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Preprints

JR Conway, A Lex, N Gehlenborg. “UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties” bioRxiv 120600; doi: https://doi.org/10.1101/120600 (2017)

J Fan, D Fan, K Slowikowski, N Gehlenborg, P Kharchenko. “UBiT2: a client-side web-application for gene expression data analysis” bioRxiv 118992; doi: https://doi.org/10.1101/118992 (2017)

M Kern, A Lex, N Gehlenborg, CR Johnson. “Interactive Visual Exploration And Refinement Of Cluster Assignments” bioRxiv 123844; doi: https://doi.org/10.1101/123844 (2017)

P Kerpedjiev, N Abdennur, F Lekschas, C McCallum, K Dinkla, H Strobelt, JM Luber, SB Ouellette, A Ahzir, N Kumar, J Hwang, BH Alver, H Pfister, LA Mirny, PJ Park, N Gehlenborg. “HiGlass: Web-based Visual Comparison And Exploration Of Genome Interaction Maps” bioRxiv 121889; doi: https://doi.org/10.1101/121889 (2017)

F Lekschas, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister. “HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples” bioRxiv 123588; doi: https://doi.org/10.1101/123588 (2017)

F Lekschas, N Gehlenborg. “SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories” bioRxiv 046755; doi: https://doi.org/10.1101/046755 (2017)

C Nobre, N Gehlenborg, H Coon, A Lex. “Lineage: Visualizing Multivariate Clinical Data in Genealogy Graphs” bioRxiv 128579; doi: https://doi.org/10.1101/128579 (2017)

2017

The Cancer Genome Atlas Research Network (incl. N Gehlenborg). “Integrated genomic characterization of oesophageal carcinomaNature 541(7636):169-175 (2017)

The Cancer Genome Atlas Research Network (incl. N Gehlenborg). “Integrated genomic and molecular characterization of cervical cancerNature 543(7645):378-384 (2017)

Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB; Cancer Genome Atlas Research Network., Weinstein JN, Zhang J, Akbani R, Levine DA. “Integrated Molecular Characterization of Uterine CarcinosarcomaCancer Cell 31(3):411-423 (2017)

Fishbein L, Leshchiner I, Walter V, Danilova L, Robertson AG, Johnson AR, Lichtenberg TM, Murray BA, Ghayee HK, Else T, Ling S, Jefferys SR, de Cubas AA, Wenz B, Korpershoek E, Amelio AL, Makowski L, Rathmell WK, Gimenez-Roqueplo AP, Giordano TJ, Asa SL, Tischler AS; Cancer Genome Atlas Research Network., Pacak K, Nathanson KL, Wilkerson MD. “Comprehensive Molecular Characterization of Pheochromocytoma and ParagangliomaCancer Cell Feb 13;31(2):181-193 (2017)

2016

Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS.. “Methods to enhance the reproducibility of precision medicinePac Symp Biocomput 21:180-182 (2016)

Campbell, JD, Alexandrov, A, Kim, J, Wala, J, Berger, AH, Pedamallu, CS, Shukla, SA, Guo, G, Brooks, AN, Murray, BA, Imielinski, M, Hu, X, Ling, S, Akbani, R, Rosenberg, M, Cibulskis, C, Ramachandran, A, Collisson, EA, Kwiatkowski, DJ, Lawrence, MS, Weinstein, JN, Verhaak, RGW, Wu, CJ, Hammerman, PS, Cherniack, AD, Getz, G, Cancer Genome Atlas Research Network (incl. N Gehlenborg), Artyomov, MN, Schreiber, R, Govindan, R, Meyerson, M.. “Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomasNat Genet 48, 607–616 (2016)

S Gratzl, A Lex, N Gehlenborg, N Cosgrove, M Streit. “From Visual Exploration to Storytelling and Back AgainComputer Graphics Forum 35:491–500 (2016)

H Stitz, S Luger, M Streit, N Gehlenborg. “AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical ResearchComputer Graphics Forum 35:481-490 (2016)

Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, incl. N Gehlenborg, Noushmehr H, Iavarone A, Verhaak RG. “Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse GliomaCell 164:550-563 (2016)

2015

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade GliomasNew England Journal of Medicine 372:2481-2498 (2015)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive Genomic Characterization of Head and Neck Squamous Cell CarcinomasNature 517:576-582 (2015)

The Cancer Genome Atlas Research Network, incl. N Gehlenborg. “The Molecular Taxonomy of Primary Prostate CancerCell 163:1011-25 (2015)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Genomic Classification of Cutaneous MelanomaCell 161:1681-96 (2015)

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, incl. Nils Gehlenborg Perou CM. “Comprehensive Molecular Portraits of Invasive Lobular Breast CancerCell 163:506-519 (2015)

2014

M Parfenov*, CS Pedamallu*, N Gehlenborg, SS Freeman, L Danilova, CA Bristow, S Lee, A Hadjipanayis, E Ivanova, MD Wilkerson, A Protopopov, L Yang, S Seth, X Song, J Tang, X Ren, J Zhang, A Pantazi, N Santoso, AW Xu, H Mahadeshwar, DA Wheeler, RI Haddad, J Jung, AI Ojesina, N Isaeva, WG Yarbrough, DN Hayes, JR Grandis, AK El-Naggar, M Meyerson, PJ Park, L Chin, JG Seidman, PS Hammerman**, R Kucherlapati**, TCGA Network. “Characterization of HPV and Host-Genome Interactions in Primary Head and Neck CancersProceedings of the National Academy of Sciences USA (2014)

M Streit*, A Lex*, S Gratzl, C Partl, D Schmalstieg, H Pfister, PJ Park** and N Gehlenborg**. “Guided Visual Exploration of Genomic Stratifications in CancerNature Methods 11:884–885 (2014)

A Lex and N Gehlenborg. “Points of View: Sets and IntersectionsNature Methods 11(8):779 (2014)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive molecular profiling of lung adenocarcinomaNature (2014)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive Molecular Characterization of Gastric AdenocarcinomaNature (2014)

JWK Ho, YL Jung, Tao Liu, BH Alver, S Lee, K Ikegami, K-A Sohn, A Minoda, MY Tolstorukov, A Appert, SCJ Parker, T Gu, A Kundaje, NC Riddle, E Bishop, TA Egelhofer, SS Hu, AA Alekseyenko, A Rechtsteiner, D Asker, JA Belsky, SK Bowman, QB Chen, RAJ Chen, DS Day, Y Dong, AC Dose, X Duan, CB Epstein, S Ercan, EA Feingold, F Ferrari, J M Garrigues, N Gehlenborg, PJ Good, P Haseley, D He, M Herrmann, MM Hoffman, TE Jeffers, PV Kharchenko, PK Zwierz, CV Kotwaliwale, N Kumar, SA Langley, EN Larschan, I Latorre, MW Libbrecht, X Lin, R Park, MJ Pazin, HN Pham, A Plachetka, B Qin, YB Schwartz, N Shoresh, P Stempor, A Vielle, C Wang, CM Whittle, H Xue, RE Kingston, JH Kim, BE Bernstein,AF Dernburg, V Pirrotta, MI Kuroda, WS Noble, TD Tullius, M Kellis, DM MacAlpine, S Strome, SCR Elgin, XS Liu, JD Lieb, J Ahringer, GH Karpen and PJ Park. “Comparative analysis of metazoan chromatin organizationNature 512:449–452 (2014)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive Molecular Characterization of Urothelial Bladder CarcinomaNature 507:315–322 (2014)

M Streit and N Gehlenborg. “Points of View: Bar Charts and Box PlotsNature Methods 11(2):117 (2014)

A Lex, N Gehlenborg, H Strobelt, R Vuillemot and H Pfister. “UpSet: Visualization of Intersecting SetsIEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14) (2014)

S Carpendale, M Chen, D Evanko, N Gehlenborg, C Görg, L Hunter, F Rowland, M-A Storey, H Strobelt. “Ontologies in Biological Data VisualizationIEEE Computer Graphics and Applications 34(2):8-15 (2014)

S Gratzl, N Gehlenborg, A Lex, H Pfister and M Streit. “Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular DatasetsIEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14) (2014)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Integrated Genomic Characterization of Papillary Thyroid CarcinomaCell 159:676–690 (2014)

KA Hoadley*, C Yau*, DM Wolf*, AD Cherniack*, D Tamborero, S Ng, MDM Leiserson, B Niu, MD McLellan, V Uzunangelov, J Zhang, C Kandoth, R Akbani, H Shen, L Omberg, A Chu, AA Margolin, LJ van’t Veer, N Lopez-Bigas, PW Laird, BJ Raphael, L Ding, AG Robertson, LA Byers, GB Mills, JN Weinstein, C Van Waes, Z Chen, EA Collisson, The Cancer Genome Atlas Network incl. N Gehlenborg, CC Benz, CM Perou, JM Stuart. “Multi-platform integration of 12 cancer types reveals cell-of-origin classes with distinct molecular signaturesCell 158:929–944 (2014)

2013

J de Ridder*, T Abeel*, M Michaut, VP Satagopam and N Gehlenborg. “Don’t Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator” Workshop Report, PLoS Computational Biology 9(1):e1002834 (2013)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive molecular characterization of clear cell renal cell carcinomaNature 499:43–49 (2013)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “The Cancer Genome Atlas Pan-Cancer analysis projectNature Genetics 45:1113–1120 (2013)

S Gratzl, A Lex, N Gehlenborg, HP Pfister and M Streit. “LineUp: Visual Analysis of Multi-Attribute RankingsIEEE Transactions on Visualization and Computer Graphics 19:2277-2286 (2013)

L Yang, LJ Luquette, N Gehlenborg, R Xi, PS Haseley, C-H Hsieh, C Zhang, X Ren, A Protopopov, L Chin, R Kucherlapati, C Lee, PJ Park and The Cancer Genome Atlas Network. “Diverse mechanisms of somatic structural variations in human cancer genomesCell 153:919-929 (2013)

CW Brennan, RG Verhaak, A McKenna, B Campos, H Noushmehr, SR Salama, S Zheng, D Chakravarty, JZ Sanborn, SH Berman, R Beroukhim, B Bernard, CJ Wu, G Genovese, I Shmulevich, J Barnholtz-Sloan, L Zou, R Vegesna, SA Shukla, G Ciriello, WK Yung, W Zhang, C Sougnez, T Mikkelsen, K Aldape, DD Bigner, EG Van Meir, M Prados, A Sloan, KL Black, J Eschbacher, G Finocchiaro, W Friedman, DW Andrews, A Guha, M Iacocca, BP O’Neill, G Foltz, J Myers, DJ Weisenberger, R Penny, R Kucherlapati, CM Perou, DN Hayes, R Gibbs, M Marra, GB Mills, E Lander, P Spellman, R Wilson, C Sander, J Weinstein, M Meyerson, S Gabriel, PW Laird, D Haussler, G Getz, L Chin, The Cancer Genome Atlas Network, incl. N Gehlenborg. “The somatic genomic landscape of glioblastomaCell 155:462-77 (2013)

N Gehlenborg, MS Noble, G Getz, L Chin and PJ Park. “Nozzle: a report generation toolkit for data analysis pipelinesBioinformatics 29:1089-1091 (2013)

S Ho Sui, E Merrill, N Gehlenborg, P Haseley, I Sytchev, R Park, P Rocca-Serra, S Corlosquet, A Gonzalez-Beltran, E Maguire, O Hofmann, PJ Park, S Das, SA Sansone, W Hide. “The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA frameworkAMIA Summits Translational Science Proceedings 2013:70 (2013)

2012

N Gehlenborg and B Wong. “Points of View: Into the Third DimensionNature Methods 9(9):851 (2012)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive genomic characterization of squamous cell lung cancersNature 489:519–525 (2012)

N Gehlenborg and B Wong. “Points of View: Power of the PlaneNature Methods 9(10):935 (2012)

N Gehlenborg and B Wong. “Points of View: NetworksNature Methods 9(2):115 (2012)

N Gehlenborg and B Wong. “Points of View: Integrating DataNature Methods 9(4):315 (2012)

N Gehlenborg and B Wong. “Points of View: Heat mapsNature Methods 9(3):213 (2012)

N Gehlenborg and B Wong. “Points of View: Mapping Quantitative Data to ColorNature Methods 9(8):769 (2012)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive molecular characterization of human colon and rectal cancerNature 487:330–337 (2012)

The Cancer Genome Atlas Network, incl. N Gehlenborg. “Comprehensive molecular portraits of human breast tumoursNature 490:61–70 (2012) (2012)

A Lex, M Streit, H-J Schulz, C Partl, D Schmalstieg, PJ Park, N Gehlenborg. “StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype CharacterizationComputer Graphics Forum 31:1175-1184 (2012). Proceedings of EuroVis Conference 2012 (2012)

J Caldas*, N Gehlenborg, E Kettunen, A Faisal, M Rönty, AG Nicholson, S Knuutila, A Brazma and S Kaski. “ Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural MesotheliomaBioinformatics 28(2):246-253 (2012)

2010

N Gehlenborg. “Visualization and Exploration of Transcriptomics DataPhD Thesis, University of Cambridge, United Kingdom (2010)

N Gehlenborg, SI O’Donoghue, NS Baliga, A Goesmann, MA Hibbs, H Kitano, O Kohlbacher, H Neuweger, R Schneider, D Tenenbaum and AC Gavin. “Visualization of Omics Data for Systems BiologyNature Methods 7(3):S56-S68 (2010)

SI O’Donoghue, AC Gavin, N Gehlenborg, DS Goodsell, JK Heriche, CB Nielsen, C North, AJ Olson, JB Procter, DW Shattuck, T Walter and B Wong. “Visualizing biological data – now and in the futureNature Methods 7(3):S2-S4 (2010)

J Peltonen, H Aidos, N Gehlenborg, A Brazma and S Kaski. “An Information Retrieval Perspective on Visualization of Gene Expression Data with Ontological Annotation” In Proceedings of the IEEE 2010 International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2010), 2178-2181 (2010)

2009

D Hwang*, IY Lee*, H Yoo*, N Gehlenborg, J Cho, B Petritis, D Baxter, R Pitstick, R Young, D Spicer, N Price, JG Hohmann, SJ DeArmond, GA Carlson and LE Hood. “A Systems Approach to Prion DiseaseMolecular Systems Biology 5:252 (2009)

N Gehlenborg, D Hwang*, IY Lee*, H Yoo, B Petritis, D Baxter, R Pitstick, B Marzolf, SJ DeArmond, GA Carlson and LE Hood. “The Prion Disease Database: A Comprehensive Transcriptome Resource for Systems Biology Research in Prion DiseasesDatabase 2009:bap011 (2009)

N Gehlenborg and A Brazma. “Visualization of Large Microarray Experiments with Space MapsBMC Bioinformatics 10(Suppl 13):O7 (2009)

J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski. “Probabilistic Retrieval and Visualization of Biologically Relevant Microarray ExperimentsBMC Bioinformatics 10(Suppl 13):P1 (2009)

N Gehlenborg, W Yan, I Lee, H Yoo, K Nieselt, D Hwang, R Aebersold, L Hood. “Prequips – An Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics DataBioinformatics 25(5):682-683 (2009)

J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski. “Probabilistic retrieval and visualization of biologically relevant microarray experimentsBioinformatics 25(12):i145-i153 (2009)

2008

A Schmidt, N Gehlenborg, B Bodenmiller, LN Mueller, D Campbell, M Mueller, R Aebersold and B Domon. “An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixturesMolecular & Cellular Proteomics 7:2138-2150 (2008)

M Corpas, N Gehlenborg, S Chandra Janga and PE Bourne. “Ten Simple Rules for Organizing a Scientific MeetingPLoS Computational Biology 4(6):e1000080 (2008)

L Peixoto, N Gehlenborg and S Chandra Janga (Eds.). “Highlights from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)BMC Bioinformatics 9(Suppl 10):I1 (2008)

2007

N Gehlenborg, M Corpas and S Chandra Janga (Eds.). “Highlights from the Third International Society for Computational Biology (ISCB) Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)BMC Bioinformatics 8(Suppl 8):I1 (2007)

2006

N Gehlenborg. “Visualization and Integration of Liquid Chromatography/Mass Spectrometry Proteomics DataDiplomarbeit (eq. Masters Thesis), University of Tübingen, Germany (2006)

J Dietzsch*, N Gehlenborg* and K Nieselt. “Mayday – A Microarray Data Analysis WorkbenchBioinformatics 22(8):1010-1012 (2006)

2005

N Gehlenborg. “Visualisierung für DNA-Chip-Analysen” in D. Spath, K. Haasis and D. Klumpp (Eds.), Aktuelle Trends in der Softwareforschung (Vol. 3), 259-270, IRB Fraunhofer Verlag, Stuttgart, Germany (2005)

N Gehlenborg, J Dietzsch and K Nieselt. “A Framework for Visualization of Microarray Data and Integrated Meta InformationInformation Visualization 4(3):164-175 (2005)

2003

N Gehlenborg. “Mayday – Microarray Data AnalysisStudienarbeit (eq. Bachelors Thesis), University of Tübingen, Germany (2003)