Meromit Singer's Homepage

I am a post-doctoral associate with Aviv Regev's group at the Broad institute.
You are welcome to contact me at:   msinger <at>

In June 2018 I will be joining the cBio Center and the Department of Biostatistics and Computational Biology at DFCI,
as well as the Department of Microbiology and Immunology at the Harvard Medical School.

I received my PhD in Computer Science from UC Berkeley, where I was advised by Lior Pachter.
Before coming to Berkeley I received a BSc in Computer Science and Biology (double major) through the Bioinformatics program at Tel-Aviv University.
During that period I was fortunate to work with Eran Segal's research group at the Weizmann Institute and with Shaul Yalovsky's research group at Tel-Aviv University. 

Selected Publications

Molecular Dissection of CD8 T cell Dysfunction
Chao Wang, Meromit Singer and Ana C. Anderson
Trends in Immunology (2017) doi:10.1016/

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells
Meromit Singer*, Chao Wang*, Le Cong, Nemanja D. Marjanovic, Monika S. Kowalczyk, Huiyuan Zhang, Jackson Nyman, Kaori Sakuishi, Sema Kurtulus, David Gennert,
Junrong Xia, John Y.H. Kwon, James Nevin, Rebecca H. Herbst, Itai Yanai, Orit Rozenblatt-Rosen, Vijay K. Kuchroo^, Aviv Regev^, Ana C. Anderson^
Cell (2016) doi:
Preview by Ryan T. Sowell and Susan M. Kaech.

Controlling for conservation in genome-wide DNA methylation studies
Meromit Singer and Lior Pachter
BMC Genomics (2015) doi:10.1186/s12864-015-1604-3
Access the recommendation on F1000Prime

A diverse epigenetic landscape at human exons with implication for expression
Meromit Singer*, Idit Kosti*, Lior Pachter and Yael Mandel-Gutfreund
Nucleic Acids Research (2015) 43(7): 3498-3508

Identification and correction of systematic error in high-throughput sequence data
Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I.K. Martin, Meromit Singer^ and Lior Pachter^
BMC Bioinformatics (2011) doi:10.1186/1471-2105-12-451
Presented at The Biology of Genomes meeting, Cold Spring Harbor Labs (2011). Download slides here.
Most viewed and most forwarded paper of BMC Bioinformatics, November 2011.

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states
David I.K. Martin* Meromit Singer*, Joseph Dhahbi, Guanxiong Mao, Lu Zhang, Gary P. Schroth, Lior Pachter and Dario Boffelli
Genome Research (2011) doi:10.1101/gr.122721.111

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains
Meromit Singer*, Alexander Engstrom*, Alexander Schoenhuth^ and Lior Pachter^
Statistical Applications in Genetics and Molecular Biology, 10 (2011), Article 43.

Nitrogen source interacts with ROP signaling in root hair tip-growth
Daria Bloch, Gabriele Monshausen, Meromit Singer, Simon Gilroy and Shaul Yalovsky.
Plant, Cell and Environment, (2011) 34, 76-88.

MetMap enables genome-scale methyltyping for determining methylation states in populations
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schoenhuth , Gary P. Schroth, David I.K. Martin and Lior Pachter
PLoS Computational Biology, 6 (2010), e1000888.

Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells
Neri Minsky, Efrat Shema, Yair Field, Meromit Schuster, Eran Segal and Moshe Oren
Nature Cell Biology (2008) 10(4):483 - 488.

* - joint first author. ^ - joint corresponding author.

Peer-Reviewed Book Chapters

Bayesian networks in the study of genomewide DNA methylation
Meromit Singer and Lior Pachter
Probabilistic Graphical Models for Genetics, Genomics and Postgenomics, (2014) Oxford University Press.


Statistical algorithms in the study of mammalian DNA methylation
Meromit Singer
University of California, Berkeley (2012) Technical Report No. UCB/EECS-2012-272


SysCall - Distinguishing heterozygous sites from systematic errors.

MetMap - Inference of Genomewide Methylation from MethylSeq Experiments.

COMPARE - Unbiased comparisons of DNA methylation tendencies.