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Single haplotype assembly of the human genome from a hydatidiform mole.
Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK. Steinberg KM, et al. Among authors: agarwala r. Genome Res. 2014 Dec;24(12):2066-76. doi: 10.1101/gr.180893.114. Epub 2014 Nov 4. Genome Res. 2014. PMID: 25373144 Free PMC article.
Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium; Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kuc… See abstract for full author list ➔ Mouse Genome Sequencing Consortium, et al. Among authors: agarwala r. Nature. 2002 Dec 5;420(6915):520-62. doi: 10.1038/nature01262. Nature. 2002. PMID: 12466850
Sequence variations in the public human genome data reflect a bottlenecked population history.
Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, Rogers A, Chakravarti A, Harpending HC, Kwok PY, Sherry ST. Marth G, et al. Among authors: agarwala r. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):376-81. doi: 10.1073/pnas.222673099. Epub 2002 Dec 26. Proc Natl Acad Sci U S A. 2003. PMID: 12502794 Free PMC article.
WindowMasker: window-based masker for sequenced genomes.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Morgulis A, et al. Among authors: agarwala r. Bioinformatics. 2006 Jan 15;22(2):134-41. doi: 10.1093/bioinformatics/bti774. Epub 2005 Nov 15. Bioinformatics. 2006. PMID: 16287941
Improved BLAST searches using longer words for protein seeding.
Shiryev SA, Papadopoulos JS, Schäffer AA, Agarwala R. Shiryev SA, et al. Among authors: agarwala r. Bioinformatics. 2007 Nov 1;23(21):2949-51. doi: 10.1093/bioinformatics/btm479. Epub 2007 Oct 6. Bioinformatics. 2007. PMID: 17921491
Initial sequence and comparative analysis of the cat genome.
Pontius JU, Mullikin JC, Smith DR; Agencourt Sequencing Team; Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G; NISC Comparative Sequencing Program; O'Brien SJ. Pontius JU, et al. Among authors: agarwala r. Genome Res. 2007 Nov;17(11):1675-89. doi: 10.1101/gr.6380007. Genome Res. 2007. PMID: 17975172 Free PMC article.
Database indexing for production MegaBLAST searches.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. Morgulis A, et al. Among authors: agarwala r. Bioinformatics. 2008 Aug 15;24(16):1757-64. doi: 10.1093/bioinformatics/btn322. Epub 2008 Jun 21. Bioinformatics. 2008. PMID: 18567917 Free PMC article.
168 results