SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data.

Peter K. Sorger https://orcid.org/0000-0002-3364-1838 https://www.wikidata.org/entity/Q42127905 https://id.loc.gov/authorities/names/n86016697 https://d-nb.info/gnd/140651241

Simon Warchol Grace Guo 0001 Johannes Knittel Dan Freeman Usha Shalla Jeremy Muhlich Peter K. Sorger Hanspeter Pfister SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data. 2026 January 484-494 32 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2025.3634794 db/journals/tvcg/tvcg32.html#WarcholGKFSMSP26 streams/journals/tvcg

Javiera Cortés-Ríos Maria Rodriguez-Fernandez Peter K. Sorger Fabian Fröhlich Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches. 1012890 2025 21 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1012890 db/journals/ploscb/ploscb21.html#CortesRiosRSF25 streams/journals/ploscb

Dong Li 0034 Guihong Wan Xintao Wu Xinyu Wu Xiaohui Chen Yi He Zhong Chen Peter K. Sorger Chen Zhao 0010 Multi-Modal Foundation Models for Computational Pathology: A Survey. 2025 2025 Trans. Mach. Learn. Res. https://openreview.net/forum?id=NZ7GSH92cY db/journals/tmlr/tmlr2025.html#LiWWWCHCSZ25 streams/journals/tmlr

Eric Mörth Kevin Sidak Zoltan Maliga Torsten Möller Nils Gehlenborg Peter K. Sorger Hanspeter Pfister Johanna Beyer Robert Krüger Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. 569-579 2025 January 31 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2024.3456406 db/journals/tvcg/tvcg31.html#MorthSMMGSPBK25 streams/journals/tvcg

Dong Li 0034 Guihong Wan Xintao Wu Xinyu Wu Ajit Johnson Nirmal Christine G. Lian Peter K. Sorger Yevgeniy R. Semenov Chen Zhao 0010 A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks. 2025 January abs/2501.15724 CoRR https://doi.org/10.48550/arXiv.2501.15724 db/journals/corr/corr2501.html#abs-2501-15724 streams/journals/corr

Dong Li 0034 Guihong Wan Xintao Wu Xinyu Wu Xiaohui Chen Yi He Christine G. Lian Peter K. Sorger Yevgeniy R. Semenov Chen Zhao 0010 Multi-Modal Foundation Models for Computational Pathology: A Survey. 2025 March abs/2503.09091 CoRR https://doi.org/10.48550/arXiv.2503.09091 db/journals/corr/corr2503.html#abs-2503-09091 streams/journals/corr

Hyun-Jic Oh Junsik Kim 0001 Zhiyi Shi Yichen Wu Yu-An Chen Peter K. Sorger Hanspeter Pfister Won-Ki Jeong Virtual Multiplex Staining for Histological Images using a Marker-wise Conditioned Diffusion Model. 2025 August abs/2508.14681 CoRR https://doi.org/10.48550/arXiv.2508.14681 db/journals/corr/corr2508.html#abs-2508-14681 streams/journals/corr

Eric Mörth Morgan L. Turner Cydney Nielsen Xianhao Carton Liu Mark S. Keller Lisa Choy John Conroy Tabassum Kakar Clarence Yapp Alex Wong Peter K. Sorger Liam McLaughlin Sanjay Jain 0006 Johanna Beyer Hanspeter Pfister Chen Zhu-Tian Nils Gehlenborg Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps. 2025 November abs/2511.04262 CoRR https://doi.org/10.48550/arXiv.2511.04262 db/journals/corr/corr2511.html#abs-2511-04262 streams/journals/corr

Guihong Wan Zoltan Maliga Boshen Yan Tuulia Vallius Yingxiao Shi Sara Khattab Crystal T. Chang Ajit Johnson Nirmal Kun-Hsing Yu David S. L. Wei Christine G. Lian Mia S. Desimone Peter K. Sorger Yevgeniy R. Semenov SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data. 2024 May 25 Briefings Bioinform. 3 https://doi.org/10.1093/bib/bbae189 db/journals/bib/bib25.html#WanMYVSKCNYWLDSS24 streams/journals/bib

Simon Warchol Jakob Troidl Jeremy Muhlich Robert Krüger John Hoffer Tica Lin Johanna Beyer Elena L. Glassman Peter K. Sorger Hanspeter Pfister psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring. 2024 43 Comput. Graph. Forum 3 https://doi.org/10.1111/cgf.15103 db/journals/cgf/cgf43.html#WarcholTMKHLBGSP24

Ajit Johnson Nirmal Peter K. Sorger SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. 6604 2024 9 J. Open Source Softw. 97 https://doi.org/10.21105/joss.06604 db/journals/jossw/jossw9.html#NirmalS24 streams/journals/jossw

Lukas Herzberger Markus Hadwiger Robert Krüger Peter K. Sorger Hanspeter Pfister Eduard Gröller Johanna Beyer Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering. 1380-1390 2024 January 30 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2023.3327193 db/journals/tvcg/tvcg30.html#HerzbergerHKSPGB24

Boshen Yan Guihong Wan Haim Schweitzer Zoltan Maliga Sara Khattab Kun-Hsing Yu Peter K. Sorger Yevgeniy R. Semenov Pass-Efficient Algorithms for Graph Spectral Clustering (Student Abstract). 23690-23692 2024 AAAI https://doi.org/10.1609/aaai.v38i21.30528 conf/aaai/2024 db/conf/aaai/aaai2024.html#YanWSMKYSS24

Changchang Liu Peter Kutchukian Nhan D. Nguyen Mohammed Alquraishi Peter K. Sorger A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. 5457-5472 2023 September 63 J. Chem. Inf. Model. 17 https://doi.org/10.1021/acs.jcim.3c00347 db/journals/jcisd/jcisd63.html#LiuKNAS23

Maulik K. Nariya Caitlin E. Mills Peter K. Sorger Artem Sokolov Paired evaluation of machine-learning models characterizes effects of confounders and outliers. 100791 2023 August 4 Patterns 8 https://doi.org/10.1016/j.patter.2023.100791 db/journals/patterns/patterns4.html#NariyaMSS23

Maulik K. Nariya Caitlin E. Mills Peter K. Sorger Artem Sokolov Correction: Paired evaluation of machine-learning models characterizes effects of confounders and outliers. 100824 2023 August 4 Patterns 8 https://doi.org/10.1016/j.patter.2023.100824 db/journals/patterns/patterns4.html#NariyaMSS23a

Simon Warchol Robert Krüger Ajit Johnson Nirmal Giorgio Gaglia Jared Jessup Cecily C. Ritch John Hoffer Jeremy Muhlich Megan L. Burger Tyler Jacks Sandro Santagata Peter K. Sorger Hanspeter Pfister Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. 106-116 2023 29 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2022.3209378 db/journals/tvcg/tvcg29.html#WarcholKNGJRHMB23

Jia-Ren Lin Shu Wang Shannon Coy Yu-An Chen Clarence Yapp Madison Tyler Maulik K. Nariya Cody N. Heiser Ken S. Lau Sandro Santagata Peter K. Sorger labsyspharm/CRC_atlas_2022. 2023 January https://doi.org/10.5281/zenodo.7554924 Zenodo streams/repo/zenodo

Lukas Herzberger Markus Hadwiger Robert Krüger Peter K. Sorger Hanspeter Pfister Eduard Gröller Johanna Beyer Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering. 2023 abs/2309.04393 CoRR https://doi.org/10.48550/arXiv.2309.04393 db/journals/corr/corr2309.html#abs-2309-04393

Jeremy Muhlich Yu-An Chen Clarence Han-Wei Yapp Douglas Russell Sandro Santagata Peter K. Sorger Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. 4613-4621 2022 38 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btac544 db/journals/bioinformatics/bioinformatics38.html#MuhlichCYRSS22

Fabian Fröhlich Peter K. Sorger Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models. 2022 18 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1010322 https://www.wikidata.org/entity/Q113308403 db/journals/ploscb/ploscb18.html#FrohlichS22

Jared Jessup Robert Krüger Simon Warchol John Hoffer Jeremy Muhlich Cecily C. Ritch Giorgio Gaglia Shannon Coy Yu-An Chen Jia-Ren Lin Sandro Santagata Peter K. Sorger Hanspeter Pfister Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. 259-269 2022 28 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2021.3114786 https://www.wikidata.org/entity/Q110894825 db/journals/tvcg/tvcg28.html#JessupKWHMRGCCL22

Marc-Joseph Antonini Deborah Plana Shriya S. Srinivasan Lyla Atta Aditya Achanta Helen L. Yang Avilash K. Cramer Jacob Freake Michael S. Sinha Sherry H. Yu Nicole R. LeBoeuf Ben Linville-Engler Peter K. Sorger A Crisis-Responsive Framework for Medical Device Development Applied to the COVID-19 Pandemic. 617106 2021 3 Frontiers Digit. Health https://doi.org/10.3389/fdgth.2021.617106 https://www.wikidata.org/entity/Q110894731 db/journals/fdgth/fdgth3.html#AntoniniPSAAYCF21

Matthew E. Berginski Nienke Moret Changchang Liu Dennis Goldfarb Peter K. Sorger Shawn M. Gomez The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. D529-D535 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa853 https://www.wikidata.org/entity/Q100739925 db/journals/nar/nar49.html#BerginskiMLGSG21

Jared Jessup Robert Krüger Simon Warchol John Hoffer Jeremy Muhlich Cecily C. Ritch Giorgio Gaglia Shannon Coy Yu-An Chen Jia-Ren Lin Sandro Santagata Peter K. Sorger Hanspeter Pfister Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. 2021 abs/2110.04875 CoRR https://arxiv.org/abs/2110.04875 db/journals/corr/corr2110.html#abs-2110-04875

John Hoffer Rumana Rashid Jeremy Muhlich Yu-An Chen Douglas Russell Juha Ruokonen Robert Krüger Hanspeter Pfister Sandro Santagata Peter K. Sorger Minerva: a light-weight, narrative image browser for multiplexed tissue images. 2579 2020 5 J. Open Source Softw. 54 https://doi.org/10.21105/joss.02579 https://www.wikidata.org/entity/Q110894979 db/journals/jossw/jossw5.html#HofferRMCRRKPSS20

Robert Krüger Johanna Beyer Won-Dong Jang Nam Wook Kim Artem Sokolov Peter K. Sorger Hanspeter Pfister Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data. 227-237 2020 26 IEEE Trans. Vis. Comput. Graph. 1 https://doi.org/10.1109/TVCG.2019.2934547 https://www.wikidata.org/entity/Q90078652 db/journals/tvcg/tvcg26.html#KrugerBJKSSP20

Salma Abdel Magid Won-Dong Jang Denis Schapiro Donglai Wei 0001 James Tompkin 0001 Peter K. Sorger Hanspeter Pfister Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. 3-13 2020 MICCAI (5) https://doi.org/10.1007/978-3-030-59722-1_1 https://www.wikidata.org/entity/Q110894814 conf/miccai/2020-5 db/conf/miccai/miccai2020-5.html#MagidJSWTSP20

Petar V. Todorov Benjamin M. Gyori John A. Bachman Peter K. Sorger INDRA-IPM: interactive pathway modeling using natural language with automated assembly. 4501-4503 2019 35 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btz289 https://www.wikidata.org/entity/Q91879998 db/journals/bioinformatics/bioinformatics35.html#TodorovGBS19

Shu Wang Jia-Ren Lin Eduardo D. Sontag Peter K. Sorger Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. 2019 15 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1007311 https://www.wikidata.org/entity/Q91757055 db/journals/ploscb/ploscb15.html#WangLSS19

John A. Bachman Benjamin M. Gyori Peter K. Sorger FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. 248:1-248:14 2018 19 BMC Bioinform. 1 https://doi.org/10.1186/s12859-018-2211-5 https://www.wikidata.org/entity/Q55505864 db/journals/bmcbi/bmcbi19.html#BachmanGS18

Qiaonan Duan Corey Flynn Mario Niepel Marc Hafner Jeremy Muhlich Nicolas F. Fernandez Andrew D. Rouillard Christopher M. Tan Edward Y. Chen Todd R. Golub Peter K. Sorger Aravind Subramanian Avi Ma'ayan LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. 449-460 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku476 https://www.wikidata.org/entity/Q33860855 db/journals/nar/nar42.html#DuanFNHMFRTCGSSM14

Evan O. Paull Daniel E. Carlin Mario Niepel Peter K. Sorger David Haussler Joshua M. Stuart Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). 2757-2764 2013 29 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btt471 https://www.wikidata.org/entity/Q37236850 db/journals/bioinformatics/bioinformatics29.html#PaullCNSHS13

Daniel C. Kirouac Julio Saez-Rodriguez Jennifer Swantek John M. Burke Douglas A. Lauffenburger Peter K. Sorger Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. 29 2012 6 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-6-29 https://www.wikidata.org/entity/Q28727977 db/journals/bmcsb/bmcsb6.html#KirouacSSBLS12

Suzanne Gaudet Sabrina L. Spencer William W. Chen Peter K. Sorger Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis. 2012 8 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1002482 https://www.wikidata.org/entity/Q28483276 db/journals/ploscb/ploscb8.html#GaudetSCS12

Melody K. Morris Julio Saez-Rodriguez David C. Clarke Peter K. Sorger Douglas A. Lauffenburger Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. 2011 7 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1001099 https://www.wikidata.org/entity/Q28477321 db/journals/ploscb/ploscb7.html#MorrisSCSL11

Kyoung Ae Kim Sabrina L. Spencer John G. Albeck John M. Burke Peter K. Sorger Suzanne Gaudet Do Hyun Kim Systematic calibration of a cell signaling network model. 202 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-202 https://www.wikidata.org/entity/Q40860549 db/journals/bmcbi/bmcbi11.html#KimSABSGK10

Bree B. Aldridge Julio Saez-Rodriguez Jeremy Muhlich Peter K. Sorger Douglas A. Lauffenburger Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. 2009 5 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1000340 https://www.wikidata.org/entity/Q33426337 db/journals/ploscb/ploscb5.html#AldridgeSMSL09

Regina Samaga Julio Saez-Rodriguez Leonidas G. Alexopoulos Peter K. Sorger Steffen Klamt The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. 2009 5 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000438 https://www.wikidata.org/entity/Q33491534 db/journals/ploscb/ploscb5.html#SamagaSASK09

Julio Saez-Rodriguez Arthur Goldsipe Jeremy Muhlich Leonidas G. Alexopoulos Bjorn Millard Douglas A. Lauffenburger Peter K. Sorger Flexible informatics for linking experimental data to mathematical models via <i>DataRail</i>. 840-847 2008 24 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btn018 https://www.wikidata.org/entity/Q31143834 db/journals/bioinformatics/bioinformatics24.html#Saez-RodriguezGMAMLS08

Leonidas G. Alexopoulos Douglas A. Lauffenburger Peter K. Sorger Modeling pro-death signaling pathways in cancer hepatocytes using multi-combinatorial treatments of inhibitors and stimuli. 1-5 2008 BIBE https://doi.org/10.1109/BIBE.2008.4696732 conf/bibe/2008 db/conf/bibe/bibe2008.html#AlexopoulosLS08

Khuloud Jaqaman Jonas F. Dorn Eugenio Marco Peter K. Sorger Gaudenz Danuser Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. 1666-1673 2007 23 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btm230 https://www.wikidata.org/entity/Q48402366 db/journals/bioinformatics/bioinformatics23.html#JaqamanDMSD07

Birgit Schoeberl Emily Pace Shavonne Howard Viara Garantcharova Art Kudla Peter K. Sorger Ulrik B. Nielsen A Data-Driven Computational Model of the ErbB Receptor Signaling Network. 53-54 2006 EMBC https://doi.org/10.1109/IEMBS.2006.259754 https://www.wikidata.org/entity/Q31133626 conf/embc/2006 db/conf/embc/embc2006.html#SchoeberlPHGKSN06

Kevin A. Janes Jason R. Kelly Suzanne Gaudet John G. Albeck Peter K. Sorger Douglas A. Lauffenburger Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data. 544-561 2004 11 J. Comput. Biol. 4 https://doi.org/10.1089/cmb.2004.11.544 https://www.wikidata.org/entity/Q33209549 db/journals/jcb/jcb11.html#JanesKGASL04

Aditya Achanta John G. Albeck Bree B. Aldridge Leonidas G. Alexopoulos Mohammed Alquraishi Marc-Joseph Antonini Lyla Atta John A. Bachman Matthew E. Berginski Johanna Beyer Megan L. Burger John M. Burke Daniel E. Carlin Crystal T. Chang Edward Y. Chen William W. Chen Xiaohui Chen Yu-An Chen Zhong Chen Lisa Choy David C. Clarke John Conroy Javiera Cortés-Ríos Shannon Coy Avilash K. Cramer Gaudenz Danuser Mia S. Desimone Jonas F. Dorn Qiaonan Duan Nicolas F. Fernandez Corey Flynn Jacob Freake Dan Freeman Fabian Fröhlich Giorgio Gaglia Viara Garantcharova Suzanne Gaudet Nils Gehlenborg Elena L. Glassman Dennis Goldfarb Arthur Goldsipe Todd R. Golub Shawn M. Gomez M. Eduard GröllerEduard Gröller Grace Guo 0001 Benjamin M. Gyori Markus Hadwiger Marc Hafner David Haussler Yi He Cody N. Heiser Lukas Herzberger John Hoffer Shavonne Howard Tyler Jacks Sanjay Jain 0006 Kevin A. Janes Won-Dong Jang Khuloud Jaqaman Won-Ki Jeong Jared Jessup Tabassum Kakar Mark S. Keller Jason R. Kelly Sara Khattab Do Hyun Kim Junsik Kim 0001 Kyoung Ae Kim Namwook KimNam Wook Kim Daniel C. Kirouac Steffen Klamt Johannes Knittel Robert Krüger Art Kudla Peter Kutchukian Ken S. Lau Douglas A. Lauffenburger Nicole R. LeBoeuf Dong Li 0034 Christine G. Lian Jia-Ren Lin Tica Lin Ben Linville-Engler Changchang Liu Xianhao Carton Liu Avi Ma'ayan Salma Abdel Magid Zoltan Maliga Eugenio Marco Liam McLaughlin Bjorn Millard Caitlin E. Mills Torsten Möller Nienke Moret Melody K. Morris Eric Mörth Jeremy Muhlich Maulik K. Nariya Nhan D. Nguyen Cydney Nielsen Ulrik B. Nielsen Mario Niepel Ajit Johnson Nirmal Hyun-Jic Oh Emily Pace Evan O. Paull Hanspeter Pfister Deborah Plana Rumana Rashid Cecily C. Ritch Maria Rodriguez-Fernandez Andrew D. Rouillard Juha Ruokonen Douglas Russell Julio Saez-Rodriguez Regina Samaga Sandro Santagata Denis Schapiro Birgit Schoeberl Haim Schweitzer Yevgeniy R. Semenov Usha Shalla Yingxiao Shi Zhiyi Shi Kevin Sidak Michael S. Sinha Artem Sokolov Eduardo D. Sontag Sabrina L. Spencer Shriya S. Srinivasan Joshua M. Stuart Aravind Subramanian Jennifer Swantek Christopher M. Tan Petar V. Todorov James Tompkin 0001 Jakob Troidl Morgan L. Turner Madison Tyler Tuulia Vallius Guihong Wan Shu Wang Simon Warchol David S. L. Wei Donglai Wei 0001 Alex Wong Xintao Wu Xinyu Wu Yichen Wu Boshen Yan Helen L. Yang Clarence Yapp Clarence Han-Wei Yapp Kun-Hsing Yu Sherry H. Yu Chen Zhao 0010 Chen Zhu-Tian