Assistant Professor
Dept. of Genetics
Dept. of Computer Science
Stanford University

Department of Genetics
300 Pasteur Dr., Lane Building, L301
Stanford, CA 94305-5120, USA [Map]

E-mail: anshul @ kundaje .net ; akundaje @ stanford .edu 
Phone: (650)-723-2353 ; Fax: (650)-725-1534

My primary research interests are computational biology and applied machine learning with a focus on gene regulation. Our research focusses on development of statistical and machine learning methods for integrative analysis of diverse functional genomic and genetic data to learn models of gene regulation. We have led the analysis efforts of the Encyclopedia of DNA Elements (ENCODE) and The Roadmap Epigenomics Projects with the development of novel methods for 
  1. Adaptive thresholding and normalization of massive collections of functional genomic data (e.g. ChIP-seq and DNase-seq)
  2. Dissecting combinatorial transcription factor co-occupancy within and across cell-types
  3. Predicting cell-type specific enhancers from chromatin state profiles
  4. Exploiting expression and chromatin co-dynamics with to predict enhancer-target gene links
  5. Jointly modeling sequence grammars at regulatory elements and their chromatin state dynamics, expression changes of regulators and functional interaction data to learn unified multi-scale gene regulation programs
  6. Elucidating the heterogeneity of chromatin architecture at regulatory elements
  7. Improving the detection and interpretation of potentially causal disease-associated variants from Genome-wide association studies
More recently, we have also been developing methods to 
  1. Decipher the functional heterogeneity of transcription factor binding
  2. Infer causal regulatory mechansisms by integrating diverse functional genomic data from temporal (e.g. differentiation/reprogramming) and perturbation (e.g. drug response, knockdown, genome-editing) experiments
  3. Model the complex relationships between genetic variation, regulatory chromatin variation and expression variation in healthy and diseased individuals
  4. Deep learning frameworks for functional genomics
For more details see our Projects


More News


2012-2013, I was a Research Scientist in Manolis Kellis' lab at MIT and The Broad Institute studying epigenomic and chromatin state dynamics across organisms, cell-types and individuals as part of the Roadmap Epigenomics Project and the mod/ENCODE (Encyclopedia for DNA elements) consortium. 

2008 - 2012, I was a Postdoctoral Research Associate with Serafim Batzoglou and Arend Sidow in the Computer Science Dept. at Stanford University. I served as one of the lead data coordinators and computational analysts for the ENCODE consortium. My primary focus was on deciphering heterogeneity of regulatory interactions in the human genome. I also developed ENCODE's ChIP-seq statistical data analysis pipeline.

2003-2008, I was a graduate student (PhD.) in Christina Leslie's lab in the Computer Science Dept. at Columbia University in New York. I developed Machine Learning methods for modeling transcriptional gene regulation in yeast and worm. 

2002-2003, I briefly worked at the IBM T.J. Watson Research Center in the Functional Genomics and Systems Biology group under Gustavo Stolovitzky. I developed one of the first statistical noise models for massively parallel sequencing data (MPSS) in a collaboration with The Institute of Systems Biology and Lynx Therapeutics.

In a past life, I was an Electrical Engineer (B.E from Mumbai University, 2001 and M.S. from Columbia University, 2002) and worked on computer networks and voice over IP.


  • An integrated encyclopedia of DNA elements in the human genome
    Dunham I, Kundaje A, ENCODE Project Consortium
    Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

  • Integrative analysis of 111 reference human epigenomes
    Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.
    Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. (PMID: 25693563)

  • Architecture of the human regulatory network derived from ENCODE data. [Website]
    Gerstein MB*, Kundaje A*, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. 
    Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.
    *Joint First Author

  • Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. [Website] [Code]
    Kundaje A*, Kyriazopoulou-Panagiotopoulou S*, Libbrecht M*, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. 
    Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.
  • Motif Discovery through predictive modeling of gene regulation  [pdf], [Website]
    Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina Leslie
    RECOMB (Research in Computational Biology), May 2005

  • Comparative analysis of regulatory information and circuits across distant species [Website/Data]
    Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.
    Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668

  • Comparative analysis of metazoan chromatin organization [Website/Data]
  • Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. 
  • Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415
    Subpages (1): Lab Photos