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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 Functional analysis of transcription factor binding sites in human promoters
by Whiteld, Troy W and Wang, Jie and Collins, Patrick J and Partridge, E Christopher and Aldred, Shelley F and Trinklein, Nathan D and Myers, Richard M and Weng, Zhiping
Genome Biology, ISSN 1474-760X, 2012, Volume 13, Issue 9, pp. R50 - R50
Background: The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells.... 
SEQUENCE FEATURES | FACTOR GABP | IN-VITRO | E2F FAMILY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PROTEIN CTCF | WIDE ANALYSIS | GENETICS & HEREDITY | INTERFERON-STIMULATED GENES | 12 DROSOPHILA GENOMES | C-MYC | CELL-CYCLE | Transcription Factors - metabolism | Cell Line | Promoter Regions, Genetic | Nucleotide Motifs | Humans | Transcription Initiation Site | YY1 Transcription Factor - metabolism | Genome, Human | Binding Sites | Index Medicus | Research
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3. Full Text A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
by Hartzell, Danette D and Trinklein, Nathan D and Mendez, Jacqui and Murphy, Nancy and Aldred, Shelley F and Wood, Keith and Urh, Marjeta
BMC Genomics, ISSN 1471-2164, 10/2009, Volume 10, Issue 1, pp. 497 - 497
Background: Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially... 
TRANSCRIPTION FACTORS | DNA INTERACTIONS | PROMOTERS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ELEMENT-BINDING-PROTEIN | TARGET GENE ACTIVATION | CHROMATIN IMMUNOPRECIPITATION | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | CROSS-LINKING | IDENTIFICATION | CAMP | Oligonucleotide Array Sequence Analysis | Signal Transduction | Genomics | Humans | Transcriptional Activation | Genes, Reporter - genetics | DNA - metabolism | Promoter Regions, Genetic - genetics | Luciferases - genetics | Cyclic AMP Response Element-Binding Protein - genetics | High-Throughput Screening Assays | Cyclic AMP Response Element-Binding Protein - metabolism | HeLa Cells | Binding Sites | Usage | Transcription factors | DNA microarrays | Physiological aspects | Cellular signal transduction | Genetic aspects | Research | Genetic regulation | Index Medicus
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4. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
02/2010
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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5. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
02/2009
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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6. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
10/2008
The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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7. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
08/2008
The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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8. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
10/2007
The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICOLIBRARIES | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | COMBINATORIAL CHEMISTRY | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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9. FUNCTIONAL ARRAYS FOR HIGH THROUGHPUT CHARACTERIZATION OF GENE EXPRESSION REGULATORY ELEMENTS
by MYERS, RICHARD, M and TRINKLEIN, NATHAN, D and ALDRED, SHELLEY, F and COOPER, SARA, J
07/2007
The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICOLIBRARIES | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | COMBINATORIAL CHEMISTRY | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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10. Functional arrays for high throughput characterization of gene expression regulatory elements
by TRINKLEIN NATHAN D and MYERS RICHARD M and ALDRED SHELLEY F and COOPER SARA J
07/2007
The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICOLIBRARIES | ENZYMOLOGY | MICROORGANISMS OR ENZYMES | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | COMPOSITIONS THEREOF | PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | COMBINATORIAL CHEMISTRY | BIOCHEMISTRY | CULTURE MEDIA | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | VINEGAR
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11. Full Text Functional profiling reveals critical role for miRNA in differentiation of human mesenchymal stem cells
by Schoolmeesters, Angela and Eklund, Teresa and Leake, Devin and Vermeulen, Annaleen and Smith, Queta and Aldred, Shelley Force and Fedorov, Yuriy
PLoS ONE, ISSN 1932-6203, 05/2009, Volume 4, Issue 5, pp. e5605 - e5605
Background: Mesenchymal stem (MS) cells are excellent candidates for cell-based therapeutic strategies to regenerate injured tissue. Although human MS cells... 
MULTIDISCIPLINARY SCIENCES | Cell Differentiation - genetics | Cell Line | Humans | Mesenchymal Stem Cells - cytology | 3' Untranslated Regions - genetics | Gene Expression Profiling - methods | MicroRNAs - genetics | MicroRNAs - physiology | Cell Differentiation - physiology | Mesenchymal Stem Cells - metabolism | MicroRNA | Gene expression | Health aspects | Stem cells | Cues | Regulators | Profiling | Mesenchyme | Cloning | Neutrophils | MiRNA | Phosphatase | Experiments | Proteins | Studies | Biomedical materials | Cell growth | Ribonucleic acids | MicroRNAs | Rodents | Bone marrow | Biocompatibility | Differentiation | Osteogenesis | Index Medicus
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12. Full Text Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
by Birney, Ewan and Stamatoyannopoulos, John A and Dutta, Anindya and Guigó, Roderic and Gingeras, Thomas R and Margulies, Elliott H and Weng, Zhiping and Snyder, Michael and Dermitzakis, Emmanouil T and Thurman, Robert E and Kuehn, Michael S and Taylor, Christopher M and Neph, Shane and Koch, Christoph M and Asthana, Saurabh and Malhotra, Ankit and Adzhubei, Ivan and Greenbaum, Jason A and Andrews, Robert M and Flicek, Paul and Boyle, Patrick J and Cao, Hua and Carter, Nigel P and Clelland, Gayle K and Davis, Sean and Day, Nathan and Dhami, Pawandeep and Dillon, Shane C and Dorschner, Michael O and Fiegler, Heike and Giresi, Paul G and Goldy, Jeff and Hawrylycz, Michael and Haydock, Andrew and Humbert, Richard and James, Keith D and Johnson, Brett E and Johnson, Ericka M and Frum, Tristan T and Rosenzweig, Elizabeth R and Karnani, Neerja and Lee, Kirsten and Lefebvre, Gregory C and Navas, Patrick A and Neri, Fidencio and Parker, Stephen C. J and Sabo, Peter J and Sandstrom, Richard and Shafer, Anthony and Vetrie, David and Weaver, Molly and Wilcox, Sarah and Yu, Man and Collins, Francis S and Dekker, Job and Lieb, Jason D and Tullius, Thomas D and Crawford, Gregory E and Sunyaev, Shamil and Noble, William S and Dunham, Ian and Denoeud, France and Reymond, Alexandre and Kapranov, Philipp and Rozowsky, Joel and Zheng, Deyou and Castelo, Robert and Frankish, Adam and Harrow, Jennifer and Ghosh, Srinka and Sandelin, Albin and Hofacker, Ivo L and Baertsch, Robert and Keefe, Damian and Dike, Sujit and Cheng, Jill and Hirsch, Heather A and Sekinger, Edward A and Lagarde, Julien and Abril, Josep F and Shahab, Atif and Flamm, Christoph and Fried, Claudia and Hackermüller, Jörg and Hertel, Jana and Lindemeyer, Manja and Missal, Kristin and Tanzer, Andrea and Washietl, Stefan and Korbel, Jan and Emanuelsson, Olof and Pedersen, Jakob S and Holroyd, Nancy and Taylor, Ruth and Swarbreck, David and Matthews, Nicholas and Dickson, Mark C and Thomas, Daryl J and Weirauch, Matthew T and Gilbert, James and ... and ENCODE Project Consortium and Baylor College of Medicine Human Genome Sequencing Center and Washington University Genome Sequencing Center and Children's Hospital Oakland Research Institute and NISC Comparative Sequencing Program and Broad Institute and The ENCODE Project Consortium
Nature, ISSN 0028-0836, 06/2007, Volume 447, Issue 7146, pp. 799 - 816
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genomeas part of the pilot... 
ANTISENSE TRANSCRIPTION | MULTIDISCIPLINARY SCIENCES | HIGH-RESOLUTION | FACTOR-BINDING-SITES | TILING ARRAYS | POLYCOMB TARGET GENES | SEQUENCE TAG ANALYSIS | TRANSCRIPTIONAL PROMOTERS | REGULATORY ELEMENTS | MAMMALIAN GENOMES | DNA-REPLICATION | Chromatin - metabolism | Conserved Sequence - genetics | Genomics | Humans | RNA, Messenger - genetics | DNA Replication | Exons - genetics | RNA, Untranslated - genetics | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Transcription Factors - metabolism | Pilot Projects | Chromatin Immunoprecipitation | Transcription Initiation Site | Protein Binding | Heterozygote | Genetic Variation - genetics | Histones - metabolism | Transcription, Genetic - genetics | Chromatin - genetics | Evolution, Molecular | Medical research | Data analysis | Deoxyribonucleic acid | DNA | Data bases | Index Medicus | Biological Sciences | Biochemistry and Molecular Biology | Naturvetenskap | Natural Sciences | Biokemi och molekylärbiologi | Biologiska vetenskaper
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