C.V.

Anshul Kundaje

Assistant Professor
Dept. of Genetics, 

Dept. of Computer Science,
Stanford University

09/2013 - Present

Address: 300 Pasteur Drive, Lane L301B

Stanford, CA 94305-5120, USA

Email: akundaje@stanford.edu

Phone: (650)-723-2353


EDUCATION / TRAINING


Research Scientist

Computer Science Dept. (Computational Biology Group)

Computer Science and Artificial Intelligence Lab (CSAIL)

Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

Mentor: Prof. Manolis Kellis


02/2012 – 08/2013

Postdoctoral Research Associate
Computer Science Dept.

Stanford University
Mentors: Prof. Serafim Batzoglou, Prof. Arend Sidow


11/2008 – 01/2012

PhD in Computer Science

Columbia University in the City of New York
Advisor: Dr. Christina Leslie


09/2003 – 10/2008

M.S. in Electrical Engineering
Columbia University in The City of New York

CGPA 3.72


09/2001 – 02/2003


B.E. in Electrical Engineering

Veermata Jijabai Technological Institute (V. J. T. I.), Mumbai University, India

Passed with Distinction,  Rank 1 in Mumbai University

07/1997 – 06/2001


AWARDS

  • NIH Director's New Innovator Award (2016-2021)
  • Alfred Sloan Foundation Research Fellowship (2014-2016)
  • Prof. P.R Dandavate Memorial Award: Highest GPA in the Bachelor’s Program. (2001)
  • D.D. & L.H. Prize: Consistent Academic Career in the Bachelor’s Program. (2001)
  • M.B.P. Memorial Foundation Award: Highest GPA in final Year of Bachelors Program. (2001)
  • National Scholarship of Central Board Of Secondary Education India for highest score (100%) in Mathematics. (1995)

PEER-REVIEWED PUBLICATIONS                                             * Joint first-author/equal contribution


  1. Corces RM, Buenrostro J, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics (2016) doi:10.1038/ng.3646
  2. Loh KM, Chen A, Koh PW, Deng T, Sinha R, Tsai JM, Barkal AA, Shen KY, Jain R, Morganti RM, Ng SC, Morganti RM, Fernhoff NB, George BM, Wernig G, Salomon RAE, Chen Z, Vogel H, Epstein JA, Kundaje A, Talbot WS, Beachy PA, Ang LT, Weissman IL. Mapping the pairwise choices and molecular transitions leading from pluripotency to human bone, heart and other mesoderm cell-types. Cell , Volume 166 , Issue 2 , 451 - 467
  3. Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB. Impact of the X Chromosome and sex on regulatory variation. Genome Res. 2016 Apr 21 [Epub ahead of print] (PMID: 27197214)
  4. Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM. An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency. Cancer Cell. 2016 May 9;29(5):697-710. doi: 10.1016/j.ccell.2016.03.003. Epub 2016 Apr 14 (PMID: 27150038)
  5. Webb AE, Kundaje A, Brunet A. Characterization of the direct targets of FOXO transcription factors throughout evolution. Aging Cell. 2016 doi: 10.1111/acel.12479. (PMID: 27061590)
  6. Grubert F*, Zaugg J*, Kasowski M*, Ursu O*, Spacek DV, Greenside P, Srivas R, Martin A, Phanstiel D, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JP, Bustamante C, Steinmetz L, Kundaje A, and Snyder M. Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell. 2015 Aug 19. pii: S0092-8674(15)00964-2. doi: 10.1016/j.cell.2015.07.048
  7. Sazonova O, Zhao Y, Nürnberg S, Miller C, Pjanic M, Castano VG, Kim JB, Salfati EL, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. PLoS Genet. 2015 May 28;11(5):e1005202. doi: 10.1371/journal.pgen.1005202. eCollection 2015 May. (PMID: 26020271)
  8. Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution. Dev Cell. 2015 Mar 23;32(6):772-4. doi: 10.1016/j.devcel.2015.03.004. (PMID: 25805139)
  9. Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P; Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet. 2015 Mar 9. doi: 10.1038/ng.3245 (PMID: 25751624)
  10. 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. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. (PMID: 25693563)
  11. Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature. 2015 Feb 19;518(7539):365-9. doi: 10.1038/nature14252. (PMID: 25693568)
  12. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985. (PMID: 25409826)
  13. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. (PMID: 25409824)
  14. Blumberg A, Sailaja BS, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D. Transcription factors bind negatively-selected sites within human mtDNA genes. Genome Biol Evol, September 22, 2014 doi:10.1093/gbe/evu210 (PMID: 25245407)
  15. Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 2014 Aug 28;512(7515):400-5. doi: 10.1038/nature13497. (PMID: 25164749)
  16. 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. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415. (PMID: 25164756)
  17. 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. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668. (PMID: 25164757)
  18. Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell. 2014 Jul 31;158(3):673-88. doi: 10.1016/j.cell.2014.06.027. (PMID: 25083876)
  19. Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res. 2014 Jul;24(7):1224-35. doi: 10.1101/gr.168807.113. (PMID: 24985916)
  20. Kellis M, Wold BJ, Snyder MP, Bernstein BE, Kundaje A*, Marinov GK*, Ward LD*, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Defining functional DNA elements in the human genome. PNAS 2014 ; April 21, 2014, doi:10.1073/pnas.1318948111 (PMID: 24753594)
  21. Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda). 2013 Dec 17. pii: g3.113.008680v1. doi: 10.1534/g3.113.008680 (PMID: 24347632)
  22. Hardee JM, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder M. STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B Cell Lymphoma. G3 (Bethesda). 2013 Oct 18. pii: g3.113.007674v1. doi: 10.1534/g3.113.007674. (PMID: 24142927)
  23. Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia Q, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive Variation in Chromatin States Across Humans. Science. 2013 Oct 17; DOI:10.1126/science.1242510 (PMID: 24136358)
  24. Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucl. Acids Res. 2012 doi:10.1093/nar/gks1284 (PMID: 23221638)
  25. Dunham I, Kundaje A**, et al., ENCODE Project Consortium. An integrated Encyclopedia of DNA Elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. (PMID: 22955616) ** First  author (non-PI) amongst 594 authors
  26. 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. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. (PMID: 22955619) ** First  author (non-PI)
  27. Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012 Sep;22(9):1735-47. (PMID: 22955985)
  28. Landt SG, Marinov GK, Kundaje A*, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31. PMID: 22955991
  29. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59. PMID: 22955986
  30. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. PMID: 22955990
  31. Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012 Sep;22(9):1646-57. PMID: 22955977
  32. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 26;13(9):R48. PMID: 22950945
  33. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Jun 13;13(9):R53. PMID: 22950368
  34. ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222
  35. Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C. A predictive model of the oxygen and heme regulatory network in yeast. PLoS Comput Biol. 2008 Nov;4(11):e1000224. PMID: 19008939
  36. Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA. Ann N Y Acad Sci. 2007 Dec;1115:178-202. PMID: 17934055
  37. Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S5. PMID: 16723008
  38. Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C. Combining sequence and time series expression data to learn transcriptional modules. IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202. PMID: 17044183
  39. Stolovitzky GA, Kundaje A*, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach JC. Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1402-7. PMID: 15668391
  40. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification. Bioinformatics. 2004 Aug 4;20. PMID: 15262804 (Also in proceedings of ISMB 2004)
  41. Sussilo D, Kundaje A, Anastassiou D, Spectrogram Analysis of Genomes, EURASIP Journal of Applied Signal Processing, 2003.



PREPRINTS


  1. Shrikumar A, Greenside P, Shcherbina A, Kundaje A. Not Just a Black Box: Learning Important Features Through Propagating Activation Differences. ArXiv e-prints [Internet]. 2016 May 1, 2016; 1605. https://arxiv.org/abs/1605.01713
  2. Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution. bioRxiv 054031; doi: http://dx.doi.org/10.1101/054031

CONFERENCE PROCEEDINGS

  1. Wang, B, Zhu, J, Pourshafeie, A, Ursu, O, Batzoglou, S, Kundaje, A. Unsupervised Learning from Noisy Networks with Applications to Hi-C Data. In Advances In Neural Information Processing Systems. pp. 3297-3305. 2016
  2. Koh PW, Pierson E, Kundaje A. Denoising genome-wide histone ChIP-seq with convolutional neural networks. Proceedings of The ICML 2016 Workshop on Computational Biology. bioRxiv doi: http://dx.doi.org/10.1101/052118 (Preprint)
  3. Lianoglou S, Kundaje A, Leslie C. Inferring active signaling pathways by boosting the phosphorylation network. Proceeding of the NIPS Workshop on Computational Biology, 2006
  4. Middendorf M, Kundaje A, Shah M, Freund Y, Wiggins C, Leslie C, Motif Discovery through predictive modeling of gene regulation, Proceeding of RECOMB, 2005.
  5. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C, Predicting genetic regulatory response using classification: Yeast stress response, Lecture Notes in Computer Science, Vol. 3318(), pp. 1-13, 2005.

INVITED / SELECTED TALKS

  1. Invited: Computational analysis of genomic data at The Center for Evolutionary Genomics and Medicine (EGM) at The Ben Gurion University of the Negev, Israel, Nov 2016
  2. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at The MIA Seminar Series, Broad Institute of MIT and Harvard, Boston, MA, Nov 2016
  3. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at Duke University CBB Seminar, Raleigh, NC, Nov 2016
  4. Invited: NHGRI Computational Genomics and Data Science Workshop at The NIH, Bethesda, MD, Sept 2016
  5. Invited: Deep learning models of transcription factor binding and chromatin accessibility in diverse human cell types and lineages at The Welcome Trust Genome Informatics Meeting, Hinxton, UK, Sept 2016
  6. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at ISMB 2016 Regulatory Genomics Special Interest Group, Orlando, FL, July 2016
  7. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at IBM TJ Watson Research Center, New York, NY, June 2016
  8. Invited: Decoding the human genome to decipher the genomic basis of disease at the Future of AI Meeting organized by Stanford AI and the White House Office of Science and Technology, Stanford, CA, June 2016
  9. Invited: How to train your DragoNN (Deep Regulatory genomic neural network) at the 2016 ENCODE Consortium Users Meeting, Stanford, CA, June 2016
  10. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at University of Massachusetts Medical School, Worcester, MA, April 2016
  11. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at Boston University Systems Biology Seminar, Boston, MA April 2016
  12. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at Microsoft Research New England, Boston, MA, April 2016
  13. Invited: Dynamics of 3D enhancer-gene associations across diverse human cell types and tissues at The Simons Institute Network Biology Workshop, Berkeley, CA, April 2016
  14. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at Illumina Inc, CA, April 2016
  15. Invited: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at The RIKEN Institute, Japan, March 2016
  16. Selected: Interpretable, integrative deep learning frameworks for regulatory genomics and epigenomics at The Cold Spring Harbor Meeting on Systems Biology: Global Regulation of Gene Expression, NY, March 2016
  17. Invited: Integrative deep learning frameworks for regulatory genomics and epigenomics at The Simons Institute Regulatory Genomics and Epigenomics Workshop, Berkeley, CA, March 2016
  18. Invited: Deep learning frameworks for regulatory genomics and epigenomics at Epigenomics 2016, Puerto Rico, Feb 2016
  19. Invited: Deep learning frameworks for regulatory genomics and epigenomics at Verily (Google Life Sciences), Mountain View, CA, Jan 2016
  20. Invited: Deep learning frameworks for regulatory genomics at Seminar Series of Computational Biology department at Memorial Sloan Kettering Cancer Center, NY, Dec 2015
  21. Invited: Deep learning frameworks for regulatory genomics at Seminar Series of the Systems Biology Department at Columbia University, NY, Dec 2015
  22. Invited: Deep learning frameworks for regulatory genomics at EMBL-Stanford Meeting on Personalised Health, Heidelberg, Germany, Nov 2015
  23. Invited: Deep learning frameworks for regulatory genomics at Calico Labs, San Francisco, CA, Nov 2015
  24. Selected: Deep learning the relationship between chromatin architecture, chromatin state and transcription factor binding at Annual meeting of The American Society of Human Genetics (ASHG) 2015., Baltimore, MD, Oct 2015
  25. Invited: Deep learning frameworks for regulatory genomics at the Genomics@JHU seminar at John's Hopkins University, Baltimore, MD, Sept 2015
  26. Invited: Leveraging reference epigenomes to decipher the genetic and molecular basis of complex diseases at CCSB Seminar at The Dana Farber Cancer Center, Boston, MA, April 1, 2015.
  27. Invited: Leveraging reference epigenomes to decipher the genetic and molecular basis of complex diseases at The Cornell-Weill Medical School, NYC, NY. Mar 18, 2015.
  28. Selected: Deep learning chromatin architecture, chromatin state and TF binding from a single assay at The 2015 ENCODE Consortium Meeting at The Cold Spring Harbor Labs, NY. Mar 16, 2015
  29. Invited: Regulatory Genomics and Epigenomics of Complex Disease at the La Jolla Institute of Allergy and Immunology in San Diego, CA. Feb 23. 2015
  30. Invited: Regulatory Genomics and Epigenomics of Complex Disease at The Epigenomics in Disease Session of the 2015 22nd Annual Molecular Medicine Tri-Conference in San Francisco, CA. Feb 16, 2015
  31. Invited: Learning and Visualizing Regulatory Landscapes across 100s of Human Tissue Types at the 2015 AAAS Meeting's session on Visualizing Biomedical Data and Processes Across Space and Time Scales, San Jose, CA. Feb 13, 2015
  32. Selected: Deep learning regulatory elements, chromatin architecture and chromatin state at The Cold Spring Harbor Systems Biology Meeting in Puerto Rico. Jan 28 2015
  33. Invited: Deciphering regulatory elements, factors, genes and pathways downstream of non-coding CRC GWAS variants at The GECCO Colorectal Cancer consortium meeting in Seattle. Jan 26 2015
  34. Invited: Three Dimensional Gene Regulation at the 2014 Neural Information Processing Systems (NIPS) workshop on Machine Learning in Computational Biology (MLCB) in Montreal, Canada. Dec 13 2015
  35. Invited: Learning three-dimensional regulatory interactomes at The Genetics/Bioinformatics and Systems Biology Colloquium at UCSD, CA. Nov 20, 2014
  36. Invited: Immune and neural epigenomics of Alzheimer’s disease in mouse and human at Big Ideas in Neuroscience Symposium. Stanford, CA. June 20 2014
  37. Invited: Integrative analysis of 111 Epigenomes at Symposium on Epigenetic Mechanisms in Cancer. Toronto, Canada, June 4 2014
  38. Invited: Learning Integrative Regulation Programs Across Diverse Human Cell Types at The 2014 Midwest Chromatin and Epigenetics meeting at The University of Wisconsin Madison. Wisconsin, MA. May 18 2014
  39. Invited: Interpreting non-coding genetic variants using functional genomic data at Novo Nordisk. Seattle, WA, April 18 2014
  40. Invited: Interpreting non-coding genetic variants using functional genomic data at the Genetic and Molecular Epidemiology (GAME) seminar series at The Fred Hutchinson Cancer Research Center. Seattle, WA. April 17 2014
  41. Invited: Integrative analysis of ENCODE data at ENCODE and Epigenomics Workshop organized by EBI-EMBL and Novartis. Boston, MA, April 15-16 2014
  42. Invited: Regulatory chromatin state variation across individuals, populations and cell types at UC Berkeley Statistics and Genomics Seminar. UC Berkeley, CA,  March 6 2014
  43. Invited: The dynamic regulatory architecture of the human genome at Stanford CS Computational Biology Dinner. Stanford, CA, January 2014
  44. Selected: Integrating Gene Expression and Sequence Data with Existing Biological Knowledge to Model Context-specific Gene Regulation at RECOMB/ISCB Conference on Regulatory and Systems Genomics 2013, Nov 2013 (Presented by Sofia KP)
  45. Selected: Epigenomic variation between species, tissues, populations and individuals. Platform Talk at American Society of Human Genetics (ASHG) 2013. Boston, MA, Oct 2013
  46. Invited: Dynamics of chromatin state and gene regulation across human cell-types and individuals. BIRS Statistical Data Integration Challenges in Computational Biology: Regulatory Networks and Personalized Medicine. Banff, Canada, Aug 2013
  47. Selected: Comparative analysis of chromatin state dynamics across organisms, cell types and individuals. Cold Spring Harbor Labs Biology of Genomes 2013. CSHL, NY. May 2013
  48. Invited: Heterogeneity of chromatin patterns are regulatory elements. American Society of Human Genetics (ASHG) 2012 - DNAnexus session. San Francisco, CA. Nov 2012
  49. Selected: Deciphering functional heterogeneity in the human genome using ENCODE data. ENCODE and modENCODE AWG/PI meeting. Cambridge, MA. May 2012
  50. Selected: Predictive models of transcription factor binding using ENCODE data. RECOMB Regulatory Genomics/Systems-Biology Meeting. New York, NY. Nov 2010
  51. Invited: Computational models for de-novo prediction of protein-ligand interactions. The Biopeople symposium on bioinformatics in the drug discovery value chain. University of Copenhagen, Denmark. Nov 2010
  52. Invited: Predictive Models of Gene Regulation- From Yeast to Humans. Stanford Biological Modeling Club, Stanford University. Oct 2010
  53. Selected: A supervised machine learning framework for integrative analysis of ENCODE data. ENCODE Consortium meeting. March 2009
  54. Invited: Predictive models of gene regulation. Broad Institute of MIT and Harvard. Cambridge, MA. 2008
  55. Selected: Hypoxia regulatory networks in yeast. Annual Yeast Molecular Biology meeting. 2006
  56. Selected: Predictive modeling of gene regulation. RECOMB Satellite Workshop on Regulatory Genomics. 2004
  57. Selected: A Classification based framework of learning gene regulatory networks. NIPS workshop on Methods in Computational Biology. 2004
  58. Invited: Using sequence and expression data to learn transcriptional modules. IBM T.J. Watson Research center. 2001

PROFESSIONAL ACTIVITIES

  • Journal Reviewer / Guest Editor (GE): 
    • Nature Methods: 2014, 2016
    • Nature Communications: 2016
    • Nature Genetics: 2016
    • Genetics: 2015
    • JAMA: 2014
    • Genome Research: 2012,2013,2014,2015
    • Genome Biology: 2012,2013,2014, 2015
    • PLOS Computational Biology: 2010, 2012, 2013, 2014, 2016
    • PLOS One: 2012
    • PLOS Genetics: 2016 (GE)
    • TCBB: 2013
    • G3: 2013
    • Bioinformatics: 2012, 2015, 2016
    • Nucleic Acids Research: 2015
    • BMC Bioinformatics: 2014
    • In-silico Biology: 2011
    • IEEE Signal Processing Magazine: 2011
    • Columbia University Undergraduate Science Journal: 2008
    • Physiological Genomics: 2008
    • Molecular Systems Biology: 2016
    • eLife: 2016 (GE)
  • Conference Reviewer / Program Committee (PC)
    • Neural Information Processing Systems (NIPS): 2007, 2012, 2013, 2014, 2015, 2016
    • NIPS Machine Learning in Computational Biology (MLCB): 2015 (PC), 2016 (PC)
    • Research in Computational Molecular Biology (RECOMB): 2010, 2011
    • RECOMB Regulatory and Systems Genomics Workshop: 2016 (PC)
    • Intelligent Systems in Molecular Biology (ISMB): 2012, 2013 (PC), 2014, 2015, 2016 (PC)
    • IEEE Computer Systems Bioinformatics: 2004
    • International Workshop on Machine Learning in Systems Biology (MLSB): 2016 (PC)

TEACHING


Stanford Courses

  • GENE236/ CS273B / BIOMEDIN273B (Deep Learning for Genomics and Biomedicine) - Autumn 2016: 9/26/2016 - 12/13/2016

  • GENE245 / BIO268 / STATS345 / CS373 / BIOMEDIN245 (Statistical and Machine Learning Methods for Genomics) - Spring 2016: 3/29/2016 - 5/31/2016

  • GENE245 / BIO268 / STATS345 / CS373 / BIOMEDIN245 (Statistical and Machine Learning Methods for Genomics) - Spring 2015: 3/30/2015 - 6/11/2015

  • GENE205 (Advanced Genetics) - Winter 2016: 1/28/2016

  • GENE205 (Advanced Genetics) - Winter 2015: 1/6/2015 - 2/19/2015

  • GENE205 (Advanced Genetics) - Winter 2014: 1/28/2014, 2/11/2014

  • GENE200 (Genetics Training Camp) - Autumn 2016

  • GENE200 (Genetics Training Camp) - Autumn 2015

  • GENE200 (Genetics Training Camp) - Autumn 2014: 9/8/2014 - 9/12/2014

  • GENE200 (Genetics Training Camp) - Autumn 2013: 9/9/2013 - 9/13/2013


Stanford Guest Lectures/Seminars
  • BIO209A (The Human Genome and Disease: 1/11/2016, 1/13/2016

  • CS300 (Computer Science): 11/02/2015

  • HUMBIO151R (Biology, Health and Big Data): 4/20/2015

  • BIO209A (The Human Genome and Disease: 4/21/2015, 4/23/2015

  • BIOMEDIN 201 (Biomedical Informatics Seminar): 7/15/2014

  • BIO209A (The Human Genome and Disease): 4/1/2014, 4/3/2014

  • BioStatistics Workshop Seminar (Stanford): 2/27/2014

  • CS300 (Computer Science): 2013


External Teaching/Courses

Teaching Assistant

  • Computational Genomics (Columbia University): Summer 2002, Spring 2004

  • Machine Learning (Columbia University): Spring 2006

  • Computer Networks (Columbia University): Spring 2002



MENTORING

Graduate Students

  1. Chuan-Sheng Foo (Computer Science, Stanford): 2013-Present (A*STAR Fellow)
  2. Oana Ursu (Genetics, Stanford): 2013-Present (HHMI International Student Fellow)
  3. Daniel Kim (Biomedical Informatics, Stanford): 2013-Present (BioX Fellow)
  4. Irene Kaplow (Computer Science, Stanford University): 2010-2011, 2013 - Present (CEHG Fellow)
  5. Peyton Greenside (Biomedical Informatics, Stanford): March 2014 - Present (BioX SIGF Fellow)
  6. Johnny Israeli (Biophysics, Stanford): Sept 2014 - Present (BioX SIGF Fellow)
  7. Avanti Shrikumar (Computer Science, Stanford): Sept 2014 - Present (BioX Fellow, HHMI International Student Fellow, Microsoft Women's Fellow)
  8. Chris Probert (Genetics, Stanford): Sept 2015 - Present (NSF Fellow)
  9. Michael Wainberg (Computer Science, Stanford): Sept 2015 - Present (BioX Fellow)
  10. Anna Scherbina (Biomedical Informatics, Stanford): Jan 2016 - Present
Postdocs
  1. Maryna Taranova (From UC Irvine, Computational Chemistry): Sept 2014-Present
  2. Jianrong Wang (From MIT): March 2016 - Present
Alumni in Industry
  1. Nathan Boley (Postdoctoral Associate): Jan 2015 - Sept 2016. Now Research Scientist at Driver Group
  2. Sofia Kyriazopoulou-Panagiotopoulou (PhD, Computer Science, Stanford, 2014) - Now Research Scientist at 10X Genomics
Qualifying exam Committee
  1. Alex Bishara (CS, Stanford)
  2. Bo Wang (CS, Stanford)
  3. Bharath Ramsundar (CS, Stanford)
  4. Johnny Israeli (Biophysics, Stanford)
  5. Jenny Hsu (Genetics, Stanford)
  6. Oana Ursu (Genetics, Stanford) 
  7. Alicia Schep (Genetics, Stanford)
  8. Emily Tsang (BMI, Stanford)
  9. Jessica Chang (Genetics, Stanford)
  10. Joe Charalel (BMI, Stanford)
  11. Ben Dulkan (MD-PhD, Stanford)
  12. Diego Calderon (BMI, Stanford)
  13. Natalie Telis (BMI, Stanford)
  14. Kristin Muench (Neuroscience, Stanford)
  15. Eli Moss (Genetics, Stanford)
  16. Brayon Fremin (Genetics, Stanford)
  17. Maxwell Mumbach (Genetics, Stanford)
  18. Devin Alpoel King (Biology, Stanford)
  19. Chris Probert (Genetics, Stanford)
Thesis Committee / Reader
  1. Lin Huang (CS, Stanford): 2016
  2. Akosua Busia (MCS undergraduate, Stanford) - Served as Reader on Thesis: 2016
  3. Sofia Kyriazopoulou-Panagiotopoulou (CS, Stanford): 2014
  4. Cristina Pop (CS, Stanford): 2014
  5. Dorna Kashef (CS, Stanford): 2015
  6. Yoni Donner (CS, Stanford): 2015
  7. Glenn Markov (Genetics, Stanford)
  8. Oana Ursu (Genetics, Stanford) 
  9. Alicia Schep (Genetics, Stanford)
  10. Aaron Daugherty (Genetics, Stanford)
  11. Joe Charalel (BMI, Stanford)
  12. Wen Torng (Bioengg, Stanford)

Other graduate student mentees

  1. Bo Wang (CS, Stanford): Jan 2014 - Present
  2. Nadine Hussami (EE, Stanford University): 2010-2011, 2016 - Present
  3. Azar Fazel (EE, Stanford): 2014
  4. Nischay Kumar (CS, MIT): 2012 - 2013
  5. Vinay Kartha (Bioinformatics, Boston University): 2012 – 2013
  6. Steve Lianoglou (CS, Columbia University): 2006-2008
Undergraduate students mentees
  1. Brian Hie (CS, Stanford): Honor's thesis: 2015-2016
  2. Akosua Busia (MCS, Stanford): 2015-2016
  3. Kayla McCue (Applied Math, Caltech): Summer 2014
  4. Kenneth Chang (CS, USC): Summer 2014
  5. Eric Kofman (CS, Stanford): 2013
  6. Sean Scott (CS, Stanford): 2013
  7. Tyler Davis (CS, Stanford): 2013-2014
  8. Hayden Metsky (CS, MIT): 2012 - 2013
  9. Max Libbrecht (CS, Stanford University): 2009-2011
  10. Jon Rodriguez (CS, Stanford University): 2010-2011
  11. Sarah Xing (Biomedical Informatics, Stanford University): 2011
High school students mentees
  1. Nikhil Cheerla (Monta Vista High School): Summer 2016
  2. Rahul Mohan (Bellarmine College Preparatory, San Jose, CA): Summer 2015, Summer 2016
  3. Pranav Reddy (Harker School, San Jose, CA): Summer 2014 (Semifinalist in Intel Science Talent Show)
  4. Aniruddh Mathukumili (Mountain Vista School, Denver, CO): Summer 2014
  5. Aathira Menon (Harker School, San Jose, CA): Summer 2014
  6. Neha Sunil (Harker School, San Jose, CA): Summer 2014

INDUSTRY EXPERIENCE

 Deep Genomics

Scientific Advisory Board

  11/2015 – Present
 Epinomics Inc.

Advisor

Clinical epigenomics startup


  09/2015 – Present

Silicon Valley Biosystems (SVBio):
Consultant

Medical genomics startup

10/2012 – 07/2013


DNAnexus Inc., https://dnanexus.com

Consultant

Cloud-based Next-generation sequencing data analysis and storage

06/2010 - 11/2010

IBM T.J. Watson Research Center, Functional Genomics and Systems Biology group.
Research software engineer

Published one of the first statistical noise models for massively parallel signature sequencing (MPSS) data in collaboration with Lynx Therapeutics and Institute for Systems biology (Alan Aderem lab) [18]

Manager: Gustavo Stolovitzky


01/2002 - 09/2002

  

OTHER ACTIVITIES

  • Founder of the Indian Students Association (ISAC) at Columbia University (2003 – 2008). Organized charitable events UTSAV 2005, 2007 and 2008. Proceeds from the event were donated to victims of Pakistan earthquake (2005), micro-financing efforts in India (2007) and a secondary school in rural India (2008)
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