Peter K. Sorger

44 papers A* 2C 1Journal 39Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data.
IEEE Trans. Vis. Comput. Graph.
Simon Warchol, Grace Guo, Johannes Knittel, Dan Freeman, Usha Shalla, Jeremy Muhlich, Peter K. Sorger, Hanspeter Pfister
2026 A* conf
Virtual Multiplex Staining for Histological Images Using a Marker-Wise Conditioned Diffusion Model.
AAAI
Hyun-Jic Oh, Junsik Kim, Zhiyi Shi, Yichen Wu, Yu-An Chen, Peter K. Sorger, Hanspeter Pfister, Won-Ki Jeong
2025 J jnl
A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks.
CoRR
Dong Li, Guihong Wan, Xintao Wu, Xinyu Wu, Ajit Johnson Nirmal, Christine G. Lian, Peter K. Sorger, Yevgeniy R. Semenov, Chen Zhao
2025 J jnl
Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data.
IEEE Trans. Vis. Comput. Graph.
Eric Mörth, Kevin Sidak, Zoltan Maliga, Torsten Möller, Nils Gehlenborg, Peter K. Sorger, Hanspeter Pfister, Johanna Beyer, Robert Krüger
2025 J jnl
Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches.
PLoS Comput. Biol.
Javiera Cortés-Ríos, Maria Rodriguez-Fernandez, Peter K. Sorger, Fabian Fröhlich
2025 J jnl
Multi-Modal Foundation Models for Computational Pathology: A Survey.
CoRR
Dong Li, Guihong Wan, Xintao Wu, Xinyu Wu, Xiaohui Chen, Yi He, Christine G. Lian, Peter K. Sorger, Yevgeniy R. Semenov, Chen Zhao
2025 J jnl
Multi-Modal Foundation Models for Computational Pathology: A Survey.
Trans. Mach. Learn. Res.
Dong Li, Guihong Wan, Xintao Wu, Xinyu Wu, Xiaohui Chen, Yi He, Zhong Chen, Peter K. Sorger, Chen Zhao
2025 J jnl
Virtual Multiplex Staining for Histological Images using a Marker-wise Conditioned Diffusion Model.
CoRR
Hyun-Jic Oh, Junsik Kim, Zhiyi Shi, Yichen Wu, Yu-An Chen, Peter K. Sorger, Hanspeter Pfister, Won-Ki Jeong
2025 J jnl
Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps.
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, Johanna Beyer, Hanspeter Pfister, Chen Zhu-Tian, Nils Gehlenborg
2024 A* conf
Pass-Efficient Algorithms for Graph Spectral Clustering (Student Abstract).
AAAI
Boshen Yan, Guihong Wan, Haim Schweitzer, Zoltan Maliga, Sara Khattab, Kun-Hsing Yu, Peter K. Sorger, Yevgeniy R. Semenov
2024 J jnl
Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering.
IEEE Trans. Vis. Comput. Graph.
Lukas Herzberger, Markus Hadwiger, Robert Krüger, Peter K. Sorger, Hanspeter Pfister, Eduard Gröller, Johanna Beyer
2024 J jnl
SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data.
J. Open Source Softw.
Ajit Johnson Nirmal, Peter K. Sorger
2024 J jnl
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data.
Briefings Bioinform.
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
2024 J jnl
psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring.
Comput. Graph. Forum
Simon Warchol, Jakob Troidl, Jeremy Muhlich, Robert Krüger, John Hoffer, Tica Lin, Johanna Beyer, Elena L. Glassman, Peter K. Sorger, Hanspeter Pfister
2023 J jnl
A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.
J. Chem. Inf. Model.
Changchang Liu, Peter Kutchukian, Nhan D. Nguyen, Mohammed AlQuraishi, Peter K. Sorger
2023 J jnl
Correction: Paired evaluation of machine-learning models characterizes effects of confounders and outliers.
Patterns
Maulik K. Nariya, Caitlin E. Mills, Peter K. Sorger, Artem Sokolov
2023 J jnl
Paired evaluation of machine-learning models characterizes effects of confounders and outliers.
Patterns
Maulik K. Nariya, Caitlin E. Mills, Peter K. Sorger, Artem Sokolov
2023 J jnl
Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering.
CoRR
Lukas Herzberger, Markus Hadwiger, Robert Krüger, Peter K. Sorger, Hanspeter Pfister, Eduard Gröller, Johanna Beyer
2023 J jnl
Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data.
IEEE Trans. Vis. Comput. Graph.
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
2022 J jnl
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models.
PLoS Comput. Biol.
Fabian Fröhlich, Peter K. Sorger
2022 J jnl
Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data.
IEEE Trans. Vis. Comput. Graph.
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
2022 J jnl
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.
Bioinform.
Jeremy Muhlich, Yu-An Chen, Clarence Han-Wei Yapp, Douglas Russell, Sandro Santagata, Peter K. Sorger
2021 J jnl
A Crisis-Responsive Framework for Medical Device Development Applied to the COVID-19 Pandemic.
Frontiers Digit. Health
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
2021 J jnl
Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data.
CoRR
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
2021 J jnl
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.
Nucleic Acids Res.
Matthew E. Berginski, Nienke Moret, Changchang Liu, Dennis Goldfarb, Peter K. Sorger, Shawn M. Gomez
2020 — conf
Channel Embedding for Informative Protein Identification from Highly Multiplexed Images.
MICCAI (5)
Salma Abdel Magid, Won-Dong Jang, Denis Schapiro, Donglai Wei, James Tompkin, Peter K. Sorger, Hanspeter Pfister
2020 J jnl
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.
IEEE Trans. Vis. Comput. Graph.
Robert Krüger, Johanna Beyer, Won-Dong Jang, Nam Wook Kim, Artem Sokolov, Peter K. Sorger, Hanspeter Pfister
2020 J jnl
Minerva: a light-weight, narrative image browser for multiplexed tissue images.
J. Open Source Softw.
John Hoffer, Rumana Rashid, Jeremy Muhlich, Yu-An Chen, Douglas Russell, Juha Ruokonen, Robert Krüger, Hanspeter Pfister, Sandro Santagata, Peter K. Sorger
2019 J jnl
INDRA-IPM: interactive pathway modeling using natural language with automated assembly.
Bioinform.
Petar V. Todorov, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger
2019 J jnl
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory.
PLoS Comput. Biol.
Shu Wang, Jia-Ren Lin, Eduardo D. Sontag, Peter K. Sorger
2018 J jnl
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.
BMC Bioinform.
John A. Bachman, Benjamin M. Gyori, Peter K. Sorger
2014 J jnl
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.
Nucleic Acids Res.
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
2013 J jnl
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).
Bioinform.
Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart
2012 J jnl
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
BMC Syst. Biol.
Daniel C. Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M. Burke, Douglas A. Lauffenburger, Peter K. Sorger
2012 J jnl
Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis.
PLoS Comput. Biol.
Suzanne Gaudet, Sabrina L. Spencer, William W. Chen, Peter K. Sorger
2011 J jnl
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli.
PLoS Comput. Biol.
Melody K. Morris, Julio Saez-Rodriguez, David C. Clarke, Peter K. Sorger, Douglas A. Lauffenburger
2010 J jnl
Systematic calibration of a cell signaling network model.
BMC Bioinform.
Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck, John M. Burke, Peter K. Sorger, Suzanne Gaudet, Do Hyun Kim
2009 J jnl
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling.
PLoS Comput. Biol.
Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy Muhlich, Peter K. Sorger, Douglas A. Lauffenburger
2009 J jnl
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
PLoS Comput. Biol.
Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt
2008 J jnl
Flexible informatics for linking experimental data to mathematical models via
Bioinform.
Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger
2008 C conf
Modeling pro-death signaling pathways in cancer hepatocytes using multi-combinatorial treatments of inhibitors and stimuli.
BIBE
Leonidas G. Alexopoulos, Douglas A. Lauffenburger, Peter K. Sorger
2007 J jnl
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics.
Bioinform.
Khuloud Jaqaman, Jonas F. Dorn, Eugenio Marco, Peter K. Sorger, Gaudenz Danuser
2006 — conf
A Data-Driven Computational Model of the ErbB Receptor Signaling Network.
EMBC
Birgit Schoeberl, Emily Pace, Shavonne Howard, Viara Garantcharova, Art Kudla, Peter K. Sorger, Ulrik B. Nielsen
2004 J jnl
Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data.
J. Comput. Biol.
Kevin A. Janes, Jason R. Kelly, Suzanne Gaudet, John G. Albeck, Peter K. Sorger, Douglas A. Lauffenburger