Publications

2015
  • Statistical inference of enhancer-gene interactions in 56 human cell and tissue types (In Review)
    Wang J, Kundaje A+ and Kellis M+
    + co-corresponding authors

  • Epigenomic and genetic variation in Alzheimer’s disease pathology across 708 individuals (In Review)
    Eaton ML, Chibnik L, Quon G, Kundaje A, Ernst J, Schneider J, Bennett DA, de Jager PL, Kellis M
     
  • Genetic control of chromatin states and gene expression in humans involves local and distal chromosomal interactions (In Review)
    Grubert F*, Zaugg J*, Kasowski M*, Ursu O*, Spacek D, Martin A, Phanstiel D, Pekowska A, Pritchard JP, Bustamante C, Steinmetz L, Kundaje A, and Snyder M
    * Equal junior contributors

  • 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)

  • Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease
    Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M.
    Nature. 2015 Feb 19;518(7539):365-9. doi: 10.1038/nature14252. (PMID: 25693568)
2014
  • A comparative encyclopedia of DNA elements in the mouse genome.
  • 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.
  • Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. (PMID: 25409824)

  • Principles of regulatory information conservation between mouse and human.
    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. 
    Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985. (PMID: 25409826)

  • Transcription factors bind negatively-selected sites within human mtDNA genes
    Blumberg A, Sailaja BS, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D
    Genome Biol Evol, September 22, 2014 doi:10.1093/gbe/evu210

  • Regulatory analysis of the C. elegans genome with spatiotemporal resolution [Website][Website]
  • 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.
  • Nature. 2014 Aug 28;512(7515):400-5. doi: 10.1038/nature13497. PMID: 25164749

  • 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

  • H3K4me3 breadth is linked to cell identity and transcriptional consistency [Website]
    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
    Cell. 2014 Jul 31;158(3):673-88. doi: 10.1016/j.cell.2014.06.027.

  • Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
    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
    Genome Res. 2014 Jul;24(7):1224-35. doi: 10.1101/gr.168807.113

  • Defining functional DNA elements in the human genome [Website/Data]
    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+
    PNAS 2014 ; April 21, 2014, doi:10.1073/pnas.1318948111
    * Equal junior contributors
    + Equal senior contributors
2013
2012
  • 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.

  • 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.

  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. [Website] [Code1] [Code2]
    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.
    Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

    *Joint First Author
2011
2008
  • A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast [pdf], [Website]
    Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C
    PLoS Computational Biology 4(11): e1000224 doi:10.1371/journal.pcbi.1000224, Nov 2008
2007
  • Learning regulatory programs that accurately predict differential expression with MEDUSA  [pdf]
    Kundaje A, Lianoglou S, Li X, Quigley D, Arias A, Wiggins CH, Zhang L, Leslie C
    Annals of the New York Academy of Sciences, July 2007
2006
  • Inferring active signaling pathways by boosting the phosphorylation network  [pdf]
    Lianoglou S, Kundaje A, Leslie C
    NIPS Workshop on Computational Biology, Nov 2006

  • A classification-based framework for predicting and analyzing gene regulatory response  [pdf], [Website]
    Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina Leslie
    BMC Bioinformatics, Vol. 7(5), Mar 2006
2005
  • 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

  • Combining Sequence and Time Series Expression Data To Learn Transcriptional Modules  [pdf], [Code]
    Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina Leslie
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2005

  • Statistical analysis of MPSS measurements: application to the study of LPS activated macrophage gene expression  [pdf]
    Gustavo Stolovitzky, Anshul Kundaje, Glenn Held, Keith Duggar, Christian Haudenschild, Daixing Zhou, Tom Vasicek, Kelly Smith, Alan Aderem, Jared Roach
    PNAS (Proceedings of the National Academy of Sciences), Vol. 102(5), pp. 1402-1407, Feb 2005

  • Predicting genetic regulatory response using classification: Yeast stress response  [pdf], [Website]
    Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina Leslie
    Lecture Notes in Computer Science, Vol. 3318(), pp. 1-13, Jan 2005
2004
Ċ
Anshul Kundaje,
Mar 22, 2013, 8:43 AM
ċ
Anshul Kundaje,
Apr 25, 2014, 2:17 AM
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