Publications by authors named "Trey Ideker"

100Publications

Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.

Cancer Cell 2020 Oct 21. Epub 2020 Oct 21.

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2020.09.014DOI Listing
October 2020

Multiscale community detection in Cytoscape.

PLoS Comput Biol 2020 Oct 23;16(10):e1008239. Epub 2020 Oct 23.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1008239DOI Listing
October 2020

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Authors:
David E Gordon Joseph Hiatt Mehdi Bouhaddou Veronica V Rezelj Svenja Ulferts Hannes Braberg Alexander S Jureka Kirsten Obernier Jeffrey Z Guo Jyoti Batra Robyn M Kaake Andrew R Weckstein Tristan W Owens Meghna Gupta Sergei Pourmal Erron W Titus Merve Cakir Margaret Soucheray Michael McGregor Zeynep Cakir Gwendolyn Jang Matthew J O'Meara Tia A Tummino Ziyang Zhang Helene Foussard Ajda Rojc Yuan Zhou Dmitry Kuchenov Ruth Hüttenhain Jiewei Xu Manon Eckhardt Danielle L Swaney Jacqueline M Fabius Manisha Ummadi Beril Tutuncuoglu Ujjwal Rathore Maya Modak Paige Haas Kelsey M Haas Zun Zar Chi Naing Ernst H Pulido Ying Shi Inigo Barrio-Hernandez Danish Memon Eirini Petsalaki Alistair Dunham Miguel Correa Marrero David Burke Cassandra Koh Thomas Vallet Jesus A Silvas Caleigh M Azumaya Christian Billesbølle Axel F Brilot Melody G Campbell Amy Diallo Miles Sasha Dickinson Devan Diwanji Nadia Herrera Nick Hoppe Huong T Kratochvil Yanxin Liu Gregory E Merz Michelle Moritz Henry C Nguyen Carlos Nowotny Cristina Puchades Alexandrea N Rizo Ursula Schulze-Gahmen Amber M Smith Ming Sun Iris D Young Jianhua Zhao Daniel Asarnow Justin Biel Alisa Bowen Julian R Braxton Jen Chen Cynthia M Chio Un Seng Chio Ishan Deshpande Loan Doan Bryan Faust Sebastian Flores Mingliang Jin Kate Kim Victor L Lam Fei Li Junrui Li Yen-Li Li Yang Li Xi Liu Megan Lo Kyle E Lopez Arthur A Melo Frank R Moss Phuong Nguyen Joana Paulino Komal Ishwar Pawar Jessica K Peters Thomas H Pospiech Maliheh Safari Smriti Sangwan Kaitlin Schaefer Paul V Thomas Aye C Thwin Raphael Trenker Eric Tse Tsz Kin Martin Tsui Feng Wang Natalie Whitis Zanlin Yu Kaihua Zhang Yang Zhang Fengbo Zhou Daniel Saltzberg Anthony J Hodder Amber S Shun-Shion Daniel M Williams Kris M White Romel Rosales Thomas Kehrer Lisa Miorin Elena Moreno Arvind H Patel Suzannah Rihn Mir M Khalid Albert Vallejo-Gracia Parinaz Fozouni Camille R Simoneau Theodore L Roth David Wu Mohd Anisul Karim Maya Ghoussaini Ian Dunham Francesco Berardi Sebastian Weigang Maxime Chazal Jisoo Park James Logue Marisa McGrath Stuart Weston Robert Haupt C James Hastie Matthew Elliott Fiona Brown Kerry A Burness Elaine Reid Mark Dorward Clare Johnson Stuart G Wilkinson Anna Geyer Daniel M Giesel Carla Baillie Samantha Raggett Hannah Leech Rachel Toth Nicola Goodman Kathleen C Keough Abigail L Lind Reyna J Klesh Kafi R Hemphill Jared Carlson-Stevermer Jennifer Oki Kevin Holden Travis Maures Katherine S Pollard Andrej Sali David A Agard Yifan Cheng James S Fraser Adam Frost Natalia Jura Tanja Kortemme Aashish Manglik Daniel R Southworth Robert M Stroud Dario R Alessi Paul Davies Matthew B Frieman Trey Ideker Carmen Abate Nolwenn Jouvenet Georg Kochs Brian Shoichet Melanie Ott Massimo Palmarini Kevan M Shokat Adolfo García-Sastre Jeremy A Rassen Robert Grosse Oren S Rosenberg Kliment A Verba Christopher F Basler Marco Vignuzzi Andrew A Peden Pedro Beltrao Nevan J Krogan

Science 2020 Oct 15. Epub 2020 Oct 15.

QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1126/science.abe9403DOI Listing
October 2020

Association of Epigenetic Metrics of Biological Age With Cortical Thickness.

JAMA Netw Open 2020 Sep 1;3(9):e2015428. Epub 2020 Sep 1.

Center for Magnetoencephalography, University of Nebraska Medical Center, Omaha.

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http://dx.doi.org/10.1001/jamanetworkopen.2020.15428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490648PMC
September 2020

Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response.

G3 (Bethesda) 2020 Sep 2;10(9):2981-2988. Epub 2020 Sep 2.

Department of Medicine, University of California, San Diego, La Jolla, California.

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http://dx.doi.org/10.1534/g3.120.401417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466999PMC
September 2020

Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.

Cell Syst 2020 Aug 2;11(2):176-185.e6. Epub 2020 Jul 2.

Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484147PMC
August 2020

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

bioRxiv 2020 Mar 22. Epub 2020 Mar 22.

QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1101/2020.03.22.002386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239059PMC
March 2020

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Authors:
David E Gordon Gwendolyn M Jang Mehdi Bouhaddou Jiewei Xu Kirsten Obernier Kris M White Matthew J O'Meara Veronica V Rezelj Jeffrey Z Guo Danielle L Swaney Tia A Tummino Ruth Hüttenhain Robyn M Kaake Alicia L Richards Beril Tutuncuoglu Helene Foussard Jyoti Batra Kelsey Haas Maya Modak Minkyu Kim Paige Haas Benjamin J Polacco Hannes Braberg Jacqueline M Fabius Manon Eckhardt Margaret Soucheray Melanie J Bennett Merve Cakir Michael J McGregor Qiongyu Li Bjoern Meyer Ferdinand Roesch Thomas Vallet Alice Mac Kain Lisa Miorin Elena Moreno Zun Zar Chi Naing Yuan Zhou Shiming Peng Ying Shi Ziyang Zhang Wenqi Shen Ilsa T Kirby James E Melnyk John S Chorba Kevin Lou Shizhong A Dai Inigo Barrio-Hernandez Danish Memon Claudia Hernandez-Armenta Jiankun Lyu Christopher J P Mathy Tina Perica Kala Bharath Pilla Sai J Ganesan Daniel J Saltzberg Ramachandran Rakesh Xi Liu Sara B Rosenthal Lorenzo Calviello Srivats Venkataramanan Jose Liboy-Lugo Yizhu Lin Xi-Ping Huang YongFeng Liu Stephanie A Wankowicz Markus Bohn Maliheh Safari Fatima S Ugur Cassandra Koh Nastaran Sadat Savar Quang Dinh Tran Djoshkun Shengjuler Sabrina J Fletcher Michael C O'Neal Yiming Cai Jason C J Chang David J Broadhurst Saker Klippsten Phillip P Sharp Nicole A Wenzell Duygu Kuzuoglu-Ozturk Hao-Yuan Wang Raphael Trenker Janet M Young Devin A Cavero Joseph Hiatt Theodore L Roth Ujjwal Rathore Advait Subramanian Julia Noack Mathieu Hubert Robert M Stroud Alan D Frankel Oren S Rosenberg Kliment A Verba David A Agard Melanie Ott Michael Emerman Natalia Jura Mark von Zastrow Eric Verdin Alan Ashworth Olivier Schwartz Christophe d'Enfert Shaeri Mukherjee Matt Jacobson Harmit S Malik Danica G Fujimori Trey Ideker Charles S Craik Stephen N Floor James S Fraser John D Gross Andrej Sali Bryan L Roth Davide Ruggero Jack Taunton Tanja Kortemme Pedro Beltrao Marco Vignuzzi Adolfo García-Sastre Kevan M Shokat Brian K Shoichet Nevan J Krogan

Nature 2020 07 30;583(7816):459-468. Epub 2020 Apr 30.

QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41586-020-2286-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431030PMC
July 2020

A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in .

J Cell Sci 2020 May 22;133(10). Epub 2020 May 22.

Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands

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http://dx.doi.org/10.1242/jcs.237628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325435PMC
May 2020

Thousands of missing variants in the UK Biobank are recoverable by genome realignment.

Ann Hum Genet 2020 05 31;84(3):214-220. Epub 2020 Mar 31.

Department of Medicine, University of California San Diego, La Jolla, California.

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http://dx.doi.org/10.1111/ahg.12383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402360PMC
May 2020

A census of pathway maps in cancer systems biology.

Nat Rev Cancer 2020 04 17;20(4):233-246. Epub 2020 Feb 17.

Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41568-020-0240-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224610PMC
April 2020

The great hairball gambit.

PLoS Genet 2019 11 26;15(11):e1008519. Epub 2019 Nov 26.

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910700PMC
November 2019

Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention.

Cereb Cortex 2020 03;30(3):1234-1243

Department of Neurological Sciences, University of Nebraska Medical Center (UNMC), Omaha, NE 68198-8440, USA.

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http://dx.doi.org/10.1093/cercor/bhz162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7132912PMC
March 2020

Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.

Cell Rep 2019 08;28(9):2317-2330.e8

Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; QB3, California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.07.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728083PMC
August 2019

Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

Curr Opin Genet Dev 2019 02 6;54:110-117. Epub 2019 Jul 6.

Cellular and Molecular Pharmacology, University of California, San Francisco, CA, United States; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2019.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6746583PMC
February 2019

A Fast and Flexible Framework for Network-Assisted Genomic Association.

iScience 2019 Jun 24;16:155-161. Epub 2019 May 24.

Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.isci.2019.05.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554232PMC
June 2019

Identifying Epistasis in Cancer Genomes: A Delicate Affair.

Cell 2019 05;177(6):1375-1383

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816465PMC
May 2019

Rare variant phasing using paired tumor:normal sequence data.

BMC Bioinformatics 2019 May 27;20(1):265. Epub 2019 May 27.

Human Biology Program, J. Craig Venter Institute, La Jolla, CA, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-019-2753-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537421PMC
May 2019

Transcriptional responses to DNA damage.

DNA Repair (Amst) 2019 07 7;79:40-49. Epub 2019 May 7.

Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15687864193000
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http://dx.doi.org/10.1016/j.dnarep.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570417PMC
July 2019

Strategies for Network GWAS Evaluated Using Classroom Crowd Science.

Cell Syst 2019 04;8(4):275-280

Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764759PMC
April 2019

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Cell 2019 04 4;177(3):572-586.e22. Epub 2019 Apr 4.

Department of Pharmacology, University of California, San Diego School of Medicine, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193027
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http://dx.doi.org/10.1016/j.cell.2019.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711371PMC
April 2019

DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Cell Syst 2019 03 13;8(3):267-273.e3. Epub 2019 Mar 13.

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712193003
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http://dx.doi.org/10.1016/j.cels.2019.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7042149PMC
March 2019

A Blueprint for Systems Biology.

Clin Chem 2019 02 28;65(2):342-344. Epub 2018 Dec 28.

Institute for Systems Biology, Seattle, WA;

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http://www.clinchem.org/lookup/doi/10.1373/clinchem.2018.291
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http://dx.doi.org/10.1373/clinchem.2018.291062DOI Listing
February 2019

Typing tumors using pathways selected by somatic evolution.

Nat Commun 2018 10 8;9(1):4159. Epub 2018 Oct 8.

Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.

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http://www.nature.com/articles/s41467-018-06464-y
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http://dx.doi.org/10.1038/s41467-018-06464-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175900PMC
October 2018

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.

Mol Cell 2018 09;71(6):882-895

Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520108PMC
September 2018

Genomic Landscape of Appendiceal Neoplasms.

JCO Precis Oncol 2018 8;2. Epub 2018 Aug 8.

, , , , and , Mount Sinai Hospital, New York, NY; , , , , , , , , , and , University of California, San Diego, La Jolla, CA; , Albany Medical College, Albany, NY; , , and , Foundation Medicine, Cambridge, MA.

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http://dx.doi.org/10.1200/PO.17.00302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7446344PMC
August 2018

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

Cell 2018 07;174(3):505-520

Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247911PMC
July 2018

Classifying tumors by supervised network propagation.

Bioinformatics 2018 07;34(13):i484-i493

Department of Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022559PMC
July 2018

Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.

J Mol Biol 2018 09 20;430(18 Pt A):2900-2912. Epub 2018 Jun 20.

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, USA.

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http://dx.doi.org/10.1016/j.jmb.2018.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097899PMC
September 2018

Visible Machine Learning for Biomedicine.

Cell 2018 06;173(7):1562-1565

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Cancer Cell Map Initiative, University of California San Diego, La Jolla, CA, USA; UCSD Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.05.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483071PMC
June 2018

pyNBS: a Python implementation for network-based stratification of tumor mutations.

Bioinformatics 2018 08;34(16):2859-2861

Bioinformatics and Systems Biology Program, Bioengineering Department, UC San Diego, La Jolla, CA, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084608PMC
August 2018

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Cell Syst 2018 Apr 28;6(4):484-495.e5. Epub 2018 Mar 28.

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cels.2018.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920724PMC
April 2018

Using deep learning to model the hierarchical structure and function of a cell.

Nat Methods 2018 04 5;15(4):290-298. Epub 2018 Mar 5.

Department of Medicine, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nmeth.4627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882547PMC
April 2018

Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping.

Mol Cell 2018 01;69(2):321-333.e3

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777277PMC
January 2018

The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins.

Mol Cell 2018 01;69(2):306-320.e4

Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.12.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6049073PMC
January 2018

Annotating gene sets by mining large literature collections with protein networks.

Pac Symp Biocomput 2018 ;23:602-613

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5806628PMC
August 2018

Correcting CRISPR for copy number.

Nat Genet 2017 11;49(12):1674-1675

Department of Medicine, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/ng.3994DOI Listing
November 2017

MHC-I Genotype Restricts the Oncogenic Mutational Landscape.

Cell 2017 Nov 26;171(6):1272-1283.e15. Epub 2017 Oct 26.

Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cell.2017.09.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711564PMC
November 2017

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Cancer Res 2017 11;77(21):e58-e61

Department of Medicine, University of California San Diego, La Jolla, California.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679399PMC
November 2017

ndexr-an R package to interface with the network data exchange.

Bioinformatics 2018 02;34(4):716-717

Department of Medical Statistics, University Medical Center Göttingen, Göttingen 37099, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6248454PMC
February 2018

Network propagation in the cytoscape cyberinfrastructure.

PLoS Comput Biol 2017 Oct 12;13(10):e1005598. Epub 2017 Oct 12.

Department of Medicine, University of California-San Diego, San Diego, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638226PMC
October 2017

Network approaches and applications in biology.

PLoS Comput Biol 2017 Oct 12;13(10):e1005771. Epub 2017 Oct 12.

Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638228PMC
October 2017

Common genetic variation in the germline influences where and how tumors develop.

Mol Cell Oncol 2017 10;4(3):e1302905. Epub 2017 Mar 10.

Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1080/23723556.2017.1302905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462515PMC
March 2017

Network propagation: a universal amplifier of genetic associations.

Nat Rev Genet 2017 09 12;18(9):551-562. Epub 2017 Jun 12.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://www.nature.com/doifinder/10.1038/nrg.2017.38
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http://dx.doi.org/10.1038/nrg.2017.38DOI Listing
September 2017

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Autophagy 2017 Jul 9;13(7):1248-1249. Epub 2017 May 9.

a Section of Molecular Biology, Division of Biological Sciences , University of California , San Diego, La Jolla , CA USA.

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http://dx.doi.org/10.1080/15548627.2017.1313946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529073PMC
July 2017

Genetic interaction mapping in mammalian cells using CRISPR interference.

Nat Methods 2017 Jun 8;14(6):577-580. Epub 2017 May 8.

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1038/nmeth.4286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584685PMC
June 2017

Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.

Mol Cell 2017 Feb 26;65(4):761-774.e5. Epub 2017 Jan 26.

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.12.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439305PMC
February 2017

Leveraging premalignant biology for immune-based cancer prevention.

Proc Natl Acad Sci U S A 2016 09 16;113(39):10750-8. Epub 2016 Sep 16.

Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047191PMC
http://dx.doi.org/10.1073/pnas.1608077113DOI Listing
September 2016

A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.

Mol Cell 2016 08 21;63(3):514-25. Epub 2016 Jul 21.

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Cancer Cell Map Initiative. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209245PMC
August 2016

Challenges in identifying cancer genes by analysis of exome sequencing data.

Nat Commun 2016 07 15;7:12096. Epub 2016 Jul 15.

Cancer Cell Map Initiative (CCMI), 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/ncomms12096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947162PMC
July 2016

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA.

Mol Cell 2016 04;62(2):157-168

Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995115PMC
April 2016

Evidence for a common evolutionary rate in metazoan transcriptional networks.

Elife 2015 Dec 18;4. Epub 2015 Dec 18.

Department of Medicine, University of California, San Diego, La Jolla, United States.

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http://dx.doi.org/10.7554/eLife.11615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764585PMC
December 2015

NDEx, the Network Data Exchange.

Cell Syst 2015 Oct;1(4):302-305

Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA ; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cels.2015.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649937PMC
October 2015

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types.

PLoS One 2015 10;10(11):e0142618. Epub 2015 Nov 10.

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142618PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640835PMC
June 2016

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

J Proteome Res 2015 Dec 20;14(12):4995-5006. Epub 2015 Oct 20.

Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706558PMC
December 2015

Molecular networks in context.

Nat Biotechnol 2015 Jul;33(7):720-1

Bioinformatics Program and Department of Medicine, University of California, San Diego, San Diego, California, USA.

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http://www.nature.com/articles/nbt.3283
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http://dx.doi.org/10.1038/nbt.3283DOI Listing
July 2015

ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer.

PLoS One 2015 17;10(6):e0126898. Epub 2015 Jun 17.

Department of Medicine, University of California San Diego, La Jolla, California, United States of America; Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126898PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470586PMC
March 2016

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.

Appl Environ Microbiol 2015 Aug 12;81(16):5639-49. Epub 2015 Jun 12.

Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, California, USA

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http://dx.doi.org/10.1128/AEM.01327-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510171PMC
August 2015

The cancer cell map initiative: defining the hallmark networks of cancer.

Mol Cell 2015 May;58(4):690-8

Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359018PMC
May 2015

Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma.

Oral Oncol 2015 May 27;51(5):470-5. Epub 2015 Feb 27.

Division of Head and Neck Surgery, University of California, San Diego, CA, USA; Department of Pharmacology, University of California, San Diego, CA, USA; Moores Cancer Center, San Diego, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.oraloncology.2015.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427339PMC
May 2015

Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy.

Mol Cell 2015 Jan 24;57(1):55-68. Epub 2014 Dec 24.

Sanford-Burnham Medical Research Institute, Development, Aging, and Regeneration Program, La Jolla, CA 92037, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765140091
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http://dx.doi.org/10.1016/j.molcel.2014.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373083PMC
January 2015

Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.

Mol Cell 2015 Jan 18;57(2):273-89. Epub 2014 Dec 18.

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.11.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706562PMC
January 2015