Joshua M Stuart

Joshua M Stuart

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Joshua M Stuart

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Biological process activity transformation of single cell gene expression for cross-species alignment.

Nat Commun 2019 Oct 25;10(1):4899. Epub 2019 Oct 25.

Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.

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http://dx.doi.org/10.1038/s41467-019-12924-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814736PMC
October 2019

PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.

Pac Symp Biocomput 2019 ;24:136-147

Dept. of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA*Currently at the Flatiron Institute & Princeton University.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417802PMC
August 2019

Reply to A. Dalla Volta et al.

J Clin Oncol 2019 Feb 17;37(4):351-352. Epub 2018 Dec 17.

Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA.

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http://dx.doi.org/10.1200/JCO.18.01487DOI Listing
February 2019

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.

J Clin Oncol 2018 08 9;36(24):2492-2503. Epub 2018 Jul 9.

Rahul Aggarwal, Li Zhang, Felix Y. Feng, Paul Lloyd, Jack Youngren, Adam Foye, Denise Playdle, Charles J. Ryan, and Eric J. Small, University of California San Francisco, San Francisco; Alana S. Weinstein, Verena Friedl, Can Zhang, Christopher K. Wong, Vlado Uzunangelov, Artem Sokolov, Yulia Newton, and Joshua M. Stuart, University of California Santa Cruz, Santa Cruz; Owen N. Witte and Matthew Rettig, University of California Los Angeles, Los Angeles; Christopher P. Evans and Primo Lara, University of California Davis, Davis, CA; Jiaoti Huang, Duke University, Durham, NC; Joshi J. Alumkal, George V. Thomas, and Tomasz M. Beer, Oregon Health Sciences University, Portland, OR; Martin Gleave and Kim N. Chi, University of British Columbia, Vancouver, British Columbia, Canada; Lawrence True, University of Washington, Seattle, WA; Himisha Beltran and Mark A. Rubin, Weill Cornell Medicine, New York, NY; and Francesca Demichelis, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1200/JCO.2017.77.6880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366813PMC
August 2018

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Cell 2018 07 19;174(3):758-769.e9. Epub 2018 Jul 19.

Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA; Department of Radiation Oncology, UCSF, San Francisco, CA, USA; Department of Urology, UCSF, San Francisco, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425931PMC
July 2018

Prophetic Granger Causality to infer gene regulatory networks.

PLoS One 2017 6;12(12):e0170340. Epub 2017 Dec 6.

University of California Santa Cruz, Department of Biomolecular Engineering, Santa Cruz, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170340PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718405PMC
January 2018

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

BMC Bioinformatics 2018 01 31;19(1):28. Epub 2018 Jan 31.

Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, M5G 0A3, Canada.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2046-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793408PMC
January 2018

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

TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES.

Pac Symp Biocomput 2017 ;22:576-587

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203771PMC
http://dx.doi.org/10.1142/9789813207813_0053DOI Listing
March 2017

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.

Pac Symp Biocomput 2016 ;21:405-16

Department of Biomolecular Engineering, University of California Santa Cruz, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856035PMC
October 2016

N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells.

Cancer Cell 2016 Apr 31;29(4):536-547. Epub 2016 Mar 31.

Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829466PMC
April 2016

Pathway-Based Genomics Prediction using Generalized Elastic Net.

PLoS Comput Biol 2016 Mar 9;12(3):e1004790. Epub 2016 Mar 9.

Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784899PMC
March 2016

A basal stem cell signature identifies aggressive prostate cancer phenotypes.

Proc Natl Acad Sci U S A 2015 Nov 12;112(47):E6544-52. Epub 2015 Oct 12.

Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095; Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095

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http://dx.doi.org/10.1073/pnas.1518007112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664352PMC
November 2015

RADIA: RNA and DNA integrated analysis for somatic mutation detection.

PLoS One 2014 18;9(11):e111516. Epub 2014 Nov 18.

University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111516PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236012PMC
July 2015

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Nat Methods 2015 Jul 18;12(7):623-30. Epub 2015 May 18.

1] Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856034PMC
July 2015

Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood Production in Normal and Regenerative Conditions.

Cell Stem Cell 2015 Jul 18;17(1):35-46. Epub 2015 Jun 18.

The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542150PMC
July 2015

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

Large-scale cytological profiling for functional analysis of bioactive compounds.

Mol Biosyst 2013 Nov;9(11):2604-17

Department of Biomolecular Engineering, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1039/c3mb70245fDOI Listing
November 2013

The Cancer Genome Atlas Pan-Cancer analysis project.

Nat Genet 2013 Oct;45(10):1113-20

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919969PMC
October 2013

The UCSC Interaction Browser: multidimensional data views in pathway context.

Nucleic Acids Res 2013 Jul 8;41(Web Server issue):W218-24. Epub 2013 Jun 8.

Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692096PMC
July 2013

Molecular pathways: extracting medical knowledge from high-throughput genomic data.

Clin Cancer Res 2013 Jun 21;19(12):3114-20. Epub 2013 Feb 21.

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-2093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686839PMC
June 2013

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Bioinformatics 2012 Sep;28(18):i640-i646

Department of Biomolecular Engineering and CBSE, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436829PMC
September 2012

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.

Nucleic Acids Res 2011 Nov 19;39(20):8792-802. Epub 2011 Jul 19.

Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203614PMC
November 2011

The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae.

Mol Biosyst 2011 Jun 12;7(6):2019-30. Epub 2011 Apr 12.

Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1039/c0mb00298dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653045PMC
June 2011

Computational integration of homolog and pathway gene module expression reveals general stemness signatures.

PLoS One 2011 Apr 29;6(4):e18968. Epub 2011 Apr 29.

Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018968PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084730PMC
April 2011

The UCSC Cancer Genomics Browser: update 2011.

Nucleic Acids Res 2011 Jan 8;39(Database issue):D951-9. Epub 2010 Nov 8.

Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkq1113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013705PMC
January 2011

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

A global analysis of genetic interactions in Caenorhabditis elegans.

J Biol 2007 26;6(3). Epub 2007 Sep 26.

Department of Medical Genetics and Microbiology, The Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College St, University of Toronto, Toronto, ON, M5S 3E1, Canada.

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http://jbiol.biomedcentral.com/articles/10.1186/jbiol58
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http://dx.doi.org/10.1186/jbiol58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373897PMC
March 2010

HALO384: a halo-based potency prediction algorithm for high-throughput detection of antimicrobial agents.

J Biomol Screen 2010 Feb 19;15(2):196-205. Epub 2010 Jan 19.

Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA.

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http://dx.doi.org/10.1177/1087057109355060DOI Listing
February 2010

Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells.

PLoS One 2010 Jan 20;5(1):e8785. Epub 2010 Jan 20.

Institute for Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008785PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808351PMC
January 2010

Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.

J Bacteriol 2009 Feb 1;191(3):782-94. Epub 2008 Dec 1.

Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA.

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http://jb.asm.org/content/191/3/782.full.pdf
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http://jb.asm.org/lookup/doi/10.1128/JB.00965-08
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http://dx.doi.org/10.1128/JB.00965-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632070PMC
February 2009

A factor graph nested effects model to identify networks from genetic perturbations.

PLoS Comput Biol 2009 Jan 30;5(1):e1000274. Epub 2009 Jan 30.

Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613752PMC
January 2009

Information-based methods for predicting gene function from systematic gene knock-downs.

BMC Bioinformatics 2008 Oct 29;9:463. Epub 2008 Oct 29.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1186/1471-2105-9-463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596148PMC
October 2008

Recommending pathway genes using a compendium of clustering solutions.

Pac Symp Biocomput 2007 :379-90

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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December 2007

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W625-32. Epub 2007 Jun 22.

Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkm295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933155PMC
July 2007

A search engine to identify pathway genes from expression data on multiple organisms.

BMC Syst Biol 2007 May 4;1:20. Epub 2007 May 4.

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1186/1752-0509-1-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1878502PMC
May 2007

Towards zoomable multidimensional maps of the cell.

Nat Biotechnol 2007 May;25(5):547-54

Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

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http://ls11-www.cs.uni-dortmund.de/people/klein/SeminarBioIn
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http://www.nature.com/doifinder/10.1038/nbt1304
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http://dx.doi.org/10.1038/nbt1304DOI Listing
May 2007

A gene-coexpression network for global discovery of conserved genetic modules.

Science 2003 Oct 21;302(5643):249-55. Epub 2003 Aug 21.

Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X-215, Stanford, CA 94305-5329, USA.

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http://dx.doi.org/10.1126/science.1087447DOI Listing
October 2003

Ontology development for a pharmacogenetics knowledge base.

Pac Symp Biocomput 2002 :65-76

Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, MSOB X-215, Stanford, CA 94305-5479, USA.

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October 2002

Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans.

Nature 2002 Aug;418(6901):975-9

Department of Developmental Biology, Stanford University Medical Center, California 94305, USA.

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http://dx.doi.org/10.1038/nature01012DOI Listing
August 2002

PharmGKB: the Pharmacogenetics Knowledge Base.

Nucleic Acids Res 2002 Jan;30(1):163-5

Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford, CA 94305-5479, USA.

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http://nar.oxfordjournals.org/content/30/1/163.full.pdf
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99138PMC
http://dx.doi.org/10.1093/nar/30.1.163DOI Listing
January 2002