Nils Gehlenborg

Nils Gehlenborg, PhD

Associate Professor of Biomedical Informatics
Director, Master of Medical Sciences in Biomedical Informatics (MMSc-BMI) Program

10 Shattuck Street, Boston, MA 02115

HIDIVE Lab

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 Medical Sciences in Biomedical Informatics (MMSc-BMI) program at Harvard Medical School.


DBMI Research Areas
DBMI Courses
SenNet Portal: Build, Optimization and Usage.
Authors: Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Gehlenborg N, Honick B, Bueckle A, Jain Y, Qaurooni D, Shirey B, Sibilla M, Métis K, Bisciotti J, Morgan RS, Betancur D, Sablosky R, Turner ML, Kim SJ, Lee PJ, Bartz J, Domanskyi S, Peters ST, Enninful A, Farzad N, Fan R, Herr BW.
bioRxiv
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Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.
Authors: Kouril D, Manz T, Clarence T, Gehlenborg N.
Bioinformatics
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Can LLMs Bridge Domain and Visualization? A Case Study on High-Dimension Data Visualization in Single-Cell Transcriptomics.
Authors: Wang Q, Liu X, Gehlenborg N.
IEEE Trans Vis Comput Graph
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An integrated view of the structure and function of the human 4D nucleome.
Authors: Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Andréa W, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepinska T, Chilinski M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park PJ, Alver BH, Schroeder AJ, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit AD, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F.
Nature
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Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools.
Authors: L'Yi S, Conroy J, Misner P, Kouril D, van den Brandt A, Choy L, Abdennur N, Gehlenborg N.
ArXiv
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Ten simple rules for making biomedical data resources accessible.
Authors: Smits TC, Weru L, Gehlenborg N, L'Yi S.
PLoS Comput Biol
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Interactive visualization of kidney micro-compartmental segmentations and associated pathomics on whole slide images.
Authors: Keller MS, Lucarelli N, Chen Y, Border S, Janowczyk A, Himmelfarb J, Kretzler M, Hodgin J, Barisoni L, Demeke D, Herlitz L, Moeckel G, Rosenberg AZ, Ding Y, Sarder P, Gehlenborg N.
ArXiv
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Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.
Authors: Kouril D, Manz T, Clarence T, Gehlenborg N.
ArXiv
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A comprehensive evaluation of life sciences data resources reveals significant accessibility barriers.
Authors: L'Yi S, Zhang HG, Mar AP, Smits TC, Weru L, Rojas S, Lex A, Gehlenborg N.
Sci Rep
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Data-driven consideration of genetic disorders for global genomic newborn screening programs.
Authors: Minten T, Bick S, Adelson S, Gehlenborg N, Amendola LM, Boemer F, Coffey AJ, Encina N, Ferlini A, Kirschner J, Russell BE, Servais L, Sund KL, Taft RJ, Tsipouras P, Zouk H, Green RC, Gold NB, Bick D, Gentile M, Orsini P, Ficarella R, Valente ML, Ponzi E, Ververi A, Koutsogianni M, Xinwen H, Rui X, Zhengyan Z, Pelo MJ, King J, Siu C, Kassahn K, Sansen S, Bertini E, Zygmunt A, Adelson S, Gentile M, Nyegaard M, Agolini E, Giordano J, O'Sullivan J, Al-Maraghi A, Jensen UG, Ojodu J, Alex K, Godler D, Orsini P, Alkuraya F, Gold N, Oza A, Akil AA, Goldenberg A, Paleologos K, Alshehri M, GoldenGrant K, Parad R, Ansel D, Goldman C, Peay H, Armstrong N, González de Aledo-Castillo JM, Pelo M, Aujla M, Gottlieb D, Philstrom C, Bailey D, Green R, Pichard D, Baker M, Greene C, Pichini A, Balciuniene J, Greenstein B, Pickering H, Barry A, Grosse S, Pirreca M, Bennetts B, Grueters A, Ponikowska M, Berenger M, Gumus G, Ponte A, Berg J, Hagman K, Posch A, Bernstein D, Hall K, Powell C, Bhatatcharjee A, Harmant A, Protopsaltis L, Bhatt S, Hartmanis S, Quevedo Y, Bick D, Hayeems R, Raia M, Bishop T, Heald R, Reimers R, Bitton A, Hegde M, Rohrwasser A, Boemer F, Heiner-Fokkema R, Rollier P, Bonhomme N, Henneman L, Rottensten L, Bowley G, Hernan B, Rtskhiladze I, Boyd B, Hobbs C, Sachedina N, Brennenstuhl H, Holm I, Sahyoun G, Brenner S, Horwitz L, Satija A, Bresnahan M, Hu Z, Schaaf C, Brewster T, Iascone M, Schleit J, Brooks PJ, Irvine K, Scott R, Broomberg K, Jin G, Scully L, Brower A, Kalbfleisch K, Seeloff S, Brown G, Kander I, Servais L, Buchanan J, Kaplun L, Shah N, Bupp C, Kasperaviciute D, Siitonen M, Cameron C, Kassahn K, Singh S, Capacchione L, Kauko L, Siu C, Carli D, Kaukonen R, Smith H, Ceballo OC, Kelly N, King LS, Chan K, Khangsar D, Sondheimer N, Chance J, King J, St George L, Charalambidou G, Kingsley C, Stark Z, Chen W, Kingsmore S, Steiner R, Chen YR, Kirmse B, Stoltze U, Chung W, Klein R, Stray-Pedersen A, Chung B, Koelker S, Sund K, Clarke M, Kousa Y, Tafas P, Clasper S, Krupoderova E, Teekakirikul P, Cole FS, Kruszka P, Thanos D, Cope H, Langley K, Thurm A, Coury S, Leckie C, To M, Cox T, Lecommandeur E, Tsipouras P, Dangouloff T, Ledbetter D, Tuff-Lacey A, Paul Daniel EJ, Lee P, Turner H, Danielsen KE, Lee B, Twiss P, Davoine E, Level C, Ulph F, Defay T, Lewis C, Uribe D, Gandhi GD, Lewis A, Urv T, Dewulf J, Liu R, Vacher C, Diller L, Longoni M, Van Den Bogaert K, Dixit P, Lundquist A, van der Burg M, Dolle M, Lunke S, Van Steijvoort E, Downie L, MacDuffie K, Veloudi Y, Drake E, Malhotra A, Vengoechea E, Drury S, Marcelis L, Voorhoeve E, Duintjer A, Martinez-Fresno M, Vu M, Duz B, Matthijs G, Wasserstein M, Eckstein D, Melbardis R, Watson M, Ellinwood M, Merritt J, Webb B, Ellsworth K, Badji RM, Wedell A, Elsea S, Metherell L, Westover T, Encina N, Mikkelsen NB, Wiedemann A, Etheredge H, Milko L, Wright M, Faivre L, Miller N, Wu C, Ferlini A, Minten T, Yeo J, Ferrie M, Morgan S, Yin-Hsiu Chien N, Finkel T, Mosiewicz K, Yusuff S, Furu P, Mütze U, Zemojtel T, Galarza-Cornejo J, Nicklen S, Zettler B, Gao Y, Niemela M, Zhao Z, Garcia-Villoria J, Niu DM, Ziff J, Gardner L, Norris S, Zimmerman R, Gaviglio A, Novelli A, Zuccolo M, Gelb M, Nusair A.
Genet Med
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