Publications
194 results found
Luis Royo J, Hidalgo C, Roncero Y, et al., 2011, Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions, PLOS ONE, Vol: 6, ISSN: 1932-6203
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- Citations: 11
Engelen E, Akinci U, Bryne JC, et al., 2011, Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes, NATURE GENETICS, Vol: 43, Pages: 607-U153, ISSN: 1061-4036
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- Citations: 187
Ragvin A, Moro E, Fredman D, et al., 2011, Erratum: Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3 (Proceedings of the National Academy of Sciences of the United States of America (2010) 107, 2, (775-780) DOI: 10.1073/pnas.0911591107), Proceedings of the National Academy of Sciences of the United States of America, Vol: 108, ISSN: 0027-8424
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- Citations: 1
Fredman D, Dong X, Lenhard B, 2011, Making enhancers from spare parts of the genome., Genome Biol, Vol: 12
New studies show that novel long-range enhancers of developmental genes can emerge by exaptation of protein-coding sequences with no previous regulatory function.
Denoeud F, Henriet S, Mungpakdee S, et al., 2010, Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate, SCIENCE, Vol: 330, Pages: 1381-1385, ISSN: 0036-8075
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- Citations: 201
Soler E, Andrieu-Soler C, De Boer E, et al., 2010, The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation (Genes & Development (2010) 24, (277-289)), Genes and Development, Vol: 24, ISSN: 0890-9369
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- Citations: 1
Ravasi T, Suzuki H, Cannistraci CV, et al., 2010, An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man, CELL, Vol: 140, Pages: 744-752, ISSN: 0092-8674
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- Citations: 539
, 2010, Erratum: The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation, Genes & development, Vol: 24, Pages: 623-623, ISSN: 0890-9369
Dong X, Navratilova P, Fredman D, et al., 2010, Exonic remnants of whole-genome duplication reveal <i>cis</i>-regulatory function of coding exons, NUCLEIC ACIDS RESEARCH, Vol: 38, Pages: 1071-1085, ISSN: 0305-1048
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- Citations: 39
Soler E, Andrieu-Soler C, de Boer E, et al., 2010, The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation, GENES & DEVELOPMENT, Vol: 24, Pages: 277-289, ISSN: 0890-9369
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- Citations: 191
Navratilova P, Fredman D, Lenhard B, et al., 2010, Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish, MOLECULAR GENETICS AND GENOMICS, Vol: 283, Pages: 171-184, ISSN: 1617-4615
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- Citations: 24
Ragvin A, Moro E, Fredman D, et al., 2010, Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to <i>HHEX</i>, <i>SOX4</i>, and <i>IRX3</i>, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 775-780, ISSN: 0027-8424
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- Citations: 151
Portales-Casamar E, Thongjuea S, Kwon AT, et al., 2010, JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, NUCLEIC ACIDS RESEARCH, Vol: 38, Pages: D105-D110, ISSN: 0305-1048
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- Citations: 468
Dong X, Akalin A, Sharma Y, et al., 2010, Translog, a web browser for studying the expression divergence of homologous genes, BMC BIOINFORMATICS, Vol: 11, ISSN: 1471-2105
Roider HG, Lenhard B, Kanhere A, et al., 2009, CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 6305-6315, ISSN: 0305-1048
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- Citations: 33
Bessa J, Tena JJ, de la Calle-Mustienes E, et al., 2009, Zebrafish Enhancer Detection (ZED) Vector: A New Tool to Facilitate Transgenesis and the Functional Analysis of <i>cis</i>-Regulatory Regions in Zebrafish, DEVELOPMENTAL DYNAMICS, Vol: 238, Pages: 2409-2417, ISSN: 1058-8388
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- Citations: 116
Fredman D, Engström PG, Lenhard B, 2009, Web-based tools and approaches to study long-range gene regulation in Metazoa., Brief Funct Genomic Proteomic, Vol: 8, Pages: 231-242
Regulatory elements can affect specific genes from megabase distances, often from within or beyond unrelated neighbouring genes. The task of computational charting of regulatory inputs in the genome can be approached from several directions. Typically, computational identification of putative regulatory elements for a gene of interest requires tools that will aid in estimating the extent of the (potentially vast) genomic region around the gene that is likely to contain regulatory elements, as well as tools for the identification and characterization of individual elements. Conversely, starting from a putative regulatory element or a regulatory variation in a non-coding region, one often wants to associate the regulatory element with the correct target gene(s). The design of tools for these purposes relies on the remarkably high level of sequence conservation of thousands of regulatory enhancers, their strong tendency to cluster around their target genes, as well as a constrained range of functional categories of the corresponding target genes, many of which are developmental regulators. Additional evolutionary information, such as conservation of synteny, and a growing body of functional genomic and epigenomic data are being rapidly added to established and emerging tools for studying developmental regulation and cross-species conservation to provide new functional insights into the roles of these regions. In this article, we give an overview of the functionality available in general purpose and new/specialized web tools for the above tasks, and discuss current and future developments in the field.
Suzuki H, Forrest ARR, van Nimwegen E, et al., 2009, The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, NATURE GENETICS, Vol: 41, Pages: 553-562, ISSN: 1061-4036
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- Citations: 349
Navratilova P, Fredman D, Hawkins TA, et al., 2009, Systematic human/zebrafish comparative identification of <i>cis</i>-regulatory activity around vertebrate developmental transcription factor genes, DEVELOPMENTAL BIOLOGY, Vol: 327, Pages: 526-540, ISSN: 0012-1606
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- Citations: 85
Akalin A, Fredman D, Arner E, et al., 2009, Transcriptional features of genomic regulatory blocks, GENOME BIOLOGY, Vol: 10, ISSN: 1474-760X
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- Citations: 77
Dong X, Fredman D, Lenhard B, 2009, Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes, GENOME BIOLOGY, Vol: 10, ISSN: 1474-760X
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- Citations: 20
Kemmer D, Podowski RM, Yusuf D, et al., 2008, Gene Characterization Index: Assessing the Depth of Gene Annotation, PLOS ONE, Vol: 3, ISSN: 1932-6203
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- Citations: 8
Yamasaki C, Murakami K, Fujii Y, et al., 2008, The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts, NUCLEIC ACIDS RESEARCH, Vol: 36, Pages: D793-D799, ISSN: 0305-1048
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- Citations: 51
Bryne JC, Valen E, Tang M-HE, et al., 2008, JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update, NUCLEIC ACIDS RESEARCH, Vol: 36, Pages: D102-D106, ISSN: 0305-1048
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- Citations: 525
Andersen MC, Engstrom PRG, Lithwick S, et al., 2008, In silico detection of sequence variations modifying transcriptional regulation, PLOS COMPUTATIONAL BIOLOGY, Vol: 4
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- Citations: 82
Engstrom PG, Fredman D, Lenhard B, 2008, Ancora:: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes, GENOME BIOLOGY, Vol: 9, ISSN: 1474-760X
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- Citations: 66
Engstrom PG, Sui SJH, Drivenes O, et al., 2007, Genomic regulatory blocks underlie extensive microsynteny conservation in insects, GENOME RESEARCH, Vol: 17, Pages: 1898-1908, ISSN: 1088-9051
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- Citations: 137
Becker TS, Lenhard B, 2007, The random versus fragile breakage models of chromosome evolution: a matter of resolution, MOLECULAR GENETICS AND GENOMICS, Vol: 278, Pages: 487-491, ISSN: 1617-4615
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- Citations: 39
Sheng Y, Engstrom PG, Lenhard B, 2007, Mammalian MicroRNA Prediction through a Support Vector Machine Model of Sequence and Structure, PLOS ONE, Vol: 2, ISSN: 1932-6203
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- Citations: 40
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