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
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, Willemin A, 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 P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, 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.
bioRxiv
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Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.
Authors: Keller MS, Gold I, McCallum C, Manz T, Kharchenko PV, Gehlenborg N.
Nat Methods
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A foundation model for clinician-centered drug repurposing.
Authors: Huang K, Chandak P, Wang Q, Havaldar S, Vaid A, Leskovec J, Nadkarni GN, Glicksberg BS, Gehlenborg N, Zitnik M.
Nat Med
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Understanding Visualization Authoring Techniques for Genomics Data in the Context of Personas and Tasks.
Authors: Brandt AVD, L'Yi S, Nguyen HN, Vilanova A, Gehlenborg N.
IEEE Trans Vis Comput Graph
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Learnable and Expressive Visualization Authoring through Blended Interfaces.
Authors: L'Yi S, Brandt AVD, Adams E, Nguyen HN, Gehlenborg N.
IEEE Trans Vis Comput Graph
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A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies.
Authors: Manz T, Lekschas F, Greene E, Finak G, Gehlenborg N.
IEEE Trans Vis Comput Graph
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Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data.
Authors: Morth E, Sidak K, Maliga Z, Moller T, Gehlenborg N, Sorger P, Pfister H, Beyer J, Kruger R.
IEEE Trans Vis Comput Graph
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A foundation model for clinician-centered drug repurposing.
Authors: Huang K, Chandak P, Wang Q, Havaldar S, Vaid A, Leskovec J, Nadkarni G, Glicksberg BS, Gehlenborg N, Zitnik M.
medRxiv
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MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data.
Authors: Sarfraz I, Wang Y, Shastry A, 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.
Genome Biol
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Determining the characteristics of genetic disorders that predict inclusion in newborn genomic sequencing programs.
Authors: Minten T, Gold NB, Bick S, Adelson S, Gehlenborg N, Amendola LM, Boemer F, Coffey AJ, Encina N, Russell BE, Servais L, Sund KL, Tsipouras P, Bick D, Taft RJ, Green RC.
medRxiv
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