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profileNils Gehlenborg, Ph.D.

TitleAssistant Professor of Biomedical Informatics
InstitutionHarvard Medical School
DepartmentBiomedical Informatics
AddressHarvard Medical School
Countway Lib CBMI
10 Shattuck St
Boston MA 02115
Phone617/432-1535
Fax617/432-0693
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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Conway JR, Lex A, Gehlenborg N. UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties. Bioinformatics. 2017 Jun 22. PMID: 28645171.
    View in: PubMed
  2. Gratzl S, Lex A, Gehlenborg N, Cosgrove N, Streit M. From Visual Exploration to Storytelling and Back Again. Comput Graph Forum. 2016 Jun; 35(3):491-500. PMID: 27942091.
    View in: PubMed
  3. Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS. METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:180-2. PMID: 26776184.
    View in: PubMed
  4. Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS. METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:180-182. PMID: 28004011.
    View in: PubMed
  5. Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. PMID: 26061751; PMCID: PMC4530011 [Available on 12/25/15].
  6. Lex A, Gehlenborg N. Response to "Plotting intersections" by Lentini. Nat Methods. 2015 Apr; 12(4):281. PMID: 25825831.
    View in: PubMed
  7. Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H. UpSet: Visualization of Intersecting Sets. IEEE Trans Vis Comput Graph. 2014 Dec; 20(12):1983-92. PMID: 26356912; PMCID: PMC4720993.
  8. Gratzl S, Gehlenborg N, Lex A, Pfister H, Streit M. Domino: Extracting, Comparing, and Manipulating Subsets Across Multiple Tabular Datasets. IEEE Trans Vis Comput Graph. 2014 Dec; 20(12):2023-32. PMID: 26356916; PMCID: PMC4719182.
  9. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15544-9. PMID: 25313082; PMCID: PMC4217452.
  10. Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg N. Guided visual exploration of genomic stratifications in cancer. Nat Methods. 2014 Sep; 11(9):884-5. PMID: 25166867; PMCID: PMC4196637.
  11. Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756; PMCID: PMC4227084.
  12. Carpendale S, Chen M, Evanko D, Gehlenborg N, Gorg C, Hunter L, Rowland F, Storey MA, Strobelt H. Ontologies in biological data visualization. IEEE Comput Graph Appl. 2014 Mar-Apr; 34(2):8-15. PMID: 24808195.
    View in: PubMed
  13. Streit M, Gehlenborg N. Bar charts and box plots. Nat Methods. 2014 Feb; 11(2):117. PMID: 24645191.
    View in: PubMed
  14. Gratzl S, Lex A, Gehlenborg N, Pfister H, Streit M. LineUp: visual analysis of multi-attribute rankings. IEEE Trans Vis Comput Graph. 2013 Dec; 19(12):2277-86. PMID: 24051794; PMCID: PMC4198697.
  15. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849; PMCID: PMC3919969.
  16. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9. PMID: 23792563; PMCID: PMC3771322.
  17. Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013 May 09; 153(4):919-29. PMID: 23663786; PMCID: PMC3704973.
  18. Ho Sui S, Merrill E, Gehlenborg N, Haseley P, Sytchev I, Park R, Rocca-Serra P, Corlosquet S, Gonzalez-Beltran A, Maguire E, Hofmann O, Park P, Das S, Sansone SA, Hide W. 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; 2013:70. PMID: 24303302.
    View in: PubMed
  19. Gehlenborg N, Noble MS, Getz G, Chin L, Park PJ. Nozzle: a report generation toolkit for data analysis pipelines. Bioinformatics. 2013 Apr 15; 29(8):1089-91. PMID: 23419376; PMCID: PMC3624805.
  20. Gehlenborg N, Wong B. Power of the plane. Nat Methods. 2012 Oct; 9(10):935. PMID: 23193562.
    View in: PubMed
  21. Gehlenborg N, Wong B. Into the third dimension. Nat Methods. 2012 Sep; 9(9):851. PMID: 23097778.
    View in: PubMed
  22. Gehlenborg N, Wong B. Points of view: Mapping quantitative data to color. Nat Methods. 2012 Aug; 9(8):769. PMID: 23019685.
    View in: PubMed
  23. Lex A, Streit M, Schulz HJ, Partl C, Schmalstieg D, Park PJ, Gehlenborg N. StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization. Comput Graph Forum. 2012 Jun; 31(33):1175-1184. PMID: 27942089.
    View in: PubMed
  24. Gehlenborg N, Wong B. Points of view: Integrating data. Nat Methods. 2012 Apr; 9(4):315. PMID: 22563597.
    View in: PubMed
  25. Gehlenborg N, Wong B. Points of View: Heat maps Nat Methods. 2012 03; 9(3):213. PMID: 27974286.
    View in: PubMed
  26. Gehlenborg N, Wong B. Points of view: Networks. Nat Methods. 2012 02; 9(2):115. PMID: 22396963.
    View in: PubMed
  27. Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S. Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics. 2012 Jan 15; 28(2):246-53. PMID: 22106335; PMCID: PMC3259436.
  28. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods. 2010 Mar; 7(3 Suppl):S56-68. PMID: 20195258.
    View in: PubMed
  29. O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B. Visualizing biological data-now and in the future. Nat Methods. 2010 Mar; 7(3 Suppl):S2-4. PMID: 20195254.
    View in: PubMed
  30. Gehlenborg N, Hwang D, Lee IY, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, Dearmond SJ, Carlson GA, Hood L. The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases. Database (Oxford). 2009; 2009:bap011. PMID: 20157484.
    View in: PubMed
  31. Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S. Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics. 2009 Jun 15; 25(12):i145-53. PMID: 19477980; PMCID: PMC2687969.
  32. Hwang D, Lee IY, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D, Price ND, Hohmann JG, Dearmond SJ, Carlson GA, Hood LE. A systems approach to prion disease. Mol Syst Biol. 2009; 5:252. PMID: 19308092; PMCID: PMC2671916.
  33. Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L. Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics. 2009 Mar 01; 25(5):682-3. PMID: 19129212; PMCID: PMC2720692.
  34. Corpas M, Gehlenborg N, Janga SC, Bourne PE. Ten simple rules for organizing a scientific meeting. PLoS Comput Biol. 2008 Jun 27; 4(6):e1000080. PMID: 18584020; PMCID: PMC2367436.
  35. Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics. 2008 Nov; 7(11):2138-50. PMID: 18511481; PMCID: PMC2577211.
  36. Dietzsch J, Gehlenborg N, Nieselt K. Mayday--a microarray data analysis workbench. Bioinformatics. 2006 Apr 15; 22(8):1010-2. PMID: 16500939.
    View in: PubMed
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