Works matching AU Sorger, Peter K.

Results: 91

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death.

Published in:

PLoS Biology, 2008, v. 6, n. 12, p. e299, doi. 10.1371/journal.pbio.0060299

By:

Albeck, John G.;
Burke, John M.;
Spencer, Sabrina L.;
Lauffenburger, Douglas A.;
Sorger, Peter K.

Publication type:

Article

GRcalculator: an online tool for calculating and mining dose-response data.

Published in:

2017

By:

Clark, Nicholas A.;
Hafner, Marc;
Kouril, Michal;
Williams, Elizabeth H.;
Muhlich, Jeremy L.;
Pilarczyk, Marcin;
Niepel, Mario;
Sorger, Peter K.;
Medvedovic, Mario

Publication type:

journal article

Analysis of growth factor signaling in genetically diverse breast cancer lines.

Published in:

BMC Biology, 2014, v. 12, n. 1, p. 20, doi. 10.1186/1741-7007-12-20

By:

Niepel, Mario;
Hafner, Marc;
Pace, Emily A;
Chung, Mirra;
Chai, Diana H;
Zhou, Lili;
Muhlich, Jeremy L;
Schoeberl, Birgit;
Sorger, Peter K

Publication type:

Article

Automated assembly of molecular mechanisms at scale from text mining and curated databases.

Published in:

Molecular Systems Biology, 2023, v. 19, n. 5, p. 1, doi. 10.15252/msb.202211325

By:

Bachman, John A;
Gyori, Benjamin M;
Sorger, Peter K

Publication type:

Article

Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.

Published in:

Molecular Systems Biology, 2023, v. 19, n. 2, p. 1, doi. 10.15252/msb.202210988

By:

Fröhlich, Fabian;
Gerosa, Luca;
Muhlich, Jeremy;
Sorger, Peter K

Publication type:

Article

Development of CDK2 and CDK5 Dual Degrader TMX‐2172.

Published in:

Angewandte Chemie, 2020, v. 132, n. 33, p. 13969, doi. 10.1002/ange.202004087

By:

Teng, Mingxing;
Jiang, Jie;
He, Zhixiang;
Kwiatkowski, Nicholas P.;
Donovan, Katherine A.;
Mills, Caitlin E.;
Victor, Chiara;
Hatcher, John M.;
Fischer, Eric S.;
Sorger, Peter K.;
Zhang, Tinghu;
Gray, Nathanael S.

Publication type:

Article

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis.

Published in:

Nature, 2009, v. 459, n. 7245, p. 428, doi. 10.1038/nature08012

By:

Spencer, Sabrina L.;
Gaudet, Suzanne;
Albeck, John G.;
Burke, John M.;
Sorger, Peter K.

Publication type:

Article

Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities.

Published in:

Nature, 2007, v. 446, n. 7138, p. 876, doi. 10.1038/nature05694

By:

Stegmeier, Frank;
Rape, Michael;
Draviam, Viji M.;
Nalepa, Grzegorz;
Sowa, Mathew E.;
Ang, Xiaolu L.;
McDonald III, E. Robert;
Li, Mamie Z.;
Hannon, Gregory J.;
Sorger, Peter K.;
Kirschner, Marc W.;
Harper, J. Wade;
Elledge, Stephen J.

Publication type:

Article

Cells on chips.

Published in:

Nature, 2006, v. 442, n. 7101, p. 403, doi. 10.1038/nature05063

By:

El-Ali, Jamil;
Sorger, Peter K.;
Jensen, Klavs F.

Publication type:

Article

Cell biology: The more MAD, the merrier.

Published in:

Nature, 2005, v. 434, n. 7033, p. 575, doi. 10.1038/434575a

By:

Hagan, Robert S.;
Sorger, Peter K.

Publication type:

Article

Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.

Published in:

Bioinformatics, 2022, v. 38, n. 19, p. 4613, doi. 10.1093/bioinformatics/btac544

By:

Muhlich, Jeremy L;
Chen, Yu-An;
Yapp, Clarence;
Russell, Douglas;
Santagata, Sandro;
Sorger, Peter K

Publication type:

Article

Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28410-9

By:

Plana, Deborah;
Fell, Geoffrey;
Alexander, Brian M.;
Palmer, Adam C.;
Sorger, Peter K.

Publication type:

Article

Collecting and organizing systematic sets of protein data.

Published in:

Nature Reviews Molecular Cell Biology, 2006, v. 7, n. 11, p. 803, doi. 10.1038/nrm2042

By:

Albeck, John G.;
MacBeath, Gavin;
White, Forest M.;
Sorger, Peter K.;
Lauffenburger, Douglas A.;
Gaudet, Suzanne

Publication type:

Article

Personal Protective Equipment for COVID-19: Distributed Fabrication and Additive Manufacturing.

Published in:

American Journal of Public Health, 2020, v. 110, n. 8, p. 1162, doi. 10.2105/AJPH.2020.305753

By:

Sinha, Michael S.;
Bourgeois, Florence T.;
Sorger, Peter K.

Publication type:

Article

A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks.

Published in:

Nature Genetics, 2014, v. 46, n. 12, p. 1363, doi. 10.1038/ng.3138

By:

AlQuraishi, Mohammed;
Koytiger, Grigoriy;
Jenney, Anne;
Sorger, Peter K;
MacBeath, Gavin

Publication type:

Article

Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010322

By:

Fröhlich, Fabian;
Sorger, Peter K.

Publication type:

Article

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03050-3

By:

Vickovic, Sanja;
Schapiro, Denis;
Carlberg, Konstantin;
Lötstedt, Britta;
Larsson, Ludvig;
Hildebrandt, Franziska;
Korotkova, Marina;
Hensvold, Aase H.;
Catrina, Anca I.;
Sorger, Peter K.;
Malmström, Vivianne;
Regev, Aviv;
Ståhl, Patrik L.

Publication type:

Article

Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer.

Published in:

NPJ Breast Cancer, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41523-023-00605-3

By:

Guerriero, Jennifer L.;
Lin, Jia-Ren;
Pastorello, Ricardo G.;
Du, Ziming;
Chen, Yu-An;
Townsend, Madeline G.;
Shimada, Kenichi;
Hughes, Melissa E.;
Ren, Siyang;
Tayob, Nabihah;
Zheng, Kelly;
Mei, Shaolin;
Patterson, Alyssa;
Taneja, Krishan L.;
Metzger, Otto;
Tolaney, Sara M.;
Lin, Nancy U.;
Dillon, Deborah A.;
Schnitt, Stuart J.;
Sorger, Peter K.

Publication type:

Article

Analysis of kinesin motor function at budding yeast kinetochores.

Published in:

Journal of Cell Biology, 2006, v. 172, n. 6, p. 861, doi. 10.1083/jcb.200509101

By:

Tytell, Jessica D.;
Sorger, Peter K.

Publication type:

Article

Spindle checkpoint proteins and chromosome--microtubule attachment in budding yeast.

Published in:

Journal of Cell Biology, 2004, v. 164, n. 4, p. 535, doi. 10.1083/jcb.200308100

By:

Gillett, Emily S.;
Espelin, Christopher W.;
Sorger, Peter K.

Publication type:

Article

SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae189

By:

Wan, Guihong;
Maliga, Zoltan;
Yan, Boshen;
Vallius, Tuulia;
Shi, Yingxiao;
Khattab, Sara;
Chang, Crystal;
Nirmal, Ajit J;
Yu, Kun-Hsing;
Liu, David;
Lian, Christine G;
DeSimone, Mia S;
Sorger, Peter K;
Semenov, Yevgeniy R

Publication type:

Article

Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.64251

By:

Vemulapalli, Vidyasiri;
Chylek, Lily A.;
Erickson, Alison;
Pfeiffer, Anamarija;
Gabriel, Khal-Hentz;
LaRochelle, Jonathan;
Subramanian, Kartik;
Cao, Ruili;
Stegmaier, Kimberley;
Mohseni, Morvarid;
LaMarche, Matthew J.;
Acker, Michael G.;
Sorger, Peter K.;
Gygi, Steven P.;
Blacklow, Stephen C.

Publication type:

Article

Systematic characterization of antibody–drug conjugate targets in central nervous system tumors.

Published in:

Neuro-Oncology, 2024, v. 26, n. 3, p. 458, doi. 10.1093/neuonc/noad205

By:

Coy, Shannon;
Lee, Jong Suk;
Chan, Sabrina J;
Woo, Terri;
Jones, Jacquelyn;
Alexandrescu, Sanda;
Wen, Patrick Y;
Sorger, Peter K;
Ligon, Keith L;
Santagata, Sandro

Publication type:

Article

Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28410-9

By:

Plana, Deborah;
Fell, Geoffrey;
Alexander, Brian M.;
Palmer, Adam C.;
Sorger, Peter K.

Publication type:

Article

Reproducibility will only come with data liberation.

Published in:

2016

By:

AlQuraishi, Mohammed;
Sorger, Peter K.

Publication type:

Editorial

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.

Published in:

Nature Protocols, 2019, v. 14, n. 10, p. 2900, doi. 10.1038/s41596-019-0206-y

By:

Du, Ziming;
Lin, Jia-Ren;
Rashid, Rumana;
Maliga, Zoltan;
Wang, Shu;
Aster, Jon C.;
Izar, Benjamin;
Sorger, Peter K.;
Santagata, Sandro

Publication type:

Article

Development of CDK2 and CDK5 Dual Degrader TMX‐2172.

Published in:

Angewandte Chemie International Edition, 2020, v. 59, n. 33, p. 13865, doi. 10.1002/anie.202004087

By:

Teng, Mingxing;
Jiang, Jie;
He, Zhixiang;
Kwiatkowski, Nicholas P.;
Donovan, Katherine A.;
Mills, Caitlin E.;
Victor, Chiara;
Hatcher, John M.;
Fischer, Eric S.;
Sorger, Peter K.;
Zhang, Tinghu;
Gray, Nathanael S.

Publication type:

Article

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2211-5

By:

Bachman, John A.;
Gyori, Benjamin M.;
Sorger, Peter K.

Publication type:

Article

INDRA-IPM: interactive pathway modeling using natural language with automated assembly.

Published in:

Bioinformatics, 2019, v. 35, n. 21, p. 4501, doi. 10.1093/bioinformatics/btz289

By:

Todorov, Petar V;
Gyori, Benjamin M;
Bachman, John A;
Sorger, Peter K

Publication type:

Article

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Published in:

Bioinformatics, 2013, v. 29, n. 21, p. 2757, doi. 10.1093/bioinformatics/btt471

By:

Paull, Evan O.;
Carlin, Daniel E.;
Niepel, Mario;
Sorger, Peter K.;
Haussler, David;
Stuart, Joshua M.

Publication type:

Article

Flexible informatics for linking experimental data to mathematical models via DataRail.

Published in:

Bioinformatics, 2008, v. 24, n. 6, p. 840, doi. 10.1093/bioinformatics/btn018

By:

Julio Saez-Rodriguez;
Arthur Goldsipe;
Jeremy Muhlich;
Leonidas G. Alexopoulos;
Bjorn Millard;
Douglas A. Lauffenburger;
Peter K. Sorger

Publication type:

Article

Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44778-2

By:

Zhang, Xue;
Pant, Shishir M.;
Ritch, Cecily C.;
Tang, Hsin-Yao;
Shao, Hongguang;
Dweep, Harsh;
Gong, Yao-Yu;
Brooks, Rebekah;
Brafford, Patricia;
Wolpaw, Adam J.;
Lee, Yool;
Weeraratna, Ashani;
Sehgal, Amita;
Herlyn, Meenhard;
Kossenkov, Andrew;
Speicher, David;
Sorger, Peter K.;
Santagata, Sandro;
Dang, Chi V.

Publication type:

Article

GeneWalk identifies relevant gene functions for a biological context using network representation learning.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02264-8

By:

Ietswaart, Robert;
Gyori, Benjamin M.;
Bachman, John A.;
Sorger, Peter K.;
Churchman, L. Stirling

Publication type:

Article

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Published in:

BMC Systems Biology, 2012, v. 6, n. 1, p. 29, doi. 10.1186/1752-0509-6-29

By:

Kirouac, Daniel C.;
Saez-Rodriguez, Julio;
Swantek, Jennifer;
Burke, John M.;
Lauffenburger, Douglas A.;
Sorger, Peter K.

Publication type:

Article

Kinetochores distinguish GTP from GDP forms of the microtubule lattice.

Published in:

Nature, 1997, v. 388, n. 6645, p. 888, doi. 10.1038/42270

By:

Severin, Fedor F.;
Sorger, Peter K.

Publication type:

Article

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method.

Published in:

Nature Communications, 2015, v. 6, n. 9, p. 8390, doi. 10.1038/ncomms9390

By:

Lin, Jia-Ren;
Fallahi-Sichani, Mohammad;
Sorger, Peter K.

Publication type:

Article

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.

Published in:

Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00943-6

By:

Patiño-Galindo, Juan Ángel;
Filip, Ioan;
Chowdhury, Ratul;
Maranas, Costas D.;
Sorger, Peter K.;
AlQuraishi, Mohammed;
Rabadan, Raul

Publication type:

Article

Systematic calibration of a cell signaling network model.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 202, doi. 10.1186/1471-2105-11-202

By:

Kyoung Ae Kim;
Spencer, Sabrina L.;
Albeck, John G.;
Burke, John M.;
Sorger, Peter K.;
Gaudet, Suzanne;
Do Hyun Kim

Publication type:

Article

Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 4, p. 1, doi. 10.1371/journal.pcbi.1002482

By:

Gaudet, Suzanne;
Spencer, Sabrina L.;
Chen, William W.;
Sorger, Peter K.

Publication type:

Article

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 3, p. 1, doi. 10.1371/journal.pcbi.1001099

By:

Morris, Melody K.;
Saez-Rodriguez, Julio;
Clarke, David C.;
Sorger, Peter K.;
Lauffenburger, Douglas A.

Publication type:

Article

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000438

By:

Samaga, Regina;
Saez-Rodriguez, Julio;
Alexopoulos, Leonidas G.;
Sorger, Peter K.;
Klamt, Steffen

Publication type:

Article

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000340

By:

Aldridge, Bree B.;
Saez-Rodriguez, Julio;
Muhlich, Jeremy L.;
Sorger, Peter K.;
Douglas A. Lauffenburger

Publication type:

Article

The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D529, doi. 10.1093/nar/gkaa853

By:

Berginski, Matthew E;
Moret, Nienke;
Liu, Changchang;
Goldfarb, Dennis;
Sorger, Peter K;
Gomez, Shawn M

Publication type:

Article

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

Published in:

Nucleic Acids Research, 2014, v. 42, n. W1, p. W449, doi. 10.1093/nar/gku476

By:

Duan, Qiaonan;
Flynn, Corey;
Niepel, Mario;
Hafner, Marc;
Muhlich, Jeremy L.;
Fernandez, Nicolas F.;
Rouillard, Andrew D.;
Tan, Christopher M.;
Chen, Edward Y.;
Golub, Todd R.;
Sorger, Peter K.;
Subramanian, Aravind;
Ma'ayan, Avi

Publication type:

Article

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01383-w

By:

Niepel, Mario;
Hafner, Marc;
Qiaonan Duan;
Zichen Wang;
Paull, Evan O.;
Mirra Chung;
Xiaodong Lu;
Stuart, Joshua M.;
Golub, Todd R.;
Subramanian, Aravind;
Ma’ayan, Avi;
Sorger, Peter K.

Publication type:

Article

The human kinetochore proteins Nnf1R and Mcm21R are required for accurate chromosome segregation.

Published in:

2009

By:

McAinsh, Andrew D.;
Meraldi, Patrick;
Draviam, Viji M.;
Toso, Alberto;
Sorger, Peter K.

Publication type:

Erratum

The human kinetochore proteins Nnf1R and Mcm21R are required for accurate chromosome segregation.

Published in:

EMBO Journal, 2006, v. 25, n. 17, p. 4033, doi. 10.1038/sj.emboj.7601293

By:

McAinsh, Andrew D.;
Meraldi, Patrick;
Draviam, Viji M.;
Toso, Alberto;
Sorger, Peter K.

Publication type:

Article

A dual role for Bub1 in the spindle checkpoint and chromosome congression.

Published in:

EMBO Journal, 2005, v. 24, n. 8, p. 1621, doi. 10.1038/sj.emboj.7600641

By:

Meraldi, Patrick;
Sorger, Peter K.

Publication type:

Article

Adaptive informatics for multifactorial and high-content biological data.

Published in:

Nature Methods, 2011, v. 8, n. 6, p. 487, doi. 10.1038/nmeth.1600

By:

Millard, Bjorn L;
Niepel, Mario;
Menden, Michael P;
Muhlich, Jeremy L;
Sorger, Peter K

Publication type:

Article

From word models to executable models of signaling networks using automated assembly.

Published in:

Molecular Systems Biology, 2017, v. 13, n. 11, p. 1, doi. 10.15252/msb.20177651

By:

Gyori, Benjamin M;
Bachman, John A;
Subramanian, Kartik;
Muhlich, Jeremy L;
Galescu, Lucian;
Sorger, Peter K

Publication type:

Article