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2020 – today
- 2025
[j29]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. IEEE Trans. Vis. Comput. Graph. 31(1): 569-579 (2025)- 2024
- [j28]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. Comput. Graph. Forum 43(3) (2024) - [j27]Ajit Johnson Nirmal, Peter K. Sorger:
SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. J. Open Source Softw. 9(97): 6604 (2024) - [j26]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. IEEE Trans. Vis. Comput. Graph. 30(1): 1380-1390 (2024) - [c4]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). AAAI 2024: 23690-23692 - 2023
- [j25]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. J. Chem. Inf. Model. 63(17): 5457-5472 (2023) - [j24]Maulik K. Nariya, Caitlin E. Mills, Peter K. Sorger, Artem Sokolov:
Paired evaluation of machine-learning models characterizes effects of confounders and outliers. Patterns 4(8): 100791 (2023) - [j23]Maulik K. Nariya, Caitlin E. Mills, Peter K. Sorger, Artem Sokolov:
Correction: Paired evaluation of machine-learning models characterizes effects of confounders and outliers. Patterns 4(8): 100824 (2023) - [j22]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. IEEE Trans. Vis. Comput. Graph. 29(1): 106-116 (2023) - [i2]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. CoRR abs/2309.04393 (2023) - 2022
- [j21]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. Bioinform. 38(19): 4613-4621 (2022) - [j20]Fabian Fröhlich, Peter K. Sorger:
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models. PLoS Comput. Biol. 18(7) (2022) - [j19]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. IEEE Trans. Vis. Comput. Graph. 28(1): 259-269 (2022) - 2021
- [j18]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. Frontiers Digit. Health 3: 617106 (2021) - [j17]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. Nucleic Acids Res. 49(Database-Issue): D529-D535 (2021) - [i1]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. CoRR abs/2110.04875 (2021) - 2020
- [j16]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. J. Open Source Softw. 5(54): 2579 (2020) - [j15]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. IEEE Trans. Vis. Comput. Graph. 26(1): 227-237 (2020) - [c3]Salma Abdel Magid, Won-Dong Jang, Denis Schapiro, Donglai Wei, James Tompkin, Peter K. Sorger, Hanspeter Pfister:
Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. MICCAI (5) 2020: 3-13
2010 – 2019
- 2019
- [j14]Petar V. Todorov, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger:
INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinform. 35(21): 4501-4503 (2019) - [j13]Shu Wang, Jia-Ren Lin, Eduardo D. Sontag, Peter K. Sorger:
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Comput. Biol. 15(12) (2019) - 2018
- [j12]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. BMC Bioinform. 19(1): 248:1-248:14 (2018) - 2014
- [j11]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. Nucleic Acids Res. 42(Webserver-Issue): 449-460 (2014) - 2013
- [j10]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). Bioinform. 29(21): 2757-2764 (2013) - 2012
- [j9]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. BMC Syst. Biol. 6: 29 (2012) - [j8]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. PLoS Comput. Biol. 8(4) (2012) - 2011
- [j7]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. PLoS Comput. Biol. 7(3) (2011) - 2010
- [j6]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. BMC Bioinform. 11: 202 (2010)
2000 – 2009
- 2009
- [j5]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. PLoS Comput. Biol. 5(4) (2009) - [j4]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. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j3]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 DataRail. Bioinform. 24(6): 840-847 (2008) - [c2]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. BIBE 2008: 1-5 - 2007
- [j2]Khuloud Jaqaman, Jonas F. Dorn, Eugenio Marco, Peter K. Sorger, Gaudenz Danuser:
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. Bioinform. 23(13): 1666-1673 (2007) - 2006
- [c1]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. EMBC 2006: 53-54 - 2004
- [j1]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. J. Comput. Biol. 11(4): 544-561 (2004)
Coauthor Index
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