- MEME SUITE: tools for motif discovery and searching
Timothy L Bailey
Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
Nucleic Acids Res 37:W202-8. 2009
..a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains...
- MicroRNA targeting specificity in mammals: determinants beyond seed pairing
Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Mol Cell 27:91-105. 2007
..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
- Mapping and analysis of chromatin state dynamics in nine human cell types
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 473:43-9. 2011
..Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease...
- Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
Mol Cell 38:576-89. 2010
..1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions. PU...
- AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
J Comput Chem 31:455-61. 2010
..Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user...
- The role of site accessibility in microRNA target recognition
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Genet 39:1278-84. 2007
..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...
- Integrins: bidirectional, allosteric signaling machines
Richard O Hynes
Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Cell 110:673-87. 2002
..Long-range conformational changes couple these functions via allosteric equilibria...
- Statistical significance for genomewide studies
John D Storey
Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 100:9440-5. 2003
..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
- Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
Cell 133:1106-17. 2008
..Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.
- TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
Nucleic Acids Res 34:D108-10. 2006
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various ..
- Histone modifications at human enhancers reflect global cell-type-specific gene expression
Nathaniel D Heintzman
Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
Nature 459:108-12. 2009
..Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression...
- Fast and effective prediction of microRNA/target duplexes
Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
RNA 10:1507-17. 2004
..Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs...
- The microRNA.org resource: targets and expression
Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
Nucleic Acids Res 36:D149-53. 2008
..The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation...
- In vivo activation of the p53 pathway by small-molecule antagonists of MDM2
Lyubomir T Vassilev
Department of Discovery Oncology, Roche Research Center, Hoffmann La Roche, Inc, Nutley, NJ 07110, USA
Science 303:844-8. 2004
..These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice...
- Identification of functional elements and regulatory circuits by Drosophila modENCODE
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
Science 330:1787-97. 2010
..Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation...
- miRWalk--database: prediction of possible miRNA binding sites by "walking" the genes of three genomes
Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, D 68167 Mannheim, Germany
J Biomed Inform 44:839-47. 2011
..we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat...
- Hfq and its constellation of RNA
Institute for Molecular Infection Biology, University of Wurzburg, Joseph Schneider Strasse, Wurzburg, Germany
Nat Rev Microbiol 9:578-89. 2011
..In this Review, we describe the salient structural and functional features of Hfq and discuss possible mechanisms by which this protein can promote RNA interactions to catalyse specific and rapid regulatory responses in vivo...
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
Richard A Friesner
Department of Chemistry, Columbia University, New York, New York 10036, USA
J Med Chem 47:1739-49. 2004
..Glide is also found to be more accurate than the recently described Surflex method...
- Identification of c-MYC as a target of the APC pathway
T C He
Howard Hughes Medical Institute and Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
Science 281:1509-12. 1998
..to be repressed by wild-type APC and activated by beta-catenin, and these effects were mediated through Tcf-4 binding sites in the c-MYC promoter...
- MatInspector and beyond: promoter analysis based on transcription factor binding sites
Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
Bioinformatics 21:2933-42. 2005
..A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy...
- FIMO: scanning for occurrences of a given motif
Charles E Grant
Department of Genome Sciences, University of Washington, Seattle, WA, USA
Bioinformatics 27:1017-8. 2011
..Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix...
- Transcriptional control of human p53-regulated genes
The Institute for Advanced Study, Princeton, New Jersey, USA
Nat Rev Mol Cell Biol 9:402-12. 2008
..In addition, we present the most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation.
- MEME-ChIP: motif analysis of large DNA datasets
Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
Bioinformatics 27:1696-7. 2011
..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...
- A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
Kevin C Miranda
Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, P O Box 218, NY 10598, USA
Cell 126:1203-17. 2006
We present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes...
- Diversity and complexity in DNA recognition by transcription factors
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Science 324:1720-3. 2009
..different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of ..
- High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
Science 318:1258-65. 2007
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genome Res 22:1798-812. 2012
..The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion...
- An oestrogen-receptor-alpha-bound human chromatin interactome
Melissa J Fullwood
Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
Nature 462:58-64. 2009
..Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin ..
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Jan Christian Bryne
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
Nucleic Acids Res 36:D102-6. 2008
..JASPAR is available at http://jaspar.genereg.net...
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
Genome Res 21:1757-67. 2011
..to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start ..
- RNAhybrid: microRNA target prediction easy, fast and flexible
Center for Biotechnology, CeBiTec, Universitat Bielefeld, 33594 Bielefeld, Germany
Nucleic Acids Res 34:W451-4. 2006
..RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid...
- Genome-wide mapping of in vivo protein-DNA interactions
David S Johnson
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
Science 316:1497-502. 2007
..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development...
- Structure of a nanobody-stabilized active state of the β(2) adrenoceptor
Søren G F Rasmussen
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
Nature 469:175-80. 2011
..This structure provides insights into the process of agonist binding and activation...
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
Kevin Y Yip
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
Genome Biol 13:R48. 2012
..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
- A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution
Sreeram V Ramagopalan
Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
Genome Res 20:1352-60. 2010
..VDR binding sites were significantly enriched near autoimmune and cancer associated genes identified from genome-wide ..
- Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
Richard A Friesner
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Med Chem 49:6177-96. 2006
..Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives...
- Targeting DNA double-strand breaks with TAL effector nucleases
Department of Plant Pathology, Iowa State University, Ames, Iowa 50011, USA
Genetics 186:757-61. 2010
..Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites...
- Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist
Ellen Y T Chien
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Science 330:1091-5. 2010
..This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications...
- VISTA: computational tools for comparative genomics
Kelly A Frazer
Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
Nucleic Acids Res 32:W273-9. 2004
..We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein...
- Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
James A Wells
Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street 503A, San Francisco, California 94156, USA
Nature 450:1001-9. 2007
..Some of these small molecules are now making their way through clinical trials, so this high-hanging fruit might not be far out of reach...
- The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist
Veli Pekka Jaakola
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
Science 322:1211-7. 2008
- miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements
Immune Disease Institute, Children s Hospital Boston, Department of Pediatrics, Harvard Medical School, MA 02115, USA
Mol Cell 35:610-25. 2009
..The E2F2 3'UTR lacks a predicted miR-24 recognition element. In fact, miR-24 regulates expression of E2F2, MYC, AURKB, CCNA2, CDC2, CDK4, and FEN1 by recognizing seedless but highly complementary sequences...
- Insights from genomic profiling of transcription factors
Peggy J Farnham
Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
Nat Rev Genet 10:605-16. 2009
..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
Nat Biotechnol 27:66-75. 2009
..The first pass identifies putative binding sites and compensates for genomic variation in the 'mappability' of sequences...
- RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, AP 565 A, Cuernavaca, Morelos 62100, Mexico
Nucleic Acids Res 39:D98-105. 2011
..RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated...
- Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31
Amy C Groth
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Genetics 166:1775-82. 2004
..These experiments demonstrate the potential for precise genetic engineering of the Drosophila genome with the phiC31 integrase system and will likely benefit research in Drosophila and other insects...
- High-resolution DNA-binding specificity analysis of yeast transcription factors
Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Res 19:556-66. 2009
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin ..
- The cyclin D1 gene is a target of the beta-catenin/LEF-1 pathway
Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 96:5522-7. 1999
..Increased beta-catenin levels may thus promote neoplastic conversion by triggering cyclin D1 gene expression and, consequently, uncontrolled progression into the cell cycle...
- The crystal structure of TAL effector PthXo1 bound to its DNA target
Amanda Nga Sze Mak
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3 025 Seattle, WA 98019, USA
Science 335:716-9. 2012
..Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition...
- Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
Stephen G Aller
Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, CB105, La Jolla, CA 92037, USA
Science 323:1718-22. 2009
..Two additional P-gp structures with cyclic peptide inhibitors demonstrate distinct drug-binding sites in the internal cavity capable of stereoselectivity that is based on hydrophobic and aromatic interactions...
- A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
Unit of Animal Genomics, Department of Animal Production, Faculty of Veterinary Medicine and Centre for Biomedical Integrative Genoproteomics, University of Liège B43, 20 Boulevard de Colonster, 4000 Liege, Belgium
Nat Genet 38:813-8. 2006
..Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation...
- Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Science 328:1036-40. 2010
..Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution...
- Crystal structure of the µ-opioid receptor bound to a morphinan antagonist
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
Nature 485:321-6. 2012
..These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nat Genet 39:457-66. 2007
..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
- Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
Mol Cell 15:185-97. 2004
..The specific role of Ago2 in guiding target RNA cleavage was confirmed independently by siRNA-based depletion of individual Ago members in combination with a sensitive positive-readout reporter assay...
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
Peter V Kharchenko
Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA
Nat Biotechnol 26:1351-9. 2008
..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.
- A quantitative analysis of kinase inhibitor selectivity
Mazen W Karaman
Ambit Biosciences, 4215 Sorrento Valley Blvd, San Diego, California 92121, USA
Nat Biotechnol 26:127-32. 2008
..We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity...
- Automated design of synthetic ribosome binding sites to control protein expression
Howard M Salis
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
Nat Biotechnol 27:946-50. 2009
..the need for trial and error optimization, we developed a predictive method for designing synthetic ribosome binding sites, enabling a rational control over the protein expression level...
- Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
Thomas A Halgren
Schrodinger, L L C, 120 W 45th Street, New York, New York 10036, USA
J Med Chem 47:1750-9. 2004
..Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01...
- Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
Mol Cell 43:327-39. 2011
..The number of binding sites per transcript, degree of HuR association, and degree of HuR-dependent RNA stabilization were positively ..
- High-resolution mapping and characterization of open chromatin across the genome
Alan P Boyle
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Cell 132:311-22. 2008
..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
- beta-catenin is a target for the ubiquitin-proteasome pathway
Max Planck Institute for Immunobiology, Department of Molecular Embryology, Freiburg, Germany
EMBO J 16:3797-804. 1997
..We show that ubiquitination of beta-catenin is greatly reduced in Wnt-expressing cells, providing the first evidence that the ubiquitin-proteasome degradation pathway may act downstream of GSK3beta in the regulation of beta-catenin...
- The role of dynamic conformational ensembles in biomolecular recognition
David D Boehr
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
Nat Chem Biol 5:789-96. 2009
- Carbohydrate-binding modules: fine-tuning polysaccharide recognition
Alisdair B Boraston
Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6
Biochem J 382:769-81. 2004
..The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands...
- The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
Alexander G Baltz
Max Delbruck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
Mol Cell 46:674-90. 2012
..and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms...
- The SR protein family of splicing factors: master regulators of gene expression
Jennifer C Long
Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH42XU, UK
Biochem J 417:15-27. 2009
..Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression...
- An alternative mode of microRNA target recognition
Sung Wook Chi
Laboratory of Neuro Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York, USA
Nat Struct Mol Biol 19:321-7. 2012
..We call position 6 the 'pivot' nucleotide and suggest a model in which a transitional 'nucleation bulge' leads to functional bulge mRNA-miRNA interactions, expanding the number of potential miRNA regulatory sites...
- UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
Daniel E Newburger
Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School and Harvard MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
Nucleic Acids Res 37:D77-82. 2009
..assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. The UniPROBE database is available at http://thebrain.bwh.harvard...
- Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2
Scott B Hansen
Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA
Nature 477:495-8. 2011
- Structure of the human histamine H1 receptor complex with doxepin
Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Kyoto 606 8501, Japan
Nature 475:65-70. 2011
..Our study sheds light on the molecular basis of H(1)R antagonist specificity against H(1)R...
- Structure of the human κ-opioid receptor in complex with JDTic
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
Nature 485:327-32. 2012
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 21:447-55. 2011
..Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites corresponding to 239 position weight matrices ..
- ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
Willem Jan Welboren
Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
EMBO J 28:1418-28. 2009
We used ChIP-Seq to map ERalpha-binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant...
- MEME: discovering and analyzing DNA and protein sequence motifs
Timothy L Bailey
Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
Nucleic Acids Res 34:W369-73. 2006
..Applications include the discovery of new transcription factor binding sites and protein domains...
- Inferring direct DNA binding from ChIP-seq
Timothy L Bailey
Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
Nucleic Acids Res 40:e128. 2012
..motif enrichment analysis' (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ..
- Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
Nucleic Acids Res 37:W247-52. 2009
..expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g...
- Structure of a beta1-adrenergic G-protein-coupled receptor
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Nature 454:486-91. 2008
- Structural basis for RNA 3'-end recognition by Hfq
Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Proc Natl Acad Sci U S A 108:13065-70. 2011
..The capacity of Hfq to occupy and sequester the RNA 3' end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation...
- A map of open chromatin in human pancreatic islets
Kyle J Gaulton
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
Nat Genet 42:255-9. 2010
..These findings illuminate the tissue-specific organization of cis-regulatory elements and show that FAIRE-seq can guide the identification of regulatory variants underlying disease susceptibility...
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
Nat Genet 42:631-4. 2010
..These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells...
- Heritable individual-specific and allele-specific chromatin signatures in humans
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
Science 328:235-9. 2010
..Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans...
- Refined structure of alpha beta-tubulin at 3.5 A resolution
MRC Laboratory of Molecular Biology, Cambridge, UK
J Mol Biol 313:1045-57. 2001
..In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues.
- Principles of activation and permeation in an anion-selective Cys-loop receptor
Ryan E Hibbs
Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
Nature 474:54-60. 2011
..GluCl provides a framework for understanding mechanisms of fast inhibitory neurotransmission and allosteric modulation of Cys-loop receptors...
- Structure of a V3-containing HIV-1 gp120 core
Chih Chin Huang
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
Science 310:1025-8. 2005
..The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization...
- Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Dev Cell 18:662-74. 2010
..Therefore, in addition to regulating muscle gene expression, MyoD binds genome wide and has the ability to broadly alter the epigenome in myoblasts and myotubes...
- Structure of an agonist-bound human A2A adenosine receptor
Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Science 332:322-7. 2011
..The results define the molecule UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration...
- RNAstructure: software for RNA secondary structure prediction and analysis
Jessica S Reuter
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
BMC Bioinformatics 11:129. 2010
..RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence...
- RNA recognition motifs: boring? Not quite
Institute for Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
Curr Opin Struct Biol 18:290-8. 2008
..The extreme structural versatility of the RRM interactions explains why RRM-containing proteins have so diverse biological functions...
- Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
Genome Biol 10:R80. 2009
- Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
Robert K Bradley
Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
PLoS Biol 8:e1000343. 2010
- A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
Teemu D Laajala
Turku Centre for Biotechnology, FI 20521 Turku, Finland
BMC Genomics 10:618. 2009
..While numerous algorithms have recently been proposed for analysing the large ChIP-seq datasets, their relative merits and potential limitations remain unclear in practical applications...
- Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
Kimberly R Blahnik
Department of Computer Science, University of California Davis, Davis, CA 95616, USA
Nucleic Acids Res 38:e13. 2010
Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome...
- Principles of microRNA-target recognition
European Molecular Biology Laboratory, Heidelberg, Germany
PLoS Biol 3:e85. 2005
- Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Gong Hong Wei
Public Health Genomics Unit, National Institute for Health and Welfare THL and Genome Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
EMBO J 29:2147-60. 2010
..The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo...
- Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor
Children s Hospital and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
Cell 96:857-68. 1999
..Within the nucleus, FKHRL1 triggers apoptosis most likely by inducing the expression of genes that are critical for cell death, such as the Fas ligand gene...
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
Jesper V Olsen
Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
Cell 127:635-48. 2006
..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...
- Benchmarking sets for molecular docking
Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143 2550, USA
J Med Chem 49:6789-801. 2006
..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
- Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
Benjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D518-24. 2010
..This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins...
- Frequent gain and loss of functional transcription factor binding sites
Scott W Doniger
Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
PLoS Comput Biol 3:e99. 2007
..We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs)...
- Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand
Jian Ping Xiong
Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
Science 296:151-5. 2002
..Ligand binding induces small changes in the orientation of alphaV relative to beta3...