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1. Full Text Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
by Matthew T. Maurano and Richard Humbert and Eric Rynes and Robert E. Thurman and Eric Haugen and Hao Wang and Alex P. Reynolds and Richard Sandstrom and Hongzhu Qu and Jennifer Brody and Anthony Shafer and Fidencio Neri and Kristen Lee and Tanya Kutyavin and Sandra Stehling-Sun and Audra K. Johnson and Theresa K. Canfield and Erika Giste and Morgan Diegel and Daniel Bates and R. Scott Hansen and Shane Neph and Peter J. Sabo and Shelly Heimfeld and Antony Raubitschek and Steven Ziegler and Chris Cotsapas and Nona Sotoodehnia and Ian Glass and Shamil R. Sunyaev and Rajinder Kaul and John A. Stamatoyannopoulos
Science, ISSN 0036-8075, 9/2012, Volume 337, Issue 6099, pp. 1190 - 1195
Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are... 
Diabetic retinopathy | Crohn disease | Nervous system diseases | Multiple sclerosis | Transcription factors | RESEARCH ARTICLE | DNA | Type 2 diabetes mellitus | Cells | Type 1 diabetes mellitus | Phenotypic traits | CELLS | EVOLUTION | CROHNS-DISEASE | VARIANTS | MULTIDISCIPLINARY SCIENCES | 22 LOCI | PROMOTER | Chromatin - ultrastructure | Chromatin - metabolism | Crohn Disease - genetics | Promoter Regions, Genetic | Genome-Wide Association Study | Transcription Factors - chemistry | Disease - genetics | Humans | Regulatory Sequences, Nucleic Acid | Fetus - metabolism | Fetal Development | Multiple Sclerosis - genetics | Transcription Factors - genetics | Gene Regulatory Networks | DNA - genetics | Genetic Variation | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Phenotype | Regulatory Elements, Transcriptional | Alleles | Electrocardiography | Polymorphism, Single Nucleotide | Genome, Human | Physiological aspects | Research | Genetic variation | Genetic diversity | Disease | Genomics | Deoxyribonucleic acid--DNA | Government regulations | Deoxyribonucleic acid | Genetics | Genomes | Gene expression | Localization | Loci | Binding sites
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2. Full Text Integrative analysis of 111 reference human epigenomes
by Roadmap Epigenomics Consortium, Epigenomics Consortium and Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and Ziller, Michael J and Amin, Viren and Whitaker, John W and Schultz, Matthew D and Ward, Lucas D and Sarkar, Abhishek and Quon, Gerald and Sandstrom, Richard S and Eaton, Matthew L and Wu, Yi-Chieh and Pfenning, Andreas R and Wang, Xinchen and Claussnitzer, Melina and Liu, Yaping and Coarfa, Cristian and Harris, R. Alan and Shoresh, Noam and Epstein, Charles B and Gjoneska, Elizabeta and Leung, Danny and Xie, Wei and Hawkins, R. David and Lister, Ryan and Hong, Chibo and Gascard, Philippe and Mungall, Andrew J and Moore, Richard and Chuah, Eric and Tam, Angela and Canfield, Theresa K and Hansen, R. Scott and Kaul, Rajinder and Sabo, Peter J and Bansal, Mukul S and Carles, Annaick and Dixon, Jesse R and Farh, Kai-How and Feizi, Soheil and Karlic, Rosa and Kim, Ah-Ram and Kulkarni, Ashwinikumar and Li, Daofeng and Lowdon, Rebecca and Elliott, Ginell and Mercer, Tim R and Neph, Shane J and Onuchic, Vitor and Polak, Paz and Rajagopal, Nisha and Ray, Pradipta and Sallari, Richard C and Siebenthall, Kyle T and Sinnott-Armstrong, Nicholas A and Stevens, Michael and Thurman, Robert E and Wu, Jie and Zhang, Bo and Zhou, Xin and Beaudet, Arthur E and Boyer, Laurie A and De Jager, Philip L and Farnham, Peggy J and Fisher, Susan J and Haussler, David and Jones, Steven J. M and Li, Wei and Marra, Marco A and McManus, Michael T and Sunyaev, Shamil and Thomson, James A and Tlsty, Thea D and Tsai, Li-Huei and Wang, Wei and Waterland, Robert A and Zhang, Michael Q and Chadwick, Lisa H and Bernstein, Bradley E and Costello, Joseph F and Ecker, Joseph R and Hirst, Martin and Meissner, Alexander and Milosavljevic, Aleksandar and Ren, Bing and Stamatoyannopoulos, John A and Wang, Ting and Kellis, Manolis and Roadmap Epigenomics Consortium
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7539, pp. 317 - 329
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a... 
TRANSCRIPTION FACTORS | RISK LOCI | DYNAMIC DNA METHYLATION | ALZHEIMERS-DISEASE | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | HISTONE MODIFICATIONS | CHROMATIN-STATE | REGULATORY REGIONS | GENOME-WIDE ASSOCIATION | MAMMALIAN GENOMES | Chromatin - metabolism | Humans | Reference Values | RNA - genetics | Organ Specificity - genetics | DNA Methylation | Base Sequence | Cell Lineage - genetics | Chromatin - chemistry | Genome-Wide Association Study | Datasets as Topic | Epigenomics | Chromosomes, Human - genetics | Cells, Cultured | Chromosomes, Human - metabolism | DNA - metabolism | Genome, Human - genetics | Chromosomes, Human - chemistry | DNA - genetics | DNA - chemistry | Epigenesis, Genetic - genetics | Enhancer Elements, Genetic - genetics | Genetic Variation - genetics | Histones - metabolism | Chromatin - genetics | Genetic research | Epigenetic inheritance | Research | Human genome | DNA methylation | Enzymes | Genomes | Gene expression | Genomics | Deoxyribonucleic acid--DNA
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3. Full Text The accessible chromatin landscape of the human genome
by Thurman, Robert E and Rynes, Eric and Humbert, Richard and Vierstra, Jeff and Maurano, Matthew T and Haugen, Eric and Sheffield, Nathan C and Stergachis, Andrew B and Wang, Hao and Vernot, Benjamin and Garg, Kavita and John, Sam and Sandstrom, Richard and Bates, Daniel and Boatman, Lisa and Canfield, Theresa K and Diegel, Morgan and Dunn, Douglas and Ebersol, Abigail K and Frum, Tristan and Giste, Erika and Johnson, Audra K and Johnson, Ericka M and Kutyavin, Tanya and Lajoie, Bryan and Lee, Bum-Kyu and Lee, Kristen and London, Darin and Lotakis, Dimitra and Neph, Shane and Neri, Fidencio and Nguyen, Eric D and Qu, Hongzhu and Reynolds, Alex P and Roach, Vaughn and Safi, Alexias and Sanchez, Minerva E and Sanyal, Amartya and Shafer, Anthony and Simon, Jeremy M and Song, Lingyun and Vong, Shinny and Weaver, Molly and Yan, Yongqi and Zhang, Zhancheng and Zhang, Zhuzhu and Lenhard, Boris and Tewari, Muneesh and Dorschner, Michael O and Hansen, R. Scott and Navas, Patrick A and Stamatoyannopoulos, George and Iyer, Vishwanath R and Lieb, Jason D and Sunyaev, Shamil R and Akey, Joshua M and Sabo, Peter J and Kaul, Rajinder and Furey, Terrence S and Dekker, Job and Crawford, Gregory E and Stamatoyannopoulos, John A
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 75 - 82
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including... 
LOCUS-CONTROL REGION | PROTEIN | MULTIDISCIPLINARY SCIENCES | TRANSCRIPTION | DISTINCT | NF-E2 | BINDING | BETA-GLOBIN LOCUS | Chromatin - metabolism | Genomics | Humans | Molecular Sequence Annotation | Mutation Rate | Promoter Regions, Genetic - genetics | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Encyclopedias as Topic | DNA - genetics | DNA Footprinting | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | DNA Methylation | Transcription Initiation Site | Transcription, Genetic | Chromatin - genetics | Evolution, Molecular | Physiological aspects | Genetic research | Chromatin | Research | Human genome | DNA | Proteins | DNA methylation | Mutation | Cells
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4. Full Text An expansive human regulatory lexicon encoded in transcription factor footprints
by Neph, Shane and Vierstra, Jeff and Stergachis, Andrew B and Reynolds, Alex P and Haugen, Eric and Vernot, Benjamin and Thurman, Robert E and John, Sam and Sandstrom, Richard and Johnson, Audra K and Maurano, Matthew T and Humbert, Richard and Rynes, Eric and Wang, Hao and Vong, Shinny and Lee, Kristen and Bates, Daniel and Diegel, Morgan and Roach, Vaughn and Dunn, Douglas and Neri, Jun and Schafer, Anthony and Hansen, R. Scott and Kutyavin, Tanya and Giste, Erika and Weaver, Molly and Canfield, Theresa and Sabo, Peter and Zhang, Miaohua and Balasundaram, Gayathri and Byron, Rachel and MacCoss, Michael J and Akey, Joshua M and Bender, M.A and Groudine, Mark and Kaul, Rajinder and Stamatoyannopoulos, John A
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 83 - 90
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution 'footprints'. Using genomic... 
RNA-POLYMERASE-II | COMPLEX | HUMAN GENOME | PROTEIN-DNA INTERACTIONS | CHROMATIN | MULTIDISCIPLINARY SCIENCES | IN-VIVO | GENE-EXPRESSION | MICE | DIFFERENTIATION | BINDING | Genomic Imprinting | Genomics | Humans | Molecular Sequence Annotation | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Encyclopedias as Topic | DNA - genetics | DNA Footprinting | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | DNA Methylation | Transcription Initiation Site | Polymorphism, Single Nucleotide - genetics | Physiological aspects | Genetic research | Transcription factors | Research | Genetic regulation | Proteins | Genes | Phylogenetics | Footprints | Genomes | Deoxyribonucleic acid--DNA | Methods | protein occupancy | regulation | chromatin | DNaseI footprinting | ENCODE
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5. Full Text Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
by Zhang, Zhihong and Kuehn, Michael S and Thurman, Robert E and Reynolds, Alex P and Noble, William S and Neph, Shane and Hesselberth, Jay R and Fields, Stanley and Sabo, Peter J and Sandstrom, Richard and Chen, Xiaoyu and Stamatoyannopoulos, John A
Nature Methods, ISSN 1548-7091, 04/2009, Volume 6, Issue 4, pp. 283 - 289
The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of... 
ELEMENTS | SPECIFICITY | CHROMATIN | TRANSCRIPTION | GENES | BIOCHEMICAL RESEARCH METHODS | FACTOR-BINDING-SITES | SACCHAROMYCES-CEREVISIAE | MAP | YEAST GENOME | Amino Acid Sequence | Transcription Factors - chemistry | Molecular Sequence Data | Transcription Factors - genetics | DNA Footprinting - methods | DNA - genetics | Protein Interaction Mapping - methods | DNA - chemistry | Algorithms | Base Sequence | Protein Binding | Binding Sites | Sequence Analysis, DNA - methods | Chromosome mapping | Usage | DNA replication | DNA microarrays | Genomics | Research | Gene expression | Methods | Protein-protein interactions | Proteins | Research methodology | Binding sites | Deoxyribonucleic acid--DNA
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6. 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 | Mouse genome | Epigenomics
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7. Full Text Conservation of trans-acting circuitry during mammalian regulatory evolution
by Stergachis, Andrew B and Neph, Shane and Sandstrom, Richard and Haugen, Eric and Reynolds, Alex P and Zhang, Miaohua and Byron, Rachel and Canfield, Theresa and Stelhing-Sun, Sandra and Lee, Kristen and Thurman, Robert E and Vong, Shinny and Bates, Daniel and Neri, Fidencio and Diegel, Morgan and Giste, Erika and Dunn, Douglas and Vierstra, Jeff and Hansen, R. Scott and Johnson, Audra K and Sabo, Peter J and Wilken, Matthew S and Reh, Thomas A and Treuting, Piper M and Kaul, Rajinder and Groudine, Mark and Bender, M.A and Borenstein, Elhanan and Stamatoyannopoulos, John A
Nature, ISSN 0028-0836, 11/2014, Volume 515, Issue 7527, pp. 365 - 370
The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence... 
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