Jacob Carlsen

Christian Showalter

Prashant Kumar Kuntala

WeizhenCai

Isaac Bermeo

Mark Slayton

  1. DNA Interacting Proteins:

Discriminative prediction of mammalian enhancers from DNA sequenceLee D, Karchin R, Beer MA. Genome Res. Dec;21(12):2167-80.

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolutionRhee HS, Pugh BF. Cell. 2011 Dec 9;147(6):1408-19.

DNaseI sensitivity QTLs are a major determinant of human expression variationJacob F Degner, AthmaAPai, Roger Pique-Regi, Jean-Baptiste Veyrieras, Daniel J Gaffney, Joseph K Pickrell, Sherryl De Leon, Katelyn Michelini, Noah Lewellen, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Nature, 482(7385), 390-394, 2012 - February 4, 2012

An expansive human regulatory lexicon encoded in transcription factor footprintsNeph S, Vierstra J, StergachisAB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.Nature, 489(7414), 83-90, Sep 2012. – September 6, 2012

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assayKheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J,Mikkelsen TS, Kellis M.Genome Research. 2013 May;23(5):800-11. – May 1, 2013

Promoter Sequence Determines the Relationship between Expression Level and NoiseCarey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E.PLoS Biol. 2013;11(4):e1001528. – April 1, 2013

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancyQ. Cheng, M. Kazemian, H. Pham, C. Blatti, S. E. Celniker, S. A. Wolfe, M. H. Brodsky, S. Sinha,PLoS Genetics. 2013 Aug;9(8):e1003571. – August 1, 2013

Single-molecule dynamics of enhanceosome assembly in embryonic stem cells Chen et al. (LA: Liu) Cell. 2014 Mar 13;156(6):1274-85.

Determination and inference of eukaryotic transcription factor sequence specificityWeirauch et al (LA: Hughes) Cell. 2014 Sep 11;158(6):1431-43.

Quantitative modeling of transcription factor binding specificities using DNA shape, Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R. PNAS 2015 Apr 14;112(15):4654-9. PMID: 26103224

The human splicing code reveals new insights into the genetic determinants of disease, Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K., ... & Frey, B. J. Science /em>3347(6218), 1254806. PMID: 25525159

  1. Networks/pathways:

An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastomaSumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. Cell. 2011 Oct 14;147(2):370-81.

Prioritizing candidate disease genes by network-based boosting of genome-wide association dataLee I, Blom UM, Wang PI, Shim JE, Marcotte EM.Genome Res. 2011 Jul;21(7):1109-21.

Guilt by association is the exception rather than the rule in gene networksGillis J, Pavlidis P.

PLoSComput Biol. 2012;8(3):e1002444 - March 29, 2012

Linking the signaling cascades and dynamic regulatory networks controlling stress responsesGitter A, Carmi M, Barkai N, Bar-Joseph ZGenome Research, 23(2), 365-376, Feb 2013. - October 11, 2012

Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancersBarozzi et al. (LA: Natoli) Mol Cell 2014 Jun 5;54(5):844-57

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotypeGagneur et al. (LA: Steinmetz) PLoS Genet. 2013;9(9):e1003803.

A method to predict the impact of regulatory variants from DNA sequence, D. Lee, D.U. Gorkin, M. Baker, B.J. Strober, A.L. Asoni, A.S. McCallion, M.A. Beer. Nat Genet. 2015 Aug;47(8):955-61. PMID: 26075791

Inferring interaction type in gene regulatory networks using co-expression data, Khosravi P, Gazestani V, Pirhaji L, Law B, Sadeghi M, GoliaeiB , Bader G. Algorithms for Molecular Biology 2015, 10:23. PMID: 26265933

Elucidating Compound Mechanism of Action by Network Perturbation Analysis, Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Cell/em>.. 2015 Jul 16;162(2):441-51. PMID: 26186195

3.Epigenomics:

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.Genome Res. 2011 Mar;21(3):447-55.

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteinsSlattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS Cell. 2011 Dec 9;147(6):1270-82.

Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism.Voss TC, Schiltz RL, Sung MH, Yen PM, Stamatoyannopoulos JA, Biddie SC, Johnson TA, Miranda TB, John S, Hager GL. Cell. 2011 Aug 19;146(4):544-54.

Mapping and analysis of chromatin state dynamics in nine human cell typesErnst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Nature. 2011 May 5;473(7345):43-9.

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shapeGordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.Cell Rep. 2013 Apr 25;3(4):1093-104 - April 1, 2013

Probing DNA shape and methylation state on a genomic scale with DNase ILazarovici A, Zhou T, Shafer A, Dantas Machado A, Riley T, Sandstrom R, Sabo P, Lu Y, Rohs R, Stamatoyannopoulos J, Bussemaker HProc Natl AcadSci U S A. 2013 Apr 16;110(16):6376-81 - April 1, 2013

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position Buenrostro et al. (LA: Greenleaf), Nat Methods. 2013 Dec;10(12):1213-8.

Enhancer loops appear stable during development and are associated with paused polymeraseGhavi-Helm et al. (LA: Furlong) Nature. 2014 Aug 7;512(7512):96-100.

Deconvolving the recognition of DNA shape from sequence, Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Cell 2015 Apr 9;161(2):307-18. PMID: 25843630

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression, Libbrecht, M. W., Ay, F., Hoffman, M. M., Gilbert, D. M., Bilmes, J. A., & Noble, W. S. Genome research25(4), 544-557. PMID: 2567718

Integration of genomic data enables selective discovery of breast cancer drivers, Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, Pe'er D. Cellem> 159(6):1461-7. PMID: 25433701

  1. Evolutionary Genomics:

A high-resolution map of human evolutionary constraint using 29 mammalsLindblad-Toh K, Garber M, Zuk O, et al.Nature. 2011 Oct 12;478(7370):476-82.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes ProjectMu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Nucleic Acids Res. 2011 Sep 1;39(16):7058-76.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals Battle et al. (LA: Koller) Genome Res. 2014 Jan;24(1):14-24.

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data Li et al. (LA: Brenner) Genome Res. 2014 Jul;24(7):1086-101.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells, Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature Biotechnology 33, 155-160, 2015. PMID: 25599176

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues, Ernst J, Kellis M. Nature Biotechnology/em> 33, 364-376, 2015. PMID: 25690853

5.Computational Methods:

A statistical framework for joint eQTL analysis in multiple tissuesTimothéeFlutre, Xiaoquan Wen, Jonathan Pritchard, Matthew StephensPLoS Genetics, 9, 5, e1003486, 2013 - May 9, 2013

A community effort to assess and improve drug sensitivity prediction algorithmsCostello et al. (LA: Stolovitzky) Nat Biotechnol. 2014 Jun 1. doi: 10.1038/nbt.2877.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites Yang et al. (LA: Rohs) Nucleic Acids Res. 2014 Jan;42(Database issue):D148-55.

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning, Alipanahi B, Delong A, Weirauch MT, Frey BJ. Nat Biotechnol 33(8):831-8. PMID: 26213851