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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL. Langmead B, et al. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4. Genome Biol. 2009. PMID: 19261174 Free PMC article.
Predicting protein secondary structure with a nearest-neighbor algorithm.
Salzberg S, Cost S. Salzberg S, et al. J Mol Biol. 1992 Sep 20;227(2):371-4. doi: 10.1016/0022-2836(92)90892-n. J Mol Biol. 1992. PMID: 1404357
Alignment of whole genomes.
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Delcher AL, et al. Nucleic Acids Res. 1999 Jun 1;27(11):2369-76. doi: 10.1093/nar/27.11.2369. Nucleic Acids Res. 1999. PMID: 10325427 Free PMC article.
DNA uptake signal sequences in naturally transformable bacteria.
Smith HO, Gwinn ML, Salzberg SL. Smith HO, et al. Res Microbiol. 1999 Nov-Dec;150(9-10):603-16. doi: 10.1016/s0923-2508(99)00130-8. Res Microbiol. 1999. PMID: 10673000 Review.
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM. Read TD, et al. Nucleic Acids Res. 2000 Mar 15;28(6):1397-406. doi: 10.1093/nar/28.6.1397. Nucleic Acids Res. 2000. PMID: 10684935 Free PMC article.
Gene index analysis of the human genome estimates approximately 120,000 genes.
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. Liang F, et al. Nat Genet. 2000 Jun;25(2):239-40. doi: 10.1038/76126. Nat Genet. 2000. PMID: 10835646
Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Eisen JA, Heidelberg JF, White O, Salzberg SL. Eisen JA, et al. Genome Biol. 2000;1(6):RESEARCH0011. doi: 10.1186/gb-2000-1-6-research0011. Epub 2000 Dec 4. Genome Biol. 2000. PMID: 11178265 Free PMC article.
The sequence of the human genome.
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. Venter JC, et al. Science. 2001 Feb 16;291(5507):1304-51. doi: 10.1126/science.1058040. Science. 2001. PMID: 11181995
A clustering method for repeat analysis in DNA sequences.
Volfovsky N, Haas BJ, Salzberg SL. Volfovsky N, et al. Genome Biol. 2001;2(8):RESEARCH0027. doi: 10.1186/gb-2001-2-8-research0027. Epub 2001 Aug 1. Genome Biol. 2001. PMID: 11532211 Free PMC article.
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