TY - JOUR AU - Margaritis, T. AU - Holstege, F. C. PY - 2008 DA - 2008// TI - Poised RNA polymerase II gives pause for thought JO - Cell VL - 133 UR - https://doi.org/10.1016/j.cell.2008.04.027 DO - 10.1016/j.cell.2008.04.027 ID - Margaritis2008 ER - TY - JOUR AU - Kershnar, E. AU - Wu, S. Y. AU - Chiang, C. M. PY - 1998 DA - 1998// TI - Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes JO - J Biol Chem VL - 273 UR - https://doi.org/10.1074/jbc.273.51.34444 DO - 10.1074/jbc.273.51.34444 ID - Kershnar1998 ER - TY - JOUR AU - Corden, J. L. AU - Cadena, D. L. AU - Ahearn, J. M. AU - Dahmus, M. E. PY - 1985 DA - 1985// TI - A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II JO - Proc Natl Acad Sci USA VL - 82 UR - https://doi.org/10.1073/pnas.82.23.7934 DO - 10.1073/pnas.82.23.7934 ID - Corden1985 ER - TY - JOUR AU - Komarnitsky, P. AU - Cho, E. J. AU - Buratowski, S. PY - 2000 DA - 2000// TI - Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription JO - Genes Dev VL - 14 UR - https://doi.org/10.1101/gad.824700 DO - 10.1101/gad.824700 ID - Komarnitsky2000 ER - TY - JOUR AU - Li, J. AU - Gilmour, D. S. PY - 2011 DA - 2011// TI - Promoter proximal pausing and the control of gene expression JO - Curr Opin Genet Dev VL - 21 UR - https://doi.org/10.1016/j.gde.2011.01.010 DO - 10.1016/j.gde.2011.01.010 ID - Li2011 ER - TY - JOUR AU - Cheng, B. AU - Price, D. H. PY - 2007 DA - 2007// TI - Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation JO - J Biol Chem VL - 282 UR - https://doi.org/10.1074/jbc.M702936200 DO - 10.1074/jbc.M702936200 ID - Cheng2007 ER - TY - JOUR AU - Core, L. J. AU - Lis, J. T. PY - 2008 DA - 2008// TI - Transcription regulation through promoter-proximal pausing of RNA polymerase II JO - Science VL - 319 UR - https://doi.org/10.1126/science.1150843 DO - 10.1126/science.1150843 ID - Core2008 ER - TY - JOUR AU - Marshall, N. F. AU - Peng, J. AU - Xie, Z. AU - Price, D. H. PY - 1996 DA - 1996// TI - Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase JO - J Biol Chem VL - 271 UR - https://doi.org/10.1074/jbc.271.43.27176 DO - 10.1074/jbc.271.43.27176 ID - Marshall1996 ER - TY - JOUR AU - Kim, T. H. AU - Barrera, L. O. AU - Zheng, M. AU - Qu, C. AU - Singer, M. A. AU - Richmond, T. A. AU - Wu, Y. AU - Green, R. D. AU - Ren, B. PY - 2005 DA - 2005// TI - A high-resolution map of active promoters in the human genome JO - Nature VL - 436 UR - https://doi.org/10.1038/nature03877 DO - 10.1038/nature03877 ID - Kim2005 ER - TY - JOUR AU - Guenther, M. G. AU - Levine, S. S. AU - Boyer, L. A. AU - Jaenisch, R. AU - Young, R. A. PY - 2007 DA - 2007// TI - A chromatin landmark and transcription initiation at most promoters in human cells JO - Cell VL - 130 UR - https://doi.org/10.1016/j.cell.2007.05.042 DO - 10.1016/j.cell.2007.05.042 ID - Guenther2007 ER - TY - JOUR AU - Alder, O. AU - Lavial, F. AU - Helness, A. AU - Brookes, E. AU - Pinho, S. AU - Chandrashekran, A. AU - Arnaud, P. AU - Pombo, A. AU - O'Neill, L. AU - Azuara, V. PY - 2010 DA - 2010// TI - Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment JO - Development VL - 137 UR - https://doi.org/10.1242/dev.048363 DO - 10.1242/dev.048363 ID - Alder2010 ER - TY - JOUR AU - Stock, J. K. AU - Giadrossi, S. AU - Casanova, M. AU - Brookes, E. AU - Vidal, M. AU - Koseki, H. AU - Brockdorff, N. AU - Fisher, A. G. AU - Pombo, A. PY - 2007 DA - 2007// TI - Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells JO - Nat Cell Biol VL - 9 UR - https://doi.org/10.1038/ncb1663 DO - 10.1038/ncb1663 ID - Stock2007 ER - TY - JOUR AU - Wilhelm, B. T. AU - Landry, J. R. PY - 2009 DA - 2009// TI - RNAseq-quantitative measurement of expression through massively parallel RNAsequencing JO - Methods VL - 48 UR - https://doi.org/10.1016/j.ymeth.2009.03.016 DO - 10.1016/j.ymeth.2009.03.016 ID - Wilhelm2009 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 RNAseq JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1226 DO - 10.1038/nmeth.1226 ID - Mortazavi2008 ER - TY - JOUR AU - Denoeud, F. AU - Aury, J. M. AU - Da Silva, C. AU - Noel, B. AU - Rogier, O. AU - Delledonne, M. AU - Morgante, M. AU - Valle, G. AU - Wincker, P. AU - Scarpelli, C. PY - 2008 DA - 2008// TI - Annotating genomes with massive-scale RNAsequencing JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-12-r175 DO - 10.1186/gb-2008-9-12-r175 ID - Denoeud2008 ER - TY - JOUR AU - Wang, E. T. AU - Sandberg, R. AU - Luo, S. AU - Khrebtukova, I. AU - Zhang, L. AU - Mayr, C. AU - Kingsmore, S. F. AU - Schroth, G. P. AU - Burge, C. B. PY - 2008 DA - 2008// TI - Alternative isoform regulation in human tissue transcriptomes JO - Nature VL - 456 UR - https://doi.org/10.1038/nature07509 DO - 10.1038/nature07509 ID - Wang2008 ER - TY - JOUR AU - Marioni, J. C. AU - Mason, C. E. AU - Mane, S. M. AU - Stephens, M. AU - Gilad, Y. PY - 2008 DA - 2008// TI - RNAseq: an assessment of technical reproducibility and comparison with gene expression arrays JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.079558.108 DO - 10.1101/gr.079558.108 ID - Marioni2008 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNAseq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - van Baren, M. J. AU - Salzberg, S. L. AU - Wold, B. J. AU - Pachter, L. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNAseq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Carson, J. P. AU - Zhang, N. AU - Frampton, G. M. AU - Gerry, N. P. AU - Lenburg, M. E. AU - Christman, M. F. PY - 2004 DA - 2004// TI - Pharmacogenomic identification of targets for adjuvant therapy with the topoisomerase poison camptothecin JO - Cancer Res VL - 64 UR - https://doi.org/10.1158/0008-5472.CAN-03-2029 DO - 10.1158/0008-5472.CAN-03-2029 ID - Carson2004 ER - TY - JOUR AU - Viegas, M. H. AU - Gehring, N. H. AU - Breit, S. AU - Hentze, M. W. AU - Kulozik, A. E. PY - 2007 DA - 2007// TI - The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm461 DO - 10.1093/nar/gkm461 ID - Viegas2007 ER - TY - JOUR AU - Scotto, L. AU - Narayan, G. AU - Nandula, S. V. AU - Arias-Pulido, H. AU - Subramaniyam, S. AU - Schneider, A. AU - Kaufmann, A. M. AU - Wright, J. D. AU - Pothuri, B. AU - Mansukhani, M. AU - Murty, V. V. PY - 2008 DA - 2008// TI - Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression JO - Genes Chromosomes Cancer VL - 47 UR - https://doi.org/10.1002/gcc.20577 DO - 10.1002/gcc.20577 ID - Scotto2008 ER - TY - JOUR AU - Chapman, R. D. AU - Heidemann, M. AU - Albert, T. K. AU - Mailhammer, R. AU - Flatley, A. AU - Meisterernst, M. AU - Kremmer, E. AU - Eick, D. PY - 2007 DA - 2007// TI - Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7 JO - Science VL - 318 UR - https://doi.org/10.1126/science.1145977 DO - 10.1126/science.1145977 ID - Chapman2007 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 ChIPseq experiments relative to controls JO - Nat Biotechnol VL - 27 UR - https://doi.org/10.1038/nbt.1518 DO - 10.1038/nbt.1518 ID - Rozowsky2009 ER - TY - JOUR AU - Jin, C. AU - Zang, C. AU - Wei, G. AU - Cui, K. AU - Peng, W. AU - Zhao, K. AU - Felsenfeld, G. PY - 2009 DA - 2009// TI - H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions JO - Nat Genet VL - 41 UR - https://doi.org/10.1038/ng.409 DO - 10.1038/ng.409 ID - Jin2009 ER - TY - JOUR AU - Brookes, E. AU - Pombo, A. PY - 2009 DA - 2009// TI - Modifications of RNA polymerase II are pivotal in regulating gene expression states JO - EMBO Rep VL - 10 UR - https://doi.org/10.1038/embor.2009.221 DO - 10.1038/embor.2009.221 ID - Brookes2009 ER - TY - JOUR AU - Core, L. J. AU - Waterfall, J. J. AU - Lis, J. T. PY - 2008 DA - 2008// TI - Nascent RNAsequencing reveals widespread pausing and divergent initiation at human promoters JO - Science VL - 322 UR - https://doi.org/10.1126/science.1162228 DO - 10.1126/science.1162228 ID - Core2008 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Sado, Y. AU - Kagawa, M. AU - Kishiro, Y. AU - Sugihara, K. AU - Naito, I. AU - Seyer, J. M. AU - Sugimoto, M. AU - Oohashi, T. AU - Ninomiya, Y. PY - 1995 DA - 1995// TI - Establishment by the rat lymph node method of epitope-defined monoclonal antibodies recognizing the six different alpha chains of human type IV collagen JO - Histochem Cell Biol VL - 104 UR - https://doi.org/10.1007/BF01464322 DO - 10.1007/BF01464322 ID - Sado1995 ER - TY - JOUR AU - Valdez, M. R. AU - Richardson, J. A. AU - Klein, W. H. AU - Olson, E. N. PY - 2000 DA - 2000// TI - Failure of Myf5 to support myogenic differentiation without myogenin, MyoD, and MRF4 JO - Developmental Biology VL - 219 UR - https://doi.org/10.1006/dbio.2000.9621 DO - 10.1006/dbio.2000.9621 ID - Valdez2000 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Berriz, G. F. AU - Beaver, J. E. AU - Cenik, C. AU - Tasan, M. AU - Roth, F. P. PY - 2009 DA - 2009// TI - Next generation software for functional trend analysis JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp498 DO - 10.1093/bioinformatics/btp498 ID - Berriz2009 ER - TY - JOUR AU - Dacwag, C. S. AU - Ohkawa, Y. AU - Pal, S. AU - Sif, S. AU - Imbalzano, A. N. PY - 2007 DA - 2007// TI - The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling JO - Molecular and Cellular Biology VL - 27 UR - https://doi.org/10.1128/MCB.01528-06 DO - 10.1128/MCB.01528-06 ID - Dacwag2007 ER -