Publications by authors named "Peter K Sorger"

100Publications

SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma.

Cell Syst 2020 Sep 7;11(3):272-285.e9. Epub 2020 Sep 7.

Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.08.001DOI Listing
September 2020

Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing.

Cell Chem Biol 2020 Aug 4. Epub 2020 Aug 4.

Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2020.07.011DOI Listing
August 2020

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

Am J Public Health 2020 08 18;110(8):1162-1164. Epub 2020 Jun 18.

Michael S. Sinha, Florence T. Bourgeois, and Peter K. Sorger are with the Harvard-MIT Center for Regulatory Science, Harvard Medical School, Boston, MA. Michael S. Sinha is also with the Program on Regulation, Therapeutics, and Law, Brigham and Women's Hospital, Boston. Florence T. Bourgeois is also with the Computational Health Informatics Program, Boston Children's Hospital, Boston. Peter K. Sorger is also with the Harvard Program in Therapeutic Science, Harvard Medical School.

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http://dx.doi.org/10.2105/AJPH.2020.305753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349433PMC
August 2020

Development of CDK2 and CDK5 Dual Degrader TMX-2172.

Angew Chem Int Ed Engl 2020 Aug 3;59(33):13865-13870. Epub 2020 Jun 3.

Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1002/anie.202004087DOI Listing
August 2020

HSF1 phase transition mediates stress adaptation and cell fate decisions.

Nat Cell Biol 2020 02 3;22(2):151-158. Epub 2020 Feb 3.

Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41556-019-0458-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135912PMC
February 2020

Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.

Elife 2020 Jan 21;9. Epub 2020 Jan 21.

Department of Systems Biology, Columbia University, New York, United States.

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http://dx.doi.org/10.7554/eLife.50342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046471PMC
January 2020

Structure-Based Design of a Potent and Selective Covalent Inhibitor for SRC Kinase That Targets a P-Loop Cysteine.

J Med Chem 2020 02 30;63(4):1624-1641. Epub 2020 Jan 30.

Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acs.jmedchem.9b01502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493195PMC
February 2020

Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nat Methods 2020 02 6;17(2):175-183. Epub 2020 Jan 6.

Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41592-019-0687-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004877PMC
February 2020

Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells.

Cell Syst 2020 01 4;10(1):66-81.e11. Epub 2019 Dec 4.

Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Ludwig Center, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000271PMC
January 2020

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory.

PLoS Comput Biol 2019 12 6;15(12):e1007311. Epub 2019 Dec 6.

Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919632PMC
December 2019

A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity.

Elife 2019 11 19;8. Epub 2019 Nov 19.

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States.

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http://dx.doi.org/10.7554/eLife.50036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6897534PMC
November 2019

Development and Characterization of a Wee1 Kinase Degrader.

Cell Chem Biol 2020 01 14;27(1):57-65.e9. Epub 2019 Nov 14.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980656PMC
January 2020

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

Nat Protoc 2019 10 18;14(10):2900-2930. Epub 2019 Sep 18.

Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41596-019-0206-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6959005PMC
October 2019

Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity.

Cell Chem Biol 2019 08 6;26(8):1067-1080.e8. Epub 2019 Jun 6.

Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936329PMC
August 2019

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

Bioinformatics 2019 11;35(21):4501-4503

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821420PMC
November 2019

Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.

Cell Chem Biol 2019 06 11;26(6):818-829.e9. Epub 2019 Apr 11.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24519456193007
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http://dx.doi.org/10.1016/j.chembiol.2019.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634314PMC
June 2019

Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries.

Cell Chem Biol 2019 05 4;26(5):765-777.e3. Epub 2019 Apr 4.

HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.02.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526536PMC
May 2019

Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype.

Cell Chem Biol 2019 06 21;26(6):792-803.e10. Epub 2019 Mar 21.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588464PMC
June 2019

A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers.

J Biol Chem 2019 05 11;294(21):8664-8673. Epub 2019 Mar 11.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA118.006805
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http://dx.doi.org/10.1074/jbc.RA118.006805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544847PMC
May 2019

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

BMC Bioinformatics 2018 06 28;19(1):248. Epub 2018 Jun 28.

Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s12859-018-2211-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022344PMC
June 2018

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.

Cell Syst 2018 06 6;6(6):664-678.e9. Epub 2018 Jun 6.

HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322215PMC
June 2018

A High Content Screen in Macrophages Identifies Small Molecule Modulators of STING-IRF3 and NFkB Signaling.

ACS Chem Biol 2018 04 19;13(4):1066-1081. Epub 2018 Mar 19.

Department of Systems Biology , Harvard Medical School , 200 Longwood Ave. , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acschembio.7b01060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996755PMC
April 2018

Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition.

Sci Signal 2018 03 6;11(520). Epub 2018 Mar 6.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scisignal.aal1601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5978689PMC
March 2018

Combination Cancer Therapy Can Confer Benefit via Patient-to-Patient Variability without Drug Additivity or Synergy.

Cell 2017 Dec;171(7):1678-1691.e13

Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741091PMC
December 2017

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Authors:
Alexandra B Keenan Sherry L Jenkins Kathleen M Jagodnik Simon Koplev Edward He Denis Torre Zichen Wang Anders B Dohlman Moshe C Silverstein Alexander Lachmann Maxim V Kuleshov Avi Ma'ayan Vasileios Stathias Raymond Terryn Daniel Cooper Michele Forlin Amar Koleti Dusica Vidovic Caty Chung Stephan C Schürer Jouzas Vasiliauskas Marcin Pilarczyk Behrouz Shamsaei Mehdi Fazel Yan Ren Wen Niu Nicholas A Clark Shana White Naim Mahi Lixia Zhang Michal Kouril John F Reichard Siva Sivaganesan Mario Medvedovic Jaroslaw Meller Rick J Koch Marc R Birtwistle Ravi Iyengar Eric A Sobie Evren U Azeloglu Julia Kaye Jeannette Osterloh Kelly Haston Jaslin Kalra Steve Finkbiener Jonathan Li Pamela Milani Miriam Adam Renan Escalante-Chong Karen Sachs Alex Lenail Divya Ramamoorthy Ernest Fraenkel Gavin Daigle Uzma Hussain Alyssa Coye Jeffrey Rothstein Dhruv Sareen Loren Ornelas Maria Banuelos Berhan Mandefro Ritchie Ho Clive N Svendsen Ryan G Lim Jennifer Stocksdale Malcolm S Casale Terri G Thompson Jie Wu Leslie M Thompson Victoria Dardov Vidya Venkatraman Andrea Matlock Jennifer E Van Eyk Jacob D Jaffe Malvina Papanastasiou Aravind Subramanian Todd R Golub Sean D Erickson Mohammad Fallahi-Sichani Marc Hafner Nathanael S Gray Jia-Ren Lin Caitlin E Mills Jeremy L Muhlich Mario Niepel Caroline E Shamu Elizabeth H Williams David Wrobel Peter K Sorger Laura M Heiser Joe W Gray James E Korkola Gordon B Mills Mark LaBarge Heidi S Feiler Mark A Dane Elmar Bucher Michel Nederlof Damir Sudar Sean Gross David F Kilburn Rebecca Smith Kaylyn Devlin Ron Margolis Leslie Derr Albert Lee Ajay Pillai

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

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

Mol Syst Biol 2017 11 24;13(11):954. Epub 2017 Nov 24.

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731347PMC
http://dx.doi.org/10.15252/msb.20177651DOI Listing
November 2017

Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics.

Sci Data 2017 11 7;4:170166. Epub 2017 Nov 7.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA.

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http://dx.doi.org/10.1038/sdata.2017.166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674849PMC
November 2017

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

Nat Commun 2017 10 30;8(1):1186. Epub 2017 Oct 30.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-017-01383-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662764PMC
October 2017

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

BMC Cancer 2017 Oct 24;17(1):698. Epub 2017 Oct 24.

LINCS-BD2K DCIC, Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45221, USA.

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http://dx.doi.org/10.1186/s12885-017-3689-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655815PMC
October 2017

Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane.

Sci Rep 2017 09 22;7(1):12150. Epub 2017 Sep 22.

HMS LINCS Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41598-017-12257-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610318PMC
September 2017

Designing Drug-Response Experiments and Quantifying their Results.

Curr Protoc Chem Biol 2017 Jun 19;9(2):96-116. Epub 2017 Jun 19.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpch.19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729909PMC
June 2017

Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells.

Curr Protoc Chem Biol 2017 Jun 19;9(2):55-74. Epub 2017 Jun 19.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpch.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538315PMC
June 2017

Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics.

Nat Biotechnol 2017 06;35(6):500-502

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668135PMC
June 2017

Fundamental trade-offs between information flow in single cells and cellular populations.

Proc Natl Acad Sci U S A 2017 05 12;114(22):5755-5760. Epub 2017 May 12.

Center for Computational Biology, University of Kansas, Lawrence, KS 66047;

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http://dx.doi.org/10.1073/pnas.1615660114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465904PMC
May 2017

Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors.

Bioorg Med Chem 2017 02 7;25(4):1320-1328. Epub 2016 Dec 7.

Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2016.11.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484535PMC
February 2017

Structure-guided development of covalent TAK1 inhibitors.

Bioorg Med Chem 2017 02 9;25(3):838-846. Epub 2016 Dec 9.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2016.11.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484537PMC
February 2017

Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging.

Curr Protoc Chem Biol 2016 Dec 7;8(4):251-264. Epub 2016 Dec 7.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpch.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5233430PMC
December 2016

Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation.

Nat Chem Biol 2017 Jan 31;13(1):38-45. Epub 2016 Oct 31.

HMS LINCS Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nchembio.2211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372219PMC
January 2017

Reproducibility will only come with data liberation.

Sci Transl Med 2016 05;8(339):339ed7

Mohammed AlQuraishi is a Fellow in Therapeutic Science at Harvard Medical School, Boston, MA 02115, USA.Peter K. Sorger is Professor of Systems Biology, Head of the Harvard Program in Therapeutic Sciences, and Director of the Laboratory of Systems Biology at Harvard Medical School, Boston, MA 02115, USA. Email:

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http://dx.doi.org/10.1126/scitranslmed.aaf0968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5084089PMC
May 2016

Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs.

Nat Methods 2016 06 2;13(6):521-7. Epub 2016 May 2.

HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887336PMC
June 2016

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

Nat Commun 2015 Sep 24;6:8390. Epub 2015 Sep 24.

HMS LINCS Center &Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 USA.

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http://dx.doi.org/10.1038/ncomms9390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587398PMC
September 2015

Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold.

Mol Syst Biol 2015 May 7;11(5):803. Epub 2015 May 7.

Department of Systems Biology, Harvard Medical School, Boston, MA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461398PMC
http://dx.doi.org/10.15252/msb.20145584DOI Listing
May 2015

Surviving apoptosis: life-death signaling in single cells.

Trends Cell Biol 2015 Aug 25;25(8):446-58. Epub 2015 Apr 25.

Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2015.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570028PMC
August 2015

A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis.

Cell 2014 Nov;159(4):844-56

Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 524, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674140135
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http://dx.doi.org/10.1016/j.cell.2014.10.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243058PMC
November 2014

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

Nat Genet 2014 Dec 2;46(12):1363-1371. Epub 2014 Nov 2.

HMS Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115.

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http://dx.doi.org/10.1038/ng.3138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244270PMC
December 2014

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

Nucleic Acids Res 2014 Jul 6;42(Web Server issue):W449-60. Epub 2014 Jun 6.

Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA

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http://dx.doi.org/10.1093/nar/gku476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086130PMC
July 2014

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

BMC Biol 2014 Mar 21;12:20. Epub 2014 Mar 21.

HMS LINCS Center, Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, WAB 444, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/1741-7007-12-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234128PMC
March 2014

Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis.

Sci Signal 2014 Mar 11;7(316):ra23. Epub 2014 Mar 11.

1Department for Bioinformatics and Functional Genomics, Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg 69120, Germany.

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http://dx.doi.org/10.1126/scisignal.2004738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208692PMC
March 2014

Decision-tree based model analysis for efficient identification of parameter relations leading to different signaling states.

PLoS One 2013 18;8(12):e82593. Epub 2013 Dec 18.

Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082593PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867358PMC
October 2014

Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines.

Sci Signal 2013 Sep 24;6(294):ra84. Epub 2013 Sep 24.

HMS LINCS Center Department of Systems Biology Harvard Medical School Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1126/scisignal.2004379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845839PMC
September 2013

Metrics other than potency reveal systematic variation in responses to cancer drugs.

Nat Chem Biol 2013 Nov 8;9(11):708-14. Epub 2013 Sep 8.

Harvard Medical School Library of Integrated Network-based Cellular Signatures Center, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nchembio.1337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947796PMC
November 2013

S. cerevisiae chromosomes biorient via gradual resolution of syntely between S phase and anaphase.

Cell 2013 Aug;154(5):1127-1139

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2013.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3802543PMC
August 2013

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

Bioinformatics 2013 Nov 27;29(21):2757-64. Epub 2013 Aug 27.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, Department of Systems Biology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115 and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799471PMC
November 2013

Modulating cell-to-cell variability and sensitivity to death ligands by co-drugging.

Phys Biol 2013 Jun 4;10(3):035002. Epub 2013 Jun 4.

Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA.

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http://dx.doi.org/10.1088/1478-3975/10/3/035002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775495PMC
June 2013

Cells surviving fractional killing by TRAIL exhibit transient but sustainable resistance and inflammatory phenotypes.

Mol Biol Cell 2013 Jul 22;24(14):2186-200. Epub 2013 May 22.

Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1091/mbc.E12-10-0737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708725PMC
July 2013

Programming biological models in Python using PySB.

Mol Syst Biol 2013 ;9:646

Department of Cancer Biology, Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://msb.embopress.org/cgi/doi/10.1038/msb.2013.1
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http://dx.doi.org/10.1038/msb.2013.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588907PMC
September 2013

Properties of cell death models calibrated and compared using Bayesian approaches.

Mol Syst Biol 2013 ;9:644

Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1038/msb.2012.69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588908PMC
September 2013

Spindle checkpoint deficiency is tolerated by murine epidermal cells but not hair follicle stem cells.

Proc Natl Acad Sci U S A 2013 Feb 4;110(8):2928-33. Epub 2013 Feb 4.

Mouse Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1217388110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581953PMC
February 2013

Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected.

Mol Cell Proteomics 2013 May 28;12(5):1204-13. Epub 2013 Jan 28.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1074/mcp.M112.025858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650332PMC
May 2013

An expanding role for cell biologists in drug discovery and pharmacology.

Mol Biol Cell 2012 Nov;23(21):4162-4

Department of Systems Biology, Center for Cell Decision Processes, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1091/mbc.E12-05-0394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484093PMC
November 2012

Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis.

PLoS Comput Biol 2012 26;8(4):e1002482. Epub 2012 Apr 26.

Department of Cancer Biology and Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343095PMC
August 2012

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

BMC Syst Biol 2012 May 1;6:29. Epub 2012 May 1.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/1752-0509-6-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436686PMC
May 2012

Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis.

Mol Syst Biol 2011 Nov 22;7:553. Epub 2011 Nov 22.

Department of Systems Biology, Center for Cell Decision Processes, Harvard Medical School, MA, USA.

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http://dx.doi.org/10.1038/msb.2011.85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261706PMC
November 2011

p31(comet) acts to ensure timely spindle checkpoint silencing subsequent to kinetochore attachment.

Mol Biol Cell 2011 Nov 30;22(22):4236-46. Epub 2011 Sep 30.

Center for Cell Decision Processes, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1091/mbc.E11-03-0216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216650PMC
November 2011