Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data. - Kevin A. Janes; Jason R. Kelly; Suzanne Gaudet; John G. Albeck; Peter K. Sorger; Douglas A. Lauffenburger (J. Comput. Biol., 2004)

A Data-Driven Computational Model of the ErbB Receptor Signaling Network. - Birgit Schoeberl; Emily Pace; Shavonne Howard; Viara Garantcharova; Art Kudla; Peter K. Sorger; Ulrik B. Nielsen (EMBC, 2006)

Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. - Khuloud Jaqaman; Jonas F. Dorn; Eugenio Marco; Peter K. Sorger; Gaudenz Danuser (Bioinform., 2007)

Modeling pro-death signaling pathways in cancer hepatocytes using multi-combinatorial treatments of inhibitors and stimuli. - Leonidas G. Alexopoulos; Douglas A. Lauffenburger; Peter K. Sorger (BIBE, 2008)

Flexible informatics for linking experimental data to mathematical models via DataRail. - Julio Saez-Rodriguez; Arthur Goldsipe; Jeremy Muhlich; Leonidas G. Alexopoulos; Bjorn Millard; Douglas A. Lauffenburger; Peter K. Sorger (Bioinform., 2008)

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. - Bree B. Aldridge; Julio Saez-Rodriguez; Jeremy Muhlich; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2009)

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. - Regina Samaga; Julio Saez-Rodriguez; Leonidas G. Alexopoulos; Peter K. Sorger; Steffen Klamt (PLoS Comput. Biol., 2009)

Systematic calibration of a cell signaling network model. - Kyoung Ae Kim; Sabrina L. Spencer; John G. Albeck; John M. Burke; Peter K. Sorger; Suzanne Gaudet; Do Hyun Kim (BMC Bioinform., 2010)

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. - Melody K. Morris; Julio Saez-Rodriguez; David C. Clarke; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2011)

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. - Daniel C. Kirouac; Julio Saez-Rodriguez; Jennifer Swantek; John M. Burke; Douglas A. Lauffenburger; Peter K. Sorger (BMC Syst. Biol., 2012)

Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis. - Suzanne Gaudet; Sabrina L. Spencer; William W. Chen; Peter K. Sorger (PLoS Comput. Biol., 2012)

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). - Evan O. Paull; Daniel E. Carlin; Mario Niepel; Peter K. Sorger; David Haussler; Joshua M. Stuart (Bioinform., 2013)

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. - 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; et al. (Nucleic Acids Res., 2014)

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. - John A. Bachman; Benjamin M. Gyori; Peter K. Sorger (BMC Bioinform., 2018)

INDRA-IPM: interactive pathway modeling using natural language with automated assembly. - Petar V. Todorov; Benjamin M. Gyori; John A. Bachman; Peter K. Sorger (Bioinform., 2019)

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. - Shu Wang; Jia-Ren Lin; Eduardo D. Sontag; Peter K. Sorger (PLoS Comput. Biol., 2019)

Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. - Salma Abdel Magid; Won-Dong Jang; Denis Schapiro; Donglai Wei 001; James Tompkin 001; Peter K. Sorger; Hanspeter Pfister (MICCAI (5), 2020)

Minerva: a light-weight, narrative image browser for multiplexed tissue images. - John Hoffer; Rumana Rashid; Jeremy Muhlich; Yu-An Chen; Douglas Russell; Juha Ruokonen; Robert Krüger; Hanspeter Pfister; Sandro Santagata; Peter K. Sorger (J. Open Source Softw., 2020)

Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data. - Robert Krüger; Johanna Beyer; Won-Dong Jang; Nam Wook Kim; Artem Sokolov; Peter K. Sorger; Hanspeter Pfister (IEEE Trans. Vis. Comput. Graph., 2020)

A Crisis-Responsive Framework for Medical Device Development Applied to the COVID-19 Pandemic. - 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; et al. (Frontiers Digit. Health, 2021)

The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. - Matthew E. Berginski; Nienke Moret; Changchang Liu; Dennis Goldfarb; Peter K. Sorger; Shawn M. Gomez (Nucleic Acids Res., 2021)

Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. - Jeremy Muhlich; Yu-An Chen; Clarence Han-Wei Yapp; Douglas Russell; Sandro Santagata; Peter K. Sorger (Bioinform., 2022)

Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models. - Fabian Fröhlich; Peter K. Sorger (PLoS Comput. Biol., 2022)

Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. - 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; et al. (IEEE Trans. Vis. Comput. Graph., 2022)

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. - 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; et al. (IEEE Trans. Vis. Comput. Graph., 2023)

labsyspharm/CRC_atlas_2022. - 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 (Zenodo, 2023)

Paired evaluation of machine-learning models characterizes effects of confounders and outliers. - Maulik K. Nariya; Caitlin E. Mills; Peter K. Sorger; Artem Sokolov (Patterns, 2023)

Correction: Paired evaluation of machine-learning models characterizes effects of confounders and outliers. - Maulik K. Nariya; Caitlin E. Mills; Peter K. Sorger; Artem Sokolov (Patterns, 2023)

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. - Changchang Liu; Peter Kutchukian; Nhan D. Nguyen; Mohammed Alquraishi; Peter K. Sorger (J. Chem. Inf. Model., 2023)

Pass-Efficient Algorithms for Graph Spectral Clustering (Student Abstract). - Boshen Yan; Guihong Wan; Haim Schweitzer; Zoltan Maliga; Sara Khattab; Kun-Hsing Yu; Peter K. Sorger; Yevgeniy R. Semenov (AAAI, 2024)

SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data. - Guihong Wan; Zoltan Maliga; Boshen Yan; Tuulia Vallius; Yingxiao Shi; Sara Khattab; Crystal Chang; Ajit Johnson Nirmal; Kun-Hsing Yu; David S. L. Wei; Christine G. Lian; Mia S. Desimone; et al. (Briefings Bioinform., 2024)

psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring. - Simon Warchol; Jakob Troidl; Jeremy Muhlich; Robert Krüger; John Hoffer; Tica Lin; Johanna Beyer; Elena L. Glassman; Peter K. Sorger; Hanspeter Pfister (Comput. Graph. Forum, 2024)

SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. - Ajit Johnson Nirmal; Peter K. Sorger (J. Open Source Softw., 2024)

Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering. - Lukas Herzberger; Markus Hadwiger; Robert Krüger; Peter K. Sorger; Hanspeter Pfister; Eduard Gröller; Johanna Beyer (IEEE Trans. Vis. Comput. Graph., 2024)

A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks. - Dong Li 034; Guihong Wan; Xintao Wu; Xinyu Wu; Ajit Johnson Nirmal; Christine G. Lian; Peter K. Sorger; Yevgeniy R. Semenov; Chen Zhao 010 (CoRR, 2025)

Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. - Eric Mörth; Kevin Sidak; Zoltan Maliga; Torsten Möller; Nils Gehlenborg; Peter K. Sorger; Hanspeter Pfister; Johanna Beyer; Robert Krüger (IEEE Trans. Vis. Comput. Graph., 2025)

Multi-Modal Foundation Models for Computational Pathology: A Survey. - Dong Li 034; Guihong Wan; Xintao Wu; Xinyu Wu; Xiaohui Chen; Yi He; Christine G. Lian; Peter K. Sorger; Yevgeniy R. Semenov; Chen Zhao 010 (CoRR, 2025)