Atul J Butte

Atul J Butte

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Atul J Butte

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Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.

Nat Commun 2019 Jul 10;10(1):3045. Epub 2019 Jul 10.

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41467-019-11069-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6620318PMC
July 2019

Robust prediction of clinical outcomes using cytometry data.

Bioinformatics 2019 Apr;35(7):1197-1203

Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449751PMC
April 2019

A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm.

J Reprod Immunol 2019 Apr 27;132:16-20. Epub 2019 Feb 27.

University of California, San Francisco, San Francisco, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jri.2019.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456418PMC
April 2019

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Nat Immunol 2019 02 14;20(2):163-172. Epub 2019 Jan 14.

Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41590-018-0276-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340744PMC
February 2019

Prototype of running clinical trials in an untrustworthy environment using blockchain.

Nat Commun 2019 02 22;10(1):917. Epub 2019 Feb 22.

Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1038/s41467-019-08874-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384889PMC
February 2019

Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.

Pharmacol Rev 2019 01 13;71(1):1-19. Epub 2018 Dec 13.

Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)

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http://pharmrev.aspetjournals.org/lookup/doi/10.1124/pr.118.
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http://dx.doi.org/10.1124/pr.118.016253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294046PMC
January 2019

A call for deep-learning healthcare.

Nat Med 2019 Jan;25(1):14-15

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA.

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http://www.nature.com/articles/s41591-018-0320-3
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http://dx.doi.org/10.1038/s41591-018-0320-3DOI Listing
January 2019

Open data informatics and data repurposing for IBD.

Nat Rev Gastroenterol Hepatol 2018 12;15(12):715-716

Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41575-018-0050-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687058PMC
December 2018

The 10,000 Immunomes Project: Building a Resource for Human Immunology.

Cell Rep 2018 Oct;25(2):513-522.e3

Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6263160PMC
October 2018

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

Genome Res 2018 04 22;28(4):423-431. Epub 2018 Mar 22.

Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.223693.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880234PMC
April 2018

Are minor alleles more likely to be risk alleles?

BMC Med Genomics 2018 01 19;11(1). Epub 2018 Jan 19.

Institute for Computational Health Sciences, University of California, 550 16th Street, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1186/s12920-018-0322-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775585PMC
January 2018

xCell: digitally portraying the tissue cellular heterogeneity landscape.

Genome Biol 2017 11 15;18(1):220. Epub 2017 Nov 15.

Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.

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http://dx.doi.org/10.1186/s13059-017-1349-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688663PMC
November 2017

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia.

PLoS One 2013 19;8(6):e65571. Epub 2013 Jun 19.

Department of Surgery, Stanford University, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065571PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686758PMC
October 2017

Comprehensive analysis of normal adjacent to tumor transcriptomes.

Nat Commun 2017 10 20;8(1):1077. Epub 2017 Oct 20.

Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1038/s41467-017-01027-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651823PMC
October 2017

Big data opens a window onto wellness.

Authors:
Atul J Butte

Nat Biotechnol 2017 08;35(8):720-721

Institute for Computational Health Sciences, University of California, San Francisco, USA.

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http://dx.doi.org/10.1038/nbt.3934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961487PMC
August 2017

Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration.

Cancer Res 2017 07 30;77(14):3740-3744. Epub 2017 Jun 30.

The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-3383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518753PMC
July 2017

Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.

Nat Commun 2017 07 12;8:16022. Epub 2017 Jul 12.

Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1038/ncomms16022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510182PMC
July 2017

Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling.

Gastroenterology 2017 06 8;152(8):2022-2036. Epub 2017 Mar 8.

Asian Liver Center and Department of Surgery, Stanford University School of Medicine, Stanford University, Stanford, California.

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http://dx.doi.org/10.1053/j.gastro.2017.02.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447464PMC
June 2017

RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.

Bioinformatics 2017 04;33(7):1101-1103

Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6041747PMC
April 2017

Solving Immunology?

Trends Immunol 2017 02 13;38(2):116-127. Epub 2016 Dec 13.

Center for Advanced Research on Diagnostic Assays, Immunology Institute, Friedman Brain Institute, and Departments of Neurology, Neuroscience, Pharmacology, and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2016.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695553PMC
February 2017

Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease.

Alzheimers Res Ther 2017 Feb 17;9(1):10. Epub 2017 Feb 17.

Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1186/s13195-017-0237-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316146PMC
February 2017

In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma.

Oncotarget 2017 Jan;8(3):4079-4095

Departments of Pathology and Laboratory Medicine, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA.

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http://dx.doi.org/10.18632/oncotarget.13385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354814PMC
January 2017

Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans.

J Biol Rhythms 2016 12 4;31(6):588-597. Epub 2016 Oct 4.

Institute for Computational Health Sciences, University of California, San Francisco, California.

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http://dx.doi.org/10.1177/0748730416668049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105327PMC
December 2016

It takes a genome to understand a village: Population scale precision medicine.

Authors:
Atul J Butte

Proc Natl Acad Sci U S A 2016 11 19;113(44):12344-12346. Epub 2016 Oct 19.

Institute for Computational Health Sciences, University of California, San Francisco, CA 94158

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http://dx.doi.org/10.1073/pnas.1615329113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098617PMC
November 2016

DO CANCER CLINICAL TRIAL POPULATIONS TRULY REPRESENT CANCER PATIENTS? A COMPARISON OF OPEN CLINICAL TRIALS TO THE CANCER GENOME ATLAS.

Pac Symp Biocomput 2016 ;21:309-20

Institute for Computational Health Sciences, University of California, San Francisco Mission Hall, 550 16th Street, San Francisco, CA 94158-2549, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961464PMC
October 2016

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.

Cell Syst 2016 10 13;3(4):374-384.e4. Epub 2016 Oct 13.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://www.cell.com/cell-systems/pdf/S2405-4712(16)30299-X.p
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http://dx.doi.org/10.1016/j.cels.2016.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358544PMC
October 2016

Digitally deconvolving the tumor microenvironment.

Genome Biol 2016 08 22;17(1):175. Epub 2016 Aug 22.

Institute for Computational Health Sciences, University of California, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158-2549, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13059-016-1036-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993002PMC
August 2016

Widespread parainflammation in human cancer.

Genome Biol 2016 07 8;17(1):145. Epub 2016 Jul 8.

The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.

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http://dx.doi.org/10.1186/s13059-016-0995-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937599PMC
July 2016

Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression.

J Am Med Inform Assoc 2016 05 11;23(3):617-26. Epub 2015 Dec 11.

Institute for Computational Health Sciences, University of California, San Francisco, Mission Hall, 550 16th Street, San Francisco, CA 94158-2549, USA

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https://academic.oup.com/jamia/article-lookup/doi/10.1093/ja
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http://dx.doi.org/10.1093/jamia/ocv166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901376PMC
May 2016

ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.

Nucleic Acids Res 2016 05 26;44(8):e80. Epub 2016 Jan 26.

Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94158, 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/gkw030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856978PMC
May 2016

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.

Sci Rep 2016 05 4;6:24799. Epub 2016 May 4.

Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America.

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http://www.nature.com/articles/srep24799
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http://dx.doi.org/10.1038/srep24799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855174PMC
May 2016

Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov.

Pac Symp Biocomput 2015 :68-79

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA, 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361221PMC
April 2016

A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets.

Pac Symp Biocomput 2015 :383-94

Stanford University, Division of System Medicine, Department of Pediatrics, Stanford, CA 94305, USA.

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http://psb.stanford.edu/psb-online/proceedings/psb15/fan-min
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299914PMC
April 2016

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.

PLoS Comput Biol 2016 Apr 26;12(4):e1004885. Epub 2016 Apr 26.

Department of Genetics, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846031PMC
April 2016

Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome.

Oncol Rep 2016 Mar 21;35(3):1519-28. Epub 2015 Dec 21.

Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China.

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http://dx.doi.org/10.3892/or.2015.4501DOI Listing
March 2016

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Immunity 2016 Jan 12;44(1):194-206. Epub 2016 Jan 12.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613150053
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http://dx.doi.org/10.1016/j.immuni.2015.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330663PMC
January 2016

Systematic pan-cancer analysis of tumour purity.

Nat Commun 2015 Dec 4;6:8971. Epub 2015 Dec 4.

Institute for Computational Health Sciences, University of California, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1038/ncomms9971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671203PMC
December 2015

Opening clinical trial data: are the voluntary data-sharing portals enough?

BMC Med 2015 Nov 11;13:280. Epub 2015 Nov 11.

Institute for Computational Health Sciences, University of California San Francisco, Mission Hall, 550 16th Street, 4th Floor, San Francisco, CA, 94158-2549, USA.

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http://dx.doi.org/10.1186/s12916-015-0525-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642633PMC
November 2015

Heterogeneity in recent-onset type 1 diabetes - a clinical trial perspective.

Diabetes Metab Res Rev 2015 Sep 23;31(6):588-94. Epub 2015 Apr 23.

Benaroya Research Institute, Seattle, WA, USA.

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http://dx.doi.org/10.1002/dmrr.2643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815427PMC
September 2015

Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment.

Arthritis Res Ther 2015 Sep 21;17:262. Epub 2015 Sep 21.

Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, Box 0110, Mission Hall 4733, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1186/s13075-015-0778-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576403PMC
September 2015

Robust meta-analysis of gene expression using the elastic net.

Nucleic Acids Res 2015 Jul 31;43(12):e79. Epub 2015 Mar 31.

Division of Systems Medicine, Department of Pediatrics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA

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http://dx.doi.org/10.1093/nar/gkv229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499117PMC
July 2015

The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue.

Diabetologia 2015 Jul 9;58(7):1579-86. Epub 2015 May 9.

Division of Endocrinology, Department of Medicine, Stanford University, 300 Pasteur Drive, Rm S025, Stanford, CA, 94305-5103, USA.

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http://dx.doi.org/10.1007/s00125-015-3603-yDOI Listing
July 2015

Anti-CD44 antibody treatment lowers hyperglycemia and improves insulin resistance, adipose inflammation, and hepatic steatosis in diet-induced obese mice.

Diabetes 2015 Mar 7;64(3):867-75. Epub 2014 Oct 7.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA Lucile Packard Children's Hospital, Palo Alto, CA

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http://dx.doi.org/10.2337/db14-0149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392898PMC
March 2015

Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records.

Sci Rep 2015 Mar 5;5:8580. Epub 2015 Mar 5.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, and Lucile Packard Children's Hospital, Palo Alto, CA, USA.

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http://www.nature.com/articles/srep08580
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http://dx.doi.org/10.1038/srep08580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894399PMC
March 2015

Variation in the human immune system is largely driven by non-heritable influences.

Cell 2015 Jan;160(1-2):37-47

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674140159
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http://dx.doi.org/10.1016/j.cell.2014.12.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302727PMC
January 2015

Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells.

Sci Rep 2014 Nov 21;4:7144. Epub 2014 Nov 21.

Hagey Laboratory for Pediatric Regenerative Medicine; Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1038/srep07144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239576PMC
November 2014

Diabetes irreversibly depletes bone marrow-derived mesenchymal progenitor cell subpopulations.

Diabetes 2014 Sep 16;63(9):3047-56. Epub 2014 Apr 16.

Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA

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http://dx.doi.org/10.2337/db13-1366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429348PMC
September 2014

Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo.

Cell Rep 2014 Jul 10;8(2):371-81. Epub 2014 Jul 10.

Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.06.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128252PMC
July 2014

Investigation of maternal environmental exposures in association with self-reported preterm birth.

Reprod Toxicol 2014 Jun 27;45:1-7. Epub 2013 Dec 27.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Lucile Packard Children's Hospital, Palo Alto, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.reprotox.2013.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316205PMC
June 2014

Whole genome sequencing in support of wellness and health maintenance.

Genome Med 2013 27;5(6):58. Epub 2013 Jun 27.

School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA ; Center for Health Discovery and Well Being, and School of Medicine, Emory University Midtown Hospital, 550 Peachtree St, Atlanta GA 30308, USA.

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http://dx.doi.org/10.1186/gm462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967117PMC
May 2014

A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.

Cancer Res 2014 May 20;74(10):2892-902. Epub 2014 Mar 20.

Authors' Affiliations: Cancer Biology Program, Division of Hematology/Oncology, Department of Pediatrics; Center for Biomedical Informatics Research, Department of Medicine; Institute for Immunity, Transplant and Infection; Department of Cardiothoracic Surgery; and Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-13-2775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084668PMC
May 2014

ImmPort: disseminating data to the public for the future of immunology.

Immunol Res 2014 May;58(2-3):234-9

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road MSOB X163, Stanford, CA, 94305-5415, USA.

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http://dx.doi.org/10.1007/s12026-014-8516-1DOI Listing
May 2014

Collaborative biomedicine in the age of big data: the case of cancer.

J Med Internet Res 2014 Apr 7;16(4):e101. Epub 2014 Apr 7.

PricewaterhouseCoopers LLP, McLean, VA, United States.

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http://dx.doi.org/10.2196/jmir.2496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004150PMC
April 2014

Disease risk factors identified through shared genetic architecture and electronic medical records.

Sci Transl Med 2014 Apr;6(234):234ra57

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1126/scitranslmed.3007191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323098PMC
April 2014

Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records.

Pac Symp Biocomput 2013 :224-35

Div. of Systems Medicine, Dept. of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA.

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December 2013

A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors.

Cancer Discov 2013 Dec 26;3(12):1364-77. Epub 2013 Sep 26.

Departments of 1Pediatrics, 2Genetics, and 5Medicine-Oncology, 3Vincent Coates Mass Spectrometry Laboratory, Stanford University, Stanford; and 4Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Cancer Center, University of California Davis School of Medicine, Sacramento, California.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864571PMC
December 2013

Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:135. Epub 2013 Mar 18.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA., 94305 USA ; Lucile Packard Children's Hospital, Palo Alto, CA., 94304 USA ; Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA. 94305, USA.

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December 2013

Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:138-42. Epub 2013 Mar 18.

Stanford Biomedical Informatics; Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814460PMC
December 2013

Systematic evaluation of personal genome services for Japanese individuals.

J Hum Genet 2013 Nov 26;58(11):734-41. Epub 2013 Sep 26.

1] Rikengenesis CO., LTD., Tokyo, Japan [2] JST, PRESTO, Tokyo, Japan.

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http://dx.doi.org/10.1038/jhg.2013.96DOI Listing
November 2013

Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia.

BMC Med 2013 Nov 6;11:236. Epub 2013 Nov 6.

Department of Pediatrics, Stanford University, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/1741-7015-11-236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226208PMC
November 2013

Altering physiological networks using drugs: steps towards personalized physiology.

BMC Med Genomics 2013 7;6 Suppl 2:S7. Epub 2013 May 7.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/1755-8794-6-S2-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654899PMC
October 2013

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.

J Exp Med 2013 Oct 14;210(11):2205-21. Epub 2013 Oct 14.

Department of Pediatrics; 2 Stanford Cardiovascular Institute; 3 Department of Cardiothoracic Surgery; 4 Stanford Center for Biomedical Informatics Research, Department of Medicine; and 5 Institute for Immunity, Transplant, and Infection; Stanford University, Stanford, CA 94305.

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http://dx.doi.org/10.1084/jem.20122709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804941PMC
October 2013

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

Bioinformatics 2013 Aug 3;29(15):1922-4. Epub 2013 Jun 3.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712221PMC
August 2013

Systematic functional regulatory assessment of disease-associated variants.

Proc Natl Acad Sci U S A 2013 Jun 20;110(23):9607-12. Epub 2013 May 20.

Biomedical Informatics Training Program, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.1219099110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677437PMC
June 2013

Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS).

BMC Med Genet 2013 Jun 20;14:62. Epub 2013 Jun 20.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS-5415, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/1471-2350-14-62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699381PMC
June 2013

Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus.

Hum Genet 2013 May 20;132(5):495-508. Epub 2013 Jan 20.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1007/s00439-012-1258-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625410PMC
May 2013

Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

PLoS Genet 2013 May 23;9(5):e1003447. Epub 2013 May 23.

Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662561PMC
May 2013

Immune response profiling identifies autoantibodies specific to Moyamoya patients.

Orphanet J Rare Dis 2013 Mar 21;8:45. Epub 2013 Mar 21.

California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA.

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http://dx.doi.org/10.1186/1750-1172-8-45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648437PMC
March 2013