James Y. Zou

Maxwell Dworkin 240
33 Oxford Street
Cambridge, MA 02138
jzou at fas harvard edu

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.


Computational Biology

Inferring parental genomic ancestries using pooled semi-Markov processes.
James Zou, Eran Halperin, Esteban Burchard, Sriram Sankararaman
Accepted by Bioinformatics (ISMB 2015).

Extended fertility and longevity: the genetic and epigenetic link.
Kerem Wainer-Katsir, James Zou, Michal Linial
Fertility and Sterility 2015.

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

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 2014, 11(3).
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.

Correcting for sample heterogeneity in epigenome-wide association studies.
James Zou
Methods in Molecular Biology forthcoming, 2015.

Locus-specific chromatin inactivation at endogenous enhancers with programmable TALE-LSD1 fusions.
Accepted by Nature Biotechnology, 2013.

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

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.
PNAS 2011, 108(36)

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. [PDF]
Bo Zhao, James Zou [co-first author], et al.
PNAS 2011, 108(36)

Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. [PDF]
B Gewurz, J Mar, M Padi, B Zhao, N Shinners, K Takasaki, E Bedoya, J Zou, E McFarland, J Quackenbush, E Kieff
Journal of Virology 2011, 85(13)

Epstein-Barr virus nuclear antigens 3C and 3A maintain lymphoblastoid cell growth by repressing p16INK4A and p14ARF expression. [PDF]
S Maruo, B Zhao, E Johannsen, E Kieff, J Zou, K Takada
PNAS 2011, 108(5)

Machine Learning/AI

Rich component analysis. [PDF]
Rong Ge, James Zou [alphabetical]. 2015

Intersecting Faces: Non-negative Matrix Factorization With New Guarantees.
Rong Ge, James Zou [alphabetical].
International Conference on Machine Learning (ICML'15), 2015

Crowdsourcing Feature Discovery via Adaptively Chosen Comparisons. [PDF]
James Zou, Kamalika Chaudhuri, Adam Tauman Kalai. 2015

Incentive Compatible Experimental Design.
Panos Toulis, David Parkes, Elery Pfeffer, James Zou.
ACM Conference on Economics and Computation (EC'15), 2015

Contrastive Learning Using Spectral Methods.
James Zou, Daniel Hsu, David Parkes, Ryan Adams.
Neural Information Processing Systems (NIPS' 13), 2013

Priors for Diversity in Generative Latent Variable Models. [PDF]
James Zou, Ryan Adams.
Neural Information Processing Systems (NIPS' 12), 2012

A Slime Mold Solver for Linear Programming Problems. [PDF]
Anders Johannson, James Zou
Lecture Notes in Computer Science, 7318, 2012

Get another worker? Active crowdlearning with sequential arrivals. [PDF]
James Zou, David Parkes
In the Proceedings of Workshop on Machine Learning in Human Computation and Crowdsourcing (ICML'12), 2012

Threats and Trade-Offs in Resource Critical Crowdsourcing Tasks Over Networks. [PDF]
S Nath, P Dayama, D Garg, Y Narahari, J Zou
In the Proceedings 8th Workshop on Internet and Network Economics (WINE'12), 2012

Tolerable Manipulability in Dynamic Assignment without Money. [PDF]
James Zou, Sujit Gujar, David Parkes
In the Proceedings 24th AAAI Conference on Artificial Intelligence (AAA'10), 2010

Dynamic House Allocation. [PDF]
Sujit Gujar, James Zou, David Parkes
In the Proceedings 5th Multidisciplinary Workshop on Advances in Preference Handling (MPREF'10), 2010

Data science and mathematical modeling

Approval voting behavior in Doodle.
James Zou, Reshef Meir, David Parkes
Accepted by CSCW 2015. Honorable mention for best paper :) Top 5% of submissions.

Are you Going to Do That? Contingent-Payment Mechanisms to Improve Coordination.
Hongyao Ma, Reshef Meir, David C. Parkes and James Zou
Preliminary version to appear at AMMA, 2015.

Incentive compatible experimental design.
Panos Toulis, David Parkes, Elery Pfeffer, James Zou, Guy Gildor
Accepted by Conference on Digital Experimentation, 2014

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, 2013

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

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


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


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