Nils Gehlenborg

Nils Gehlenborg, PhD

Associate Professor of Biomedical Informatics
Director, Master of Biomedical Informatics (MBI) Program

10 Shattuck Street, Boston, MA 02115

Nils Gehlenborg  received his PhD from the University of Cambridge and was a predoctoral fellow at the European Bioinformatics Institute (EMBL-EBI).

The goal of Gehlenborg’s research is to improve human health by developing computational techniques and interfaces that enable scientists and clinicians to efficiently interact with biomedical data. Tight integration of algorithmic approaches from biomedical informatics with advanced data visualization techniques is central to his efforts, as is close collaboration with clinicians and experimentalists. Currently, Gehlenborg is researching and developing novel tools to visualize heterogeneous data from large-scale cancer genomics studies such as The Cancer Genome Atlas, integrating visual and computational approaches to support sense-making in biology, and using software to support reproducible collaborative research in epigenomics and genomics.

Gehlenborg is a co-founder and former general chair of BioVis, the Symposium on Biological Data Visualization, and co-founder of VIZBI, the annual workshop on Visualizing Biological Data. Occasionally, he contributes to the “Points of View” data visualization column in Nature Methods.

Gehlenborg currently serves as the Director of the Master of Biomedical Informatics (MBI) program at Harvard Medical School.


DBMI Research Areas
DBMI Courses
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).
Authors: Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP.
Nat Cell Biol
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How surgeons use risk calculators and non-clinical factors for informed consent and shared decision making: A qualitative study.
Authors: Panton J, Beaulieu-Jones BR, Marwaha JS, Woods AP, Nakikj D, Gehlenborg N, Brat GA.
Am J Surg
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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Authors: Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldas A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR.
Histochem Cell Biol
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The chromatin landscape of healthy and injured cell types in the human kidney.
Authors: Gisch DL, Brennan M, Lake BB, Basta J, Keller M, Ferreira RM, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Jefferson N, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT.
bioRxiv
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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Authors: Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldas AK, Kyoda K, de la Villegeorges ALT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR.
bioRxiv
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Potential pitfalls in the use of real-world data for studying long COVID.
Authors: Zhang HG, Honerlaw JP, Maripuri M, Samayamuthu MJ, Beaulieu-Jones BR, Baig HS, L'Yi S, Ho YL, Morris M, Panickan VA, Wang X, Weber GM, Liao KP, Visweswaran S, Tan BWQ, Yuan W, Gehlenborg N, Muralidhar S, Ramoni RB, Kohane IS, Xia Z, Cho K, Cai T, Brat GA.
Nat Med
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New Ways for Patients to Make Sense of Their Electronic Health Record Data Using the Discovery Web Application: Think-Aloud Evaluation Study.
Authors: Nakikj D, Kreda D, Gehlenborg N.
JMIR Form Res
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DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples.
Authors: Wang Q, L'Yi S, Gehlenborg N.
Proc SIGCHI Conf Hum Factor Comput Syst
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Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data.
Authors: Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD.
bioRxiv
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Cistrome Explorer: An Interactive Visual Analysis Tool for Large-Scale Epigenomic Data.
Authors: L'Yi S, Keller MS, Dandawate A, Taing L, Chen CH, Brown M, Meyer CA, Gehlenborg N.
Bioinformatics
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