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1. 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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2. Full Text Comparative analysis of metazoan chromatin organization
by Ho, Joshua W. K and Jung, Youngsook L and Liu, Tao and Alver, Burak H and Lee, Soohyun and Ikegami, Kohta and Sohn, Kyung-Ah and Minoda, Aki and Tolstorukov, Michael Y and Appert, Alex and Parker, Stephen C. J and Gu, Tingting and Kundaje, Anshul and Riddle, Nicole C and Bishop, Eric and Egelhofer, Thea A and Hu, Sheng'En Shawn and Alekseyenko, Artyom A and Rechtsteiner, Andreas and Asker, Dalal and Belsky, Jason A and Bowman, Sarah K and Chen, Q. Brent and Chen, Ron A.-J and Day, Daniel S and Dong, Yan and Dose, Andrea C and Duan, Xikun and Epstein, Charles B and Ercan, Sevinc and Feingold, Elise A and Ferrari, Francesco and Garrigues, Jacob M and Gehlenborg, Nils and Good, Peter J and Haseley, Psalm and He, Daniel and Herrmann, Moritz and Hoffman, Michael M and Jeffers, Tess E and Kharchenko, Peter V and Kolasinska-Zwierz, Paulina and Kotwaliwale, Chitra V and Kumar, Nischay and Langley, Sasha A and Larschan, Erica N and Latorre, Isabel and Libbrecht, Maxwell W and Lin, Xueqiu and Park, Richard and Pazin, Michael J and Pham, Hoang N and Plachetka, Annette and Qin, Bo and Schwartz, Yuri B and Shoresh, Noam and Stempor, Przemyslaw and Vielle, Anne and Wang, Chengyang and Whittle, Christina M and Xue, Huiling and Kingston, Robert E and Kim, Ju Han and Bernstein, Bradley E and Dernburg, Abby F and Pirrotta, Vincenzo and Kuroda, Mitzi I and Noble, William S and Tullius, Thomas D and Kellis, Manolis and MacAlpine, David M and Strome, Susan and Elgin, Sarah C. R and Liu, Xiaole Shirley and Lieb, Jason D and Ahringer, Julie and Karpen, Gary H and Park, Peter J
Nature (London), ISSN 0028-0836, 08/2014, Volume 512, Issue 7515, pp. 449 - 452
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Chromatin - metabolism | Species Specificity | Histones - chemistry | Nucleosomes - chemistry | Epigenesis, Genetic | Humans | Chromatin Assembly and Disassembly - genetics | Centromere - metabolism | Drosophila melanogaster - genetics | Promoter Regions, Genetic - genetics | Heterochromatin - chemistry | Heterochromatin - metabolism | Nuclear Lamina - metabolism | Chromatin - chemistry | Cell Line | Caenorhabditis elegans - genetics | Molecular Sequence Annotation | Drosophila melanogaster - cytology | Nucleosomes - metabolism | Nucleosomes - genetics | Animals | Caenorhabditis elegans - cytology | Heterochromatin - genetics | Centromere - genetics | DNA Replication - genetics | Enhancer Elements, Genetic - genetics | Histones - metabolism | Chromatin - genetics | Studies | Chromatin | Genes | Genomes | Comparative analysis | Chromosomes | Methods | Index Medicus
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3. Full Text Comparative analysis of the transcriptome across distant species
by Gerstein, Mark B and Rozowsky, Joel and Yan, Koon-Kiu and Wang, Daifeng and Cheng, Chao and Brown, James B and Davis, Carrie A and Hillier, Ladeana and Sisu, Cristina and Li, Jingyi Jessica and Pei, Baikang and Harmanci, Arif O and Duff, Michael O and Djebali, Sarah and Alexander, Roger P and Alver, Burak H and Auerbach, Raymond and Bell, Kimberly and Bickel, Peter J and Boeck, Max E and Boley, Nathan P and Booth, Benjamin W and Cherbas, Lucy and Cherbas, Peter and Di, Chao and Dobin, Alex and Drenkow, Jorg and Ewing, Brent and Fang, Gang and Fastuca, Megan and Feingold, Elise A and Frankish, Adam and Gao, Guanjun and Good, Peter J and Guigó, Roderic and Hammonds, Ann and Harrow, Jen and Hoskins, Roger A and Howald, Cédric and Hu, Long and Huang, Haiyan and Hubbard, Tim J. P and Huynh, Chau and Jha, Sonali and Kasper, Dionna and Kato, Masaomi and Kaufman, Thomas C and Kitchen, Robert R and Ladewig, Erik and Lagarde, Julien and Lai, Eric and Leng, Jing and Lu, Zhi and MacCoss, Michael and May, Gemma and McWhirter, Rebecca and Merrihew, Gennifer and Miller, David M and Mortazavi, Ali and Murad, Rabi and Oliver, Brian and Olson, Sara and Park, Peter J and Pazin, Michael J and Perrimon, Norbert and Pervouchine, Dmitri and Reinke, Valerie and Reymond, Alexandre and Robinson, Garrett and Samsonova, Anastasia and Saunders, Gary I and Schlesinger, Felix and Sethi, Anurag and Slack, Frank J and Spencer, William C and Stoiber, Marcus H and Strasbourger, Pnina and Tanzer, Andrea and Thompson, Owen A and Wan, Kenneth H and Wang, Guilin and Wang, Huaien and Watkins, Kathie L and Wen, Jiayu and Wen, Kejia and Xue, Chenghai and Yang, Li and Yip, Kevin and Zaleski, Chris and Zhang, Yan and Zheng, Henry and Brenner, Steven E and Graveley, Brenton R and Celniker, Susan E and Gingeras, Thomas R and Waterston, Robert
Nature (London), ISSN 0028-0836, 08/2014, Volume 512, Issue 7515, pp. 445 - 448
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Caenorhabditis elegans - growth & development | Caenorhabditis elegans - genetics | Humans | Molecular Sequence Annotation | Gene Expression Regulation, Developmental - genetics | Gene Expression Profiling | Transcriptome - genetics | Caenorhabditis elegans - embryology | Drosophila melanogaster - genetics | Promoter Regions, Genetic - genetics | RNA, Untranslated - genetics | Pupa - genetics | Animals | Sequence Analysis, RNA | Larva - growth & development | Drosophila melanogaster - growth & development | Larva - genetics | Models, Genetic | Histones - metabolism | Pupa - growth & development | Chromatin - genetics | Cluster Analysis | Proteins | Accuracy | Transcription factors | Organisms | Gene expression | Comparative analysis | Index Medicus | Caenorhabditis elegans | Embriologia | Genètica | Regulació genètica | Transcriptomics | Comparative genomics | Drosòfila
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4. 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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5. Full Text Defining functional DNA elements in the human genome
by Manolis Kellis and Barbara Wold and Michael P. Snyderd and Bradley E. Bernstein and Anshul Kundaje and Georgi K. Marinov and Lucas D. Ward and Ewan Birney and Gregory E. Crawford and Job Dekker and Ian Dunham and Laura L. Elnitski and Peggy J. Farnham and Elise A. Feingold and Mark Gerstein and Morgan C. Giddings and David M. Gilbert and Thomas R. Gingeras and Eric D. Green and Roderic Guigo and Tim Hubbard and Jim Kent and Jason D. Lieb and Richard M. Myerst and Michael J. Pazin and Bing Ren and John A. Stamatoyannopoulos and Zhiping Weng and Kevin P. White and Ross C. Hardison
Proceedings of the National Academy of Sciences - PNAS, ISSN 0027-8424, 4/2014, Volume 111, Issue 17, pp. 6131 - 6138
Human genome | RNA | PERSPECTIVE | DNA | Genomics | Genes | Evolution | Evolutionary genetics | Genomes | Biochemistry | Human genetics | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Biological Evolution | DNA - genetics | Disease - genetics | Humans | Software | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Genetic research | Research | Nucleotide sequencing | DNA sequencing | Human subjects | Deoxyribonucleic acid--DNA | Index Medicus | Biological Sciences
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6. Full Text Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions
by Michael Shogren-Knaak and Haruhiko Ishii and Jian-Min Sun and Michael J. Pazin and James R. Davie and Craig L. Peterson
Science (American Association for the Advancement of Science), ISSN 0036-8075, 2/2006, Volume 311, Issue 5762, pp. 844 - 847
Proteins | Circles | Chromatin | Ligation | Gels | DNA | Histones | Nucleosomes | Reports | Biochemistry | Acetylation | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Chromatin. Chromosome | Molecular and cellular biology | Molecular genetics | Recombinant Proteins - metabolism | Chromatin - metabolism | Histones - chemistry | Nucleosomes - chemistry | Electrophoresis, Polyacrylamide Gel | Humans | Chromatin Assembly and Disassembly | Nucleosomes - metabolism | DNA - metabolism | Drosophila Proteins - metabolism | Protein Folding | Transcription Factors - metabolism | Magnesium Chloride - pharmacology | Adenosine Triphosphate - metabolism | Protein Conformation | Electrophoretic Mobility Shift Assay | Lysine - metabolism | Protein Processing, Post-Translational | HeLa Cells | Histones - metabolism | Chromatin - chemistry | Eukaryotes | Research | Enzymes | Index Medicus
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7. Full Text Perspectives on ENCODE
by Snyder, Michael P and Gingeras, Thomas R and Moore, Jill E and Weng, Zhiping and Gerstein, Mark B and Ren, Bing and Hardison, Ross C and Stamatoyannopoulos, John A and Graveley, Brenton R and Feingold, Elise A and Pazin, Michael J and Pagan, Michael and Gilchrist, Daniel A and Hitz, Benjamin C and Cherry, J. Michael and Bernstein, Bradley E and Mendenhall, Eric M and Zerbino, Daniel R and Frankish, Adam and Flicek, Paul and Myers, Richard M and ENCODE Project Consortium and The ENCODE Project Consortium
Nature (London), ISSN 0028-0836, 07/2020, Volume 583, Issue 7818, pp. 693 - 698
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Consortia | Genomic libraries | Terminology | Bibliographic databases | Management | Nucleotide sequencing | History | Collections and collecting | Service enhancement | DNA sequencing | Medical research | Chromatin | Transcription factors | Ontology | Gene regulation | Genomics | Genes | Metadata | Genomes | Regulatory sequences | Experiments | Standards | Proteins | Annotations | Isoforms | Quality control | Binding sites | Deoxyribonucleic acid--DNA | Index Medicus | Epigenetics | Epigenomics | Genome | Transcriptomics
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