TY - JOUR AU - Pepke, S. AU - Wold, B. AU - Mortazavi, A. PY - 2009 DA - 2009// TI - Computation for ChIP-seq and RNA-seq studies JO - Nat Methods. VL - 6 UR - https://doi.org/10.1038/nmeth.1371 DO - 10.1038/nmeth.1371 ID - Pepke2009 ER - TY - JOUR AU - Wilbanks, E. G. AU - Facciotti, M. T. PY - 2010 DA - 2010// TI - Evaluation of algorithm performance in ChIP-seq peak detection JO - PLoS One. VL - 5 UR - https://doi.org/10.1371/journal.pone.0011471 DO - 10.1371/journal.pone.0011471 ID - Wilbanks2010 ER - TY - CHAP AU - Kulakovskiy, I. V. AU - Makeev, V. J. PY - 2014 DA - 2014// TI - Motif discovery and motif finding in ChIP-Seq data BT - Genome analysis: current procedures and applications PB - Caister Academic Press CY - Norfolk ID - Kulakovskiy2014 ER - TY - JOUR AU - Park, P. J. PY - 2009 DA - 2009// TI - ChIP-seq: advantages and challenges of a maturing technology JO - Nat Rev Genet. VL - 10 UR - https://doi.org/10.1038/nrg2641 DO - 10.1038/nrg2641 ID - Park2009 ER - TY - JOUR AU - Zang, C. AU - Schones, D. E. AU - Zeng, C. AU - Cui, K. AU - Zhao, K. AU - Peng, W. PY - 2009 DA - 2009// TI - A clustering approach for identification of enriched domains from histone modification ChIP-Seq data JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp340 DO - 10.1093/bioinformatics/btp340 ID - Zang2009 ER - TY - JOUR AU - Hower, V. AU - Evans, S. N. AU - Pachter, L. PY - 2011 DA - 2011// TI - Shape-based peak identification for ChIP-seq JO - BMC Bioinform. VL - 12 UR - https://doi.org/10.1186/1471-2105-12-15 DO - 10.1186/1471-2105-12-15 ID - Hower2011 ER - TY - JOUR AU - Mendoza-Parra, M. A. AU - Nowicka, M. AU - Gool, W. AU - Gronemeyer, H. PY - 2013 DA - 2013// TI - Characterising ChIP-seq binding patterns by model-based peak shape deconvolution JO - BMC Genomics. VL - 14 UR - https://doi.org/10.1186/1471-2164-14-834 DO - 10.1186/1471-2164-14-834 ID - Mendoza-Parra2013 ER - TY - JOUR AU - Mahony, S. AU - Edwards, M. D. AU - Mazzoni, E. O. AU - Sherwood, R. I. AU - Kakumanu, A. AU - Morrison, C. A. AU - Wichterle, H. AU - Gifford, D. K. PY - 2014 DA - 2014// TI - An integrated model of multiple condition ChIP-seq data reveals predeterminants of Cdx2 binding JO - PLoS Comput Biol. VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003501 DO - 10.1371/journal.pcbi.1003501 ID - Mahony2014 ER - TY - JOUR AU - Hu, H. AU - Ji, H. PY - 2014 DA - 2014// TI - PolyaPeak, detecting transcription factor binding sites from ChIP-seq using peak shape information JO - PLoS One. VL - 9 UR - https://doi.org/10.1371/journal.pone.0089694 DO - 10.1371/journal.pone.0089694 ID - Hu2014 ER - TY - JOUR AU - Schweikert, G. AU - Cseke, B. AU - Clouaire, T. AU - Bird, A. AU - Sanguinetti, G. PY - 2013 DA - 2013// TI - MMDiff: quantitative testing for shape changes in ChIP-seq data sets JO - BMC Genomics. VL - 14 UR - https://doi.org/10.1186/1471-2164-14-826 DO - 10.1186/1471-2164-14-826 ID - Schweikert2013 ER - TY - STD TI - SIC-ChIP software. http://cgsb.genomics.iit.it/wiki/projects/SIC-ChIP. UR - http://cgsb.genomics.iit.it/wiki/projects/SIC-ChIP ID - ref11 ER - TY - JOUR AU - Bao, Y. AU - Vinciotti, V. AU - Wit, E. AU - AC’t Hown, P. PY - 2013 DA - 2013// TI - Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data JO - BMC Bioinform. VL - 14 UR - https://doi.org/10.1186/1471-2105-14-169 DO - 10.1186/1471-2105-14-169 ID - Bao2013 ER - TY - JOUR AU - Papadopoulos, G. L. AU - Karkoulia, E. AU - Tsamardinos, I. AU - Porcher, C. AU - Ragoussis, J. AU - Bungert, J. AU - Strouboulis, J. PY - 2013 DA - 2013// TI - GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis JO - Nucleic Acids Res. VL - 41 UR - https://doi.org/10.1093/nar/gkt167 DO - 10.1093/nar/gkt167 ID - Papadopoulos2013 ER - TY - JOUR AU - Wu, J. AU - Zhou, L. Q. AU - Yu, W. AU - Zhao, Z. G. AU - Xie, X. M. AU - Wang, W. T. AU - Xiong, J. AU - Li, M. AU - Xue, Z. AU - Wang, X. AU - Zhang, P. AU - Mao, B. B. AU - Hao, D. L. AU - Lv, X. AU - Liu, D. P. PY - 2014 DA - 2014// TI - PML4 facilitates erythroid differentiation by enhancing the transcriptional activity of GATA-1 JO - Blood. VL - 123 UR - https://doi.org/10.1182/blood-2013-02-483289 DO - 10.1182/blood-2013-02-483289 ID - Wu2014 ER - TY - JOUR AU - Fujiwara, T. AU - O'Geen, H. AU - Keles, S. AU - Blahnik, K. AU - Linnemann, A. K. AU - Kang, Y. A. AU - Choi, K. AU - Farnham, P. J. AU - Bresnick, E. H. PY - 2009 DA - 2009// TI - Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy JO - Mol Cell. VL - 36 UR - https://doi.org/10.1016/j.molcel.2009.11.001 DO - 10.1016/j.molcel.2009.11.001 ID - Fujiwara2009 ER - TY - JOUR PY - 2012 DA - 2012// TI - An integrated encyclopedia of DNA elements in the human genome JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11247 DO - 10.1038/nature11247 ID - ref16 ER - TY - STD TI - Encyclopedia of DNA Elements (ENCODE) Project. https://www.encodeproject.org. UR - https://www.encodeproject.org ID - ref17 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. AU - Eeckhoute, J. AU - Johnson, D. AU - Bernstein, B. AU - Nusbaum, C. AU - Myers, R. AU - Brown, M. AU - Li, W. AU - Liu, X. S. PY - 2008 DA - 2008// TI - Model-based analysis of ChIP-seq (MACS) JO - Genome Biol. VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Shimizu, R. AU - Engel, J. D. AU - Yamamoto, M. PY - 2008 DA - 2008// TI - GATA1-related leukaemias JO - Nat Rev Cancer. VL - 8 UR - https://doi.org/10.1038/nrc2348 DO - 10.1038/nrc2348 ID - Shimizu2008 ER - TY - JOUR AU - Pan, X. AU - Ohneda, O. AU - Ohneda, K. AU - Lindeboom, F. AU - Iwata, F. AU - Shimizu, R. AU - Nagano, M. AU - Suwabe, N. AU - Philipsen, S. AU - Lim, K. C. AU - Engel, J. D. AU - Yamamoto, M. PY - 2005 DA - 2005// TI - Graded levels of GATA-1 expression modulate survival, proliferation, and differentiation of erythroid progenitors JO - J Biol Chem. VL - 280 UR - https://doi.org/10.1074/jbc.M500081200 DO - 10.1074/jbc.M500081200 ID - Pan2005 ER - TY - JOUR AU - Evans, T. AU - Reitman, M. AU - Felsenfeld, G. PY - 1988 DA - 1988// TI - An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes JO - Proc Natl Acad Sci U S A. VL - 85 UR - https://doi.org/10.1073/pnas.85.16.5976 DO - 10.1073/pnas.85.16.5976 ID - Evans1988 ER - TY - JOUR AU - Martin, D. I. AU - Orkin, S. H. PY - 1990 DA - 1990// TI - Transcriptional activation and DNA binding by the erythroid factor GF-1/NF-E1/Eryf 1 JO - Genes Dev. VL - 4 UR - https://doi.org/10.1101/gad.4.11.1886 DO - 10.1101/gad.4.11.1886 ID - Martin1990 ER - TY - JOUR AU - Ko, L. J. AU - Engel, J. D. PY - 1993 DA - 1993// TI - DNA-binding specificities of the GATA transcription factor family JO - Mol Cell Biol VL - 13 UR - https://doi.org/10.1128/MCB.13.7.4011 DO - 10.1128/MCB.13.7.4011 ID - Ko1993 ER - TY - JOUR AU - Tijssen, M. R. AU - Cvejic, A. AU - Joshi, A. AU - Hannah, R. L. AU - Ferreira, R. AU - Forrai, A. AU - Bellissimo, D. C. AU - Oram, S. H. AU - Smethurst, P. A. AU - Wilson, N. K. AU - Wang, X. AU - Ottersbach, K. AU - Stemple, D. L. AU - Green, A. R. AU - Ouwehand, W. H. AU - Göttgens, B. PY - 2011 DA - 2011// TI - Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators JO - Dev Cell. VL - 20 UR - https://doi.org/10.1016/j.devcel.2011.04.008 DO - 10.1016/j.devcel.2011.04.008 ID - Tijssen2011 ER - TY - JOUR AU - Chlon, T. M. AU - Doré, L. C. AU - Crispino, J. D. PY - 2012 DA - 2012// TI - Cofactor-mediated restriction of GATA-1 chromatin occupancy coordinates lineage-specific gene expression JO - Mol Cell. VL - 47 UR - https://doi.org/10.1016/j.molcel.2012.05.051 DO - 10.1016/j.molcel.2012.05.051 ID - Chlon2012 ER - TY - JOUR AU - Yu, M. AU - Riva, L. AU - Xie, H. AU - Schindler, Y. AU - Moran, T. B. AU - Cheng, Y. AU - Yu, D. AU - Hardison, R. AU - Weiss, M. J. AU - Orkin, S. H. AU - Bernstein, B. E. AU - Fraenkel, E. AU - Cantor, A. B. PY - 2009 DA - 2009// TI - Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis JO - Mol Cell. VL - 36 UR - https://doi.org/10.1016/j.molcel.2009.11.002 DO - 10.1016/j.molcel.2009.11.002 ID - Yu2009 ER - TY - JOUR AU - Lan, X. AU - Witt, H. AU - Katsumura, K. AU - Ye, Z. AU - Wang, Q. AU - Bresnick, E. H. AU - Farnham, P. J. AU - Jin, V. X. PY - 2012 DA - 2012// TI - Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages JO - Nucleic Acids Res. VL - 40 UR - https://doi.org/10.1093/nar/gks501 DO - 10.1093/nar/gks501 ID - Lan2012 ER - TY - JOUR AU - Boes, M. AU - Dake, B. L. AU - Bar, R. S. PY - 1991 DA - 1991// TI - Interactions of cultured endothelial cells with TGF-beta, bFGF, PDGF and IGF-I JO - Life Sci VL - 48 UR - https://doi.org/10.1016/0024-3205(91)90097-U DO - 10.1016/0024-3205(91)90097-U ID - Boes1991 ER - TY - JOUR AU - Kassouf, M. T. AU - Hughes, J. R. AU - Taylor, S. AU - McGowan, S. J. AU - Soneji, S. AU - Green, A. L. AU - Vyas, P. AU - Porcher, C. PY - 2010 DA - 2010// TI - Genome-wide identification of TAL1's functional targets: insights into its mechanisms of action in primary erythroid cells JO - Genome Res. VL - 20 UR - https://doi.org/10.1101/gr.104935.110 DO - 10.1101/gr.104935.110 ID - Kassouf2010 ER - TY - JOUR AU - Rhee, H. S. AU - Pugh, B. F. PY - 2011 DA - 2011// TI - Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution JO - Cell. VL - 147 UR - https://doi.org/10.1016/j.cell.2011.11.013 DO - 10.1016/j.cell.2011.11.013 ID - Rhee2011 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler Transform JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Rye, M. B. AU - Sætrom, P. AU - Drabløs, F. PY - 2011 DA - 2011// TI - A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs JO - Nucleic Acids Res. VL - 39 UR - https://doi.org/10.1093/nar/gkq1187 DO - 10.1093/nar/gkq1187 ID - Rye2011 ER - TY - BOOK AU - Ramsay, J. O. AU - Silverman, B. W. PY - 2005 DA - 2005// TI - Functional data analysis PB - Springer CY - New York ID - Ramsay2005 ER - TY - JOUR AU - Evans, S. N. AU - Hower, V. AU - Pachter, L. PY - 2010 DA - 2010// TI - Coverage statistics for sequence census methods JO - BMC Bioinform. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-430 DO - 10.1186/1471-2105-11-430 ID - Evans2010 ER - TY - BOOK AU - Johnson, R. A. AU - Wichern, D. W. PY - 2007 DA - 2007// TI - Applied multivariate statistical analysis PB - Pearson CY - Upper Saddle River ID - Johnson2007 ER - TY - BOOK AU - Hastie, T. AU - Tibshirani, R. AU - Friedman, J. PY - 2009 DA - 2009// TI - The elements of statistical learning PB - Springer CY - New York UR - https://doi.org/10.1007/978-0-387-84858-7 DO - 10.1007/978-0-387-84858-7 ID - Hastie2009 ER - TY - JOUR AU - McLean, C. Y. AU - Bristor, D. AU - Hiller, M. AU - Clarke, S. L. AU - Schaar, B. T. AU - Lowe, C. B. AU - Wenger, A. M. AU - Bejerano, G. PY - 2010 DA - 2010// TI - GREAT improves functional interpretation of cis-regulatory regions JO - Nat Biotechnol. VL - 28 UR - https://doi.org/10.1038/nbt.1630 DO - 10.1038/nbt.1630 ID - McLean2010 ER - TY - JOUR AU - Machanick, P. AU - Bailey, T. L. PY - 2011 DA - 2011// TI - MEME-ChIP: motif analysis of large DNA datasets JO - Bioinformatics. VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr189 DO - 10.1093/bioinformatics/btr189 ID - Machanick2011 ER - TY - STD TI - Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2010. http://www.repeatmasker.org. Accessed 25 Feb 2015. UR - http://www.repeatmasker.org ID - ref39 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random forests JO - Mach Learn. VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 ER - TY - JOUR AU - Menze, B. H. AU - Kelm, B. M. AU - Masuch, R. AU - Himmelreich, U. AU - Bachert, P. AU - Petrich, W. AU - Hamprecht, F. A. PY - 2009 DA - 2009// TI - A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data JO - BMC Bioinform. VL - 10 UR - https://doi.org/10.1186/1471-2105-10-213 DO - 10.1186/1471-2105-10-213 ID - Menze2009 ER - TY - BOOK AU - Greenacre, M. PY - 2007 DA - 2007// TI - Correspondence analysis in practice PB - Hall/CRC CY - London UR - https://doi.org/10.1201/9781420011234 DO - 10.1201/9781420011234 ID - Greenacre2007 ER -