TY - JOUR AU - Kim, T. H. AU - Ren, B. PY - 2006 DA - 2006// TI - Genome-wide analysis of protein-DNA interactions JO - Annual Review of Genomics and Human Genetics VL - 7 UR - https://doi.org/10.1146/annurev.genom.7.080505.115634 DO - 10.1146/annurev.genom.7.080505.115634 ID - Kim2006 ER - TY - JOUR AU - Mardis, E. R. PY - 2008 DA - 2008// TI - ChIP-seq: welcome to the new frontier JO - Nature Methods VL - 4 UR - https://doi.org/10.1038/nmeth0807-613 DO - 10.1038/nmeth0807-613 ID - Mardis2008 ER - TY - JOUR AU - Ji, H. AU - Wong, W. H. PY - 2005 DA - 2005// TI - TileMap: create chromosomal map of tiling array hybridizations JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti593 DO - 10.1093/bioinformatics/bti593 ID - Ji2005 ER - TY - JOUR AU - Li, W. AU - Meyer, C. A. AU - Liu, X. S. PY - 2005 DA - 2005// TI - A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1046 DO - 10.1093/bioinformatics/bti1046 ID - Li2005 ER - TY - JOUR AU - Du, J. AU - Rozowsky, J. S. AU - Korbel, J. O. AU - Zhang, Z. D. AU - Royce, T. E. AU - Schultz, M. H. AU - Snyder, M. AU - Gerstein, M. PY - 2006 DA - 2006// TI - A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl515 DO - 10.1093/bioinformatics/btl515 ID - Du2006 ER - TY - JOUR AU - Munch, K. AU - Gardner, P. AU - Arctander, P. AU - Krogh, A. PY - 2006 DA - 2006// TI - A hidden Markov model approach for determining expression from genomic tiling micro arrays JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-239 DO - 10.1186/1471-2105-7-239 ID - Munch2006 ER - TY - JOUR AU - Humburg, P. AU - Bulger, D. AU - Stone, G. PY - 2008 DA - 2008// TI - Parameter estimation for robust HMM analysis of ChIP-chip data JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-343 DO - 10.1186/1471-2105-9-343 ID - Humburg2008 ER - TY - JOUR AU - Huber, W. AU - Toedling, J. AU - Steinmetz, L. M. PY - 2006 DA - 2006// TI - Transcript mapping with high-density oligonucleotide tiling arrays JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl289 DO - 10.1093/bioinformatics/btl289 ID - Huber2006 ER - TY - JOUR AU - Johnson, D. S. AU - Mortazavi, A. AU - Myers, R. M. AU - Wold, B. PY - 2007 DA - 2007// TI - Genome-wide mapping of in vivo protein-DNA interactions JO - Science VL - 316 UR - https://doi.org/10.1126/science.1141319 DO - 10.1126/science.1141319 ID - Johnson2007 ER - TY - JOUR AU - Mortazavi, A. AU - Williams, B. A. AU - McCue, K. AU - Schaeffer, L. AU - Wold, B. PY - 2008 DA - 2008// TI - Mapping and quantifying mammalian transcriptomes by RNA-Seq JO - Nature Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1226 DO - 10.1038/nmeth.1226 ID - Mortazavi2008 ER - TY - JOUR AU - Robertson, G. AU - Hirst, M. AU - Bainbridge, M. AU - Bilenky, M. AU - Zhao, Y. AU - Zeng, T. AU - Euskirchen, G. AU - Bernier, B. AU - Varhol, R. AU - Delaney, A. AU - Thiessen, N. AU - Griffith, O. L. AU - He, A. AU - Marra, M. AU - Snyder, M. AU - Jones, S. PY - 2007 DA - 2007// TI - Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing JO - Nature Methods VL - 4 UR - https://doi.org/10.1038/nmeth1068 DO - 10.1038/nmeth1068 ID - Robertson2007 ER - TY - JOUR AU - Mikkelsen, T. S. AU - Ku, M. AU - Jaffe, D. B. AU - Issac, B. AU - Lieberman, E. AU - Giannoukos, G. AU - Alvarez, P. AU - Brockman, W. AU - Kim, T. K. AU - Koche, R. P. AU - Lee, W. AU - Mendenhall, E. AU - O'Donovan, A. AU - Presser, A. AU - Russ, C. AU - Xie, X. AU - Meissner, A. AU - Wernig, M. AU - Jaenisch, R. AU - Nusbaum, C. AU - Lander, E. S. AU - Bernstein, B. E. PY - 2007 DA - 2007// TI - Genome-wide maps of chromatin state in pluripotent and lineage-committed cells JO - Nature VL - 448 UR - https://doi.org/10.1038/nature06008 DO - 10.1038/nature06008 ID - Mikkelsen2007 ER - TY - JOUR AU - Rozowsky, J. AU - Euskirchen, G. AU - Auerbach, R. K. AU - Zhang, Z. D. AU - Gibson, T. AU - Bjornson, R. AU - Carriero, N. AU - Snyder, M. AU - Gerstein, M. B. PY - 2009 DA - 2009// TI - PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls JO - Nature Biotechnology VL - 27 UR - https://doi.org/10.1038/nbt.1518 DO - 10.1038/nbt.1518 ID - Rozowsky2009 ER - TY - STD TI - Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, Bernstein B, Nussbaum C, Myers R, Brown M, Li W, Liu X: Model-based analysis of ChIP-Seq (MACS). Genome Biology 2008., 9(9): 10.1186/gb-2008-9-9-r137 ID - ref14 ER - TY - JOUR AU - Valouev, A. AU - Johnson, D. S. AU - Sundquist, A. AU - Medina, C. AU - Anton, E. AU - Batzoglou, S. AU - Myers, R. M. AU - Sidow, A. PY - 2008 DA - 2008// TI - Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data JO - Nature Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1246 DO - 10.1038/nmeth.1246 ID - Valouev2008 ER - TY - JOUR AU - Fejes, A. P. AU - Robertson, G. AU - Bilenky, M. AU - Varhol, R. AU - Bainbridge, M. AU - Jones, S. J. PY - 2008 DA - 2008// TI - FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn305 DO - 10.1093/bioinformatics/btn305 ID - Fejes2008 ER - TY - JOUR AU - Jothi, R. AU - Cuddapah, S. AU - Barski, A. AU - Cui, K. AU - Zhao, K. PY - 2008 DA - 2008// TI - Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data JO - Nucleic Acids Research VL - 36 UR - https://doi.org/10.1093/nar/gkn488 DO - 10.1093/nar/gkn488 ID - Jothi2008 ER - TY - JOUR AU - Kharchenko, P. V. AU - Tolstorukov, M. Y. AU - Park, P. J. PY - 2008 DA - 2008// TI - Design and analysis of ChIP-seq experiments for DNA-binding proteins JO - Nature Biotechnology VL - 26 UR - https://doi.org/10.1038/nbt.1508 DO - 10.1038/nbt.1508 ID - Kharchenko2008 ER - TY - JOUR AU - Nix, D. AU - Courdy, S. AU - Boucher, K. PY - 2008 DA - 2008// TI - Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-523 DO - 10.1186/1471-2105-9-523 ID - Nix2008 ER - TY - JOUR AU - Dempster, A. AU - Laird, N. M. AU - Rubin, D. B. PY - 1977 DA - 1977// TI - Maximum likelihood from incomplete data via the EM algorithm JO - Journal of the Royal Statistical Society. Series B (Methodological) VL - 39 ID - Dempster1977 ER - TY - BOOK AU - Gelman, A. AU - Carlin, J. B. AU - Stern, H. S. AU - Rubin, D. B. PY - 2003 DA - 2003// TI - Bayesian Data Analysis PB - Hall/CRC CY - London ID - Gelman2003 ER - TY - JOUR AU - Baum, L. E. AU - Petrie, T. AU - Soules, G. AU - Weiss, N. PY - 1970 DA - 1970// TI - A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains JO - The Annals of Mathematical Statistics VL - 41 UR - https://doi.org/10.1214/aoms/1177697196 DO - 10.1214/aoms/1177697196 ID - Baum1970 ER - TY - JOUR AU - Scott, S. L. PY - 2002 DA - 2002// TI - Bayesian methods for hidden Markov models: recursive computing in the 21st century JO - Journal of the American Statistical Association VL - 97 UR - https://doi.org/10.1198/016214502753479464 DO - 10.1198/016214502753479464 ID - Scott2002 ER - TY - STD TI - Schmidt D, Stark R, Wilson MD, Brown GD, Odom DT: Genome-scale validation of deep-sequencing libraries. PLoS ONE 2008., 3(11): 10.1371/journal.pone.0003713 ID - ref24 ER - TY - JOUR AU - Wilson, M. D. AU - Barbosa-Morais, N. L. AU - Schmidt, D. AU - Conboy, C. M. AU - Vanes, L. AU - Tybulewicz, V. L. AU - Fisher, E. M. AU - Tavaré, S. AU - Odom, D. T. PY - 2008 DA - 2008// TI - Species-specific transcription in mice carrying human chromosome 21 JO - Science VL - 322 UR - https://doi.org/10.1126/science.1160930 DO - 10.1126/science.1160930 ID - Wilson2008 ER - TY - CHAP AU - Gelman, A. AU - Meng, X. L. ED - Gilks, W. R. ED - Richardson, S. ED - Spiegelhalter, D. J. PY - 1995 DA - 1995// TI - Model checking and model improvement BT - Markov chain Monte Carlo in practice PB - Hall/CRC CY - London ID - Gelman1995 ER - TY - JOUR AU - Odom, D. T. AU - Dowell, R. D. AU - Jacobsen, E. S. AU - Gordon, W. AU - Danford, T. W. AU - Macisaac, K. D. AU - Rolfe, A. P. AU - Conboy, C. M. AU - Gifford, D. K. AU - Fraenkel, E. PY - 2007 DA - 2007// TI - Tissue-specific transcriptional regulation has diverged significantly between human and mouse JO - Nature Genetics VL - 39 UR - https://doi.org/10.1038/ng2047 DO - 10.1038/ng2047 ID - Odom2007 ER - TY - JOUR AU - Frith, M. C. AU - Fu, Y. AU - Yu, L. AU - Chen, J. F. AU - Hansen, U. AU - Weng, Z. PY - 2004 DA - 2004// TI - Detection of functional DNA motifs via statistical over-representation JO - Nucleic Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh299 DO - 10.1093/nar/gkh299 ID - Frith2004 ER - TY - STD TI - Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B: A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Research 2006, (34 Database):D95-D97. 10.1093/nar/gkj115 ID - ref29 ER - TY - JOUR AU - Mortazavi, A. AU - Evonne AU - Garcia, S. T. AU - Myers, R. M. AU - Wold, B. PY - 2006 DA - 2006// TI - Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.4997306 DO - 10.1101/gr.4997306 ID - Mortazavi2006 ER - TY - JOUR AU - Wilson, N. K. AU - Miranda-Saavedra, D. AU - Kinston, S. AU - Bonadies, N. AU - Foster, S. D. AU - Calero-Nieto, F. AU - Dawson, M. A. AU - Donaldson, I. J. AU - Dumon, S. AU - Frampton, J. AU - Janky, R. AU - Sun, X. H. AU - Teichmann, S. A. AU - Bannister, A. J. AU - Göttgens, B. PY - 2009 DA - 2009// TI - The transcriptional programme controlled by the stem cell leukaemia gene Scl/Tal1 during early embryonic haematopoietic development JO - Blood VL - 113 UR - https://doi.org/10.1182/blood-2009-01-200048 DO - 10.1182/blood-2009-01-200048 ID - Wilson2009 ER - TY - JOUR AU - Choi, H. AU - Nesvizhskii, A. I. AU - Ghosh, D. AU - Qin, Z. S. PY - 2009 DA - 2009// TI - Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp312 DO - 10.1093/bioinformatics/btp312 ID - Choi2009 ER - TY - STD TI - BayesPeak: Bayesian analysis of ChIP-seq data[http://www.compbio.group.cam.ac.uk/Resources/BayesPeak/csbayespeak.html] UR - http://www.compbio.group.cam.ac.uk/Resources/BayesPeak/csbayespeak.html ID - ref33 ER - TY - JOUR AU - Brooks, S. AU - Gelman, A. PY - 1998 DA - 1998// TI - General methods for monitoring convergence of iterative simulations JO - Journal of Computational and Graphical Statistics VL - 7 ID - Brooks1998 ER - TY - CHAP AU - Geweke, J. ED - Berger, J. O. ED - Dawid, A. P. ED - Smith, A. F. M. PY - 1992 DA - 1992// TI - Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments BT - Bayesian Statistics PB - Oxford University Press CY - Oxford ID - Geweke1992 ER - TY - JOUR AU - Heidelberger, P. AU - Welch, P. D. PY - 1983 DA - 1983// TI - Simulation run length control in the presence of an initial transient JO - Operations Research VL - 31 UR - https://doi.org/10.1287/opre.31.6.1109 DO - 10.1287/opre.31.6.1109 ID - Heidelberger1983 ER -