:10.1101/2021.08.27.457854Cold Spring Harbor Laboratory Press2021-08-28
<![CDATA[
Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma
]]>
https://biorxiv.org/cgi/content/short/2022.01.12.475925v1?rss=1"
Coy, S.Wang, S.Stopka, S. A.Lin, J.-R.Rashid, R.Yapp, C.Ritch, C. C.Khadka, P.Regan, M.Hwang, J.Wen, P. Y.Bandopadhayay, P.Ligon, K. L.Agar, N. Y.Sorger, P. K.Touat, M.Santagata, S.2022-01-12doi:10.1101/2022.01.12.475925Cold Spring Harbor Laboratory Press2022-01-12
<![CDATA[
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
]]>
https://biorxiv.org/cgi/content/short/2022.02.17.480899v1?rss=1"
Froehlich, F.Gerosa, L.Muhlich, J. L.Sorger, P. K.2022-02-18doi:10.1101/2022.02.17.480899Cold Spring Harbor Laboratory Press2022-02-18
<![CDATA[
Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data
]]>
https://biorxiv.org/cgi/content/short/2022.05.09.490039v1?rss=1"
Warchol, S.Krueger, R.Nirmal, A. J.Gaglia, G.Jessup, J.Ritch, C. C.Hoffer, J.Muhlich, J. L.Burger, M.Jacks, T. L.Santagata, S.Sorger, P. K.Pfister, H.2022-05-09doi:10.1101/2022.05.09.490039Cold Spring Harbor Laboratory Press2022-05-09
<![CDATA[
A community-based approach to image analysis of cells, tissues and tumors
]]>
https://biorxiv.org/cgi/content/short/2021.07.22.451363v1?rss=1"
CSBC/PS-ON Image Analysis Working Group,Vizcarra, J. C.Burlingame, E. A.Hug, C. B.Goltsev, Y.White, B. S.Tyson, D. R.Sokolov, A.2021-07-25doi:10.1101/2021.07.22.451363Cold Spring Harbor Laboratory Press2021-07-25
<![CDATA[
Design principles to assemble drug combinations for effective tuberculosis therapy using interpretable pairwise drug response measurements
]]>
https://biorxiv.org/cgi/content/short/2021.12.05.471248v1?rss=1"
500 combinations among twelve antibiotics. Our classifiers performed well on test data and predicted many novel combinations to be improved over bedaquiline + pretomanid + linezolid, an effective regimen for multidrug-resistant tuberculosis that also shortens treatment in BALB/c mice compared to the standard of care. To understand the design features of effective drug combinations, we reformulated classifiers as simple rulesets to reveal guiding principles of constructing combination therapies for both preclinical and clinical outcomes. One example ruleset is to include a drug pair that is synergistic in dormancy and another pair that is potent in a cholesterol-rich growth environment. These rulesets are predictive, intuitive, and practical, thus enabling rational construction of effective drug combinations based on in vitro pairwise drug synergies and potencies. As more preclinical and clinical drug combination data become available, we expect to improve predictions and combination design rules.
]]>Larkins-Ford, J.Degefu, Y. N.Van, N.Sokolov, A.Aldridge, B. B.2021-12-06doi:10.1101/2021.12.05.471248Cold Spring Harbor Laboratory Press2021-12-06
<![CDATA[
Systematic measurement of combination drug landscapes to predict in vivo treatment outcomes for tuberculosis
]]>
https://biorxiv.org/cgi/content/short/2021.02.03.429579v1?rss=1"
Larkins-Ford, J.Greenstein, T.Van, N.Degefu, Y. N.Olson, M. C.Sokolov, A.Aldridge, B. B.2021-02-04doi:10.1101/2021.02.03.429579Cold Spring Harbor Laboratory Press2021-02-04
<![CDATA[
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data
]]>
https://biorxiv.org/cgi/content/short/722918v1?rss=1"
Krueger, R.Beyer, J.Jang, W.-D.Kim, N. W.Sokolov, A.Sorger, P. K.Pfister, H.2019-08-02doi:10.1101/722918Cold Spring Harbor Laboratory Press2019-08-02
<![CDATA[
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer
]]>
https://biorxiv.org/cgi/content/short/704114v1?rss=1"
Rashid, R.Gaglia, G.Chen, Y.-A.Lin, J.-R.Du, Z.Maliga, Z.Schapiro, D.Yapp, C.Muhlich, J.Sokolov, A.Sorger, P.Santagata, S.2019-07-17doi:10.1101/704114Cold Spring Harbor Laboratory Press2019-07-17
<![CDATA[
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
]]>
https://biorxiv.org/cgi/content/short/2021.09.10.459803v1?rss=1"
Gyori, B. M.Hoyt, C. T.Steppi, A.2021-09-11doi:10.1101/2021.09.10.459803Cold Spring Harbor Laboratory Press2021-09-11
<![CDATA[
Robustness and parameter geography in post-translational modification systems
]]>
https://biorxiv.org/cgi/content/short/862003v1?rss=1"
Nam, K.-M.Gyori, B. M.Amethyst, S. V.Bates, D. J.Gunawardena, J.2019-12-02doi:10.1101/862003Cold Spring Harbor Laboratory Press2019-12-02
<![CDATA[
Capturing scientific knowledge in computable form
]]>
https://biorxiv.org/cgi/content/short/2021.03.10.382333v1?rss=1"
Wong, J. V.Franz, M.Siper, M. C.Fong, D.Durupinar, F.Dallago, C.Luna, A.Giorgi, J. M.Rodchenkov, I.Babur, O.Gyori, B. M.Bachman, J. A.Demir, E.Bader, G. D.Sander, C.2021-03-11doi:10.1101/2021.03.10.382333Cold Spring Harbor Laboratory Press2021-03-11
<![CDATA[
Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language
]]>
https://biorxiv.org/cgi/content/short/536409v1?rss=1"
Hoyt, C.Domingo-Fernandez, D.Aldisi, R.Xu, L.Kolpeja, K.Spalek, S.Wollert, E.Bachman, J.Gyori, B.Greene, P.Hofmann-Apitius, M.2019-01-31doi:10.1101/536409Cold Spring Harbor Laboratory Press2019-01-31
<![CDATA[
Transitions in the proteome and phospho-proteome during early embryonic development in Xenopus
]]>
https://biorxiv.org/cgi/content/short/2021.08.05.455309v1?rss=1"
Van Itallie, E.Kalocsay, M.Wuhr, M.Peshkin, L.Kirschner, M. W.2021-08-06doi:10.1101/2021.08.05.455309Cold Spring Harbor Laboratory Press2021-08-06
<![CDATA[
Time-resolved proteomic profiling of the ciliary Hedgehog response reveals that GPR161 and PKA undergo regulated co-exit from cilia
]]>
https://biorxiv.org/cgi/content/short/2020.07.29.225797v1?rss=1"
May, E. A.Kalocsay, M.Galtier D'Auriac, I.Gygi, S. P.Nachury, M. V.Mick, D. U.2020-07-29doi:10.1101/2020.07.29.225797Cold Spring Harbor Laboratory Press2020-07-29
<![CDATA[
Orphan nuclear receptor COUP-TFII drives the myofibroblast metabolic shift leading to fibrosis
]]>
https://biorxiv.org/cgi/content/short/2020.06.05.135889v1?rss=1"
Li, L.Galichon, P.Xiao, X.Figueroa-Ramirez, A. C.Tamayo, D.Lee, J. J.Kalocsay, M.Gonzalez-Sanchez, D.Chancay, M. S.McCracken, K.Lemos, D.Lee, N.Ichimura, T.Mori, Y.Valerius, M. T.Sun, X.Edelman, E. R.Bonventre, J. V.2020-06-05doi:10.1101/2020.06.05.135889Cold Spring Harbor Laboratory Press2020-06-05
<![CDATA[
The Kinase Chemogenomic Set (KCGS): An open science resource for kinase vulnerability identification
]]>
https://biorxiv.org/cgi/content/short/2019.12.22.886523v1?rss=1"
Wells, C. I.Al-Ali, H.Andrews, D. M.Asquith, C. R. M.Axtman, A. D.Chung, M.Dikic, I.Ebner, D.Elkins, J.Ettmayer, P.Fischer, C.Frederiksen, M.Gray, N. S.Hatch, S. B.Knapp, S.Lee, S.Lucking, U.Michaelides, M.Mills, C. E.Muller, S.Owen, D.Picado, A.Ramadan, K.Saikatendu, K. S.Schroder, M.Stolz, A.Tellechea, M.Treiber, D. K.Turunen, B. J.Vilar, S.Wang, J.Zuercher, W.Willson, T. M.Drewry, D. H.2019-12-23doi:10.1101/2019.12.22.886523Cold Spring Harbor Laboratory Press2019-12-23
<![CDATA[
Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity
]]>
https://biorxiv.org/cgi/content/short/2020.09.13.276923v1?rss=1"
Inde, Z.Yapp, C.Joshi, G. N.Spetz, J.Fraser, C.Deskin, B.Ghelfi, E.Sodhi, C.Hackam, D.Kobzik, L.Croker, B.Brownfield, D.Jia, H.Sarosiek, K. A.2020-09-13doi:10.1101/2020.09.13.276923Cold Spring Harbor Laboratory Press2020-09-13
<![CDATA[
Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER
]]>
https://biorxiv.org/cgi/content/short/507566v1?rss=1"
Saka, S. K.Wang, Y.Kishi, J. Y.Zhu, A.Zeng, Y.Xie, W.Kirli, K.Yapp, C.Cicconet, M.Beliveau, B. J.Lapan, S. W.Yin, S.Lin, M.Boyden, E. S.Kaeser, P. S.Pihan, G.Church, G. M.Yin, P.2018-12-28doi:10.1101/507566Cold Spring Harbor Laboratory Press2018-12-28
<![CDATA[
STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs
]]>
https://biorxiv.org/cgi/content/short/2021.08.17.456616v1?rss=1"
Balabin, H.Hoyt, C. T.Birkenbihl, C.Gyori, B. M.Bachman, J. A.Tom Kodamullil, A.Ploeger, P. G.Hofmann-Apitius, M.Domingo-Fernandez, D.2021-08-18doi:10.1101/2021.08.17.456616Cold Spring Harbor Laboratory Press2021-08-18
<![CDATA[
Crosstalk and Ultrasensitivity in Protein Degradation Pathways
]]>
https://biorxiv.org/cgi/content/short/594085v1?rss=1"
Mallela, A.Nariya, M. K.Deeds, E. J.2019-03-30doi:10.1101/594085Cold Spring Harbor Laboratory Press2019-03-30
<![CDATA[
The Bioregistry: Unifying the Identification of Biomedical Entities through an Integrative, Open, Community-driven Metaregistry
]]>
https://biorxiv.org/cgi/content/short/2022.07.08.499378v1?rss=1"
Hoyt, C. T.Balk, M.Callahan, T. J.Domingo-Fernandez, D.Haendel, M. A.Hegde, H. B.Himmelstein, D. S.Karis, K.Kunze, J.Lubiana, T.Matentzoglu, N.McMurry, J.Moxon, S.Mungall, C. J.Rutz, A.Unni, D. R.Willighagen, E.Winston, D.Gyori, B. M.2022-07-10doi:10.1101/2022.07.08.499378Cold Spring Harbor Laboratory Press2022-07-10
<![CDATA[
Automated assembly of molecular mechanisms at scale from text mining and curated databases
]]>
https://biorxiv.org/cgi/content/short/2022.08.30.505688v1?rss=1"
Bachman, J. A.Gyori, B. M.Sorger, P. K.2022-08-31doi:10.1101/2022.08.30.505688Cold Spring Harbor Laboratory Press2022-08-31
<![CDATA[
A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets
]]>
https://biorxiv.org/cgi/content/short/2022.08.18.504436v1?rss=1"
Creason, A. L.Watson, C.Gu, Q.Persson, D.Sargent, L. L.Chen, Y.-A.Lin, J.-R.Sivagnanam, S.Wünnemann, F.Nirmal, A. J.Chin, K.Feiler, H. S.Coussens, L. M.Schapiro, D.Grüning, B. A.Sorger, P. K.Sokolov, A.Goecks, J.2022-08-19doi:10.1101/2022.08.18.504436Cold Spring Harbor Laboratory Press2022-08-19
<![CDATA[
Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma
]]>
https://biorxiv.org/cgi/content/short/2022.08.11.503237v1?rss=1"
Gaglia, G.Burger, M.Ritch, C. C.Rammos, D.Dai, Y.Crossland, G. E.Tavana, S. Z.Warchol, S.Jaeger, A. M.Naranjo, S.Coy, S.Johnson, A.Krueger, R.Lin, J.-R.Pfister, H.Sorger, P. K.Jacks, T.Santagata, S.2022-08-13doi:10.1101/2022.08.11.503237Cold Spring Harbor Laboratory Press2022-08-13
<![CDATA[
Paired evaluation defines performance landscapes for machine learning models
]]>
https://biorxiv.org/cgi/content/short/2022.09.07.507020v1?rss=1"
Nariya, M. K.Mills, C. E.Sorger, P. K.Sokolov, A.2022-09-12doi:10.1101/2022.09.07.507020Cold Spring Harbor Laboratory Press2022-09-12
<![CDATA[
Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section
]]>
https://biorxiv.org/cgi/content/short/2022.09.28.509927v1?rss=1"
Lin, J.-R.Chen, Y.-A.Campton, D.Cooper, J.Coy, S.Yapp, C.Tefft, J.McCarty, E.Ligon, K.Rodig, S. J.Reese, S.George, T.Santagata, S.Sorger, P. K.2022-09-30doi:10.1101/2022.09.28.509927Cold Spring Harbor Laboratory Press2022-09-30
<![CDATA[
Multi range ERK responses shape the proliferative trajectory of single cells following oncogene induced senescence
]]>
https://biorxiv.org/cgi/content/short/2022.10.06.511142v1?rss=1"
Chen, J.-Y.Hug, C.Reyes, J.Tian, C.Gerosa, L.Fröhlich, F.Ponsioen, B.Snippert, H. J. G.Spencer, S. L.Jambhekar, A.Sorger, P. K.Lahav, G.2022-10-07doi:10.1101/2022.10.06.511142Cold Spring Harbor Laboratory Press2022-10-07
<![CDATA[
Resolving deleterious and near-neutral effects requires different pooled fitness assay designs
]]>
https://biorxiv.org/cgi/content/short/2022.08.19.504558v1?rss=1"
Limdi, A.Baym, M.2022-08-20doi:10.1101/2022.08.19.504558Cold Spring Harbor Laboratory Press2022-08-20
<![CDATA[
Parallel changes in gene essentiality over 50,000 generations of evolution
]]>
https://biorxiv.org/cgi/content/short/2022.05.17.492023v1?rss=1"
Limdi, A.Owen, S. V.Herren, C.Lenski, R. E.Baym, M.2022-05-17doi:10.1101/2022.05.17.492023Cold Spring Harbor Laboratory Press2022-05-17
<![CDATA[
Decreased thermal tolerance as a trade-off of antibiotic resistance
]]>
https://biorxiv.org/cgi/content/short/2021.04.05.438396v1?rss=1"
Herren, C. M.Baym, M.2021-04-05doi:10.1101/2021.04.05.438396Cold Spring Harbor Laboratory Press2021-04-05
<![CDATA[
Swapped genetic code blocks viral infections and gene transfer
]]>
https://biorxiv.org/cgi/content/short/2022.07.08.499367v1?rss=1"
Nyerges, A.Vinke, S.Flynn, R.Owen, S. V.Rand, E. A.Budnik, B.Keen, E.Narasimhan, K.Marchand, J. A.Baas-Thomas, M.Liu, M.Chen, K.Chiappino-Pepe, A.Hu, F.Baym, M.Church, G. M.2022-07-10doi:10.1101/2022.07.08.499367Cold Spring Harbor Laboratory Press2022-07-10
<![CDATA[
Simplitigs as an efficient and scalable representation of de Bruijn graphs
]]>
https://biorxiv.org/cgi/content/short/2020.01.12.903443v1?rss=1"
Brinda, K.Baym, M.Kucherov, G.2020-01-12doi:10.1101/2020.01.12.903443Cold Spring Harbor Laboratory Press2020-01-12
<![CDATA[
The gut bacterial natural product colibactin triggers induction of latent viruses in diverse bacteria
]]>
https://biorxiv.org/cgi/content/short/2021.05.24.445430v1?rss=1"
Silpe, J. E.Wong, J. W. H.Owen, S. V.Baym, M.Balskus, E. P.2021-05-24doi:10.1101/2021.05.24.445430Cold Spring Harbor Laboratory Press2021-05-24
<![CDATA[
Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria
]]>
https://biorxiv.org/cgi/content/short/261750v1?rss=1"
Herren, C.Baym, M.2018-02-08doi:10.1101/261750Cold Spring Harbor Laboratory Press2018-02-08
<![CDATA[
Prophage-encoded phage defence proteins with cognate self-immunity
]]>
https://biorxiv.org/cgi/content/short/2020.07.13.199331v1?rss=1"
Owen, S. V.Wenner, N.Dulberger, C. L.Rodwell, E. V.Bowers-Barnard, A.Quinones-Olvera, N.Rigden, D. J.Rubin, E. J.Garner, E. C.Baym, M.Hinton, J. C. D.2020-07-13doi:10.1101/2020.07.13.199331Cold Spring Harbor Laboratory Press2020-07-13
<![CDATA[
Lineage calling can identify antibiotic resistant clones within minutes
]]>
https://biorxiv.org/cgi/content/short/403204v1?rss=1"
Brinda, K.Callendrello, A.Cowley, L.Charalampous, T.Lee, R. S.MacFadden, D. R.Kucherov, G.O'Grady, J.Baym, M.Hanage, W. P.2018-08-29doi:10.1101/403204Cold Spring Harbor Laboratory Press2018-08-29
<![CDATA[
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
]]>
https://biorxiv.org/cgi/content/short/2022.08.08.503176v1?rss=1"
Lakrisenko, P.Stapor, P.Grein, S.Paszkowski, ŁukaszPathirana, D.Fröhlich, F.Lines, G. T.Weindl, D.Hasenauer, J.2022-08-11doi:10.1101/2022.08.08.503176Cold Spring Harbor Laboratory Press2022-08-11
<![CDATA[
KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data
]]>
https://biorxiv.org/cgi/content/short/2022.05.02.490362v1?rss=1"
Tagore, S.Wang, Y.Biermann, J.Rabadan, R.Azizi, E.Izar, B.2022-05-04doi:10.1101/2022.05.02.490362Cold Spring Harbor Laboratory Press2022-05-04
<![CDATA[
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513552v1?rss=1"
Pillich, R. T.Chen, J.Churas, C.Fong, D.Gyori, B. M.Ideker, T.Karis, K.Liu, S. N.Ono, K.Pico, A.Pratt, D.2022-10-25doi:10.1101/2022.10.24.513552Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
]]>
https://biorxiv.org/cgi/content/short/2022.11.20.517210v1?rss=1"
Ahdritz, G.Bouatta, N.Kadyan, S.Xia, Q.Gerecke, W.O'Donnell, T. J.Berenberg, D.Fisk, I.Zanichelli, N.Zhang, B.Nowaczynski, A.Wang, B.Stepniewska-Dziubinska, M. M.Zhang, S.Ojewole, A.Guney, M. E.Biderman, S.Watkins, A. M.Ra, S.Lorenzo, P. R.Nivon, L.Weitzner, B.Ban, Y.-E. A.Sorger, P. K.Mostaque, E.Zhang, Z.Bonneau, R.AlQuraishi, M.2022-11-22doi:10.1101/2022.11.20.517210Cold Spring Harbor Laboratory Press2022-11-22
<![CDATA[
Characterization of metabolic compartmentalization in the liver using spatially resolved metabolomics
]]>
https://biorxiv.org/cgi/content/short/2021.12.13.472421v1?rss=1"
van der Reest, J.Stopka, S. A.Abdelmoula, W. M.Ruiz, D. F.Joshi, S.Ringel, A.Haigis, M. C.Agar, N. Y. R.2021-12-13doi:10.1101/2021.12.13.472421Cold Spring Harbor Laboratory Press2021-12-13
<![CDATA[
A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments
]]>
https://biorxiv.org/cgi/content/short/2023.01.26.525375v1?rss=1"
Chidley, C.Darnell, A. M.Gaudio, B. L.Lien, E. C.Barbeau, A. M.Vander Heiden, M. G.Sorger, P. K.2023-01-26doi:10.1101/2023.01.26.525375Cold Spring Harbor Laboratory Press2023-01-26
<![CDATA[
3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding
]]>
https://biorxiv.org/cgi/content/short/2022.12.09.519807v1?rss=1"
Burlingame, E.Ternes, L.Lin, J.-R.Chen, Y.-A.Kim, E. N.Gray, J. W.Santagata, S.Sorger, P. K.Chang, Y. H.2022-12-12doi:10.1101/2022.12.09.519807Cold Spring Harbor Laboratory Press2022-12-12
<![CDATA[
Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518386v1?rss=1"
Hoyt, C. T.Hoyt, A. L.Gyori, B. M.2022-12-02doi:10.1101/2022.11.29.518386Cold Spring Harbor Laboratory Press2022-12-02
<![CDATA[
Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways
]]>
https://biorxiv.org/cgi/content/short/2023.02.01.526526v1?rss=1"
Jain, A.Gyori, B.Hakim, S.Bunga, S.Taub, D. G.Ruiz-Cantero, M. C.Tong-Li, C.Andrews, N.Sorger, P. K.Woolf, C. J.2023-02-03doi:10.1101/2023.02.01.526526Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531314v1?rss=1"
Wang, Y.Sarfraz, I.Teh, W. K.Sokolov, A.Herb, B. R.Creasy, H. H.Virshup, I.Dries, R.Degatano, K.Mahurkar, A.Schnell, D. J.Madrigal, P.Hilton, J.Gehlenborg, N.Tickle, T.Campbell, J. D.2023-03-07doi:10.1101/2023.03.06.531314Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Diverse and Abundant Viruses Exploit Conjugative Plasmids
]]>
https://biorxiv.org/cgi/content/short/2023.03.19.532758v1?rss=1"
Quinones-Olvera, N.Owen, S. V.McCully, L. M.Marin, M. G.Rand, E. A.Fan, A. C.Dosumu, O. J. M.Paul, K.Castano, C. E. S.Paull, J. S.Petherbridge, R.Baym, M.2023-03-19doi:10.1101/2023.03.19.532758Cold Spring Harbor Laboratory Press2023-03-19
<![CDATA[
Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence
]]>
https://biorxiv.org/cgi/content/short/2023.04.03.535435v1?rss=1"
Maliga, Z.Kim, D. Y.Bui, A.-T. N.Lin, J.-R.Dewan, A. K.Murphy, G. F.Nirmal, A. J.Lian, C. G.Sorger, P. K.LeBoeuf, N. R.2023-04-05doi:10.1101/2023.04.03.535435Cold Spring Harbor Laboratory Press2023-04-05
<![CDATA[
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression
]]>
https://biorxiv.org/cgi/content/short/2023.04.15.536996v1?rss=1"
Brinda, K.Lima, L.Pignotti, S.Quinones-Olvera, N.Salikhov, K.Chikhi, R.Kucherov, G.Iqbal, Z.Baym, M.2023-04-16doi:10.1101/2023.04.15.536996Cold Spring Harbor Laboratory Press2023-04-16
<![CDATA[
Addressing persistent challenges in digital image analysis of cancerous tissues
]]>
https://biorxiv.org/cgi/content/short/2023.07.21.548450v1?rss=1"
Prabhakaran, S.Yapp, C.Baker, G. J.Beyer, J.Chang, Y. H.Creason, A. L.Krueger, R.Muhlich, J.Patterson, N. H.Sidak, K.Sudar, D.Taylor, A. J.Ternes, L.Troidl, J.Yubin, X.Sokolov, A.Tyson, D. R.Participants of the Cell Imaging Hackathon 2022,2023-07-24doi:10.1101/2023.07.21.548450Cold Spring Harbor Laboratory Press2023-07-24
<![CDATA[
2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer
]]>
https://biorxiv.org/cgi/content/short/2023.11.07.566063v1?rss=1"
Coy, S.Cheng, B.Lee, J. S.Rashid, R.Browning, L.Xu, Y.Chakrabarty, S. S.Yapp, C.Chan, S.Tefft, J. B.Spektor, A.Ligon, K. L.Baker, G. J.Pellman, D.Sorger, P. K.Santagata, S.2023-11-11doi:10.1101/2023.11.07.566063Cold Spring Harbor Laboratory Press2023-11-11
<![CDATA[
Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565120v1?rss=1"
Baker, G. J.Novikov, E.Zhao, Z.Vallius, T.Davis, J. A.Lin, J.-R.Muhlich, J. L.Mittendorf, E. A.Santagata, S.Guerriero, J. L.Sorger, P. K.2023-11-01doi:10.1101/2023.11.01.565120Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images
]]>
https://biorxiv.org/cgi/content/short/2023.11.15.567196v1?rss=1"
Nirmal, A. J.Yapp, C.Santagata, S.Sorger, P.2023-11-17doi:10.1101/2023.11.15.567196Cold Spring Harbor Laboratory Press2023-11-17
<![CDATA[
Multiplexed 3D Analysis of Cell Plasticity and Immune Niches in Melanoma
]]>
https://biorxiv.org/cgi/content/short/2023.11.10.566670v1?rss=1"
Yapp, C.Nirmal, A. J.Zhou, F. Y.Maliga, Z.Montero Llopis, P.Murphy, G. F.Lian, C.Danuser, G.Santagata, S.Sorger, P. K.2023-11-15doi:10.1101/2023.11.10.566670Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data
]]>
https://biorxiv.org/cgi/content/short/2023.11.10.566378v1?rss=1"
Wan, G.Maliga, Z.Yan, B.Vallius, T.Shi, Y.Khattab, S.Chang, C.Nirmal, A. J.Yu, K.-H.Liu, D.Lian, C. G.DeSimone, M. S.Sorger, P. K.Semenov, Y. R.2023-11-14doi:10.1101/2023.11.10.566378Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
ASCT2 is the primary serine transporter in cancer cells
]]>
https://biorxiv.org/cgi/content/short/2023.10.09.561530v1?rss=1"
Conger, K. O.Chidley, C.Ozgurses, M. E.Zhao, H.Kim, Y.Semina, S. E.Burns, P. A.Rawat, V.Sheldon, R.Ben-Sahra, I.Frasor, J.Sorger, P. K.DeNicola, G. M.Coloff, J. L.2023-10-11doi:10.1101/2023.10.09.561530Cold Spring Harbor Laboratory Press2023-10-11
<![CDATA[
Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches.
]]>
https://biorxiv.org/cgi/content/short/2023.09.29.560006v1?rss=1"
100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in TRM biology and suggests a novel mechanism for rapid reactivation of resting TRM in tissue upon antigen encounter.
]]>Smith, N. P.Yan, Y.Pan, Y.Williams, J. B.Manakongtreecheep, K.Pant, S.Zhao, J.Tian, T.Pan, T.Stingley, C.Wu, K.Zhang, J.Kley, A. L.Sorger, P. K.Villani, A.-C.Kupper, T. S.2023-10-02doi:10.1101/2023.09.29.560006Cold Spring Harbor Laboratory Press2023-10-02
<![CDATA[
Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers
]]>
https://biorxiv.org/cgi/content/short/2023.09.27.557464v1?rss=1"
Creason, A. L.Egger, J.Watson, C.Sivagnanam, S.Chin, K.MacPherson, K.Lin, J.-R.Chen, Y.-A.Johnson, B. E.Feiler, H. S.Galipeau, D.Navin, N. E.Demir, E.Chang, Y. H.Corless, C. L.Mitri, Z. I.Thomas, G.Sorger, P. K.Adey, A. C.Coussens, L. M.Gray, J. W.Mills, G. B.Goecks, J.2023-09-29doi:10.1101/2023.09.27.557464Cold Spring Harbor Laboratory Press2023-09-29
<![CDATA[
TYK2 as a novel therapeutic target in Alzheimer Disease
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.595773v1?rss=1"
Konig, L.Rodriguez, S.Hug, C.Daneshvari, S.Chung, A.Bradshaw, G.Sahin, A.Zhou, G.Eisert, R.Piccioni, F.Das, S.Kalocsay, M.Sokolov, A.Sorger, P.Root, D.Albers, M. W.2024-06-06doi:10.1101/2024.06.04.595773Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Persistent Neurological Deficits in Mouse PASC Reveal Antiviral Drug Limitations
]]>
https://biorxiv.org/cgi/content/short/2024.06.02.596989v1?rss=1"
Verma, A. K.Lowery, S.Lin, L.-C.Duraisami, E.Abrahante, J. E. K.Qiu, Q.Hefti, M. M.Yu, R. C.Albers, M. W.Perlman, S.2024-06-03doi:10.1101/2024.06.02.596989Cold Spring Harbor Laboratory Press2024-06-03
<![CDATA[
Spatial Profiling of Metals through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging
]]>
https://biorxiv.org/cgi/content/short/2024.05.22.594980v1?rss=1"
Stopka, S.Bodineau, C.Baquer, G.Lin, J.-R.Hossain, M. A.Regan, M. S.Ruiz, D. F.Fletcher, S.-M.Pourquie, O.Lutsenko, S.Payne, C.Agar, J. N.Mazitschek, R.McDannold, N.Sorger, P. K.Santagata, S.Agar, N.2024-05-23doi:10.1101/2024.05.22.594980Cold Spring Harbor Laboratory Press2024-05-23
<![CDATA[
psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring
]]>
https://biorxiv.org/cgi/content/short/2024.04.11.589087v1?rss=1"
Warchol, S.Troidl, J.Muhlich, J. L.Krueger, R.Hoffer, J.Lin, T.Beyer, J.Glassman, E.Sorger, P. K.Pfister, H.2024-04-15doi:10.1101/2024.04.11.589087Cold Spring Harbor Laboratory Press2024-04-15
<![CDATA[
A general algorithm for consensus 3D cell segmentation from 2D segmented stacks
]]>
https://biorxiv.org/cgi/content/short/2024.05.03.592249v1?rss=1"
70,000 cells, spanning single cells, cell aggregates, and tissue. Moreover, u-Segment3D is competitive with native 3D segmentation, even exceeding when cells are crowded and have complex morphologies.
]]>Zhou, F. Y.Yapp, C.Shang, Z.Daetwyler, S.Marin, Z.Islam, M. T.Nanes, B. A.Jenkins, E.Gihana, G. M.Chang, B.-J.Weems, A.Dustin, M.Morrison, S. J.Fiolka, R. P.Dean, K. M.Jamieson, A.Sorger, P. K.Danuser, G. K.2024-05-06doi:10.1101/2024.05.03.592249Cold Spring Harbor Laboratory Press2024-05-06
<![CDATA[
Sendai virus persistence questions the transient naive reprogramming method for iPSC generation
]]>
https://biorxiv.org/cgi/content/short/2024.03.07.583804v1?rss=1"
De Los Angeles, A.Hug, C. B.Gladyshev, V. N.Church, G. M.Velychko, S.2024-03-12doi:10.1101/2024.03.07.583804Cold Spring Harbor Laboratory Press2024-03-12
<![CDATA[
PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation
]]>
https://biorxiv.org/cgi/content/short/2024.07.26.605293v1?rss=1"
Fang, R.Vallius, T.Zhang, A.Van Cura, D.Alicandri, F.Fischer, G.Draper, E.Xu, S.Pelletier, R.Katsyv, I.Sorger, P. K.Murphy, G. F.Lian, C. G.2024-07-26doi:10.1101/2024.07.26.605293Cold Spring Harbor Laboratory Press2024-07-26
<![CDATA[
Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement
]]>
https://biorxiv.org/cgi/content/short/2024.06.25.598921v1?rss=1"
de Bruijn, I.Nikolov, M.Lau, C.Clayton, A.Gibbs, D. L.Mitraka, E.Pozhideyeva, D.Lash, A.Sumer, S. O.Altreuter, J.Anton, K.DeFelice, M.Li, X.Lisman, A.Longabaugh, W. J. R.Muhlich, J.Sandro, S.Nandakumar, S.Peter, S. K.Suver, C.Schultz, N.Taylor, A. J.Thorsson, V.Cerami, E.Eddy, J. A.2024-06-30doi:10.1101/2024.06.25.598921Cold Spring Harbor Laboratory Press2024-06-30
<![CDATA[
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress
]]>
https://biorxiv.org/cgi/content/short/2022.08.16.503984v1?rss=1"
Hsu, P. P.Do, B. T.Vermeulen, S. Y.Wang, Z.Hirz, T.Aziz, N.Replogle, J. M.Abbott, K. L.Block, S.Darnell, A. M.Ferreira, R.Milosevic, J. T.Schmidt, D. R.Chidley, C.Su, X. A.Harris, I. S.Weissman, J. S.Cheloufi, S.Sykes, D. B.Vander Heiden, M. G.2022-08-16doi:10.1101/2022.08.16.503984Cold Spring Harbor Laboratory Press2022-08-16
<![CDATA[
Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
]]>
https://biorxiv.org/cgi/content/short/2024.09.25.615007v1?rss=1"
Kader, T.Lin, J.-R.Hug, C.Coy, S.Chen, Y.-A.de Bruijn, I.Shih, N.Jung, E.Pelletier, R. J.Leon, M. L.Mingo, G.Omran, D. K.Lee, J. S.Yapp, C.Satravada, B. A.Kundra, R.Xu, Y.Chan, S.Tefft, J.Muhlich, J. L.Kim, S.Gysler, S. M.Agudo, J.Heath, J. R.Schultz, N.Drescher, C.Sorger, P. K.Drapkin, R.Santagata, S.2024-09-27doi:10.1101/2024.09.25.615007Cold Spring Harbor Laboratory Press2024-09-27
<![CDATA[
Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers
]]>
https://biorxiv.org/cgi/content/short/2024.09.24.614701v1?rss=1"
Wala, J.de Bruijn, I.Coy, S.Gagne, A.Chan, S.Chen, Y.-A.Hoffer, J.Muhlich, J.Schultz, N.Santagata, S.Sorger, P.2024-09-26doi:10.1101/2024.09.24.614701Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data
]]>
https://biorxiv.org/cgi/content/short/2025.07.19.665696v1?rss=1"
Warchol, S.Guo, G.Knittel, J.Freeman, D.Bhalla, U.Muhlich, J.Sorger, P. K.Pfister, H.2025-07-22doi:10.1101/2025.07.19.665696Cold Spring Harbor Laboratory Press2025-07-22
<![CDATA[
Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches
]]>
https://biorxiv.org/cgi/content/short/2025.02.20.639240v1?rss=1"
Cortes-Rios, J.Rodriguez-Fernandez, M.Sorger, P. K.Fröhlich, F.2025-02-26doi:10.1101/2025.02.20.639240Cold Spring Harbor Laboratory Press2025-02-26
<![CDATA[
Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders
]]>
https://biorxiv.org/cgi/content/short/2025.06.23.661064v1?rss=1"
Baker, G. J.Novikov, E.Coy, S.Chen, Y.-A.Hug, C. B.Ahmed, Z.Ordonez, S. A. C.Huang, S.Yapp, C.Sokolov, A.Pfister, H.Santagata, S.Sorger, P. K.2025-06-27doi:10.1101/2025.06.23.661064Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma
]]>
https://biorxiv.org/cgi/content/short/2025.06.21.660851v1?rss=1"
Vallius, T.Shi, Y.Novikov, E.Pant, S. M.Pelletier, R.Chen, Y.-A.Tefft, J. B.Nirmal, A. J.Maliga, Z.Wan, G.Murphy, G.Santagata, S.Semenov, Y.Liu, D.Lian, C. G.Sorger, P. K.2025-06-24doi:10.1101/2025.06.21.660851Cold Spring Harbor Laboratory Press2025-06-24
<![CDATA[
Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas.
]]>
https://biorxiv.org/cgi/content/short/2025.03.10.642376v1?rss=1"
Jain, N.Ogbanna, E. C.Maliga, Z.Jacobson, C. A.Zhang, L.Shih, A. R.Rosenberg, J. M.Kalam, H.Gagne, A.Solomon, I. H.Santagata, S.Sorger, P. K.Aldridge, B. B.Martinot, A. J.2025-03-13doi:10.1101/2025.03.10.642376Cold Spring Harbor Laboratory Press2025-03-13
<![CDATA[
Ribosome-associated quality control of aberrant protein production during amino acid limitation
]]>
https://biorxiv.org/cgi/content/short/2026.01.14.699605v1?rss=1"
Darnell, A. M.Chidley, C.Paradise, V.Cui, D. S.Davidsen, K.Lincoln, S. C.Abbott, K. L.Elbashir, R.Vander Heiden, C. P.Sorger, P. K.Sullivan, L. B.Davis, J. H.Vander Heiden, M. G.2026-01-15doi:10.64898/2026.01.14.699605Cold Spring Harbor Laboratory Press2026-01-15
<![CDATA[
In vivo evidence for bleb-induced survival signaling in metastatic melanoma
]]>
https://biorxiv.org/cgi/content/short/2026.01.05.697601v1?rss=1"
View larger version (61K):
org.highwire.dtl.DTLVardef@1770384org.highwire.dtl.DTLVardef@87e567org.highwire.dtl.DTLVardef@1e5d6b2org.highwire.dtl.DTLVardef@724c5f_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Weems, A. D.Islam, M. T.Borges, H.Yapp, C.Perez-Castro, L.Nogueira, P.Lin, J.Maliga, Z.Lewis, A. J.Kutter, C.Mannino, M.Vallius, T.Santagata, S.Sorger, P. K.Conacci-Sorrell, M.Dean, K. M.Danuser, G. M.2026-01-05doi:10.64898/2026.01.05.697601Cold Spring Harbor Laboratory Press2026-01-05
<![CDATA[
Mechanisms of tumor persistence in metastatic melanoma following successful immunotherapy
]]>
https://biorxiv.org/cgi/content/short/2025.12.11.692633v1?rss=1"
Shi, Y.Maliga, Z.Vallius, T.Pant, S. M.Pelletier, R.Kobs, B.Solanky, P.He, Y.Van Allen, E.Santagata, S.Ott, P.Lian, C. G.Buchbinder, E.Liu, D.Sorger, P. K.2025-12-15doi:10.64898/2025.12.11.692633Cold Spring Harbor Laboratory Press2025-12-15
<![CDATA[
Integrative single-cell and spatial mapping of oxidative stress response uncovers GCLC+ mesenchymal tumor cell state linked with favorable outcomes in triple negative breast cancer
]]>
https://biorxiv.org/cgi/content/short/2025.11.06.686771v1?rss=1"
Girnius, N.Vallius, T.Chen, W.Launonen, I.-M.Palomino-Echeverria, S.Lin, J.-R.Mills, C. E.Kauppila, S.Kronqvist, P.Ellonen, A.Perala, M.Withnell, E.Chen, Y.-A.Secrier, M.Santagata, S.Sorger, P. K.Farkkila, A.2025-11-07doi:10.1101/2025.11.06.686771Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
Spatially organized lymphocytic microenvironments in high grade primary prostate tumors
]]>
https://biorxiv.org/cgi/content/short/2025.09.21.677465v1?rss=1"
Amiryousefi, A.Wala, J.Lin, J.-R.Labadie, B. W.Atmakuri, A.Maliga, Z.Toye, E.Chaudagar, K.Torcasso, M. S.Coy, S.Fanelli, G. N.Kobs, B.Socciarelli, F.Gagne, A.Van Allen, E.Patnaik, A.Sorger, P. K.2025-09-21doi:10.1101/2025.09.21.677465Cold Spring Harbor Laboratory Press2025-09-21
<![CDATA[
Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679282v1?rss=1"
Tarantino, G.Zaremba, A.Vallius, T.Woodnorth, M.Hua, Y.Pelletier, R.Lopez Leon, M.Shi, Y.Maliga, Z.Makhzami, S.Aprati, T. J.Karlas, B.Glutsch, V.Schilling, B.Hassel, J.Berking, C.Utikal, J.Meier, F.Meiss, F.Heinzerling, L.Kahler, K.Chen, J.Zimmer, L.Sucker, A.Livingstone, E.Hadaschik, E.Lian, C.Murphy, G.Semenov, Y. R.Boland, G. M.Sorger, P. K.Rambow, F.Liu, D.Schadendorf, D.2025-10-02doi:10.1101/2025.10.01.679282Cold Spring Harbor Laboratory Press2025-10-02
<![CDATA[
Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours
]]>
https://biorxiv.org/cgi/content/short/2025.07.23.666465v1?rss=1"
Burn, T. N.Schroeder, J.Gandolfo, L. C.Osman, M.Wainwright, E. N.Lam, E. Y. N.McDonald, K. M.Evans, R. B.Lee, S.Rawlinson, D.Dryburgh, L.Zaid, A.Maliga, Z.Schienstock, D.Meiser, P.Lee, H. J.Lai, H.Moreira, M. L.Zareie, P.Lee, H.-Y.Huq, L.Christo, S. N.Seow, J. J. W.Ching, K. A.Guillaume, S. M.Knezevic, K.Park, S. L.Evrard, M.Waithman, J.Gebhardt, T.Mueller, S. N.Riddiough, G. E.Perini, M. V.Tsao, S. C. H.Speed, T. P.Sorger, P.Loi, S.Carbone, F. R.Gras, S.Fisher, T. S.Baaten, B. J.Dawson, M. A.Mackay, L. K.2025-07-23doi:10.1101/2025.07.23.666465Cold Spring Harbor Laboratory Press2025-07-23