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1. Full Text An integrated encyclopedia of DNA elements in the human genome
by Dunham, Ian and Kundaje, Anshul and Aldred, Shelley F and Collins, Patrick J and Davis, Carrie A and Doyle, Francis and Epstein, Charles B and Frietze, Seth and Harrow, Jennifer and Kaul, Rajinder and Khatun, Jainab and Lajoie, Bryan R and Landt, Stephen G and Lee, Bum-Kyu and Pauli, Florencia and Rosenbloom, Kate R and Sabo, Peter and Safi, Alexias and Sanyal, Amartya and Shoresh, Noam and Simon, Jeremy M and Song, Lingyun and Trinklein, Nathan D and Altshuler, Robert C and Birney, Ewan and Brown, James B and Cheng, Chao and Djebali, Sarah and Dong, Xianjun and Ernst, Jason and Furey, Terrence S and Gerstein, Mark and Giardine, Belinda and Greven, Melissa and Hardison, Ross C and Harris, Robert S and Herrero, Javier and Hoffman, Michael M and Iyer, Sowmya and Kellis, Manolis and Kheradpour, Pouya and Lassmann, Timo and Li, Qunhua and Lin, Xinying and Marinov, Georgi K and Merkel, Angelika and Mortazavi, Ali and Parker, Stephen C. J and Reddy, Timothy E and Rozowsky, Joel and Schlesinger, Felix and Thurman, Robert E and Wang, Jie and Ward, Lucas D and Whitfield, Troy W and Wilder, Steven P and Wu, Weisheng and Xi, Hualin S and Yip, Kevin Y and Zhuang, Jiali and Bernstein, Bradley E and Green, Eric D and Gunter, Chris and Snyder, Michael and Pazin, Michael J and Lowdon, Rebecca F and Dillon, Laura A. L and Adams, Leslie B and Kelly, Caroline J and Zhang, Julia and Wexler, Judith R and Good, Peter J and Feingold, Elise A and Crawford, Gregory E and Dekker, Job and Elnitski, Laura and Farnham, Peggy J and Giddings, Morgan C and Gingeras, Thomas R and Guigó, Roderic and Hubbard, Timothy J and Kent, W. James and Lieb, Jason D and Margulies, Elliott H and Myers, Richard M and Stamatoyannopoulos, John A and Tenenbaum, Scott A and Weng, Zhiping and White, Kevin P and Wold, Barbara and Yu, Yanbao and Wrobel, John and Risk, Brian A and Gunawardena, Harsha P and Kuiper, Heather C and Maier, Christopher W and Xie, Ling and Chen, Xian and Mikkelsen, Tarjei S and Gillespie, Shawn and ... and ENCODE Project Consortium and The ENCODE Project Consortium
Nature (London), ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 57 - 74
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Fundamental and applied biological sciences. Psychology | Classical genetics, quantitative genetics, hybrids | Human | Biological and medical sciences | Genetics of eukaryotes. Biological and molecular evolution | Mammals - genetics | Chromatin - metabolism | Histones - chemistry | Genomics | Humans | Promoter Regions, Genetic - genetics | Encyclopedias as Topic | DNA-Binding Proteins - metabolism | Chromatin Immunoprecipitation | Neoplasms - genetics | Genetic Predisposition to Disease - genetics | Genome-Wide Association Study | Chromosomes, Human - genetics | Molecular Sequence Annotation | Exons - genetics | DNA Methylation - genetics | Binding Sites - genetics | Chromosomes, Human - metabolism | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | DNA - genetics | DNA Footprinting | Proteins - genetics | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Animals | Sequence Analysis, RNA | Alleles | Polymorphism, Single Nucleotide - genetics | Genetic Variation - genetics | Histones - metabolism | Transcription, Genetic - genetics | Chromatin - genetics | Genetic research | Genetic transcription | Research | Human genome | Proteins | Studies | Genes | DNA methylation | Genetics | Deoxyribonucleic acid--DNA | Index Medicus | Genètica | Genòmica | Genoma humà | Life Sciences
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2. Full Text Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
by Trapnell, Cole and Mortazavi, Ali and Kwan, Gordon and Williams, Brian A and Salzberg, Steven L and Pertea, Geo and Pachter, Lior and Wold, Barbara J and van Baren, Marijke J
Nature biotechnology, ISSN 1087-0156, 05/2010, Volume 28, Issue 5, pp. 511 - 515
Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Fundamental and applied biological sciences. Psychology | Biotechnology | Biological and medical sciences | Diverse techniques | Molecular and cellular biology | Cell Line | Oligonucleotide Array Sequence Analysis - methods | RNA, Messenger - genetics | RNA, Messenger - analysis | Gene Expression Profiling - methods | RNA, Messenger - metabolism | Proto-Oncogene Proteins c-myc - metabolism | Sequence Analysis, RNA - methods | Cell Differentiation - genetics | Algorithms | Animals | Protein Isoforms - metabolism | Mice | Proto-Oncogene Proteins c-myc - genetics | Software | Genome | Protein Isoforms - genetics | Messenger RNA | Genetic aspects | Research | Genetic transcription | Properties | Cell differentiation | Gene expression | Cellular biology | Ribonucleic acid--RNA | Open source software | Index Medicus
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3. Full Text Assessment of transcript reconstruction methods for RNA-seq
by Steijger, Tamara and Abril, Josep F and Engström, Pär G and Kokocinski, Felix and Akerman, Martin and Alioto, Tyler and Ambrosini, Giovanna and Antonarakis, Stylianos E and Behr, Jonas and Bertone, Paul and Bohnert, Regina and Bucher, Philipp and Cloonan, Nicole and Derrien, Thomas and Djebali, Sarah and Du, Jiang and Dudoit, Sandrine and Gerstein, Mark and Gingeras, Thomas R and Gonzalez, David and Grimmond, Sean M and Guigó, Roderic and Habegger, Lukas and Harrow, Jennifer and Hubbard, Tim J and Iseli, Christian and Jean, Géraldine and Kahles, André and Lagarde, Julien and Leng, Jing and Lefebvre, Gregory and Lewis, Suzanna and Mortazavi, Ali and Niermann, Peter and Rätsch, Gunnar and Reymond, Alexandre and Ribeca, Paolo and Richard, Hugues and Rougemont, Jacques and Rozowsky, Joel and Sammeth, Michael and Sboner, Andrea and Schulz, Marcel H and Searle, Steven M. J and Solorzano, Naryttza Diaz and Solovyev, Victor and Stanke, Mario and Stevenson, Brian J and Stockinger, Heinz and Valsesia, Armand and Weese, David and White, Simon and Wold, Barbara J and Wu, Jie and Wu, Thomas D and Zeller, Georg and Zerbino, Daniel and Zhang, Michael Q and RGASP Consortium and The RGASP Consortium
Nature methods, ISSN 1548-7091, 12/2013, Volume 10, Issue 12, pp. 1177 - 1184
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Computational Biology - methods | RNA Splice Sites | Exons | Introns | Humans | Gene Expression Profiling | RNA, Messenger - metabolism | Sequence Analysis, RNA - methods | Caenorhabditis elegans | RNA Splicing | Algorithms | Animals | Software | Genome | Drosophila melanogaster | RNA sequencing | Exon (Molecular genetics) | Genetic research | Research | Genetic transcription | Methods | Computational biology | Computers | Ribonucleic acid--RNA | Gene expression | Index Medicus | Empalmament (Genètica) | Biologia computacional | Life Sciences | Quantitative Methods | Bioinformatics | Computer Science
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4. Full Text ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
by Landt, Stephen G and Marinov, Georgi K and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E and Bickel, Peter and Brown, James B and Cayting, Philip and Chen, Yiwen and DeSalvo, Gilberto and Epstein, Charles and Fisher-Aylor, Katherine I and Euskirchen, Ghia and Gerstein, Mark and Gertz, Jason and Hartemink, Alexander J and Hoffman, Michael M and Iyer, Vishwanath R and Jung, Youngsook L and Karmakar, Subhradip and Kellis, Manolis and Kharchenko, Peter V and Li, Qunhua and Liu, Tao and Liu, X. Shirley and Ma, Lijia and Milosavljevic, Aleksandar and Myers, Richard M and Park, Peter J and Pazin, Michael J and Perry, Marc D and Raha, Debasish and Reddy, Timothy E and Rozowsky, Joel and Shoresh, Noam and Sidow, Arend and Slattery, Matthew and Stamatoyannopoulos, John A and Tolstorukov, Michael Y and White, Kevin P and Xi, Simon and Farnham, Peggy J and Lieb, Jason D and Wold, Barbara J and Snyder, Michael
Genome research, ISSN 1088-9051, 09/2012, Volume 22, Issue 9, pp. 1813 - 1831
Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Transcription Factors - metabolism | Guidelines as Topic | Animals | Humans | Genome - genetics | Databases, Genetic | Chromatin Immunoprecipitation - methods | Histones - metabolism | Internet | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Index Medicus | Resource
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5. Full Text A comparative encyclopedia of DNA elements in the mouse genome
by Yue, Feng and Cheng, Yong and Breschi, Alessandra and Vierstra, Jeff and Wu, Weisheng and Ryba, Tyrone and Sandstrom, Richard and Ma, Zhihai and Davis, Carrie and Pope, Benjamin D and Shen, Yin and Pervouchine, Dmitri D and Djebali, Sarah and Thurman, Robert E and Kaul, Rajinder and Rynes, Eric and Kirilusha, Anthony and Marinov, Georgi K and Williams, Brian A and Trout, Diane and Amrhein, Henry and Fisher-Aylor, Katherine and Antoshechkin, Igor and DeSalvo, Gilberto and See, Lei-Hoon and Fastuca, Meagan and Drenkow, Jorg and Zaleski, Chris and Dobin, Alex and Prieto, Pablo and Lagarde, Julien and Bussotti, Giovanni and Tanzer, Andrea and Denas, Olgert and Li, Kanwei and Bender, M.A and Zhang, Miaohua and Byron, Rachel and Groudine, Mark T and McCleary, David and Pham, Long and Ye, Zhen and Kuan, Samantha and Edsall, Lee and Wu, Yi-Chieh and Rasmussen, Matthew D and Bansal, Mukul S and Kellis, Manolis and Keller, Cheryl A and Morrissey, Christapher S and Mishra, Tejaswini and Jain, Deepti and Dogan, Nergiz and Harris, Robert S and Cayting, Philip and Kawli, Trupti and Boyle, Alan P and Euskirchen, Ghia and Kundaje, Anshul and Lin, Shin and Lin, Yiing and Jansen, Camden and Malladi, Venkat S and Cline, Melissa S and Erickson, Drew T and Kirkup, Vanessa M and Learned, Katrina and Sloan, Cricket A and Rosenbloom, Kate R and De Sousa, Beatriz Lacerda and Beal, Kathryn and Pignatelli, Miguel and Flicek, Paul and Lian, Jin and Kahveci, Tamer and Lee, Dongwon and Kent, W. James and Santos, Miguel Ramalho and Herrero, Javier and Notredame, Cedric and Johnson, Audra and Vong, Shinny and Lee, Kristen and Bates, Daniel and Neri, Fidencio and Diegel, Morgan and Canfield, Theresa and Sabo, Peter J and Wilken, Matthew S and Reh, Thomas A and Giste, Erika and Shafer, Anthony and Kutyavin, Tanya and Haugen, Eric and Dunn, Douglas and Reynolds, Alex P and Neph, Shane and Humbert, Richard and Hansen, R. Scott and De Bruijn, Marella and ... and Mouse ENCODE Consortium and The Mouse ENCODE Consortium
Nature (London), ISSN 0028-0836, 11/2014, Volume 515, Issue 7527, pp. 355 - 364
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Chromatin - metabolism | Mice - genetics | Conserved Sequence - genetics | Genome-Wide Association Study | Gene Regulatory Networks - genetics | Species Specificity | Gene Expression Regulation - genetics | Genomics | Humans | Molecular Sequence Annotation | Genome - genetics | Transcriptome - genetics | Regulatory Sequences, Nucleic Acid - genetics | RNA - genetics | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Animals | DNA Replication - genetics | Chromatin - genetics | Cell Lineage - genetics | Human beings | Genetic research | Mice | Genetic aspects | Genomes | Man | Comparative analysis | Transcription factors | Rodents | Mammals | Gene expression | Deoxyribonucleic acid--DNA | Index Medicus | Mouse genome | Epigenomics
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6. Full Text Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity
by Zhang, Jingli A and Mortazavi, Ali and Williams, Brian A and Wold, Barbara J and Rothenberg, Ellen V
Cell (Cambridge), ISSN 0092-8674, 04/2012, Volume 149, Issue 2, pp. 467 - 482
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Proto-Oncogene Proteins - metabolism | Promoter Regions, Genetic | Genome-Wide Association Study | Signal Transduction | Receptors, Notch - metabolism | Epigenesis, Genetic | Mice, Inbred C57BL | Gene Expression Regulation