TY - JOUR AU - Tagle, D. A. AU - Koop, B. F. AU - Goodman, M. AU - Slightom, J. L. AU - Hess, D. L. AU - Jones, R. T. PY - 1988 DA - 1988// TI - Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. JO - J Mol Biol VL - 203 UR - https://doi.org/10.1016/0022-2836(88)90011-3 DO - 10.1016/0022-2836(88)90011-3 ID - Tagle1988 ER - TY - JOUR AU - Fickett, J. W. AU - Wasserman, W. W. PY - 2000 DA - 2000// TI - Discovery and modeling of transcriptional regulatory regions. JO - Curr Opin Biotechnol VL - 11 UR - https://doi.org/10.1016/S0958-1669(99)00049-X DO - 10.1016/S0958-1669(99)00049-X ID - Fickett2000 ER - TY - JOUR AU - Levy, S. AU - Hannenhalli, S. AU - Workman, C. PY - 2001 DA - 2001// TI - Enrichment of regulatory signals in conserved non-coding genomic sequence. JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.10.871 DO - 10.1093/bioinformatics/17.10.871 ID - Levy2001 ER - TY - JOUR AU - Boffelli, D. AU - McAuliffe, J. AU - Ovcharenko, D. AU - Lewis, K. D. AU - Ovcharenko, I. AU - Pachter, L. AU - Rubin, E. M. PY - 2003 DA - 2003// TI - Phylogenetic shadowing of primate sequences to find functional regions of the human genome. JO - Science VL - 299 UR - https://doi.org/10.1126/science.1081331 DO - 10.1126/science.1081331 ID - Boffelli2003 ER - TY - JOUR AU - Chapman, M. A. AU - Donaldson, I. J. AU - Gilbert, J. AU - Grafham, D. AU - Rogers, J. AU - Green, A. R. AU - Gottgens, B. PY - 2004 DA - 2004// TI - Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1759004 DO - 10.1101/gr.1759004 ID - Chapman2004 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Morgenstern, B. AU - Frech, K. AU - Dress, A. AU - Werner, T. PY - 1998 DA - 1998// TI - DIALIGN: finding local similarities by multiple sequence alignment. JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.3.290 DO - 10.1093/bioinformatics/14.3.290 ID - Morgenstern1998 ER - TY - JOUR AU - Morgenstern, B. PY - 1999 DA - 1999// TI - DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.3.211 DO - 10.1093/bioinformatics/15.3.211 ID - Morgenstern1999 ER - TY - JOUR AU - Bray, N. AU - Pachter, L. PY - 2003 DA - 2003// TI - MAVID multiple alignment server. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg623 DO - 10.1093/nar/gkg623 ID - Bray2003 ER - TY - JOUR AU - Bray, N. AU - Pachter, L. PY - 2004 DA - 2004// TI - MAVID: constrained ancestral alignment of multiple sequences. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1960404 DO - 10.1101/gr.1960404 ID - Bray2004 ER - TY - JOUR AU - Brudno, M. AU - Do, C. B. AU - Cooper, G. M. AU - Kim, M. F. AU - Davydov, E. AU - Green, E. D. AU - Sidow, A. AU - Batzoglou, S. PY - 2003 DA - 2003// TI - LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.926603 DO - 10.1101/gr.926603 ID - Brudno2003 ER - TY - JOUR AU - Major, M. B. AU - Jones, D. A. PY - 2004 DA - 2004// TI - Identification of a gadd45beta 3' enhancer that mediates SMAD3- and SMAD4-dependent transcriptional induction by transforming growth factor beta. JO - J Biol Chem VL - 279 UR - https://doi.org/10.1074/jbc.M311517200 DO - 10.1074/jbc.M311517200 ID - Major2004 ER - TY - JOUR AU - Wasserman, W. W. AU - Fickett, J. W. PY - 1998 DA - 1998// TI - Identification of regulatory regions which confer muscle-specific gene expression. JO - J Mol Biol VL - 278 UR - https://doi.org/10.1006/jmbi.1998.1700 DO - 10.1006/jmbi.1998.1700 ID - Wasserman1998 ER - TY - JOUR AU - Abrahams, B. S. AU - Mak, G. M. AU - Berry, M. L. AU - Palmquist, D. L. AU - Saionz, J. R. AU - Tay, A. AU - Tan, Y. H. AU - Brenner, S. AU - Simpson, E. M. AU - Venkatesh, B. PY - 2002 DA - 2002// TI - Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci. JO - Genomics VL - 80 UR - https://doi.org/10.1006/geno.2002.6795 DO - 10.1006/geno.2002.6795 ID - Abrahams2002 ER - TY - JOUR AU - Aparicio, S. AU - Morrison, A. AU - Gould, A. AU - Gilthorpe, J. AU - Chaudhuri, C. AU - Rigby, P. AU - Krumlauf, R. AU - Brenner, S. PY - 1995 DA - 1995// TI - Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. JO - Proc Natl Acad Sci USA VL - 92 UR - https://doi.org/10.1073/pnas.92.5.1684 DO - 10.1073/pnas.92.5.1684 ID - Aparicio1995 ER - TY - JOUR AU - Bagheri-Fam, S. AU - Ferraz, C. AU - Demaille, J. AU - Scherer, G. AU - Pfeifer, D. PY - 2001 DA - 2001// TI - Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. JO - Genomics VL - 78 UR - https://doi.org/10.1006/geno.2001.6648 DO - 10.1006/geno.2001.6648 ID - Bagheri-Fam2001 ER - TY - JOUR AU - Montpetit, A. AU - Sinnett, D. PY - 2001 DA - 2001// TI - Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human. JO - Oncogene VL - 20 UR - https://doi.org/10.1038/sj.onc.1204444 DO - 10.1038/sj.onc.1204444 ID - Montpetit2001 ER - TY - JOUR AU - Nobrega, M. A. AU - Ovcharenko, I. AU - Afzal, V. AU - Rubin, E. M. PY - 2003 DA - 2003// TI - Scanning human gene deserts for long-range enhancers. JO - Science VL - 302 UR - https://doi.org/10.1126/science.1088328 DO - 10.1126/science.1088328 ID - Nobrega2003 ER - TY - JOUR AU - Santini, S. AU - Boore, J. L. AU - Meyer, A. PY - 2003 DA - 2003// TI - Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.700503 DO - 10.1101/gr.700503 ID - Santini2003 ER - TY - JOUR AU - Sandelin, A. AU - Bailey, P. AU - Bruce, S. AU - Engstrom, P. G. AU - Klos, J. M. AU - Wasserman, W. W. AU - Ericson, J. AU - Lenhard, B. PY - 2004 DA - 2004// TI - Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. JO - BMC Genomics VL - 5 UR - https://doi.org/10.1186/1471-2164-5-99 DO - 10.1186/1471-2164-5-99 ID - Sandelin2004 ER - TY - JOUR AU - Woolfe, A. AU - Goodson, M. AU - Goode, D. K. AU - Snell, P. AU - McEwen, G. K. AU - Vavouri, T. AU - Smith, S. F. AU - North, P. AU - Callaway, H. AU - Kelly, K. PY - 2005 DA - 2005// TI - Highly conserved non-coding sequences are associated with vertebrate development. JO - PLoS Biol VL - 3 ID - Woolfe2005 ER - TY - JOUR AU - Aparicio, S. AU - Chapman, J. AU - Stupka, E. AU - Putnam, N. AU - Chia, J. M. AU - Dehal, P. AU - Christoffels, A. AU - Rash, S. AU - Hoon, S. AU - Smit, A. PY - 2002 DA - 2002// TI - Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. JO - Science VL - 297 UR - https://doi.org/10.1126/science.1072104 DO - 10.1126/science.1072104 ID - Aparicio2002 ER - TY - JOUR AU - Brenner, S. AU - Elgar, G. AU - Sandford, R. AU - Macrae, A. AU - Venkatesh, B. AU - Aparicio, S. PY - 1993 DA - 1993// TI - Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. JO - Nature VL - 366 UR - https://doi.org/10.1038/366265a0 DO - 10.1038/366265a0 ID - Brenner1993 ER - TY - JOUR AU - Venkatesh, B. AU - Gilligan, P. AU - Brenner, S. PY - 2000 DA - 2000// TI - Fugu: a compact vertebrate reference genome. JO - FEBS Lett VL - 476 UR - https://doi.org/10.1016/S0014-5793(00)01659-8 DO - 10.1016/S0014-5793(00)01659-8 ID - Venkatesh2000 ER - TY - JOUR AU - Elemento, O. AU - Tavazoie, S. PY - 2005 DA - 2005// TI - Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. JO - Genome Biol VL - 6 UR - https://doi.org/10.1186/gb-2005-6-2-r18 DO - 10.1186/gb-2005-6-2-r18 ID - Elemento2005 ER - TY - JOUR AU - Blanchette, M. AU - Tompa, M. PY - 2002 DA - 2002// TI - Discovery of regulatory elements by a computational method for phylogenetic footprinting. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.6902 DO - 10.1101/gr.6902 ID - Blanchette2002 ER - TY - JOUR AU - Blanchette, M. AU - Tompa, M. PY - 2003 DA - 2003// TI - FootPrinter: A program designed for phylogenetic footprinting. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg606 DO - 10.1093/nar/gkg606 ID - Blanchette2003 ER - TY - JOUR AU - Bailey, T. L. AU - Elkan, C. PY - 1995 DA - 1995// TI - The value of prior knowledge in discovering motifs with MEME. JO - Proc Int Conf Intell Syst Mol Biol VL - 3 ID - Bailey1995 ER - TY - JOUR AU - Hertz, G. Z. AU - Hartzell, G. W. AU - Stormo, G. D. PY - 1990 DA - 1990// TI - Identification of consensus patterns in unaligned DNA sequences known to be functionally related. JO - Comput Appl Biosci VL - 6 ID - Hertz1990 ER - TY - JOUR AU - Hertz, G. Z. AU - Stormo, G. D. PY - 1999 DA - 1999// TI - Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.7.563 DO - 10.1093/bioinformatics/15.7.563 ID - Hertz1999 ER - TY - JOUR AU - Lawrence, C. E. AU - Altschul, S. F. AU - Boguski, M. S. AU - Liu, J. S. AU - Neuwald, A. F. AU - Wootton, J. C. PY - 1993 DA - 1993// TI - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. JO - Science VL - 262 UR - https://doi.org/10.1126/science.8211139 DO - 10.1126/science.8211139 ID - Lawrence1993 ER - TY - JOUR AU - McCue, L. AU - Thompson, W. AU - Carmack, C. AU - Ryan, M. P. AU - Liu, J. S. AU - Derbyshire, V. AU - Lawrence, C. E. PY - 2001 DA - 2001// TI - Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.3.774 DO - 10.1093/nar/29.3.774 ID - McCue2001 ER - TY - JOUR AU - Cliften, P. F. AU - Hillier, L. W. AU - Fulton, L. AU - Graves, T. AU - Miner, T. AU - Gish, W. R. AU - Waterston, R. H. AU - Johnston, M. PY - 2001 DA - 2001// TI - Surveying Saccharomycesgenomes to identify functional elements by comparative DNA sequence analysis. JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.182901 DO - 10.1101/gr.182901 ID - Cliften2001 ER - TY - JOUR AU - Hughes, J. D. AU - Estep, P. W. AU - Tavazoie, S. AU - Church, G. M. PY - 2000 DA - 2000// TI - Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. JO - J Mol Biol VL - 296 UR - https://doi.org/10.1006/jmbi.2000.3519 DO - 10.1006/jmbi.2000.3519 ID - Hughes2000 ER - TY - CHAP AU - Workman, C. T. AU - Stormo, G. D. PY - 2000 DA - 2000// TI - ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. BT - Pac Symp Biocomput ID - Workman2000 ER - TY - CHAP AU - Liu, X. AU - Brutlag, D. L. AU - Liu, J. S. PY - 2001 DA - 2001// TI - BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. BT - Pac Symp Biocomput ID - Liu2001 ER - TY - JOUR AU - Thijs, G. AU - Lescot, M. AU - Marchal, K. AU - Rombauts, S. AU - De Moor, B. AU - Rouze, P. AU - Moreau, Y. PY - 2001 DA - 2001// TI - A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.12.1113 DO - 10.1093/bioinformatics/17.12.1113 ID - Thijs2001 ER - TY - JOUR AU - Thijs, G. AU - Moreau, Y. AU - De Smet, F. AU - Mathys, J. AU - Lescot, M. AU - Rombauts, S. AU - Rouze, P. AU - De Moor, B. AU - Marchal, K. PY - 2002 DA - 2002// TI - INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.2.331 DO - 10.1093/bioinformatics/18.2.331 ID - Thijs2002 ER - TY - JOUR AU - Thijs, G. AU - Marchal, K. AU - Lescot, M. AU - Rombauts, S. AU - De Moor, B. AU - Rouze, P. AU - Moreau, Y. PY - 2002 DA - 2002// TI - A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. JO - J Comput Biol VL - 9 UR - https://doi.org/10.1089/10665270252935566 DO - 10.1089/10665270252935566 ID - Thijs2002 ER - TY - JOUR AU - Tompa, M. AU - Li, N. AU - Bailey, T. L. AU - Church, G. M. AU - De Moor, B. AU - Eskin, E. AU - Favorov, A. V. AU - Frith, M. C. AU - Fu, Y. AU - Kent, W. J. PY - 2005 DA - 2005// TI - Assessing computational tools for the discovery of transcription factor binding sites. JO - Nat Biotechnol VL - 23 UR - https://doi.org/10.1038/nbt1053 DO - 10.1038/nbt1053 ID - Tompa2005 ER - TY - JOUR AU - Pennacchio, L. A. PY - 2003 DA - 2003// TI - Insights from human/mouse genome comparisons. JO - Mamm Genome VL - 14 UR - https://doi.org/10.1007/s00335-002-4001-1 DO - 10.1007/s00335-002-4001-1 ID - Pennacchio2003 ER - TY - JOUR AU - Elgar, G. AU - Sandford, R. AU - Aparicio, S. AU - Macrae, A. AU - Venkatesh, B. AU - Brenner, S. PY - 1996 DA - 1996// TI - Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). JO - Trends Genet VL - 12 UR - https://doi.org/10.1016/0168-9525(96)10018-4 DO - 10.1016/0168-9525(96)10018-4 ID - Elgar1996 ER - TY - JOUR AU - Wasserman, W. W. AU - Krivan, W. PY - 2003 DA - 2003// TI - In silicoidentification of metazoan transcriptional regulatory regions. JO - Naturwissenschaften VL - 90 ID - Wasserman2003 ER - TY - STD TI - Supplementary Website. [http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_VanHel_2005/SuppWebsite.html] UR - http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_VanHel_2005/SuppWebsite.html ID - ref44 ER - TY - JOUR AU - Marchal, K. AU - De Keersmaecker, S. AU - Monsieurs, P. AU - van Boxel, N. AU - Lemmens, K. AU - Thijs, G. AU - Vanderleyden, J. AU - De Moor, B. PY - 2004 DA - 2004// TI - In silico identification and experimental validation of PmrAB targets in Salmonella typhimuriumby regulatory motif detection. JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-2-r9 DO - 10.1186/gb-2004-5-2-r9 ID - Marchal2004 ER - TY - JOUR AU - Scemama, J. L. AU - Hunter, M. AU - McCallum, J. AU - Prince, V. AU - Stellwag, E. PY - 2002 DA - 2002// TI - Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. JO - J Exp Zool VL - 294 UR - https://doi.org/10.1002/jez.90009 DO - 10.1002/jez.90009 ID - Scemama2002 ER - TY - JOUR AU - Kammandel, B. AU - Chowdhury, K. AU - Stoykova, A. AU - Aparicio, S. AU - Brenner, S. AU - Gruss, P. PY - 1999 DA - 1999// TI - Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. JO - Dev Biol VL - 205 UR - https://doi.org/10.1006/dbio.1998.9128 DO - 10.1006/dbio.1998.9128 ID - Kammandel1999 ER - TY - JOUR AU - Gottgens, B. AU - Barton, L. M. AU - Chapman, M. A. AU - Sinclair, A. M. AU - Knudsen, B. AU - Grafham, D. AU - Gilbert, J. G. AU - Rogers, J. AU - Bentley, D. R. AU - Green, A. R. PY - 2002 DA - 2002// TI - Transcriptional regulation of the stem cell leukemia gene (SCL) - comparative analysis of five vertebrate SCL loci. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.45502 DO - 10.1101/gr.45502 ID - Gottgens2002 ER - TY - JOUR AU - Kent, W. J. AU - Sugnet, C. W. AU - Furey, T. S. AU - Roskin, K. M. AU - Pringle, T. H. AU - Zahler, A. M. AU - Haussler, D. PY - 2002 DA - 2002// TI - The human genome browser at UCSC. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229102. Article published online before print in May 2002 DO - 10.1101/gr.229102. Article published online before print in May 2002 ID - Kent2002 ER - TY - STD TI - UCSC Genome Browser. [http://genome.ucsc.edu/] UR - http://genome.ucsc.edu/ ID - ref50 ER - TY - JOUR AU - Karolchik, D. AU - Baertsch, R. AU - Diekhans, M. AU - Furey, T. S. AU - Hinrichs, A. AU - Lu, Y. T. AU - Roskin, K. M. AU - Schwartz, M. AU - Sugnet, C. W. AU - Thomas, D. J. PY - 2003 DA - 2003// TI - The UCSC Genome Browser Database. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg129 DO - 10.1093/nar/gkg129 ID - Karolchik2003 ER - TY - JOUR AU - Blanchette, M. AU - Kent, W. J. AU - Riemer, C. AU - Elnitski, L. AU - Smit, A. F. AU - Roskin, K. M. AU - Baertsch, R. AU - Rosenbloom, K. AU - Clawson, H. AU - Green, E. D. PY - 2004 DA - 2004// TI - Aligning multiple genomic sequences with the threaded blockset aligner. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1933104 DO - 10.1101/gr.1933104 ID - Blanchette2004 ER - TY - STD TI - UCR Browser. [http://mordor.cgb.ki.se/UCRbrowse/] UR - http://mordor.cgb.ki.se/UCRbrowse/ ID - ref53 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT - the BLAST-like alignment tool. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER - TY - JOUR AU - Wingender, E. AU - Chen, X. AU - Fricke, E. AU - Geffers, R. AU - Hehl, R. AU - Liebich, I. AU - Krull, M. AU - Matys, V. AU - Michael, H. AU - Ohnhauser, R. PY - 2001 DA - 2001// TI - The TRANSFAC system on gene expression regulation. JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.1.281 DO - 10.1093/nar/29.1.281 ID - Wingender2001 ER - TY - JOUR AU - Margulies, E. H. AU - Blanchette, M. AU - Haussler, D. AU - Green, E. D. PY - 2003 DA - 2003// TI - Identification and characterization of multi-species conserved sequences. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1602203 DO - 10.1101/gr.1602203 ID - Margulies2003 ER - TY - JOUR AU - Ureta-Vidal, A. AU - Ettwiller, L. AU - Birney, E. PY - 2003 DA - 2003// TI - Comparative genomics: genome-wide analysis in metazoan eukaryotes. JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1043 DO - 10.1038/nrg1043 ID - Ureta-Vidal2003 ER - TY - JOUR AU - Boffelli, D. AU - Nobrega, M. A. AU - Rubin, E. M. PY - 2004 DA - 2004// TI - Comparative genomics at the vertebrate extremes. JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1350 DO - 10.1038/nrg1350 ID - Boffelli2004 ER - TY - JOUR PY - 2004 DA - 2004// TI - The ENCODE (ENCyclopedia Of DNA Elements) Project. JO - Science VL - 306 UR - https://doi.org/10.1126/science.1105136 DO - 10.1126/science.1105136 ID - ref59 ER - TY - JOUR AU - Thomas, J. W. AU - Touchman, J. W. AU - Blakesley, R. W. AU - Bouffard, G. G. AU - Beckstrom-Sternberg, S. M. AU - Margulies, E. H. AU - Blanchette, M. AU - Siepel, A. C. AU - Thomas, P. J. AU - McDowell, J. C. PY - 2003 DA - 2003// TI - Comparative analyses of multi-species sequences from targeted genomic regions. JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01858 DO - 10.1038/nature01858 ID - Thomas2003 ER - TY - JOUR AU - Down, T. A. AU - Hubbard, T. J. PY - 2005 DA - 2005// TI - NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki282 DO - 10.1093/nar/gki282 ID - Down2005 ER - TY - STD TI - Ensembl Genome Browser. [http://www.ensembl.org] UR - http://www.ensembl.org ID - ref62 ER - TY - JOUR AU - Barton, L. M. AU - Göttgens, B. AU - Gering, M. AU - Gilbert, J. G. AU - Grafham, D. AU - Rogers, J. AU - Bentley, D. AU - Patient, R. AU - Green, A. R. PY - 2001 DA - 2001// TI - Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes. JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.101532998 DO - 10.1073/pnas.101532998 ID - Barton2001 ER - TY - JOUR AU - Tatusova, T. A. AU - Madden, T. L. PY - 1999 DA - 1999// TI - BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. JO - FEMS Microbiol Lett VL - 174 UR - https://doi.org/10.1111/j.1574-6968.1999.tb13575.x DO - 10.1111/j.1574-6968.1999.tb13575.x ID - Tatusova1999 ER - TY - JOUR AU - Bray, N. AU - Dubchak, I. AU - Pachter, L. PY - 2003 DA - 2003// TI - AVID: A global alignment program. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.789803 DO - 10.1101/gr.789803 ID - Bray2003 ER - TY - JOUR AU - Frazer, K. A. AU - Pachter, L. AU - Poliakov, A. AU - Rubin, E. M. AU - Dubchak, I. PY - 2004 DA - 2004// TI - VISTA: computational tools for comparative genomics. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh458 DO - 10.1093/nar/gkh458 ID - Frazer2004 ER - TY - JOUR AU - Enright, A. J. AU - Van Dongen, S. AU - Ouzounis, C. A. PY - 2002 DA - 2002// TI - An efficient algorithm for large-scale detection of protein families. JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.7.1575 DO - 10.1093/nar/30.7.1575 ID - Enright2002 ER - TY - JOUR AU - Marchal, K. AU - Thijs, G. AU - De Keersmaecker, S. AU - Monsieurs, P. AU - De Moor, B. AU - Vanderleyden, J. PY - 2003 DA - 2003// TI - Genome-specific higher-order background models to improve motif detection. JO - Trends Microbiol VL - 11 UR - https://doi.org/10.1016/S0966-842X(02)00030-6 DO - 10.1016/S0966-842X(02)00030-6 ID - Marchal2003 ER - TY - STD TI - BLAT Search Genome. [http://genome.ucsc.edu/cgi-bin/hgBlat] UR - http://genome.ucsc.edu/cgi-bin/hgBlat ID - ref69 ER - TY - JOUR AU - Aerts, S. AU - Thijs, G. AU - Coessens, B. AU - Staes, M. AU - Moreau, Y. AU - De Moor, B. PY - 2003 DA - 2003// TI - Toucan: deciphering the cis-regulatory logic of coregulated genes. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg268 DO - 10.1093/nar/gkg268 ID - Aerts2003 ER - TY - JOUR AU - Coessens, B. AU - Thijs, G. AU - Aerts, S. AU - Marchal, K. AU - De Smet, F. AU - Engelen, K. AU - Glenisson, P. AU - Moreau, Y. AU - Mathys, J. AU - De Moor, B. PY - 2003 DA - 2003// TI - INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg615 DO - 10.1093/nar/gkg615 ID - Coessens2003 ER - TY - STD TI - BioI@SCD Software. [http://homes.esat.kuleuven.be/~dna/Bioi/Software.html] UR - http://homes.esat.kuleuven.be/~dna/Bioi/Software.html ID - ref72 ER - TY - JOUR AU - Kato, M. AU - Hata, N. AU - Banerjee, N. AU - Futcher, B. AU - Zhang, M. Q. PY - 2004 DA - 2004// TI - Identifying combinatorial regulation of transcription factors and binding motifs. JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-8-r56 DO - 10.1186/gb-2004-5-8-r56 ID - Kato2004 ER - TY - STD TI - MAVID Multiple Alignment Server. [http://baboon.math.berkeley.edu/mavid/] UR - http://baboon.math.berkeley.edu/mavid/ ID - ref74 ER - TY - STD TI - Miller Lab. [http://bio.cse.psu.edu/] UR - http://bio.cse.psu.edu/ ID - ref75 ER - TY - STD TI - E Margulies FTP Site. [ftp://kronos.nhgri.nih.gov/pub/outgoing/elliott/tba/] UR - ftp://kronos.nhgri.nih.gov/pub/outgoing/elliott/tba/ ID - ref76 ER -