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Items: 39

1.

HiGlass: web-based visual exploration and analysis of genome interaction maps.

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.

Genome Biol. 2018 Aug 24;19(1):125. doi: 10.1186/s13059-018-1486-1.

2.

Lineage: Visualizing Multivariate Clinical Data in Genealogy Graphs.

Nobre C, Gehlenborg N, Coon H, Lex A.

IEEE Trans Vis Comput Graph. 2018 Mar 6. doi: 10.1109/TVCG.2018.2811488. [Epub ahead of print]

PMID:
29993603
3.

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

Lekschas F, Gehlenborg N.

Bioinformatics. 2018 Apr 1;34(7):1200-1207. doi: 10.1093/bioinformatics/btx739.

4.

Interactive visual exploration and refinement of cluster assignments.

Kern M, Lex A, Gehlenborg N, Johnson CR.

BMC Bioinformatics. 2017 Sep 12;18(1):406. doi: 10.1186/s12859-017-1813-7.

5.

HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.

Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):522-531. doi: 10.1109/TVCG.2017.2745978. Epub 2017 Aug 29.

6.

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

Conway JR, Lex A, Gehlenborg N.

Bioinformatics. 2017 Sep 15;33(18):2938-2940. doi: 10.1093/bioinformatics/btx364.

7.

METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE.

Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS.

Pac Symp Biocomput. 2016;21:180-182. No abstract available.

8.

From Visual Exploration to Storytelling and Back Again.

Gratzl S, Lex A, Gehlenborg N, Cosgrove N, Streit M.

Comput Graph Forum. 2016 Jun;35(3):491-500. Epub 2016 Jul 4.

9.

AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research.

Stitz H, Luger S, Streit M, Gehlenborg N.

Comput Graph Forum. 2016 Jun;35(3):481-490. doi: 10.1111/cgf.12924. Epub 2016 Jul 4.

10.

Domino: Extracting, Comparing, and Manipulating Subsets Across Multiple Tabular Datasets.

Gratzl S, Gehlenborg N, Lex A, Pfister H, Streit M.

IEEE Trans Vis Comput Graph. 2014 Dec;20(12):2023-32. doi: 10.1109/TVCG.2014.2346260.

11.

UpSet: Visualization of Intersecting Sets.

Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H.

IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92. doi: 10.1109/TVCG.2014.2346248.

12.

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

Cancer Genome Atlas Research Network, 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 Jr, 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 Jr, 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.

N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

13.

Response to "Plotting intersections" by Lentini.

Lex A, Gehlenborg N.

Nat Methods. 2015 Apr;12(4):281. doi: 10.1038/nmeth.3331. No abstract available.

PMID:
25825831
14.

Characterization of HPV and host genome interactions in primary head and neck cancers.

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; Cancer Genome Atlas Network.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13.

15.

Guided visual exploration of genomic stratifications in cancer.

Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg N.

Nat Methods. 2014 Sep;11(9):884-885. doi: 10.1038/nmeth.3088. No abstract available.

16.

Comparative analysis of metazoan chromatin organization.

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.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

17.

Ontologies in biological data visualization.

Carpendale S, Chen M, Evanko D, Gehlenborg N, Gorg C, Hunter L, Rowland F, Storey MA, Strobelt H.

IEEE Comput Graph Appl. 2014 Mar-Apr;34(2):8-15. doi: 10.1109/MCG.2014.33.

PMID:
24808195
18.

Bar charts and box plots.

Streit M, Gehlenborg N.

Nat Methods. 2014 Feb;11(2):117. No abstract available.

PMID:
24645191
19.

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

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.

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

PMID:
24303302
20.

LineUp: visual analysis of multi-attribute rankings.

Gratzl S, Lex A, Gehlenborg N, Pfister H, Streit M.

IEEE Trans Vis Comput Graph. 2013 Dec;19(12):2277-86. doi: 10.1109/TVCG.2013.173.

21.

Diverse mechanisms of somatic structural variations in human cancer genomes.

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.

Cell. 2013 May 9;153(4):919-29. doi: 10.1016/j.cell.2013.04.010. Erratum in: Cell. 2014 Jun 19;157(7):1736.

22.

Nozzle: a report generation toolkit for data analysis pipelines.

Gehlenborg N, Noble MS, Getz G, Chin L, Park PJ.

Bioinformatics. 2013 Apr 15;29(8):1089-91. doi: 10.1093/bioinformatics/btt085. Epub 2013 Feb 17.

23.

Power of the plane.

Gehlenborg N, Wong B.

Nat Methods. 2012 Oct;9(10):935. No abstract available.

PMID:
23193562
24.

Into the third dimension.

Gehlenborg N, Wong B.

Nat Methods. 2012 Sep;9(9):851. No abstract available.

PMID:
23097778
25.

Points of view: Mapping quantitative data to color.

Gehlenborg N, Wong B.

Nat Methods. 2012 Aug;9(8):769. No abstract available.

PMID:
23019685
26.

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization.

Lex A, Streit M, Schulz HJ, Partl C, Schmalstieg D, Park PJ, Gehlenborg N.

Comput Graph Forum. 2012 Jun;31(33):1175-1184. Epub 2012 Jun 25.

27.

Points of view: Integrating data.

Gehlenborg N, Wong B.

Nat Methods. 2012 Apr;9(4):315. No abstract available.

PMID:
22563597
28.

Points of view: Networks.

Gehlenborg N, Wong B.

Nat Methods. 2012 Feb;9(2):115. No abstract available.

PMID:
22396963
29.

Points of View: Heat maps

Gehlenborg N, Wong B.

Nat Methods. 2012 Mar;9(3):213. No abstract available.

PMID:
27974286
30.

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

Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.

Bioinformatics. 2012 Jan 15;28(2):246-53. doi: 10.1093/bioinformatics/btr634. Epub 2011 Nov 20.

31.

Visualization of omics data for systems biology.

Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC.

Nat Methods. 2010 Mar;7(3 Suppl):S56-68. doi: 10.1038/nmeth.1436. Review.

PMID:
20195258
32.

Visualizing biological data-now and in the future.

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.

Nat Methods. 2010 Mar;7(3 Suppl):S2-4. doi: 10.1038/nmeth.f.301.

PMID:
20195254
33.

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

Gehlenborg N, Hwang D, Lee IY, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, Dearmond SJ, Carlson GA, Hood L.

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

34.

Probabilistic retrieval and visualization of biologically relevant microarray experiments.

Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.

Bioinformatics. 2009 Jun 15;25(12):i145-53. doi: 10.1093/bioinformatics/btp215.

35.

A systems approach to prion disease.

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.

Mol Syst Biol. 2009;5:252. doi: 10.1038/msb.2009.10. Epub 2009 Mar 24.

36.

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.

Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L.

Bioinformatics. 2009 Mar 1;25(5):682-3. doi: 10.1093/bioinformatics/btp005. Epub 2009 Jan 6.

37.

Ten simple rules for organizing a scientific meeting.

Corpas M, Gehlenborg N, Janga SC, Bourne PE.

PLoS Comput Biol. 2008 Jun 27;4(6):e1000080. doi: 10.1371/journal.pcbi.1000080. No abstract available.

38.

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

Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B.

Mol Cell Proteomics. 2008 Nov;7(11):2138-50. doi: 10.1074/mcp.M700498-MCP200. Epub 2008 May 29.

39.

Mayday--a microarray data analysis workbench.

Dietzsch J, Gehlenborg N, Nieselt K.

Bioinformatics. 2006 Apr 15;22(8):1010-2. Epub 2006 Feb 24.

PMID:
16500939

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