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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, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 57 - 74
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA... 
TRANSCRIPTION FACTOR-BINDING | CHROMATIN | MAPS | DETERMINANTS | HUMAN-CELLS | MULTIDISCIPLINARY SCIENCES | IN-VIVO | REGIONS | MOUSE | WIDE | CHROMOSOME CONFORMATION CAPTURE | 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 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, ISSN 0028-0836, 11/2014, Volume 515, Issue 7527, pp. 355 - 364
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two... 
TRANSCRIPTION FACTOR-BINDING | GENE | LANDSCAPE | PERVASIVE TRANSCRIPTION | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | ENCODE DATA | TRANSPOSABLE ELEMENTS | EVOLUTIONARY DYNAMICS | CHROMATIN INTERACTIONS | EXPRESSION | Human beings | Genetic research | Mice | Genetic aspects | Genomes | Man | Comparative analysis | Transcription factors | Genomics | Rodents | Mammals | Gene expression | Deoxyribonucleic acid--DNA | Index Medicus | Mouse genome | Epigenomics
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3. 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
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the... 
TRANSCRIPTION FACTOR-BINDING | CHROMATIN IMMUNOPRECIPITATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | METHYLATIONS | MACROPHAGE | IDENTIFICATION | ELEMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | REGIONS | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | ASSOCIATION | EXPRESSION | 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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4. 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 and Medicinska fakulteten and Institutionen för molekylärbiologi (Medicinska fakulteten) and Umeå universitet
Nature, ISSN 0028-0836, 08/2014, Volume 512, Issue 7515, pp. 449 - 452
Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies... 
CENTROMERIC CHROMATIN | ELEMENTS | METHYLATION | DROSOPHILA GENOME | ELEGANS | MULTIDISCIPLINARY SCIENCES | TRANSCRIPTION | STATE | MODENCODE | DOMAINS | ENCODE | 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 | Medical Biotechnology | Medical and Health Sciences | Medicin och hälsovetenskap | Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) | Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci) | Medicinsk bioteknologi
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5. 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, ISSN 0028-0836, 08/2014, Volume 512, Issue 7515, pp. 445 - 448
The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the... 
CELLS | EVOLUTION | LANDSCAPE | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | TISSUES | GENOME | 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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