Mark A Jensen

Mark A Jensen

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Mark A Jensen

Mark A Jensen

Publications by authors named "Mark A Jensen"

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The NCI Genomic Data Commons as an engine for precision medicine.

Blood 2017 07 9;130(4):453-459. Epub 2017 Jun 9.

Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD.

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http://www.bloodjournal.org/lookup/doi/10.1182/blood-2017-03
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http://dx.doi.org/10.1182/blood-2017-03-735654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533202PMC
July 2017

A Practical Guide to The Cancer Genome Atlas (TCGA).

Methods Mol Biol 2016 ;1418:111-41

Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, USA.

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http://dx.doi.org/10.1007/978-1-4939-3578-9_6DOI Listing
December 2016

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Interferon regulatory factors: critical mediators of human lupus.

Transl Res 2015 Feb 13;165(2):283-95. Epub 2014 Oct 13.

Division of Rheumatology, Department of Immunology, Mayo Clinic, Rochester, Minn. Electronic address:

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http://dx.doi.org/10.1016/j.trsl.2014.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306637PMC
February 2015

Independent modulation of contractile performance by cardiac troponin I Ser43 and Ser45 in the dynamic sarcomere.

J Mol Cell Cardiol 2015 Feb 3;79:264-74. Epub 2014 Dec 3.

Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.yjmcc.2014.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301988PMC
February 2015

Effect of body mass and activity on the metabolic rate and ammonia-N excretion of the spiny lobster Sagmariasus verreauxi during ontogeny.

Comp Biochem Physiol A Mol Integr Physiol 2013 Sep 10;166(1):191-8. Epub 2013 Jun 10.

Institute for Marine and Antarctic Studies, Private Bag 49, Hobart, Tasmania 7001, Australia.

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http://dx.doi.org/10.1016/j.cbpa.2013.06.003DOI Listing
September 2013

The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition.

Appl Environ Microbiol 2013 Sep 12;79(18):5710-20. Epub 2013 Jul 12.

Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1128/AEM.00950-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754162PMC
September 2013

Functional genetic polymorphisms in ILT3 are associated with decreased surface expression on dendritic cells and increased serum cytokines in lupus patients.

Ann Rheum Dis 2013 Apr 17;72(4):596-601. Epub 2012 Aug 17.

Correspondence to Professor Timothy B Niewold, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, 5841 S. Maryland Ave., MC0930 Chicago, IL 60637, USA.

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http://dx.doi.org/10.1136/annrheumdis-2012-202024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910490PMC
April 2013

BIO::Phylo-phyloinformatic analysis using perl.

BMC Bioinformatics 2011 Feb 27;12:63. Epub 2011 Feb 27.

School of Biological Sciences, University of Reading, UK.

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http://dx.doi.org/10.1186/1471-2105-12-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056726PMC
February 2011

HIV-1 with predicted CXCR4 genotype identified in clade C from India.

Mol Diagn Ther 2009 ;13(1):19-24

Department of Clinical Virology, Christian Medical College, Vellore, India.

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http://dx.doi.org/10.1007/bf03256311DOI Listing
August 2009

Targeting of myelin protein zero in a spontaneous autoimmune polyneuropathy.

J Immunol 2008 Dec;181(12):8753-60

Department of Neurology, The University of Chicago, Chicago, IL 60637, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745060PMC
http://dx.doi.org/10.4049/jimmunol.181.12.8753DOI Listing
December 2008

Predicting disease outcomes in the clinic.

Authors:
Mark A Jensen

Nat Biotechnol 2008 Jun;26(6):611-2; author reply 6112-3

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http://www.nature.com/articles/nbt0608-611
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http://dx.doi.org/10.1038/nbt0608-611DOI Listing
June 2008

HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report.

Clin Infect Dis 2007 Aug 10;45(4):501-9. Epub 2007 Jul 10.

Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1086/520024DOI Listing
August 2007

HIV-specific probabilistic models of protein evolution.

PLoS One 2007 Jun 6;2(6):e503. Epub 2007 Jun 6.

Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000503PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876811PMC
June 2007

A novel Fc gamma receptor ligand augments humoral responses by targeting antigen to Fc gamma receptors.

Eur J Immunol 2007 Apr;37(4):1139-48

Department of Neurology, University of Chicago, Chicago, IL 60637, USA.

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http://doi.wiley.com/10.1002/eji.200636321
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http://dx.doi.org/10.1002/eji.200636321DOI Listing
April 2007

Coping with viral diversity in HIV vaccine design.

PLoS Comput Biol 2007 Apr;3(4):e75

Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857809PMC
April 2007

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes.

Evol Bioinform Online 2007 Jan 13;2:53-76. Epub 2007 Jan 13.

Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland, New Zealand.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674662PMC
January 2007

Modeling the role of bacteriophage in the control of cholera outbreaks.

Proc Natl Acad Sci U S A 2006 Mar 14;103(12):4652-7. Epub 2006 Mar 14.

Department of Biology, Emory University, Atlanta, GA 30332, USA.

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http://dx.doi.org/10.1073/pnas.0600166103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450226PMC
March 2006

Molecular clock-like evolution of human immunodeficiency virus type 1.

Virology 2004 Nov;329(1):101-8

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, United States.

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http://dx.doi.org/10.1016/j.virol.2004.08.014DOI Listing
November 2004

Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection.

Genetics 2004 Mar;166(3):1155-64

Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195-8070, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470792PMC
http://dx.doi.org/10.1534/genetics.166.3.1155DOI Listing
March 2004

Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy.

AIDS 2004 Mar;18(4):F1-9

BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, the Faculty of Medicine, University of British Columbia, 603-1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6.

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http://dx.doi.org/10.1097/00002030-200403050-00001DOI Listing
March 2004

Predicting HIV-1 coreceptor usage with sequence analysis.

AIDS Rev 2003 Apr-Jun;5(2):104-12

Department of Microbiology, Box 358070, University of Washington School of Medicine, Seattle, WA 98195-8070, USA.

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August 2003

Potential impact of recombination on sitewise approaches for detecting positive natural selection.

Genet Res 2003 Apr;81(2):115-21

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA.

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http://dx.doi.org/10.1017/s0016672303006128DOI Listing
April 2003

Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans.

Genetics 2002 Feb;160(2):493-507

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637-1573, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461959PMC
February 2002

Eicosenoids Modify Experimental Allergic Encephalomyelitis.

Am J Ther 1995 Sep;2(9):711-720

The University of Chicago Department of Neurology, and the Brain Research Institute Chicago, USA.

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http://dx.doi.org/10.1097/00045391-199509000-00020DOI Listing
September 1995