TY - JOUR AU - Loots, G. G. AU - Ovcharenko, I. AU - Pachter, L. AU - Dubchak, I. AU - Rubin, E. M. PY - 2002 DA - 2002// TI - rVista for comparative sequence-based discovery of functional transcription factor binding sites. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.225502. Article published online before print in April 2002 DO - 10.1101/gr.225502. Article published online before print in April 2002 ID - Loots2002 ER - TY - JOUR AU - Lenhard, B. AU - Sandelin, A. AU - Mendoza, L. AU - Engstrom, P. AU - Jareborg, N. AU - Wasserman, W. W. PY - 2003 DA - 2003// TI - Identification of conserved regulatory elements by comparative genome analysis. JO - J Biol VL - 2 UR - https://doi.org/10.1186/1475-4924-2-13 DO - 10.1186/1475-4924-2-13 ID - Lenhard2003 ER - TY - JOUR AU - Ludwig, M. Z. PY - 2002 DA - 2002// TI - Functional evolution of noncoding DNA. JO - Curr Opin Genet Dev VL - 12 UR - https://doi.org/10.1016/S0959-437X(02)00355-6 DO - 10.1016/S0959-437X(02)00355-6 ID - Ludwig2002 ER - TY - JOUR AU - Maduro, M. AU - Pilgrim, D. PY - 1996 DA - 1996// TI - Conservation of function and expression of unc-119 from two Caenorhabditisspecies despite divergence of non-coding DNA. JO - Gene VL - 183 UR - https://doi.org/10.1016/S0378-1119(96)00491-X DO - 10.1016/S0378-1119(96)00491-X ID - Maduro1996 ER - TY - JOUR AU - Stone, J. R. AU - Wray, G. A. PY - 2001 DA - 2001// TI - Rapid evolution of cis-regulatory sequences via local point mutations. JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003964 DO - 10.1093/oxfordjournals.molbev.a003964 ID - Stone2001 ER - TY - JOUR AU - Dermitzakis, E. T. AU - Clark, A. G. PY - 2002 DA - 2002// TI - Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004169 DO - 10.1093/oxfordjournals.molbev.a004169 ID - Dermitzakis2002 ER - TY - JOUR AU - Ludwig, M. Z. AU - Bergman, C. AU - Patel, N. H. AU - Kreitman, M. PY - 2000 DA - 2000// TI - Evidence for stabilizing selection in a eukaryotic enhancer element. JO - Nature VL - 403 UR - https://doi.org/10.1038/35000615 DO - 10.1038/35000615 ID - Ludwig2000 ER - TY - JOUR AU - Ludwig, M. Z. AU - Palsson, A. AU - Alekseeva, E. AU - Bergman, C. M. AU - Nathan, J. AU - Kreitman, M. PY - 2005 DA - 2005// TI - Functional evolution of a cis-regulatory module. JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030093 DO - 10.1371/journal.pbio.0030093 ID - Ludwig2005 ER - TY - JOUR AU - Ludwig, M. Z. AU - Patel, N. H. AU - Kreitman, M. PY - 1998 DA - 1998// TI - Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. JO - Development VL - 125 ID - Ludwig1998 ER - TY - JOUR AU - Frith, M. C. AU - Ponjavic, J. AU - Fredman, D. AU - Kai, C. AU - Kawai, J. AU - Carninci, P. AU - Hayashizaki, Y. AU - Sandelin, A. PY - 2006 DA - 2006// TI - Evolutionary turnover of mammalian transcription start sites. JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.5031006 DO - 10.1101/gr.5031006 ID - Frith2006 ER - TY - JOUR AU - Carter, A. J. AU - Wagner, G. P. PY - 2002 DA - 2002// TI - Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model. JO - Proc Biol Sci VL - 269 UR - https://doi.org/10.1098/rspb.2002.1968 DO - 10.1098/rspb.2002.1968 ID - Carter2002 ER - TY - JOUR AU - Gerland, U. AU - Hwa, T. PY - 2002 DA - 2002// TI - On the selection and evolution of regulatory DNA motifs. JO - J Mol Evol VL - 55 UR - https://doi.org/10.1007/s00239-002-2335-z DO - 10.1007/s00239-002-2335-z ID - Gerland2002 ER - TY - JOUR AU - Wray, G. A. AU - Hahn, M. W. AU - Abouheif, E. AU - Balhoff, J. P. AU - Pizer, M. AU - Rockman, M. V. AU - Romano, L. A. PY - 2003 DA - 2003// TI - The evolution of transcriptional regulation in eukaryotes. JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg140 DO - 10.1093/molbev/msg140 ID - Wray2003 ER - TY - JOUR AU - MacArthur, S. AU - Brookfield, J. F. Y. PY - 2004 DA - 2004// TI - Expected rates and modes of evolution of enhancer sequences. JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh105 DO - 10.1093/molbev/msh105 ID - MacArthur2004 ER - TY - JOUR AU - Lee, A. P. AU - Koh, E. G. AU - Tay, A. AU - Brenner, S. AU - Venkatesh, B. PY - 2006 DA - 2006// TI - Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0601492103 DO - 10.1073/pnas.0601492103 ID - Lee2006 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 - Ruvinsky, I. AU - Ruvkun, G. PY - 2003 DA - 2003// TI - Functional tests of enhancer conservation between distantly related species. JO - Development VL - 130 UR - https://doi.org/10.1242/dev.00711 DO - 10.1242/dev.00711 ID - Ruvinsky2003 ER - TY - BOOK AU - Davidson, E. H. PY - 2001 DA - 2001// TI - Genomic Regulatory Systems: Development and Evolution PB - Academic Press CY - San Diego, CA ID - Davidson2001 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 - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Huang, W. AU - Umbach, D. M. AU - Li, L. PY - 2006 DA - 2006// TI - Accurate anchoring alignment of divergent sequences. JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti772 DO - 10.1093/bioinformatics/bti772 ID - Huang2006 ER - TY - JOUR AU - Notredame, C. AU - Higgins, D. G. AU - Heringa, J. PY - 2000 DA - 2000// TI - T-Coffee: A novel method for fast and accurate multiple sequence alignment. JO - J Mol Biol VL - 302 UR - https://doi.org/10.1006/jmbi.2000.4042 DO - 10.1006/jmbi.2000.4042 ID - Notredame2000 ER - TY - JOUR AU - McClure, M. A. AU - Vasi, T. K. AU - Fitch, W. M. PY - 1994 DA - 1994// TI - Comparative analysis of multiple protein-sequence alignment methods. JO - Mol Biol Evol VL - 11 ID - McClure1994 ER - TY - JOUR AU - Sauder, J. M. AU - Arthur, J. W. AU - Dunbrack, R. L. PY - 2000 DA - 2000// TI - Large-scale comparison of protein sequence alignment algorithms with structure alignments. JO - Proteins VL - 40 UR - https://doi.org/3.0.CO;2-7 DO - 3.0.CO;2-7 ID - Sauder2000 ER - TY - JOUR AU - Thompson, J. D. AU - Plewniak, F. AU - Poch, O. PY - 1999 DA - 1999// TI - A comprehensive comparison of multiple sequence alignment programs. JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.13.2682 DO - 10.1093/nar/27.13.2682 ID - Thompson1999 ER - TY - JOUR AU - Lassmann, T. AU - Sonnhammer, E. L. PY - 2002 DA - 2002// TI - Quality assessment of multiple alignment programs. JO - FEBS Lett VL - 529 UR - https://doi.org/10.1016/S0014-5793(02)03189-7 DO - 10.1016/S0014-5793(02)03189-7 ID - Lassmann2002 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 - Pollard, D. A. AU - Bergman, C. M. AU - Stoye, J. AU - Celniker, S. E. AU - Eisen, M. B. PY - 2004 DA - 2004// TI - Benchmarking tools for the alignment of functional noncoding DNA. JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-6 DO - 10.1186/1471-2105-5-6 ID - Pollard2004 ER - TY - JOUR AU - Pollard, D. A. AU - Moses, A. M. AU - Iyer, V. N. AU - Eisen, M. B. PY - 2006 DA - 2006// TI - Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-376 DO - 10.1186/1471-2105-7-376 ID - Pollard2006 ER - TY - JOUR AU - DeGregori, J. AU - Leone, G. AU - Miron, A. AU - Jakoi, L. AU - Nevins, J. R. PY - 1997 DA - 1997// TI - Distinct roles for E2F proteins in cell growth control and apoptosis. JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.14.7245 DO - 10.1073/pnas.94.14.7245 ID - DeGregori1997 ER - TY - JOUR AU - Muller, H. AU - Bracken, A. P. AU - Vernell, R. AU - Moroni, M. C. AU - Christians, F. AU - Grassilli, E. AU - Prosperini, E. AU - Vigo, E. AU - Oliner, J. D. AU - Helin, K. PY - 2001 DA - 2001// TI - E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. JO - Genes Dev VL - 15 UR - https://doi.org/10.1101/gad.864201 DO - 10.1101/gad.864201 ID - Muller2001 ER - TY - JOUR AU - Bernard, S. AU - Eilers, M. PY - 2006 DA - 2006// TI - Control of cell proliferation and growth by Myc proteins. JO - Results Probl Cell Differ VL - 42 UR - https://doi.org/10.1007/400_004 DO - 10.1007/400_004 ID - Bernard2006 ER - TY - JOUR AU - Amati, B. AU - Littlewood, T. D. AU - Evan, G. I. AU - Land, H. PY - 1993 DA - 1993// TI - The c-Myc protein induces cell cycle progression and apoptosis through dimerization with Max. JO - EMBO J VL - 12 ID - Amati1993 ER - TY - JOUR AU - La Thangue, N. B. PY - 2002 DA - 2002// TI - Transcription. Chromatin control - a place for E2F and Myc to meet. JO - Science VL - 296 UR - https://doi.org/10.1126/science.1072446 DO - 10.1126/science.1072446 ID - La Thangue2002 ER - TY - JOUR AU - Ogawa, H. AU - Ishiguro, K. AU - Gaubatz, S. AU - Livingston, D. M. AU - Nakatani, Y. PY - 2002 DA - 2002// TI - A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. JO - Science VL - 296 UR - https://doi.org/10.1126/science.1069861 DO - 10.1126/science.1069861 ID - Ogawa2002 ER - TY - JOUR AU - Ditsworth, D. AU - Zong, W. X. PY - 2004 DA - 2004// TI - NF-kappaB: key mediator of inflammation-associated cancer. JO - Cancer Biol Ther VL - 3 UR - https://doi.org/10.4161/cbt.3.12.1391 DO - 10.4161/cbt.3.12.1391 ID - Ditsworth2004 ER - TY - JOUR AU - Dobrovolskaia, M. A. AU - Kozlov, S. V. PY - 2005 DA - 2005// TI - Inflammation and cancer: when NF-kappaB amalgamates the perilous partnership. JO - Curr Cancer Drug Targets VL - 5 UR - https://doi.org/10.2174/1568009054629645 DO - 10.2174/1568009054629645 ID - Dobrovolskaia2005 ER - TY - JOUR AU - Luo, J. L. AU - Kamata, H. AU - Karin, M. PY - 2005 DA - 2005// TI - IKK/NF-kappaB signaling: balancing life and death - a new approach to cancer therapy. JO - J Clin Invest VL - 115 UR - https://doi.org/10.1172/JCI26322 DO - 10.1172/JCI26322 ID - Luo2005 ER - TY - JOUR AU - Vlieghe, D. AU - Sandelin, A. AU - De Bleser, P. J. AU - Vleminckx, K. AU - Wasserman, W. W. AU - van Roy, F. AU - Lenhard, B. PY - 2006 DA - 2006// TI - A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj115 DO - 10.1093/nar/gkj115 ID - Vlieghe2006 ER - TY - JOUR AU - Hasegawa, M. AU - Kishino, H. AU - Yano, T. PY - 1985 DA - 1985// TI - Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. JO - J Mol Evol VL - 22 UR - https://doi.org/10.1007/BF02101694 DO - 10.1007/BF02101694 ID - Hasegawa1985 ER - TY - JOUR AU - Bieda, M. AU - Xu, X. AU - Singer, M. A. AU - Green, R. AU - Farnham, P. J. PY - 2006 DA - 2006// TI - Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4887606 DO - 10.1101/gr.4887606 ID - Bieda2006 ER - TY - JOUR AU - Ren, B. AU - Cam, H. AU - Takahashi, Y. AU - Volkert, T. AU - Terragni, J. AU - Young, R. A. AU - Dynlacht, B. D. PY - 2002 DA - 2002// TI - E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. JO - Genes Dev VL - 16 UR - https://doi.org/10.1101/gad.949802 DO - 10.1101/gad.949802 ID - Ren2002 ER - TY - JOUR AU - Yan, Z. AU - DeGregori, J. AU - Shohet, R. AU - Leone, G. AU - Stillman, B. AU - Nevins, J. R. AU - Williams, R. S. PY - 1998 DA - 1998// TI - Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells. JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.7.3603 DO - 10.1073/pnas.95.7.3603 ID - Yan1998 ER - TY - JOUR AU - Hateboer, G. AU - Wobst, A. AU - Petersen, B. O. AU - Le Cam, L. AU - Vigo, E. AU - Sardet, C. AU - Helin, K. PY - 1998 DA - 1998// TI - Cell cycle-regulated expression of mammalian CDC6 is dependent on E2F. JO - Mol Cell Biol VL - 18 UR - https://doi.org/10.1128/MCB.18.11.6679 DO - 10.1128/MCB.18.11.6679 ID - Hateboer1998 ER - TY - JOUR AU - Ohtani, K. AU - Tsujimoto, A. AU - Ikeda, M. AU - Nakamura, M. PY - 1998 DA - 1998// TI - Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F. JO - Oncogene VL - 17 UR - https://doi.org/10.1038/sj.onc.1202105 DO - 10.1038/sj.onc.1202105 ID - Ohtani1998 ER - TY - JOUR AU - Siepel, A. AU - Haussler, D. PY - 2004 DA - 2004// TI - Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh039 DO - 10.1093/molbev/msh039 ID - Siepel2004 ER - TY - JOUR AU - Ogurtsov, A. Y. AU - Sunyaev, S. AU - Kondrashov, A. S. PY - 2004 DA - 2004// TI - Indel-based evolutionary distance and mouse-human divergence. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2450504 DO - 10.1101/gr.2450504 ID - Ogurtsov2004 ER - TY - JOUR AU - Schlisio, S. AU - Halperin, T. AU - Vidal, M. AU - Nevins, J. R. PY - 2002 DA - 2002// TI - Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function. JO - EMBO J VL - 21 UR - https://doi.org/10.1093/emboj/cdf577 DO - 10.1093/emboj/cdf577 ID - Schlisio2002 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. 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 - Huang, W. AU - Umbach, D. M. AU - Ohler, U. AU - Li, L. PY - 2006 DA - 2006// TI - Optimized mixed Markov models for motif identification. JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-279 DO - 10.1186/1471-2105-7-279 ID - Huang2006 ER - TY - JOUR AU - Yeo, G. AU - Burge, C. B. PY - 2004 DA - 2004// TI - Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. JO - J Comput Biol VL - 11 UR - https://doi.org/10.1089/1066527041410418 DO - 10.1089/1066527041410418 ID - Yeo2004 ER - TY - JOUR AU - Arnosti, D. N. AU - Kulkarni, M. M. PY - 2005 DA - 2005// TI - Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? JO - J Cell Biochem VL - 94 UR - https://doi.org/10.1002/jcb.20352 DO - 10.1002/jcb.20352 ID - Arnosti2005 ER - TY - JOUR AU - Mustonen, V. AU - Lassig, M. PY - 2005 DA - 2005// TI - Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0505537102 DO - 10.1073/pnas.0505537102 ID - Mustonen2005 ER - TY - JOUR AU - Margulies, E. H. AU - Chen, C. W. AU - Green, E. D. PY - 2006 DA - 2006// TI - Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. JO - Trends Genet VL - 22 UR - https://doi.org/10.1016/j.tig.2006.02.005 DO - 10.1016/j.tig.2006.02.005 ID - Margulies2006 ER - TY - JOUR AU - Morgenstern, B. AU - Dress, A. AU - Werner, T. PY - 1996 DA - 1996// TI - Multiple DNA and protein sequence alignment based on segment-to-segment comparison. JO - Proc Natl Acad Sci USA VL - 93 UR - https://doi.org/10.1073/pnas.93.22.12098 DO - 10.1073/pnas.93.22.12098 ID - Morgenstern1996 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 - JOUR AU - Loytynoja, A. AU - Goldman, N. PY - 2005 DA - 2005// TI - An algorithm for progressive multiple alignment of sequences with insertions. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409137102 DO - 10.1073/pnas.0409137102 ID - Loytynoja2005 ER - TY - JOUR AU - Do, C. B. AU - Mahabhashyam, M. S. AU - Brudno, M. AU - Batzoglou, S. PY - 2005 DA - 2005// TI - ProbCons: Probabilistic consistency-based multiple sequence alignment. JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.2821705 DO - 10.1101/gr.2821705 ID - Do2005 ER - TY - STD TI - Weichun Huang's Research Domain. [http://biomedempire.org] UR - http://biomedempire.org ID - ref61 ER - TY - STD TI - Uwe Ohler's Gene Regulation Webpage. [http://tools.genome.duke.edu/generegulation] UR - http://tools.genome.duke.edu/generegulation ID - ref62 ER - TY - JOUR AU - Blanco, E. AU - Messeguer, X. AU - Smith, T. F. AU - Guigo, R. PY - 2006 DA - 2006// TI - Transcription factor map alignment of promoter regions. JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020049 DO - 10.1371/journal.pcbi.0020049 ID - Blanco2006 ER - TY - JOUR AU - Quandt, K. AU - Frech, K. AU - Karas, H. AU - Wingender, E. AU - Werner, T. PY - 1995 DA - 1995// TI - MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. JO - Nucleic Acids Res VL - 23 UR - https://doi.org/10.1093/nar/23.23.4878 DO - 10.1093/nar/23.23.4878 ID - Quandt1995 ER - TY - JOUR AU - Sandelin, A. AU - Alkema, W. AU - Engstrom, P. AU - Wasserman, W. W. AU - Lenhard, B. PY - 2004 DA - 2004// TI - JASPAR: an open-access database for eukaryotic transcription factor binding profiles. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh012 DO - 10.1093/nar/gkh012 ID - Sandelin2004 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. R. ED - Munro, M. N. PY - 1969 DA - 1969// TI - Evolution of protein molecules. BT - Mammalian Protein Metabolism PB - Academic Press CY - New York UR - https://doi.org/10.1016/B978-1-4832-3211-9.50009-7 DO - 10.1016/B978-1-4832-3211-9.50009-7 ID - Jukes1969 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach. JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Kimura, M. PY - 1980 DA - 1980// TI - A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. JO - J Mol Evol VL - 16 UR - https://doi.org/10.1007/BF01731581 DO - 10.1007/BF01731581 ID - Kimura1980 ER - TY - JOUR AU - Tamura, K. AU - Nei, M. PY - 1993 DA - 1993// TI - Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. JO - Mol Biol Evol VL - 10 ID - Tamura1993 ER - TY - JOUR AU - Lanave, C. AU - Preparata, G. AU - Saccone, C. AU - Serio, G. PY - 1984 DA - 1984// TI - A new method for calculating evolutionary substitution rates. JO - J Mol Evol VL - 20 UR - https://doi.org/10.1007/BF02101990 DO - 10.1007/BF02101990 ID - Lanave1984 ER - TY - JOUR AU - Tavare, S. PY - 1986 DA - 1986// TI - Some probabilistic and statisical problems on the analysis of DNA sequences. JO - Lect Math Life Sci VL - 17 ID - Tavare1986 ER - TY - JOUR AU - Rodriguez, F. AU - Oliver, J. L. AU - Marin, A. AU - Medina, J. R. PY - 1990 DA - 1990// TI - The general stochastic model of nucleotide substitution. JO - J Theor Biol VL - 142 UR - https://doi.org/10.1016/S0022-5193(05)80104-3 DO - 10.1016/S0022-5193(05)80104-3 ID - Rodriguez1990 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. JO - J Mol Evol VL - 39 UR - https://doi.org/10.1007/BF00160154 DO - 10.1007/BF00160154 ID - Yang1994 ER - TY - JOUR AU - Waddell, P. J. AU - Steel, M. A. PY - 1997 DA - 1997// TI - General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. JO - Mol Phylogenet Evol VL - 8 UR - https://doi.org/10.1006/mpev.1997.0452 DO - 10.1006/mpev.1997.0452 ID - Waddell1997 ER - TY - JOUR AU - Cartwright, R. A. PY - 2005 DA - 2005// TI - DNA assembly with gaps (Dawg): simulating sequence evolution. JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1200 DO - 10.1093/bioinformatics/bti1200 ID - Cartwright2005 ER - TY - JOUR AU - Schwartz, S. AU - Kent, W. J. AU - Smit, A. AU - Zhang, Z. AU - Baertsch, R. AU - Hardison, R. C. AU - Haussler, D. AU - Miller, W. PY - 2003 DA - 2003// TI - Human-mouse alignments with BLASTZ. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.809403 DO - 10.1101/gr.809403 ID - Schwartz2003 ER - TY - JOUR AU - Kurtz, S. AU - Phillippy, A. AU - Delcher, A. L. AU - Smoot, M. AU - Shumway, M. AU - Antonescu, C. AU - Salzberg, S. L. PY - 2004 DA - 2004// TI - Versatile and open software for comparing large genomes. JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-2-r12 DO - 10.1186/gb-2004-5-2-r12 ID - Kurtz2004 ER - TY - JOUR AU - Rambaldi, D. AU - Guffanti, A. AU - Morandi, P. AU - Cassata, G. PY - 2005 DA - 2005// TI - NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae. JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-S4-S22 DO - 10.1186/1471-2105-6-S4-S22 ID - Rambaldi2005 ER - TY - JOUR AU - Lee, C. AU - Grasso, C. AU - Sharlow, M. F. PY - 2002 DA - 2002// TI - Multiple sequence alignment using partial order graphs. JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.452 DO - 10.1093/bioinformatics/18.3.452 ID - Lee2002 ER - TY - JOUR AU - Katoh, K. AU - Kuma, K. AU - Toh, H. AU - Miyata, T. PY - 2005 DA - 2005// TI - MAFFT version 5: improvement in accuracy of multiple sequence alignment. JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki198 DO - 10.1093/nar/gki198 ID - Katoh2005 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity. JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Crooks, G. E. AU - Hon, G. AU - Chandonia, J. M. AU - Brenner, S. E. PY - 2004 DA - 2004// TI - WebLogo: a sequence logo generator. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.849004 DO - 10.1101/gr.849004 ID - Crooks2004 ER -