Publications

For my most recent work please see my Google Scholar profile and bioRxiv.

Peer-Reviewed Journal & Conference Papers

The Cancer Genome Atlas Network, incl. N Gehlenborg, “Integrated Genomic Characterization of Papillary Thyroid Carcinoma”. Cell 159:676–690 (2014). Featured in Clinical Sequencing News, Deutsches Ärtzeblatt, Cancer Research UK News.

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 Cancers”, Proceedings of the National Academy of Sciences USA 2014. Published online ahead of print.

A Lex, N Gehlenborg, H Strobelt, R Vuillemot and H Pfister, “UpSet: Visualization of Intersecting Sets”. To appear in IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14).

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

M Streit*, A Lex*, S Gratzl, C Partl, D Schmalstieg, H Pfister, PJ Park** and N Gehlenborg**, “Guided Visual Exploration of Genomic Stratifications in Cancer“. Nature Methods 11:884–885 (2014). Featured in GenomeWeb, Harvard Medical School News, The Crimson, Harvard SEAS News, JKU Campus News.

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 organization“. Nature 512:449–452 (2014).
Featured in New York Times, The Scientist.

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 signatures”, Cell 158:929–944 (2014).

The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive Molecular Characterization of Gastric Adenocarcinoma”, Nature. Published online ahead of print.

The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular profiling of lung adenocarcinoma“, Nature. Published online ahead of print.

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

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

S Gratzl, A Lex, N Gehlenborg, HP Pfister and M Streit, “LineUp: Visual Analysis of Multi-Attribute Rankings“, IEEE Transactions on Visualization and Computer Graphics 19:2277-2286 (2013). IEEE InfoVis 2013 Best Paper Award | Featured in IEEE Computing NowHarvard SEAS NewsForbes, Scientific Computing, Der Standard

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 glioblastoma“, Cell 155:462-77 (2013).

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

The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular characterization of clear cell renal cell carcinoma“, Nature 499:43–49 (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 genomes, Cell 153:919-929 (2013).

N Gehlenborg, MS Noble, G Getz, L Chin and PJ Park, “Nozzle: a report generation toolkit for data analysis pipelines“, Bioinformatics 29:1089-1091 (2013). Featured in GenomeWeb Bioinformatics Papers of Note for February 2013.

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

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

The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular characterization of human colon and rectal cancer“, Nature 487:330–337 (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 Characterization“, Computer Graphics Forum 31:1175-1184 (2012). Proceedings of EuroVis Conference 2012 - 3rd Best Paper Award.

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 Mesothelioma“, Bioinformatics 28(2):246-253 (2012).

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 Biology“, Nature Methods 7(3):S56-S68 (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).

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 Diseases“, Database 2009:bap011 (2009).

J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski, “Probabilistic retrieval and visualization of biologically relevant microarray experiments“, Bioinformatics 25(12):i145-i153 (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 Disease“, Molecular Systems Biology 5:252 (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 Data“, Bioinformatics 25(5):682-683 (2009).

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 mixtures“, Molecular & Cellular Proteomics 7:2138-2150 (2008).

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

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

Commentaries, Editorials, Book Chapters & Published Abstracts

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

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

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 framework“, AMIA Summits Translational Science Proceedings 2013:70 (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). Most viewed article in PLoS Computational Biology during February/March 2013 with more than 12,000 views in 30 days.

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

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

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

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

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

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

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 future“. Nature Methods 7(3):S2-S4 (2010).

N Gehlenborg and A Brazma, “Visualization of Large Microarray Experiments with Space Maps” (Abstract), BMC 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 Experiments” (Abstract), BMC Bioinformatics 10(Suppl 13):P1 (2009).

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).

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

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).

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). In German.

* equally contributing authors

Theses

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

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

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