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Two rounds of whole genome duplication in the ancestral vertebrate.
Dehal P, Boore JL. Dehal P, et al. PLoS Biol. 2005 Oct;3(10):e314. doi: 10.1371/journal.pbio.0030314. Epub 2005 Sep 6. PLoS Biol. 2005. PMID: 16128622 Free PMC article.
MicrobesOnline: an integrated portal for comparative and functional genomics.
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. Dehal PS, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906701 Free PMC article.
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.
Dehal PS, Boore JL. Dehal PS, et al. BMC Bioinformatics. 2006 Apr 11;7:201. doi: 10.1186/1471-2105-7-201. BMC Bioinformatics. 2006. PMID: 16608522 Free PMC article.
Orthologous transcription factors in bacteria have different functions and regulate different genes.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. PLoS Comput Biol. 2007 Sep;3(9):1739-50. doi: 10.1371/journal.pcbi.0030175. PLoS Comput Biol. 2007. PMID: 17845071 Free PMC article.
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. Genome Biol. 2008 Jan 7;9(1):R4. doi: 10.1186/gb-2008-9-1-r4. Genome Biol. 2008. PMID: 18179685 Free PMC article.
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.
Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. Aparicio S, et al. Among authors: dehal p. Science. 2002 Aug 23;297(5585):1301-10. doi: 10.1126/science.1072104. Epub 2002 Jul 25. Science. 2002. PMID: 12142439
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS. Dehal P, et al. Science. 2002 Dec 13;298(5601):2157-67. doi: 10.1126/science.1080049. Science. 2002. PMID: 12481130
Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19.
Kim J, Gordon L, Dehal P, Badri H, Christensen M, Groza M, Ha C, Hammond S, Vargas M, Wehri E, Wagner M, Olsen A, Stubbs L. Kim J, et al. Among authors: dehal p. Genomics. 2001 Jun 1;74(2):129-41. doi: 10.1006/geno.2001.6521. Genomics. 2001. PMID: 11386749
Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.
Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Ecale Zhou CL, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, Richardson P, Rokhsar D, Uberbacher E, Hawkins T, Branscomb E, Stubbs L. Dehal P, et al. Science. 2001 Jul 6;293(5527):104-11. doi: 10.1126/science.1060310. Science. 2001. PMID: 11441184
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077. Epub 2009 Apr 17. Mol Biol Evol. 2009. PMID: 19377059 Free PMC article.
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