Preprints | |
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) |
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Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Sarah Arena, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe'er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger. "MITI Minimum Information guidelines for highly multiplexed tissue images" arXiv:2108.09499 (2021) |
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Hutch, Meghan R. and Son, Jiyeon and Le, Trang T. and Hong, Chuan and Wang, Xuan and Shakeri Hossein Abad, Zahra and Morris, Michele and Gutiérrez-Sacristán, Alba and Klann, Jeffrey G. and Spiridou, Anastasia and Bellazzi, Riccardo and Benoit, Vincent and Bonzel, Clara-Lea and Bryant, William A. and Cho, Kelly and Das, Priyam and Hanauer, David A. and Henderson, Darren W. and Ho, Yuk-Lam and Loh, Ne Hooi Will and Makoudjou, Adeline and Malovini, Alberto and Moal, Bertrand and Mowery, Danielle L. and Samayamuthu, Malarkodi Jebathilagam and Sanz Vidorreta, Fernando J. and Schriver, Emily R. and Schubert, Petra and Talbert, Jeffrey and Tan, Amelia LM and Tan, Byorn WL and Tan, Bryce WQ and Tibollo, Valentina and Yuan, William and Avillach, Paul and Gehlenborg, Nils and Omenn, Gilbert S. and Characterization of COVID-19 by EHR (4CE), The Consortium for Clinical and Visweswaran, Shyam and Cai, Tianxi and Luo, Yuan and Xia, Zongqi. SSRN Preprints 10.2196/preprints.31400 (2022) |
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M S Keller, I Gold, C McCallum, T Manz, P V Kharchenko, and N Gehlenborg. OSF Preprints doi:10.31219/osf.io/y8thv (2021) |
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S Mataraso, V Socrates, F Lekschas, N Gehlenborg. "Halyos: A patient-facing visual EHR interface for longitudinal risk awareness" bioRxiv 597583 (2019) |
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U Gisladottir, D Nakikj, R Jhunjhunwala, G Brat, N Gehlenborg. medrxiv:2020.03.25.20038398 (2020) |
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2024 | |
L Taing, A Dandawate, S L'Yi, N Gehlenborg, M Brown, C A Meyer. "Cistrome Data Browser: integrated search, analysis and visualization of chromatin data" Nucleic Acids Research 52(D1), D61-D66 (2024) |
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2023 | |
Q Wang, S L'Yi, N Gehlenborg. "Drava: Concept-Driven Exploration of Small Multiples using Interpretable Latent Vectors" Proceedings of ACM CHI 2023, 1-15 (2023) |
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Qianwen Wang, Xiao Liu, Man Qing Liang, Sehi L’Yi, Nils Gehlenborg. "Enabling Multimodal User Interactions for Genomics Visualization Creation" Proceedings of IEEE VIS 2023, 101-105 (2023) |
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Trevor Manz, Sehi L'Yi, Nils Gehlenborg. "Gos: a declarative library for interactive genomics visualization in Python" Bioinformatics 39(1), btad050. (2023) |
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S L'Yi, Q Wang, N Gehlenborg. "The Role of Visualization in Genomics Data Analysis Workflows: The Interview" Proceedings of IEEE VIS 2023, 101-105 (2023) |
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Sehi L'Yi, Mark S Keller, Ariaki Dandawate, Len Taing, Chen-Hao Chen, Myles Brown, Clifford A Meyer, Nils Gehlenborg. "Cistrome Explorer: An Interactive Visual Analysis Tool for Large-Scale Epigenomic Data" Bioinformatics 39(2), btad018. (2023) |
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S L'Yi, D Maziec, V Stevens, T Manz, A Veit, M Berselli, P J. Park, D Głodzik, N Gehlenborg. "Chromoscope: interactive multiscale visualization for structural variation in human genomes" Nature Methods 20, 1834–1835 (2023) |
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Harrison Zhang, Jacqueline Honerlaw, Monika Maripuri, Malarkodi Jebathilagam Samayamuthu, Brendin Beaulieu-Jones, Huma Baig, Sehi L'Yi, Yuk-Lam Ho, Michele Morris, Vidul Ayakulangara Panickan, Xuan Wang, Griffin Weber, Katherine P Liao, Shyam Visweswaran, Bryce Tan, William Yuan, Nils Gehlenborg, Sumitra Muralidhar, Rachel Ramoni, The Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Isaac Kohane, Zongqi Xia, Kelly Cho, and Tianxi Cai. "Potential pitfalls in the use of real world data to study Long COVID" Nature Medicine 29, 1040–1043 (2023) |
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2022 | |
Furui Cheng, Mark S Keller, Huamin Qu, Nils Gehlenborg, Qianwen Wang. "Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis" Accepted at IEEE VIS 2022 and IEEE Transactions on Visualization and Computer Graphics. (2022) |
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Qianwen Wang, Kexin Huang, Payal Chandak, Marinka Zitnik, Nils Gehlenborg. "Extending the Nested Model for User-Centric XAI: A Design Study on GNN-based Drug Repurposing" Accepted at IEEE VIS 2022 and IEEE Transactions on Visualization and Computer Graphics. (2022) |
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T Manz, I Gold, NH Patterson, C McCallum, MS Keller, BW Herr II, K Börner, J Spraggins, N Gehlenborg. "Viv: Multiscale Visualization of High-Resolution Multiplexed Bioimaging Data on the Web" Nature Methods 19 515–516 (2022) |
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Sehi L'Yi, Nils Gehlenborg. "Multi-View Design Patterns and Responsive Visualization for Genomics Data" Accepted at IEEE VIS 2022 and IEEE Transactions on Visualization and Computer Graphics. (2022) |
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T.S. Liaw and N. Gehlenborg. "User-Centric Process of Designing a Molecular & Cellular Query Interface for Biomedical Research" International Design Conference - DESIGN 2022 (2022) |
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Chuan Hong, Harrison G Zhang, Sehi L'Yi, Griffin Weber, Paul Avillach, Bryce WQ Tan, Alba Gutiérrez-Sacristán, Clara-Lea Bonzel, Nathan P Palmer, Alberto Malovini, Valentina Tibollo, Yuan Luo, Meghan R Hutch, Molei Liu, Florence Bourgeois, Riccardo Bellazzi, Luca Chiovato, Fernando J Sanz Vidorreta, Trang T Le, Xuan Wang, William Yuan, Antoine Neuraz, Vincent Benoit, Bertrand Moal, Michele Morris, David A Hanauer, Sarah Maidlow, Kavishwar Wagholikar, Shawn Murphy, Hossein Estiri, Adeline Makoudjou, Patric Tippmann, Jeffery Klann, Robert W Follett, Nils Gehlenborg, Gilbert S Omenn, Zongqi Xia, Arianna Dagliati, Shyam Visweswaran, Lav P Patel, Danielle L Mowery, Emily R Schriver, Malarkodi Jebathilagam Samayamuthu, Ramakanth Kavuluru, Sara Lozano-Zahonero, Daniela Zöller, Amelia LM Tan, Byorn WL Tan, Kee Yuan Ngiam, John H Holmes, Petra Schubert, Kelly Cho, Yuk-Lam Ho, Brett K Beaulieu-Jones, Miguel Pedrera-Jiménez, Noelia García-Barrio, Pablo Serrano-Balazote, Isaac Kohane, Andrew South, Gabriel A Brat, T Cai. BMJ open 12 (6):e057725 (2022) |
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Aditeya Pandey, Sehi L'Yi, Qianwen Wang, Michelle A Borkin, Nils Gehlenborg. "GenoREC: A Recommendation System for Interactive Genomics Data Visualization" Accepted at IEEE VIS 2022 and IEEE Transactions on Visualization and Computer Graphics. (2022) |
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G Weber, C Hong, Z Xia, N Palmer, P Avillach, S L’Yi, M Keller, S Murphy, A Gutiérrez-Sacristán, C Bonzel, A Serret-Larmande, A Neuraz, G Omenn, S Visweswaran, J Klann, A South, N Loh, M Cannataro, B Beaulieu-Jones, R Bellazzi, G Agapito, M Alessiani, B Aronow, D Bell, V Benoit, F Bourgeois, L Chiovato, K Cho, A Dagliati, S DuVall, N Barrio, D Hanauer, Y Ho, J Holmes, R Issitt, M Liu, Y Luo, K Lynch, S Maidlow, A Malovini, K Mandl, C Mao, M Matheny, J Moore, J Morris, M Morris, D Mowery, K Ngiam, L Patel, M Pedrera-Jimenez, R Ramoni, E Schriver, P Schubert, P Balazote, A Spiridou, A Tan, B Tan, V Tibollo, C Torti, E Trecarichi, X Wang, J Aaron, A Albayrak, G Albi, A Alloni, D Amendola, F Angoulvant, L Anthony, F Ashraf, A Atz, P Avillach, P Azevedo, J Balshi, B Beaulieu-Jones, A Bellasi, V Benoit, M Beraghi, J Bernal-Sobrino, M Bernaux, R Bey, S Bhatnagar, A Blanco-Martínez, M Boeker, J Booth, S Bosari, R Bradford, G Brat, S Bréant, N Brown, R Bruno, W Bryant, M Bucalo, E Bucholz, A Burgun, T Cai, A Carmona, C Caucheteux, J Champ, K Chen, J Chen, L Chiudinelli, K Cho, J Cimino, T Colicchio, S Cormont, S Cossin, J Craig, J Cruz-Bermúdez, J Cruz-Rojo, M Daniar, C Daniel, P Das, B Devkota, A Dionne, R Duan, J Dubiel, L Esteve, H Estiri, S Fan, R Follett, T Ganslandt, N García-Barrio, L Garmire, N Gehlenborg, E Getzen, A Geva, T Gradinger, A Gramfort, R Griffier, N Griffon, O Grisel, A Gutiérrez-Sacristán, L Han, D Hanauer, C Haverkamp, D Hazard, B He, D Henderson, M Hilka, K Huling, M Hutch, R Issitt, A Jannot, V Jouhet, R Kavuluru, C Kennedy, K Kernan, D Key, K Kirchoff, J Klann, I Kohane, I Krantz, D Kraska, A Krishnamurthy, T Le, J Leblanc, G Lemaitre, L Lenert, D Leprovost, M Liu, Q Long, S Lozano-Zahonero, S Mahmood, S Maidlow, A Makoudjou, A Maram, P Martel, M Martins, J Marwaha, A Masino, M Mazzitelli, A Mensch, M Milano, M Minicucci, B Moal, T Ahooyi, J Moore, C Moraleda, J Morris, K Moshal, S Mousavi, D Murad, S Murphy, T Naughton, C Neto, J Newburger, K Ngiam, W Njoroge, J Norman, J Obeid, M Okoshi, K Olson, G Omenn, N Orlova, B Ostasiewski, N Palmer, N Paris, L Patel, M Pedrera-Jiménez, A Pfaff, E Pfaff, D Pillion, S Pizzimenti, H Prokosch, R Prudente, A Prunotto, V Quirós-González, R Ramoni, M Raskin, S Rieg, G Roig-Domínguez, P Rojo, P Rubio-Mayo, P Sacchi, C Sáez, E Salamanca, M Samayamuthu, L Sanchez-Pinto, A Sandrin, N Santhanam, J Santos, F Sanz Vidorreta, M Savino, J Schuettler, L Scudeller, N Sebire, P Serrano-Balazote, P Serre, A Serret-Larmande, M Shah, Z Abad, D Silvio, P Sliz, J Son, C Sonday, A South, F Sperotto, Z Strasser, A Tan, B Tan, S Tanni, D Taylor, A Terriza-Torres, P Tippmann, E Toh, Y Tseng, A Vallejos, G Varoquaux, M Vella, G Verdy, J Vie, S Visweswaran, M Vitacca, K Wagholikar, L Waitman, D Wassermann, G Weber, M Wolkewitz, S Wong, Z Xia, X Xiong, Y Ye, N Yehya, W Yuan, A Zambelli, H Zhang, D Zöller, V Zuccaro, C Zucco, I Kohane, T Cai, G Brat, The Consortium for Clinical Characterization of COVID-19 by EHR (4CE). npj Digital Medicine 5, 74 (2022) (2022) |
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2021 | |
Qianwen Wang, Tali Mazor, Theresa Harbig, Ethan Cerami, Nils Gehlenborg. "ThreadStates: State-based Visual Analysis of Disease Progression" Accepted at IEEE VIS 2021 and IEEE Transactions on Visualization and Computer Graphics. (2021) |
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S L'Yi, Q Wang, F Lekschas, and N Gehlenborg. "Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization" Accepted at IEEE VIS 2021 and IEEE Transactions on Visualization and Computer Graphics. (2021) |
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Theresa Harbig, Sabrina Nusrat, Tali Mazor, Qianwen Wang, Alexander Thomson, Hans Bitter, Ethan Cerami, Nils Gehlenborg. "OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data" Bioinformatics (Proceedings of ISMB/ECCB 2021), Volume 37, Issue Supplement_1, July 2021, Pages i59–i66, https://doi.org/10.1093/bioinformatics/btab289 (2021) |
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G Weber, H Zhang, S L'Yi, C Bonzel, C Hong, P Avillach, A Gutiérrez-Sacristán, N Palmer, A Tan, X Wang, W Yuan, N Gehlenborg, A Alloni, D Amendola, A Bellasi, R Bellazzi, M Beraghi, M Bucalo, L Chiovato, K Cho, A Dagliati, H Estiri, R Follett, N García-Barrio, D Hanauer, D Henderson, Y Ho, J Holmes, M Hutch, R Kavuluru, K Kirchoff, J Klann, A Krishnamurthy, T Le, M Liu, N Loh, S Lozano-Zahonero, Y Luo, S Maidlow, A Makoudjou, A Malovini, B Moal, M Morris, D Mowery, S Murphy, A Neuraz, K Ngiam, M Okoshi, G Omenn, L Patel, M Pedrera-Jiménez, R Prudente, M Samayamuthu, J Sanz, E Schriver, P Schubert, P Serrano-Balazote, B Tan, S Tanni, V Tibollo, S Visweswaran, K Wagholikar, Z Xia, D Zoeller, The Consortium For Clinical Characterization Of COVID-19 By EHR (4CE), I Kohane, T Cai, A South, G Brat. J Med Internet Res 2021;23(10):e31400. doi: https://doi.org/10.2196/31400 (2021) |
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Bourgeois F, Gutiérrez-Sacristán A, Keller M, Liu M, Hong C, Bonzel C, Tan A, Aronow B, Boeker M, Booth J, Cruz Rojo J, Devkota B, García Barrio N, Gehlenborg N, Geva A, Hanauer D, Hutch M, Issitt R, Klann J, Luo Y, Mandl K, Mao C, Moal B, Moshal K, Murphy S, Neuraz A, Yuan Ngiam K, Omenn G, Patel L, Pedrera Jiménez M, Sebire N, Serrano Balazote P, Serret-Larmande A, South A, Spiridou A, Taylor D, Tippmann P, Visweswaran S, Weber G, Kohane I, Cai T, Avillach P; for the Consortium for Clinical Characterization of COVID-19 by EHR (4CE). JAMA Netw Open 4:e2112596 (2021) |
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2020 | |
F Lekschas, X Zhou, W Chen, N Gehlenborg, B Bach, H Pfister. "A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling" IEEE Transactions on Visualization and Computer Graphics, to appear. DOI: https://doi.org/10.1109/TVCG.2020.3028948 (2020) |
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F Lekschas, B Peterson, D Haehn, E Ma, N Gehlenborg, H Pfister. Computer Graphics Forum 39 167-179 (2020) |
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Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce Aronow, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H. Scheuermann, Deanne Taylor, Nicole Vasilevsky, Laura Clarke, Nils Gehlenborg, Jim Kent, John Marioni, Sarah Teichmann, Alvis Brazma & Irene Papatheodorou . "Guidelines for reporting single-cell RNA-seq experiments" Nature Biotechnology (2020) |
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G Brat, G Weber, N Gehlenborg, P Avillach, N Palmer, L Chiovato, J Cimino, L Waitman, G Omenn, A Malovini, J Moore, B Beaulieu-Jones, V Tibollo, S Murphy, S L'Yi, M Keller, R Bellazzi, D Hanauer, A Serret-Larmande, A Gutierrez-Sacristan, J Holmes, D Bell, K Mandl, R Follett, J Klann, D Murad, L Scudeller, M Bucalo, K Kirchoff, J Craig, J Obeid, V Jouhet, R Griffier, S Cossin, B Moal, L Pate, A Bellasi, H Prokosch, D Kraska, P Sliz, A Tan, K Ngiam, A Zambelli, D Mowery, E Schiver, B Devkota, R Bradford, M Daniar, C Daniel, V Benoit, R Bey, N Paris, P Serre, N Orlova, J Dubiel, M Hilka, A Jannot, S Breant, J Leblanc, N Griffon, A Burgun, M Bernaux, A Sandrin, E Salamanca, T Ganslandt, T Gradinger, J Champ, M Boeker, P Martel, L Esteve, A Gramfort, O Grisel, D Leprovost, T Moreau, G Varoquaux, J Vie, D Wassermann, A Mensch, C Caucheteux, C Haverkamp, G Lemaitre, C Haverkamp, T Cai, I Kohane. "International Electronic Health Record-Derived COVID-19 Clinical Course Profiles: the 4CE Consortium" npj Digital Medicine 3, 109 (2020) |
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2019 | |
S Nusrat, T Harbig, N Gehlenborg. "Tasks, Techniques, and Tools for Genomic Data Visualization" Computer Graphics Forum 38 781-805 (2019) |
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B Morrow, T Manz, AE Chung, N Gehlenborg, D Gotz. "Periphery Plots for Contextualizing Heterogeneous Time-Based Charts" Proceedings of IEEE VIS 2019, to appear (2019) |
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F Lekschas, M Behrisch, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister. "Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets" IEEE Transactions on Visualization and Computer Graphics, to appear. DOI: https://doi.org/10.1109/TVCG.2019.2934555 (2019) |
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MP Snyder, S Lin, A Posgai, M Atkinson, A Regev, J Rood, O Rosen, L Gaffney, A Hupalowska, R Satija, N Gehlenborg, J Shendure, J Laskin, P Harbury, NA Nystrom, Z Bar-Joseph, K Zhang, K Borner, Y Lin, R Conroy, D Procaccini, AL Roy, A Pillai, M Brown, ZS Galis (for the HuBMAP Consortium). "The human body at cellular resolution: the NIH Human Biomolecular Atlas Program" Nature 574 187-192 (2019) |
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2018 | |
C Nobre, N Gehlenborg, H Coon, A Lex. "Lineage: Visualizing Multivariate Clinical Data in Genealogy Graphs" IEEE Transactions on Visualization and Computer Graphics 25 1543-1558. doi: https://doi.org/10.1109/TVCG.2018.2811488 (2018) |
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F Lekschas, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister. "HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples" IEEE Transactions on Visualization and Computer Graphics 24:1 (2018) |
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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 exploration and analysis of genome interaction maps" Genome Biology 201819:125 (2018); https://doi.org/10.1186/s13059-018-1486-1 (2018) |
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M Behrisch, R Krueger, F Lekschas, T Schreck, N Gehlenborg, H Pfister. "Visual Pattern-Driven Exploration of Big Data" Proceedings of International Symposium on Big Data Visual and Immersive Analytics, doi:10.1109/BDVA.2018.8534028 (2018) |
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2017 | |
F Lekschas, N Gehlenborg. "SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories" Bioinformatics, btx739, https://doi.org/10.1093/bioinformatics/btx739 (2017) |
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M Kern, A Lex, N Gehlenborg, CR Johnson. "Interactive Visual Exploration And Refinement Of Cluster Assignments" BMC Bioinformatics 18:406 (2017) |
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The Cancer Genome Atlas Research Network (incl. N Gehlenborg). "Integrated genomic characterization of oesophageal carcinoma" Nature 541(7636):169-175 (2017) |
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The Cancer Genome Atlas Research Network (incl. N Gehlenborg). "Integrated genomic and molecular characterization of cervical cancer" Nature 543(7645):378-384 (2017) |
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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 Carcinosarcoma" Cancer Cell 31(3):411-423 (2017) |
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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 Paraganglioma" Cancer Cell Feb 13;31(2):181-193 (2017) |
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JR Conway, A Lex, N Gehlenborg. "UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties" Bioinformatics 33: 2938–2940; doi: https://doi.org/10.1093/bioinformatics/btx364 (2017) |
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2016 | |
Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS.. "Methods to enhance the reproducibility of precision medicine" Pac Symp Biocomput 21:180-182 (2016) |
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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 carcinomas" Nat Genet 48, 607–616 (2016) |
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S Gratzl, A Lex, N Gehlenborg, N Cosgrove, M Streit. "From Visual Exploration to Storytelling and Back Again" Computer Graphics Forum 35:491–500 (2016) |
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H Stitz, S Luger, M Streit, N Gehlenborg. "AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research" Computer Graphics Forum 35:481-490 (2016) |
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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. Cell 164:550-563 (2016) |
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2015 | |
The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade Gliomas" New England Journal of Medicine 372:2481-2498 (2015) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive Genomic Characterization of Head and Neck Squamous Cell Carcinomas" Nature 517:576-582 (2015) |
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The Cancer Genome Atlas Research Network, incl. N Gehlenborg. "The Molecular Taxonomy of Primary Prostate Cancer" Cell 163:1011-25 (2015) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Genomic Classification of Cutaneous Melanoma" Cell 161:1681-96 (2015) |
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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 Cancer" Cell 163:506-519 (2015) |
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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 Cancers" Proceedings of the National Academy of Sciences USA (2014) |
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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) |
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A Lex and N Gehlenborg. "Points of View: Sets and Intersections" Nature Methods 11(8):779 (2014) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive molecular profiling of lung adenocarcinoma" Nature (2014) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive Molecular Characterization of Gastric Adenocarcinoma" Nature (2014) |
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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) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive Molecular Characterization of Urothelial Bladder Carcinoma" Nature 507:315–322 (2014) |
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M Streit and N Gehlenborg. "Points of View: Bar Charts and Box Plots" Nature Methods 11(2):117 (2014) |
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A Lex, N Gehlenborg, H Strobelt, R Vuillemot and H Pfister. "UpSet: Visualization of Intersecting Sets" IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14) (2014) |
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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) |
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S Gratzl, N Gehlenborg, A Lex, H Pfister and M Streit. "Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets" IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14) (2014) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Integrated Genomic Characterization of Papillary Thyroid Carcinoma" Cell 159:676–690 (2014) |
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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. Cell 158:929–944 (2014) |
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2013 | |
J de Ridder\*, T Abeel\*, M Michaut, VP Satagopam and N Gehlenborg. Workshop Report, PLoS Computational Biology 9(1):e1002834 (2013) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive molecular characterization of clear cell renal cell carcinoma" Nature 499:43–49 (2013) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "The Cancer Genome Atlas Pan-Cancer analysis project" Nature Genetics 45:1113–1120 (2013) |
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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) |
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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) |
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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) |
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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) |
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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. AMIA Summits Translational Science Proceedings 2013:70 (2013) |
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2012 | |
N Gehlenborg and B Wong. "Points of View: Into the Third Dimension" Nature Methods 9(9):851 (2012) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive genomic characterization of squamous cell lung cancers" Nature 489:519–525 (2012) |
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N Gehlenborg and B Wong. "Points of View: Power of the Plane" Nature Methods 9(10):935 (2012) |
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N Gehlenborg and B Wong. Nature Methods 9(2):115 (2012) |
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N Gehlenborg and B Wong. "Points of View: Integrating Data" Nature Methods 9(4):315 (2012) |
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N Gehlenborg and B Wong. Nature Methods 9(3):213 (2012) |
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N Gehlenborg and B Wong. "Points of View: Mapping Quantitative Data to Color" Nature Methods 9(8):769 (2012) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive molecular characterization of human colon and rectal cancer" Nature 487:330–337 (2012) |
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The Cancer Genome Atlas Network, incl. N Gehlenborg. "Comprehensive molecular portraits of human breast tumours" Nature 490:61–70 (2012) (2012) |
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A Lex, M Streit, H-J Schulz, C Partl, D Schmalstieg, PJ Park, N Gehlenborg. Computer Graphics Forum 31:1175-1184 (2012). Proceedings of EuroVis Conference 2012 (2012) |
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J Caldas\*, N Gehlenborg, E Kettunen, A Faisal, M Rönty, AG Nicholson, S Knuutila, A Brazma and S Kaski. Bioinformatics 28(2):246-253 (2012) |
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2010 | |
N Gehlenborg. "Visualization and Exploration of Transcriptomics Data" PhD Thesis, University of Cambridge, United Kingdom (2010) |
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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) |
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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) |
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J Peltonen, H Aidos, N Gehlenborg, A Brazma and S Kaski. In Proceedings of the IEEE 2010 International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2010), 2178-2181 (2010) |
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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) |
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N Gehlenborg, D Hwang\*, IY Lee\*, H Yoo, B Petritis, D Baxter, R Pitstick, B Marzolf, SJ DeArmond, GA Carlson and LE Hood. Database 2009:bap011 (2009) |
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N Gehlenborg and A Brazma. "Visualization of Large Microarray Experiments with Space Maps" BMC Bioinformatics 10(Suppl 13):O7 (2009) |
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J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski. "Probabilistic Retrieval and Visualization of Biologically Relevant Microarray Experiments" BMC Bioinformatics 10(Suppl 13):P1 (2009) |
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N Gehlenborg, W Yan, I Lee, H Yoo, K Nieselt, D Hwang, R Aebersold, L Hood. Bioinformatics 25(5):682-683 (2009) |
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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) |
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2008 | |
A Schmidt, N Gehlenborg, B Bodenmiller, LN Mueller, D Campbell, M Mueller, R Aebersold and B Domon. Molecular & Cellular Proteomics 7:2138-2150 (2008) |
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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) |
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L Peixoto, N Gehlenborg and S Chandra Janga (Eds.). BMC Bioinformatics 9(Suppl 10):I1 (2008) |
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2007 | |
N Gehlenborg, M Corpas and S Chandra Janga (Eds.). BMC Bioinformatics 8(Suppl 8):I1 (2007) |
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2006 | |
N Gehlenborg. "Visualization and Integration of Liquid Chromatography/Mass Spectrometry Proteomics Data" Diplomarbeit (eq. Masters Thesis), University of Tübingen, Germany (2006) |
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J Dietzsch\*, N Gehlenborg\* and K Nieselt. "Mayday – A Microarray Data Analysis Workbench" Bioinformatics 22(8):1010-1012 (2006) |
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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) |
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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) |
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2003 | |
N Gehlenborg. "Mayday – Microarray Data Analysis" Studienarbeit (eq. Bachelors Thesis), University of Tübingen, Germany (2003) |