Yakir Reshef 1stnamelastinitial at broadinstitute.org

I'm an MD/PhD computer scientist interested in the immune system. I'm currently a fellow in rheumatology at Brigham and Women's Hospital. My research focuses on developing quantitative methods for characterizing immune state from high-dimensional molecular data.

In 2020, I completed an MD at Harvard Medical School and the Massachusetts Institute of Technology. I wrote my MD thesis with Soumya Raychaudhuri on analysis of single-cell data.

In 2018, I completed a PhD in computer science at Harvard University, advised by Ryan Adams and Michael Mitzenmacher and working on problems in statistics, machine learning, and statistical genetics. I also collaborated closely with Alkes Price and Pardis Sabeti.

In 2011, I was a Fulbright scholar in the Department of Applied Math and Computer Science at the Weizmann Institute of Science.

In 2009, I graduated from Harvard College with a BA in mathematics. I wrote my BA thesis on pseudorandomness with Salil Vadhan.

Selected publications (full list on Google Scholar)

Powerful and accurate case-control analysis of spatial molecular data
Y Reshef#, L Sood, M Curtis, L Rumker, D Stein, M Palshikar, S Nayar, A Filer, AH Jonsson, I Korsunsky, S Raychaudhuri#
(# co-corresponding)
bioRxiv 2025
[pre-print]

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics
[Y Reshef, L Rumker], J Kang, A Nathan, I Korsunsky, S Asgari, M Murray, DB Moody, S Raychaudhuri
[...] equal contribution
Nature Biotechnology 2021
[abstract] [talk] [bibtex]

Equitability, interval estimation, and statistical power
Y Reshef*, D Reshef*, P Sabeti**, M Mitzenmacher**
* co-first authors; ** co-last authors
Statistical Science 2020
[abstract] [pdf] [bibtex]

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk
Y Reshef#, H Finucane, D Kelley, A Gusev, D Kotliar, J Ulirsch, F Hormozdiari, J Nasser, L OConnor, B van de Geijn, P Loh, S Grossman, G Bhatia, S Gazal, P Francesco Palamara, L Pinello, N Patterson, R Adams, A Price#
(# co-corresponding)
Nature Genetics 2018
[abstract] [pdf] [talk] [bibtex]

Sequential regulatory activity prediction across chromosomes with convolutional neural networks
D. Kelley, Y Reshef, M Bileschi, D Belanger, C McLean, J Snoek
Genome Research 2018
[abstract] [pdf] [bibtex]

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
H Finucane, Y Reshef, V Anttila, K Slowikowski, A Gusev, A Byrnes, S Gazal, P Loh, C Lareau, N Shoresh, G Genovese, A Saunders, E Macosko, S Pollack, The Brainstorm Consortium, J Perry, J Buenrostro, B Bernstein, S Raychaudhuri, S McCarroll, B Neale, A Price
Nature Genetics 2018
[abstract] [bioRxiv] [bibtex]

An empirical study of the maximal and total information coefficients and leading measures of dependence
D Reshef*, Y Reshef*, P Sabeti**, M Mitzenmacher**
* co-first authors; ** co-last authors
Annals of Applied Statistics 2018
[abstract] [arXiv] [bibtex]

Measuring dependence powerfully and equitably
Y Reshef*, D Reshef*, H Finucane, P Sabeti**, M Mitzenmacher**
* co-first authors; ** co-last authors
Journal of Machine Learning Research 2016
[abstract] [pdf] [bibtex]

Comment on "Equitability, Mutual Information, and the Maximal Information Coefficient"
[D Reshef, Y Reshef], [M Mitzenmacher, P Sabeti]
[...] equal contribution, listed alphabetically, co-corresponding
[[...]] equal contribution
PNAS 2014
[abstract] [pdf] [bibtex]

On Extractors and Exposure-Resilient Functions for Sublogarithmic Entropy
Y Reshef, S Vadhan
Random Structures and Algorithms 2012
[abstract] [arXiv] [bibtex]

Detecting Novel Associations in Large Datasets
[D Reshef, Y Reshef], H Finucane, S Grossman, G McVean, P Turnbaugh, E Lander, [[M Mitzenmacher, P Sabeti]]
[...] equal contribution, listed alphabetically, co-corresponding
[[...]] equal contribution
Science 2011.
[abstract] [talk] [bibtex] [paper website] [accompanying Science perspective] [FAQ]

On Resilient and Exposure-Resilient Functions
Y Reshef
My undergraduate thesis (2009), advised by Salil Vadhan.
[pdf] [bibtex]

Funding

I'm grateful for prior funding from the NIH Medical Scientist Training Program, the PD Soros foundation, the National Defense Science and Engineering Graduate (NDSEG) fellowship, and the United States Fulbright Program.