Publications

Lab members are underlined in bold
* co-corresponding or co-first authorship

Preprints
Peer-reviewed Journal Publications, Conference Proceedings, Extended Abstracts

2019
  • Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts [Code]
    Nair S, Kim DS, Perricone J, Kundaje A
    bioRxiv 605717 doi: https://doi.org/10.1101/605717
    (Accepted to ISMB 2019. To be published in Bioinformatics)

  • Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines Using Integrated Gradients [Code] [Videos]
    Shrikumar A, Prakash E, Kundaje A.
    bioRxiv 457606; doi: https://doi.org/10.1101/457606
    (Accepted to ISMB 2019. To be published in Bioinformatics)

  • Kipoi: accelerating the community exchange and reuse of predictive models for regulatory genomics [Website] [Code] [Preprint]
    Avsec Z, Kreuzhuber R, Israeli JXu NCheng J, Shrikumar A, Banerjee A, Kim DSKundaje A*, Stegle O*, Gagneur J*
    (Accepted, In Press)


  • Transcriptome-wide association studies: opportunities and challenges [Preprint]
    Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles D, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Bjorkegren JLM, Im HY, Pasaniuc B, Rivas MA, Kundaje A
    Nature Genetics, Volume 51, pages 592–599 (2019) (PMID:)

  • mtDNA Chromatin-like Organization is Gradually Established During Mammalian Embryogenesis
  • Marom S, Blumberg A, Kundaje A, Mishmar D
  • iScience. 2019 Jan DOI: 10.1016/j.isci.2018.12.032 (PMID: 30684873)

  • Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses [Preprint]
    Benayoun BA, Pollina E, Singh PP, Mahmoudi S, Harel I, Casey K, Dulken B, Kundaje A, Brunet A
    Genome Res. 2019 Mar 11. doi: 10.1101/gr.240093.118 (PMID: 30858345)

  • Measuring the reproducibility and quality of Hi-C data [Preprint]
  • Yardimci G, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS
  • Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7 (PMID: 30890172)
2018
  • Discovery of common and rare genetic risk variants for colorectal cancer 
    Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U.
    Nat Genet. 2018 Dec 3. doi: 10.1038/s41588-018-0286-6. (PMID: 30510241)

  • Discovering epistatic feature interactions from neural network models of regulatory DNA sequences [Preprint] [Code]
    Greenside PG, Shimko T, Fordyce P, Kundaje A
    Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i629–i637 (PMID: 30423062)
    (Proceedings of ECCB 2018)
     
  • Intertumoral heterogeneity in SCLC is influenced by the cell type of origin
    Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM
    Cancer Discov. 2018 Sep 18 DOI: 10.1158/2159-8290.CD-17-0987 (PMID: 30228179)

  • Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers
    Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. 
    Nucleic Acids Res. 2018 Aug 22. doi: 10.1093/nar/gky753. (PMID: 30137428)


  • Umap and Bismap: quantifying genome and methylome mappability [Website] [Code] [Preprint]
    Karimzadeh M, Ernst C, Kundaje A, Hoffman MH
    Nucleic Acids Research, Sept 1, 2018, gky677, https://doi.org/10.1093/nar/gky677 (PMID: 30169659)
     

  • A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization [Preprint]
  • Blumberg A, Danko CG, Kundaje A, Mishmar D
    Genome Res. 2018 Aug;28(8):1158-1168. doi: 10.1101/gr.230409.117. Epub 2018 Jul 12. (PMID: 30002158)


  • Kipoi: accelerating the community exchange and reuse of predictive models for regulatory genomics [Website] [Code]
    Avsec Z, Kreuzhuber R, Israeli J, Cheng J, Urban L, Banerjee A, Xu N, Shrikumar A, Ouwehand WH, Kundaje A*, Stegle O*, Gagneur J*
    ICML 2018 Workshop for Computational Biology

  • A Sequence-to-sequence Regression of Genome-wide Chromatin Data through Adversarial Training [pdf]
    Min J, Israeli J, Kundaje A
    ICML 2018 Workshop for Computational Biology

  • Selective Classification via Curve Optimization [pdf]
    Alexandari A, Shrikumar A, Kundaje A
    ArXiv e-prints [Internet]. 2018 Feb 20
    ICML 2018 Workshop for Computational Biology (Highlighted Paper) 

  • BPNet: Learning single-nucleotide resolution predictive models of in vivo transcription factor binding from ChIP-nexus data [pdf]
    Avsec Z, Israeli J
    , Fropf R, Weilert M, Zeitlinger J, Kundaje A
    ICML 2018 Workshop for Computational Biology 

  • Opportunities And Obstacles For Deep Learning In Biology And Medicine [Preprint]
    Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Gitter A, Greene CS (Note: Author order is randomized)
    J. R. Soc. Interface 2018 15 20170387; DOI: 10.1098/rsif.2017.0387. Published 4 April 2018 (PMID: 29618526)
    Highlighted in
    - Nature's 2017 year in review's most read preprints table 
    - Nature
    - Nature's Tech Blog
    - F1000 Prime
    - Eureka Alert  

  • GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs [Code] [Preprint]
  • Ursu O, Boley N, Taranova M, Rachel WYX, Yardimci GG, Noble WS, Kundaje A

  • Bioinformatics, March 2018 , bty164, https://doi.org/10.1093/bioinformatics/bty164 (PMID: 29554289) 

    • ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation
      GK Marinov, A Kundaje
      Briefings in Functional Genomics, Feb 2018. https://doi.org/10.1093/bfgp/ely004 (
      PMID: 29529131) 

    2017
    • Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.
      Bien SA, Auer PL, Harrison TA, Qu C, Connolly CM, Greenside PG, Chen S, Berndt SI, Bézieau S, Kang HM, Huyghe J, Brenner H, Casey G, Chan AT, Hopper JL, Banbury BL, Chang-Claude J, Chanock SJ, Haile RW, Hoffmeister M, Fuchsberger C, Jenkins MA, Leal SM, Lemire M, Newcomb PA, Gallinger S, Potter JD, Schoen RE, Slattery ML, Smith JD, Le Marchand L, White E, Zanke BW, Abeçasis GR, Carlson CS, Peters U, Nickerson DA, Kundaje A*, Hsu L*; GECCO and CCFR.
      PLoS One. 2017 Nov 21;12(11):e0186518. doi: 10.1371/journal.pone.0186518. eCollection 2017. (PMID: 29161273)
      (* Equal contribution)

    • Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans [Preprint]
      Daugherty AC, Yeo R, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A
      Published in Advance November 15, 2017, doi:10.1101/gr.226233.117 Genome Res. 2017. (PMID: 29141961)

    • Vicus: Exploiting local structures to improve network-based analysis of biological data
    • Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A
    • PLoS Comput Biol. 2017 Oct 12;13(10):e1005621. doi: 10.1371/journal.pcbi.1005621. eCollection 2017 Oct. (PMID: 29023470)

    • Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures [Code] [Dataset]
      Greenside PG, Hillenmeyer M, Kundaje A
      Pac Symp Biocomput. 2018;23:20-31. (PMID: 29218866)

    • Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements [Preprint]
    • Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY
    • Nature Genetics (2017) doi:10.1038/ng.3963 (PMID: 28945252)

    • An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues [Preprint]
      Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY 
      Nat Meth. 2017. doi: 10.1038/nmeth.4396 (PMID: 28846090)

    • Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
    • Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. 
    • Nature Genetics (2017) doi:10.1038/ng.3935 (PMID: 28805829)

    • Denoising genome-wide histone ChIP-seq with convolutional neural networks [Code] [Preprint]
    • Koh PW, Pierson E, Kundaje A
      Bioinformatics (2017) 33 (14): i225-i233 (
    • PMID: 28881977)
      2017 Intelligent Systems in Molecular Biology (ISMB) Conference

    • Separable Fully Connected Layers Improve Deep Learning Models For Genomics [Code]
      Alexandari AM, Shrikumar A, Kundaje A
      bioRxiv 146431; doi: https://doi.org/10.1101/146431
      2017 ICML Workshop on Computational Biology
      (Best Poster Award)

    • High-Throughput Characterization of Cascade Type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences.
      Fu BXH, Wainberg M, Kundaje A*, Fire AZ*.
      Genetics. 2017 Jun 20. pii: genetics.117.202580. doi: 10.1534/genetics.117.202580. (PMID: 28634160)
      (* co-corresponding authors)

    • Learning Important Features Through Propagating Activation Differences [Code], [Videos], [Preprint]
      Shrikumar A, Greenside P,  Kundaje A
      Proceedings of the 34th International Conference on Machine Learning (ICML), PMLR 70:3145-3153, 2017

    • Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.
      Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC.
      Nat Commun. 2017 May 5;8:15178. doi: 10.1038/ncomms15178. (PMID: 28474669)

    • Predicting gene expression in massively parallel reporter assays: a comparative study
      Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.
      Hum Mutat. 2017 Feb 21. doi: 10.1002/humu.23197 (PMID: 28220625)

    • Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis.
    • Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, Li JB, Kundaje A, Winslow MM
    • Nat Med. 2017 Feb 13. doi: 10.1038/nm.4285 (PMID: 28191885)

    • Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution [Preprint]
      Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.
      Genome Res. 2017 Jan 3. pii: gr.209924.116. doi: 10.1101/gr.209924.116. (PMID: 28049628)

    2016 
    • An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.
      Koh PW, Sinha R*, Barkal AA, Morganti RM, Chen A, Weissman IL, Ang LT, Kundaje A*, Loh KM. 
      Sci. Data 3:160109 doi: 10.1038/sdata.2016.109 (2016) (PMID: 27996962)
      (* Corresponding author)

    • Unsupervised Learning from Noisy Networks with Applications to Hi-C Data
      Wang, B, Zhu, J, Pourshafeie, A, Ursu, O, Batzoglou, S, Kundaje, A
      In 2016 Advances In Neural Information Processing Systems (NIPS) (pp. 3297-3305)

    • Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
      Corces RM, Buenrostro J, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY
      Nature Genetics (2016) doi:10.1038/ng.3646 (PMID: 27526324)

    • Mapping the pairwise choices and molecular transitions leading from pluripotency to human bone, heart and other mesoderm cell-types
    • 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
    • Cell , Volume 166 , Issue 2 , 451 - 467 (PMID: 27419872)

    • Denoising genome-wide histone ChIP-seq with convolutional neural networks [Code]
    • Koh PW, Pierson E, Kundaje A
    • bioRxiv doi: http://dx.doi.org/10.1101/052118 
      Accepted to ICML 2016 Workshop on Computational Biology
      (Best paper award)

    • Impact of the X Chromosome and sex on regulatory variation.
    • 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.
    • Genome Res. 2016 Apr 21 [Epub ahead of print] (
    • PMID: 27197214)

    • An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency
    • Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM.
    • Cancer Cell. 2016 May 9;29(5):697-710. doi: 10.1016/j.ccell.2016.03.003. Epub 2016 Apr 14 (PMID: 27150038)

    • Characterization of the direct targets of FOXO transcription factors throughout evolution
      Webb AE, Kundaje A, Brunet A. 
      Aging Cell. 2016 doi: 10.1111/acel.12479. (PMID: 27061590)
    2015
    • Genetic control of chromatin states in humans involves local and distal chromosomal interactions [Website]
      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
      Cell. 2015 Aug 19. pii: S0092-8674(15)00964-2. doi: 10.1016/j.cell.2015.07.048 (PMID: 26300125)
      * Equal junior contributors
    • Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci.
    • 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.
    • PLoS Genet. 2015 May 28;11(5):e1005202. doi: 10.1371/journal.pgen.1005202. eCollection 2015 May. (PMID: 26020271)

    • Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution
    • Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M.
    • Dev Cell. 2015 Mar 23;32(6):772-4. doi: 10.1016/j.devcel.2015.03.004. (PMID: 25805139)

    • Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.
    • 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. 
    • Nat Genet. 2015 Mar 9. doi: 10.1038/ng.3245

    • Integrative analysis of 111 reference human epigenomes [Website]
      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
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    Anshul Kundaje,
    Mar 22, 2013, 8:43 AM
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    spectrofish.zip
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    Anshul Kundaje,
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