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Nils Gehlenborg, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. U24HG010263 (TAYLOR, JAMES PETER) Sep 21, 2018 - Jun 30, 2023
    NIH/NHGRI
    Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)
    Role: Co-Principal Investigator
  2. OT2OD026677 (GEHLENBORG, NILS) Sep 21, 2018 - Sep 20, 2022
    NIH
    HuBMAP HIVE Tools Component
    Role: Principal Investigator
  3. R00HG007583 (GEHLENBORG, NILS) Aug 18, 2015 - Jul 31, 2018
    NIH/NHGRI
    Visualization of (Epi)Genomic Data for Discovery of Disease-Associated Variants
    Role: Principal Investigator
  4. K99HG007583 (GEHLENBORG, NILS) Jan 1, 2014 - Dec 31, 2015
    NIH/NHGRI
    Visualization of (Epi)Genomic Data for Discovery of Disease-Associated Variants
    Role: Principal Investigator

Bibliographic
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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018 08 24; 19(1):125. PMID: 30143029.
    Citations: 3     Fields:    
  2. Lekschas F, Gehlenborg N. SATORI: a system for ontology-guided visual exploration of biomedical data repositories. Bioinformatics. 2018 04 01; 34(7):1200-1207. PMID: 29186292.
    Citations: 1     Fields:    Translation:HumansAnimals
  3. Nobre C, Gehlenborg N, Coon H, Lex A. Lineage: Visualizing Multivariate Clinical Data in Genealogy Graphs. IEEE Trans Vis Comput Graph. 2019 Mar; 25(3):1543-1558. PMID: 29993603.
    Citations:    Fields:    
  4. Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017 Sep 15; 33(18):2938-2940. PMID: 28645171.
    Citations: 18     Fields:    
  5. Kern M, Lex A, Gehlenborg N, Johnson CR. Interactive visual exploration and refinement of cluster assignments. BMC Bioinformatics. 2017 Sep 12; 18(1):406. PMID: 28899361.
    Citations:    Fields:    Translation:Humans
  6. Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H. HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. IEEE Trans Vis Comput Graph. 2018 01; 24(1):522-531. PMID: 28866592.
    Citations: 2     Fields:    
  7. 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.
    Citations: 2     
  8. Stitz H, Luger S, Streit M, Gehlenborg N. AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research. Comput Graph Forum. 2016 Jun; 35(3):481-490. PMID: 29973745.
    Citations:    
  9. 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.
    Citations:    
  10. 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.
    Citations: 1     Fields:    Translation:Humans
  11. 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.
    Citations: 392     Fields:    Translation:HumansCells
  12. Lex A, Gehlenborg N. Response to "Plotting intersections" by Lentini. Nat Methods. 2015 Apr; 12(4):281. PMID: 25825831.
    Citations:    Fields:    
  13. 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.
    Citations: 59     Fields:    
  14. 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.
    Citations: 3     Fields:    Translation:Humans
  15. 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.
    Citations: 67     Fields:    Translation:HumansCells
  16. 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):884-885. PMID: 25166867.
    Citations: 5     Fields:    Translation:HumansAnimals
  17. 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.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  18. 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.
    Citations: 1     Fields:    
  19. Streit M, Gehlenborg N. Bar charts and box plots. Nat Methods. 2014 Feb; 11(2):117. PMID: 24645191.
    Citations: 6     Fields:    Translation:Humans
  20. 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.
    Citations: 4     Fields:    
  21. 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.
    Citations: 799     Fields:    Translation:Humans
  22. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9. PMID: 23792563.
    Citations: 712     Fields:    Translation:HumansCells
  23. 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.
    Citations: 89     Fields:    Translation:Humans
  24. 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.
    Citations: 1     
  25. 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.
    Citations: 8     Fields:    Translation:Humans
  26. Gehlenborg N, Wong B. Power of the plane. Nat Methods. 2012 Oct; 9(10):935. PMID: 23193562.
    Citations:    Fields:    
  27. Gehlenborg N, Wong B. Into the third dimension. Nat Methods. 2012 Sep; 9(9):851. PMID: 23097778.
    Citations: 4     Fields:    
  28. Gehlenborg N, Wong B. Points of view: Mapping quantitative data to color. Nat Methods. 2012 Aug; 9(8):769. PMID: 23019685.
    Citations: 3     Fields:    Translation:HumansAnimals
  29. 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.
    Citations: 9     
  30. Gehlenborg N, Wong B. Points of view: Integrating data. Nat Methods. 2012 Apr; 9(4):315. PMID: 22563597.
    Citations: 1     Fields:    
  31. Gehlenborg N, Wong B. Points of View: Heat maps Nat Methods. 2012 03; 9(3):213. PMID: 27974286.
    Citations: 1     Fields:    Translation:Humans
  32. Gehlenborg N, Wong B. Points of view: Networks. Nat Methods. 2012 02; 9(2):115. PMID: 22396963.
    Citations: 4     Fields:    
  33. 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.
    Citations: 5     Fields:    Translation:HumansAnimals
  34. 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.
    Citations: 143     Fields:    Translation:Cells
  35. 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.
    Citations: 33     Fields:    
  36. 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.
    Citations: 14     Fields:    
  37. 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.
    Citations: 15     Fields:    
  38. 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.
    Citations: 103     Fields:    Translation:HumansAnimalsCells
  39. 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.
    Citations: 4     Fields:    
  40. 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.
    Citations: 3     Fields:    
  41. 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.
    Citations: 51     Fields:    Translation:AnimalsCells
  42. Dietzsch J, Gehlenborg N, Nieselt K. Mayday--a microarray data analysis workbench. Bioinformatics. 2006 Apr 15; 22(8):1010-2. PMID: 16500939.
    Citations: 22     Fields:    
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.