Publications

12. Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Lee SW, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 9:204.
11. Ming, R, Hou, S, Feng, Y, Yu, Q, Dionne-Laporte, A, Saw, JH, Senin, P, Wang, W, Ly, BV, Lewis, KLT, Salzberg, SL, Feng, L, Jones, MR, Skelton, RL, Murray, JE, Chen, C, Qian, W, Shen, J, Du, P, Eustice, M, Tong, E, Tang, H, Lyons, E, Paull, RE, Michael, TP, Wall, K, Rice, DW, Albert, H, Wang, M, Zhu, YJ, Schatz, M, Nagarajan, N, Acob, RA, Guan, P, Blas, A, Wai, CM, Ackerman, CM, Ren, Y, Liu, C, Wang, J, Wang, J, Na, J, Shakirov, EV, Haas, B, Thimmapuram, J, Nelson, D, Wang, X, Bowers, JE, Gschwend, AR, Delcher, AL, Singh, R, Suzuki, JY, Tripathi, S, Neupane, K, Wei, H, Irikura, B, Paidi, M, Jiang, N, Zhang, W, Presting, G, Windsor, A, Navajas-Perez, R, Torres, MJ, Feltus, FA, Porter, B, Li, Y, Burroughs, AM, Luo, M, Liu, L, Christopher, DA, Mount, SM, Moore, PH, Sugimura, T, Jiang, J, Schuler, MA, Friedman, V, Mitchell-Olds, T, Shippen, DE, dePamphilis, CW, Palmer, JD, Freeling, M, Paterson, AH, Gonsalves, D, Wang, L, Alam, M.  (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Nature 452, 991-996.
10. Phillippy, A.M., Schatz, M.C., Pop, M. (2008) Genome Assembly forensics: finding the elusive mis-assembly. Genome Biology 9:R55.
9. Schatz, M.C., Trapnell, C., Delcher, A.L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics 8:474.
8.
Drosophila 12 Genomes Consortium. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.  (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature Nov 8;450(7167):203-18.
7. Ghedin, E., Wang,S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J.E., Delcher, A.L., Guiliano,D.B., Miranda-Saavedra, D., Angiuoli, S.V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N.M., Wortman, J.R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S.L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G.J., Carlow, C.K.S., Crawford, M.J., Daub, J., Dimmic, M.W., Estes, C.F., Foster, J.M., Ganatra, M., Gregory, W.F., Johnson, N.M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B., Li, W., Lindblom, T.H., Lustigman, S., Ma, D., Maina, C.V., Martin, D.M.A., McCarter, J.P., McReynolds, L., Mitreva, M., Nutman, T.B., Parkinson, J., Peregrin-Alvarez, J.M., Poole, C., Ren, Q., Saunders, L., Sluder, A.E., Smith, K., Stanke, M., Unnasch, T.R., Ware, J., Wei, A.D., Weil, G., Williams, D.J., Zhang, Y., Williams, S.A., Fraser-Liggett, C., Slatko, B., Blaxter, M.L., Scott, A.L. Draft Genome of the Filarial Nematode Parasite Brugia malayi. (2007) Science 317(5845):1756-1760
6.
Desjardins, C.A., Gundersen-Rindal, D.E., Hostetler, J.B., Tallon, L.J., Fuester, R.W., Schatz, M.C., Pedroni, M.J., Fadrosh, D.W., Haas, B.J., Toms, B.S., Chen, D., Nene, V. Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus (2007) BMC Microbiology 7:61
5.
Nene, V., Wortman, J.R., Lawson, D., Haas, B., Kodira, C., Tu, Z., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E.M., Lobo, N.F., Campbell, K.S., Brown, S.E., Bonaldo, M.F., Zhu, J., Sinkins, S.P., Hogenkamp, D.G., Amedeo, P., Arensburger, P., Atkinson, P.W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R.V., Costas, J., Coy, M.R., Crabtree, J., Crawford, M., deBruyn, B., DeCaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W.M., Gomes, S.L., Hammond, M., Hannick, L.I., Hogan, J.R., Holmes, M.H., Jaffe, D., Johnston, J.S., Kennedy, R.C., Koo, H., Kravitz, S., Kriventseva, E.V., Kulp, D., LaButti,K., Lee, E., Li, S., Lovin, D.D., Mao, C., Mauceli, E., Menck, C.F.M., Miller, J.R., Montgomery, P., Mori, A., Nascimento, A.L., Naveira, H.F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach,K.R., Rogers, Y., Roth, C.W., Schneider, J.R., Schatz, M., Shumway, M., Stanke, M., Stinson, E.O., Tubio, J.M.C., VanZee, J.P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C.A., Raikhel, A.S., Soares, M.B., Knudson, D.L., Lee, N.H., Galagan, J., Salzberg, S.L., Paulsen, I.T., Dimopoulos, G., Collins, F.H., Birren, B., Fraser-Liggett, C.M., Severson, D.W. (2007) Genome Sequence of Aedes aegypti, a Major Arbovirus Vector Science 316(5832), 1718-1723.
4.
Schatz, M.C., Phillippy, A.M., Shneiderman, B., Salzberg, S.L. (2007) Hawkeye: a visual analytics tool for genome assemblies. Genome Biology 8:R34.
3.
Carlton, J.M., Hirt, R.P., Silva, J.C., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark, U.C.M., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van de Peer, Y., Miranda-Saavedra, D., Barton, G.J., Westrop, G.D., Müller, S., Dessi, D., Fiori, P.L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F.D., Simoes-Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, R., Smith, A.J., Vanacova, S., Villalvazo, M., Haas, B.J., Pertea, M., Feldblyum, T.V., Utterback, T.R., Shu, C., Osoegawa, K., de Jong, P.J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S., Logsdon, J.M., Henze, K., Gupta, A., Wang, C.C., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tang, P., Chiu, C., Lee, Y., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., and Johnson, P.L. (2007) Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis Science 315 (5809), 207-212.
2.Fouts, D.E., Mongodin, E.F., Mandrell, R.E., Miller, W.G., Rasko, D.A., Ravel, J., Brinkac, L.M., DeBoy, R.T., Parker, C.T., Daugherty, S.C., Dodson, R.J., Durkin, A.S., Madupu, R., Sullivan, S.A., Shetty, J.U., Ayodeji, M.A., Shvartsbeyn, A., Schatz, M.C., Badger, J.H., Fraser, C.M., Nelson, K.E. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 3 (1):e15.
1.Gajer, P., Schatz, M., Salzberg, S.L. (2004) Automated correction of genome sequence errors. Nucleic Acids Res 32 (2):562-569.