James Zou
Microsoft Research New England and MIT
One Memorial Drive, Cambridge, MA 02142
jamesyzou at gmail dot com

I work on machine learning and computational biology at Microsoft Research New England and MIT. I received my Ph.D. from Harvard University in May 2014 and also spent half time at the Broad Institute, supported by a NSF Graduate Fellowship. Before this, I completed Part III in Mathematics at the University of Cambridge (thanks to the generous support of a Gates Scholarship). In Spring 2014, I was very fortunate to be a Simons research fellow at U.C. Berkeley.

I will join Stanford as an assistant professor in Fall 2016.

machine learning    |   computational biology   |   talks   |   teaching   |   fun

Computational biology

Quantifying the unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects. [arXiv]
James Zou, Greg Valiant, Paul Valiant, Konrad Karczewski, Siu On Chan, Kaitlin Samocha, Monkol Lek, Exome Aggregation Consortium, Shamil Sunyaev, Mark Daly, Daniel MacArthur
Under review (2016).

Analysis of protein-coding genetic variation in 60,706 humans. [arXiv]
Exome Aggregation Consortium.
Nature in press (2016).

A genetic and socio-economic study of mate choice in Latinos reveals novel assortment patterns. [PDF] [Press]
James Zou [corresponding author], Danny Park, Esteban Burchard, Dara Torgerson, Maria Pino-Yanes, Yun Song, Sriram Sankararaman, Eran Halperin, Noah Zaitlen
Proceedings of the National Academy of Sciences 112(44):13621-6 (2015).

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, James Zou, Eran Halperin.
Nature Methods in press (2016).

Genetics of assortative mating in human marriages.
James Zou.
Encyclopedia of Life Sciences. Invited review Wiley (2015).

Inferring parental genomic ancestries using pooled semi-Markov processes. [PDF]
James Zou [corresponding author], Eran Halperin, Esteban Burchard, Sriram Sankararaman.
Bioinformatics 31(12):i190-6 (2015).

Correcting for sample heterogeneity in epigenome-wide association studies. [PDF]
James Zou.
Methods Mol Biol. (2015).

Undesired usage and the robust self-assembly of heterogeneous structures. [PDF]
Arvind Murugan, James Zou, Michael Brenner.
Nature Communications 11;6:6203 (2015).

Extended fertility and longevity: the genetic and epigenetic link. [PDF]
Kerem Wainer-Katsir, James Zou, Michal Linial.
Fertil Steril. 103(5):1117-24 (2015).

Epigenome-wide association studies without the need for cell-type composition. [PDF]
James Zou [corresponding author], Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten.
Nature Methods 11(3):309-11 (2014).
Highlight talk at ISMB 2015.
Highlight talk at RECOMB 2015.
Platform presentation at the 2013 Wellcome Trust Epigenomics of Common Diseases conference.
Platform presentation at the 2013 Machine Learning in Computational Biology meeting.

Genome-wide chromatin state transitions elicited by developmental and environmental cues. [PDF]
Jiang Zhu, Mazhar Adli, James Zou, et al.
Cell 152(3):642-54 (2013).

Locus-specific chromatin inactivation at endogenous enhancers with programmable TALE-LSD1 fusions. [PDF]
Eric Mendenhall, Kaylyn Williamson, Deepak Reyon, James Zou, et al.
Nature Biotechnology 31(12):1133-6 (2013).

Getting the biggest birch for the bang: restoring and expanding upland birchwoods in the Scottish Highlands by managing red deer. [PDF]
Andrew Tanentzap, James Zou, David Coomes.
Ecology and Evolution 3(7):1890-901 (2013).

Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. [PDF]
Hongfang Wang, James Zou [co-first author, corresponding author], et al.
Proceedings of the National Academy of Sciences 108(36):14908-13 (2011).

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. [PDF]
Bo Zhao, James Zou [co-first author], et al.
Proceedings of the National Academy of Sciences 108(36):14902-7 (2011).

Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. [PDF]
Ben Gewurz, Jessica Mar, Megha Padi, Bo Zhao, Nicholas Shinners, Kaoru Takasaki, Edward Bedoya, James Zou, et al.
Journal of Virology 85(13):6764-73 (2011).

Epstein-Barr virus nuclear antigens 3C and 3A maintain lymphoblastoid cell growth by repressing p16INK4A and p14ARF expression. [PDF]
Seiji Maruo, Bo Zhao, Eric Johannsen, Elliott Kieff, James Zou, Kenzo Takada.
Proceedings of the National Academy of Sciences 108(5):1919-24 (2011).

Religion and HIV in Tanzania: influence of religious beliefs on HIV stigma, disclosure, and treatment attitudes. [PDF]
James Zou [corresponding author], Yvonne Yamanaka, et al.
BMC Public Health 9:75 (2009).

Machine learning and AI

Quantifying the accuracy of approximate diffusions and Markov chains. [arXiv]
Jonathan Huggins, James Zou.
Submitted 2016.

Man is to Computer Programmer as Woman is to Homemaker? Debiasing Word Embeddings [arXiv] [TechReview] [Vice] [NPR]
Tolga Bolukbasi, Kai-Wei Chang, James Zou, Venkatesh Saligrama, Adam Kalai.
Neural Information Processing Systems (NIPS 2016).

Rich component analysis. [arXiv]
Rong Ge, James Zou [alphabetical].
International Conference on Machine Learning (ICML 2016).

Controlling bias in adaptive data analysis using information theory. [arXiv]
Daniel Russo, James Zou [alphabetical].
Preliminary version accepted at AISTATS 2016 (full oral; top 7% of submissions).
Information Theory and Applications (ITA) invited talk.

Clustering with a reject option: interactive clustering as Bayesian prior elicitation.
Akash Srivastava, James Zou, Ryan Adams, Charles Sutton.
ArXiv (2016).

Intersecting faces: non-negative matrix factorization with new guarantees. [PDF]
Rong Ge, James Zou [alphabetical].
International Conference on Machine Learning (ICML 2015).

Crowdsourcing feature discovery via adaptively chosen comparisons. [PDF]
James Zou, Kamalika Chaudhuri, Adam Kalai.
HCOMP (2015); CrowdML workshop (ICML 2015); Feature extraction workshop (NIPS 2015)
Invited to Journal of Machine Learning Research (JMLR) special issue (2015).

Incentive compatible experimental design. [PDF]
Panos Toulis, David Parkes, Elery Pfeffer, James Zou.
ACM Conference on Economics and Computation (EC 2015).

Approval voting behavior in Doodle. [PDF]
James Zou, Reshef Meir, David Parkes.
ACM Conference CSCW (2015). Honorable mention for best paper (top 5% of submissions).

Coordination through contingent payment mechanisms.
Hongyao Ma, Reshef Meir, David C. Parkes, James Zou.
Conference on Auctions, Market Mechanisms and Their Applications (2015). INFORMS (2015)

Contrastive learning using spectral methods. [PDF]
James Zou, Daniel Hsu, David Parkes, Ryan Adams.
Neural Information Processing Systems (NIPS 2013).

Priors for diversity in generative latent variable models. [PDF]
James Zou, Ryan Adams.
Neural Information Processing Systems (NIPS 2012).

A slime mold solver for linear programming problems. [PDF]
Anders Johannson, James Zou [alphabetical].
Lecture Notes in Computer Science 7318 (2012).

Get another worker? Active crowdlearning with sequential arrivals.
James Zou, David Parkes.
Proceedings of Workshop on Machine Learning in Human Computation and Crowdsourcing (ICML 2012).

Threats and trade-Offs in resource critical crowdsourcing tasks over networks. [arXiv]
Swaprava Nath, Pankaj Dayama, Dinesh Garg, Y. Narahari, James Zou.
Proceedings 8th Workshop on Internet and Network Economics (WINE 2012).

Tolerable manipulability in dynamic assignment without money. [PDF]
James Zou, Sujit Gujar, David Parkes.
Proceedings 24th AAAI Conference on Artificial Intelligence (AAAI 2010).

Dynamic House Allocation.
Sujit Gujar, James Zou, David Parkes.
Proceedings 5th Multidisciplinary Workshop on Advances in Preference Handling (MPREF 2010).

Systems and methods for quantifiable signaling in multi-user environments.
James Zou, David Parkes.
U.S. Provisional Application No.: 61/837,843 .

Recent/upcoming talks

  • 3/21/16     U Mass Amherst CS Colloquium
  • 3/9/16       Broad Institute Models, Inference, and Algorithms seminar
  • 3/7/16       NYU CS Colloquium
  • 3/4/16       UCSD CS Colloquium
  • 2/25/16     Yale CS Colloquium
  • 2/23/16     CMU CS Colloquium
  • 2/16/16     Stanford CS Colloquium
  • 2/9/16       University of Pennsylvania CIS Colloquium
  • 2/5/16       Information Theory and Applications (ITA) invited talk
  • 2/3/16       MIT Bioinformatics seminar
  • 2/1/16       Yale Biostatistics special seminar
  • 1/28/16     Stanford Biostatistics workshop
  • 1/27/16     Stanford Information Systems Colloquium
  • 1/25/16     UC Berkeley NCD seminar
  • 1/22/16     Johns Hopkins Biostatistics special seminar
  • 1/19/16     Harvard Biostatistics special seminar
  • 1/10/16     Banff Workshop on Quantitative Problems in Human Genetics and Health
  • 12/14/15   Deep Genomics invited talk
  • 12/11/15   Neural Information Processing (NIPS'15)
  • 11/23/15   MIT Machine Learning Tea
  • 11/11/15   Conference on Human Computation & Crowdsourcing (HOMP'15)
  • 11/10/15   UCSD Computer Science & Engineering Colloquium


Teaching Fellow (Fall 2011), CS281: Advanced Machine Learning.


I am a co-organizer for the 2015 Computational Aspects of Biological Information.

I enjoy writing and journalism, and have been a columnist for The Budapest Sun and The Chronicle. I have also been fortunate to serve as the president of the Harvard Graduate Dormitory Council. When not indoors, I completed 5 marathons: Berlin, Atlanta, Lake Balaton, Budapest and Philadelphia.