Nils Gehlenborg

Nils Gehlenborg

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Nils Gehlenborg

Nils Gehlenborg

Publications by authors named "Nils Gehlenborg"

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38Publications

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Visual Pattern-Driven Exploration of Big Data.

2018 Int Symp Big Data Vis Immers Analyt (BDVA) (2018) 2018 Oct 15;2018. Epub 2018 Nov 15.

Harvard University, Cambridge, USA.

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http://dx.doi.org/10.1109/BDVA.2018.8534028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687327PMC
October 2018

SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

Bioinformatics 2018 04;34(7):1200-1207

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031061PMC
April 2018

METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE.

Pac Symp Biocomput 2016 ;21:180-182

Department of Biomedical Informatics, Harvard Medical School, Boston, MA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167531PMC
February 2018

UpSetR: an R package for the visualization of intersecting sets and their properties.

Bioinformatics 2017 Sep;33(18):2938-2940

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870712PMC
September 2017

Interactive visual exploration and refinement of cluster assignments.

BMC Bioinformatics 2017 Sep 12;18(1):406. Epub 2017 Sep 12.

Scientific Computing and Imaging Institute, University of Utah, 72 Sout Central Campus Drive, Salt Lake City, 84112, USA.

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http://dx.doi.org/10.1186/s12859-017-1813-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596943PMC
September 2017

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

Response to "Plotting intersections" by Lentini.

Nat Methods 2015 Apr;12(4):281

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3331DOI Listing
April 2015

Guided visual exploration of genomic stratifications in cancer.

Nat Methods 2014 Sep;11(9):884-885

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196637PMC
September 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Bar charts and box plots.

Nat Methods 2014 Feb;11(2):117

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February 2014

LineUp: visual analysis of multi-attribute rankings.

IEEE Trans Vis Comput Graph 2013 Dec;19(12):2277-86

Johannes Kepler University Linz.

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http://dx.doi.org/10.1109/TVCG.2013.173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198697PMC
December 2013

The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:70. Epub 2013 Mar 18.

Harvard School of Public Health, Biostatistics, Boston, MA, USA ; Harvard Stem Cell Institute, Cambridge, MA, USA.

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December 2013

Nozzle: a report generation toolkit for data analysis pipelines.

Bioinformatics 2013 Apr 17;29(8):1089-91. Epub 2013 Feb 17.

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624805PMC
April 2013

Power of the plane.

Nat Methods 2012 Oct;9(10):935

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October 2012

Into the third dimension.

Nat Methods 2012 Sep;9(9):851

Harvard Medical School, USA.

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September 2012

Points of view: Mapping quantitative data to color.

Nat Methods 2012 Aug;9(8):769

Harvard Medical School, USA.

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August 2012

Points of view: Integrating data.

Nat Methods 2012 Apr;9(4):315

Harvard Medical School, USA.

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April 2012

Points of View: Heat maps

Nat Methods 2012 03;9(3):213

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March 2012

Points of view: Networks.

Nat Methods 2012 02;9(2):115

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February 2012

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

Bioinformatics 2012 Jan 20;28(2):246-53. Epub 2011 Nov 20.

Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btr634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259436PMC
January 2012

The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.

Database (Oxford) 2009 17;2009:bap011. Epub 2009 Sep 17.

Institute for Systems Biology, Seattle, WA 98103, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, I-Bio Program & Department of Chemical Engineering, POSTECH, Pohang, 790-784, Republic of Korea, McLaughlin Research Institute, Great Falls, MT 59405 and Department of Pathology, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/database/bap011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790306PMC
September 2009

Probabilistic retrieval and visualization of biologically relevant microarray experiments.

Bioinformatics 2009 Jun;25(12):i145-53

Department of Information and Computer Science, Helsinki Institute for Information Technology, Helsinki University of Technology, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btp215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687969PMC
June 2009

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.

Mol Cell Proteomics 2008 Nov 29;7(11):2138-50. Epub 2008 May 29.

Institute of Molecular Systems Biology and section signCompetence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, Wolfgang-Pauli-Str. 16, 8093 Zurich, Switzerland.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M700498-MCP2
Publisher Site
http://dx.doi.org/10.1074/mcp.M700498-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577211PMC
November 2008

Ten simple rules for organizing a scientific meeting.

PLoS Comput Biol 2008 Jun 27;4(6):e1000080. Epub 2008 Jun 27.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1000080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367436PMC
June 2008

Mayday--a microarray data analysis workbench.

Bioinformatics 2006 Apr 24;22(8):1010-2. Epub 2006 Feb 24.

Center for Bioinformatics Tübingen, Department of Information and Cognitive Sciences, University of Tübingen, Sand 14, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btl070DOI Listing
April 2006