Anshul Kundaje

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Research Scientist
Kellis lab
Computer Science Dept.
MIT (Massachusetts Institute of Technology)

Address
MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) 
32 Vassar Street, 32D-514,
Cambridge, MA 02139. 
[Map]

E-mail
anshul at kundaje dot net

My research interests include computational biology and applied machine learning. I am in interested in developing algorithms for learning models of gene regulation from high-throughput functional genomics data.

I am currently a research scientist in Manolis Kellis' lab working on integrative analysis of next-generation sequencing data as part of the Roadmap Epigenomics Project and the mod/ENCODE (Encyclopedia for DNA elements) consortium.

I was a postdoc with Serafim Batzoglou and Arend Sidow in the Computer Science Dept. at Stanford University from Nov 2008 to Feb 2012 during which I worked with the ENCODE consortium.

I completed my PhD in Computer Science (Computational Biology) from Columbia University in New York in August 2008. My advisor was Dr. Christina Leslie.

Recent Talks/Publications

  • An Integrated Encyclopedia of DNA Elements in the Human Genome
    Ian Dunham, Anshul Kundaje et al. (The ENCODE Project Consortium)
    Nature 2012 (In Press)

  • Analysis of the human regulatory network using ENCODE data
    Mark Gerstein*, Anshul Kundaje* et al., Michael Snyder
    Joint First Author
    Nature 2012 (In Press)

  • Ubiquitous heterogeneity and asymmetry of the chromatin landscape at transcription regulatory elements
    Anshul Kundaje*, Sofia KP*, Max Libbrecht*, Cheryl Smith, Debashish Raha, Elliot Winters, Steven Johnson, Michael Snyder, Serafim Batzoglou, and Arend Sidow
    Genome Research 2012 (In Press)

  • ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia
    Stephen G. Landt*, Georgi Marinov*, Anshul Kundaje*, Pouya Kheradpour, et al., Michael Snyder
    Joint First Author
    Genome Research 2012 (In Press)
  • Linking disease associations with regulatory information in the human genome
    Marc Schaub, Alan Boyle, Anshul Kundaje, Serafim Batzoglou, Michael Snyder
    Genome Research 2012 (In Press)
  • Long non-coding RNAs are rarely translated
    Balázs Bánfai, Hui Jia, Jainab Khatun, Emily Wood, Brian Risk, Will Gundling, Anshul Kundaje, Harsha Gunawardena, Yanbao Yu, Ling Xie, Krzysztof Krajewski, Brian Strahl, Xian Chen, Peter Bickel, Morgan Giddings, James Brown & Leonard Lipovich
    Genome Research 2012 (In Press)

  • Genome-wide analysis of the binding sites of more than 100 transcription-related factors defines different types of genomic regions with distinct biological properties
    Kevin Y. Yip, Chao Cheng, Nitin Bhardwaj, James B. Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter J. Bickel, Michael Snyder and Mark Gerstein
    Genome Biology 2012 (In Press)

  • Genome-wide mapping of the binding sites of 126 human transcription factors (Submitted)
    Jie Wang, Jiali Zhuang, Sowmya Iyer, XinYing Lin, Troy Whitfield, Shelley Force, Aldred, Nathan Trinklein, Xianjun Dong, Melissa Greven, Anshul Kundaje, Ewan Birney, Richard Myers, William S. Noble, Michael Snyder, Zhiping Weng
    Genome Research 2012 (In Press) 
  • Predictive models of transcription factor binding using ENCODE data
    Selected talk at RECOMB Regulatory Genomics/Systems-Biology Meeting, Nov 2010

  • A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast [Website], [pdf]
    Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina Leslie.
    PLoS Computational Biology 4(11): e1000224 doi:10.1371/journal.pcbi.1000224, Nov 2008