2008
Roberts M, Zimin A, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke JA Improving Phrap-based assembly of the rat using reliable overlaps. PLoS ONE, 3:3 2008 PDF More details »
Navlakha Saket, Rastogi Rajeev, Shrivastava Nisheeth Graph Summarization with Bounded Error SIGMOD, 2008 More details »
BJ Haas, SL Salzberg, W Zhu, M Pertea, JE Allen, J Orvis, O White, CR Buell, JR Wortman Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology, 9:R7 2008 More details »
JR White, M Roberts, JA Yorke, M Pop Figaro: a novel statistical method for vector sequence removal. Bioinformatics, 24:462-7 2008 More details »
Myers D. S., Myers D. S., Bazinet A.L., Bazinet A.L., Cummings M.P., Cummings M.P. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational Biology, 71-85 2008 More details »
M Pop, SL Salzberg Bioinformatics challenges of new sequencing technology. Trends Genet, 24:142-9 2008 More details »
AM Phillippy, MC Schatz, M Pop Genome assembly forensics: finding the elusive mis-assembly. Genome Biol, 9:R55 2008 More details »
2007
The Drosophila 12 Genomes Consortium- led by Prof. Andrew Clark of Cornell University The Drosophila 12 Genomes Consortium publishes its analysis of 12 species of the fruit fly Drosophila in the journal Nature Nature, 405:203-218 2007 More details »
E Ghedin, S Wang, D Spiro, E Caler, Q Zhao, J Crabtree, JE Allen, AL Delcher, DB Guiliano, D Miranda-Saavedra, SV Angiuoli, T Creasy, P Amedeo, B Haas, NM El-Sayed, JR Wortman, T Feldblyum, L Tallon, M Schatz, M Shumway, H Koo, SL Salzberg, S Schobel, M Pertea, M Pop, O White, GJ Barton, CK Carlow, MJ Crawford, J Daub, MW Dimmic, CF Estes, JM Foster, M Ganatra, WF Gregory, NM Johnson, J Jin, R Komuniecki, I Korf, S Kumar, S Laney, BW Li, W Li, TH Lindblom, S Lustigman, D Ma, CV Maina, DM Martin, JP McCarter, L McReynolds, M Mitreva, TB Nutman, J Parkinson, JM Peregrín-Alvarez, C Poole, Q Ren, L Saunders, AE Sluder, K Smith, M Stanke, TR Unnasch, J Ware, AD Wei, G Weil, DJ Williams, Y Zhang, SA Williams, C Fraser-Liggett, B Slatko, ML Blaxter, AL Scott Draft genome of the filarial nematode parasite Brugia malayi. Science, 317:1756-60 2007 More details »
M Pertea, M Pertea, S.L. Salzberg, S.L. Salzberg Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding. Algorithms in Bioinformatics, 208-215 2007 More details »
C Kingsford, AL Delcher, SL Salzberg A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Mol Biol Evol, 24:2091-8 2007 More details »
SL Salzberg, C Kingsford, G Cattoli, DJ Spiro, DA Janies, MM Aly, IH Brown, E Couacy-Hymann, GM De Mia, do H Dung, A Guercio, T Joannis, AS Maken Ali, A Osmani, I Padalino, MD Saad, V Savić, NA Sengamalay, S Yingst, J Zaborsky, O Zorman-Rojs, E Ghedin, I Capua Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases, 13:713-8 2007 More details »
J Grand, MP Cummings, TG Rebelo, TH Ricketts, MC Neel Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters, 10:364-74 2007 More details »
A. L. Bazinet, D. S. Myers, J. Fuetsch, M.P. Cummings Grid Services Base Library: a high-level, procedural application program interface for writing Globus-based Grid services. Future Generation Computer Systems, 23:517-522 2007 More details »
S. Lee, T.D. Wang, N. Hashmi, Cummings. M.P. Bio-STEER: a Semantic Web workflow tool for Grid computing in the life sciences Future Generation Computer Systems, 23:497-509 2007 More details »
V Nene, JR Wortman, D Lawson, B Haas, C Kodira, ZJ Tu, B Loftus, Z Xi, K Megy, M Grabherr, Q Ren, EM Zdobnov, NF Lobo, KS Campbell, SE Brown, MF Bonaldo, J Zhu, SP Sinkins, DG Hogenkamp, P Amedeo, P Arensburger, PW Atkinson, S Bidwell, J Biedler, E Birney, RV Bruggner, J Costas, MR Coy, J Crabtree, M Crawford, B Debruyn, D Decaprio, K Eiglmeier, E Eisenstadt, H El-Dorry, WM Gelbart, SL Gomes, M Hammond, LI Hannick, JR Hogan, MH Holmes, D Jaffe, JS Johnston, RC Kennedy, H Koo, S Kravitz, EV Kriventseva, D Kulp, K Labutti, E Lee, S Li, DD Lovin, C Mao, E Mauceli, CF Menck, JR Miller, P Montgomery, A Mori, AL Nascimento, HF Naveira, C Nusbaum, S O'leary, J Orvis, M Pertea, H Quesneville, KR Reidenbach, YH Rogers, CW Roth, JR Schneider, M Schatz, M Shumway, M Stanke, EO Stinson, JM Tubio, JP Vanzee, S Verjovski-Almeida, D Werner, O White, S Wyder, Q Zeng, Q Zhao, Y Zhao, CA Hill, AS Raikhel, MB Soares, DL Knudson, NH Lee, J Galagan, SL Salzberg, IT Paulsen, G Dimopoulos, FH Collins, B Birren, CM Fraser-Liggett, DW Severson Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316:1718-23 2007 More details »
M Pertea, SM Mount, SL Salzberg A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics, 8:159 2007 More details »
AM Phillippy, JA Mason, K Ayanbule, DD Sommer, E Taviani, A Huq, RR Colwell, IT Knight, SL Salzberg Comprehensive DNA signature discovery and validation. PLoS Comput Biol, 3:e98 2007 More details »
MC Schatz, AM Phillippy, B Shneiderman, SL Salzberg Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biology, 8:R34 2007 More details »
CL Kingsford, K Ayanbule, SL Salzberg Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology, 8:R22 2007 More details »
SL Salzberg Genome re-annotation: a wiki solution? Genome Biology, 8:102 2007 More details »
DD Sommer, AL Delcher, SL Salzberg, M Pop Minimus: a fast, lightweight genome assembler. BMC Bioinformatics, 8:64 2007 More details »
JM Carlton, RP Hirt, JC Silva, AL Delcher, M Schatz, Q Zhao, JR Wortman, SL Bidwell, UC Alsmark, S Besteiro, T Sicheritz-Ponten, CJ Noel, JB Dacks, PG Foster, C Simillion, Y Van de Peer, D Miranda-Saavedra, GJ Barton, GD Westrop, S Müller, D Dessi, PL Fiori, Q Ren, I Paulsen, H Zhang, FD Bastida-Corcuera, A Simoes-Barbosa, MT Brown, RD Hayes, M Mukherjee, CY Okumura, R Schneider, AJ Smith, S Vanacova, M Villalvazo, BJ Haas, M Pertea, TV Feldblyum, TR Utterback, CL Shu, K Osoegawa, PJ de Jong, I Hrdy, L Horvathova, Z Zubacova, P Dolezal, SB Malik, JM Logsdon, K Henze, A Gupta, CC Wang, RL Dunne, JA Upcroft, P Upcroft, O White, SL Salzberg, P Tang, CH Chiu, YS Lee, TM Embley, GH Coombs, JC Mottram, J Tachezy, CM Fraser-Liggett, PJ Johnson Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315:207-12 2007 More details »
MC Schatz, C Trapnell, AL Delcher, A Varshney High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics, 8:474 2007 More details »
CA Desjardins, DE Gundersen-Rindal, JB Hostetler, LJ Tallon, RW Fuester, MC Schatz, MJ Pedroni, DW Fadrosh, BJ Haas, BS Toms, D Chen, V Nene Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiol, 7:61 2007 More details »
2006
JA Eisen, RS Coyne, M Wu, D Wu, M Thiagarajan, JR Wortman, JH Badger, Q Ren, P Amedeo, KM Jones, LJ Tallon, AL Delcher, SL Salzberg, JC Silva, BJ Haas, WH Majoros, M Farzad, JM Carlton, RK Smith, J Garg, RE Pearlman, KM Karrer, L Sun, G Manning, NC Elde, AP Turkewitz, DJ Asai, DE Wilkes, Y Wang, H Cai, K Collins, BA Stewart, SR Lee, K Wilamowska, Z Weinberg, WL Ruzzo, D Wloga, J Gaertig, J Frankel, CC Tsao, MA Gorovsky, PJ Keeling, RF Waller, NJ Patron, JM Cherry, NA Stover, CJ Krieger, C del Toro, HF Ryder, SC Williamson, RA Barbeau, EP Hamilton, E Orias Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol, 4:e286 2006 More details »
J Quackenbush, SL Salzberg It is time to end the patenting of software. Bioinformatics, 22:1416-7 2006 More details »
JE Allen, SL Salzberg A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms for Molecular Biology, 1:14 2006 More details »
JE Allen, WH Majoros, M Pertea, SL Salzberg JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biology, 7 Suppl 1:S9.1-13 2006 More details »
SR Gill, M Pop, RT Deboy, PB Eckburg, PJ Turnbaugh, BS Samuel, JI Gordon, DA Relman, CM Fraser-Liggett, KE Nelson Metagenomic analysis of the human distal gut microbiome. Science, 312:1355-9 2006 More details »
M. Pop, M. Pop DNA sequence assembly algorithms. Yearbook of Science and Technology, 2006 More details »
RL Malek, HY Wang, AE Kwitek, AS Greene, N Bhagabati, G Borchardt, L Cahill, T Currier, B Frank, X Fu, M Hasinoff, E Howe, N Letwin, TV Luu, A Saeed, H Sajadi, SL Salzberg, R Sultana, M Thiagarajan, J Tsai, K Veratti, J White, J Quackenbush, HJ Jacob, NH Lee Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet, 38:234-9 2006 More details »
AP Chan, G Pertea, F Cheung, D Lee, L Zheng, C Whitelaw, AC Pontaroli, P SanMiguel, Y Yuan, J Bennetzen, WB Barbazuk, J Quackenbush, PD Rabinowicz The TIGR Maize Database. Nucleic Acids Res, 34:D771-6 2006 More details »
F Bringaud, DC Bartholomeu, G Blandin, A Delcher, T Baltz, NM El-Sayed, E Ghedin The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion. Mol Biol Evol, 23:411-20 2006 More details »
2005
SL Salzberg, JA Yorke Beware of mis-assembled genomes. Bioinformatics, 21:4320-1 2005 More details »
S.L. Salzberg Nature journal club article about viruses as living organisms Nature, 438:133 2005 More details »
R Seshadri, L Adrian, DE Fouts, JA Eisen, AM Phillippy, BA Methe, NL Ward, WC Nelson, RT Deboy, HM Khouri, JF Kolonay, RJ Dodson, SC Daugherty, LM Brinkac, SA Sullivan, R Madupu, KE Nelson, KH Kang, M Impraim, K Tran, JM Robinson, HA Forberger, CM Fraser, SH Zinder, JF Heidelberg Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science, 307:105-8 2005 More details »
NM El-Sayed, PJ Myler, G Blandin, M Berriman, J Crabtree, G Aggarwal, E Caler, H Renauld, EA Worthey, C Hertz-Fowler, E Ghedin, C Peacock, DC Bartholomeu, BJ Haas, AN Tran, JR Wortman, UC Alsmark, S Angiuoli, A Anupama, J Badger, F Bringaud, E Cadag, JM Carlton, GC Cerqueira, T Creasy, AL Delcher, A Djikeng, TM Embley, C Hauser, AC Ivens, SK Kummerfeld, JB Pereira-Leal, D Nilsson, J Peterson, SL Salzberg, J Shallom, JC Silva, J Sundaram, S Westenberger, O White, SE Melville, JE Donelson, B Andersson, KD Stuart, N Hall Comparative genomics of trypanosomatid parasitic protozoa. Science, 309:404-9 2005 More details »
NM El-Sayed, PJ Myler, DC Bartholomeu, D Nilsson, G Aggarwal, AN Tran, E Ghedin, EA Worthey, AL Delcher, G Blandin, SJ Westenberger, E Caler, GC Cerqueira, C Branche, B Haas, A Anupama, E Arner, L Aslund, P Attipoe, E Bontempi, F Bringaud, P Burton, E Cadag, DA Campbell, M Carrington, J Crabtree, H Darban, JF da Silveira, P de Jong, K Edwards, PT Englund, G Fazelina, T Feldblyum, M Ferella, AC Frasch, K Gull, D Horn, L Hou, Y Huang, E Kindlund, M Klingbeil, S Kluge, H Koo, D Lacerda, MJ Levin, H Lorenzi, T Louie, CR Machado, R McCulloch, A McKenna, Y Mizuno, JC Mottram, S Nelson, S Ochaya, K Osoegawa, G Pai, M Parsons, M Pentony, U Pettersson, M Pop, JL Ramirez, J Rinta, L Robertson, SL Salzberg, DO Sanchez, A Seyler, R Sharma, J Shetty, AJ Simpson, E Sisk, MT Tammi, R Tarleton, S Teixeira, S Van Aken, C Vogt, PN Ward, B Wickstead, J Wortman, O White, CM Fraser, KD Stuart, B Andersson The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science, 309:409-15 2005 More details »
SL Salzberg, JC Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen, WC Nelson Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology, 6:R23 2005 More details »
WH Majoros, M Pertea, AL Delcher, SL Salzberg Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics, 6:16 2005 More details »
M. P. Cummings, M. P. Cummings, Huskamp J.C., Huskamp J.C. Grid computing EDUCAUSE Review, 116-117 2005 More details »
E Ghedin, NA Sengamalay, M Shumway, J Zaborsky, T Feldblyum, V Subbu, DJ Spiro, J Sitz, H Koo, P Bolotov, D Dernovoy, T Tatusova, Y Bao, K St George, J Taylor, DJ Lipman, CM Fraser, JK Taubenberger, SL Salzberg Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature, 437:1162-6 2005 More details »
MP Cummings, A Meyer Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena), 108:329-36 2005 More details »
EC Holmes, E Ghedin, N Miller, J Taylor, Y Bao, K St George, BT Grenfell, SL Salzberg, CM Fraser, DJ Lipman, JK Taubenberger Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol, 3:e300 2005 More details »
M Berriman, E Ghedin, C Hertz-Fowler, G Blandin, H Renauld, DC Bartholomeu, NJ Lennard, E Caler, NE Hamlin, B Haas, U Böhme, L Hannick, MA Aslett, J Shallom, L Marcello, L Hou, B Wickstead, UC Alsmark, C Arrowsmith, RJ Atkin, AJ Barron, F Bringaud, K Brooks, M Carrington, I Cherevach, TJ Chillingworth, C Churcher, LN Clark, CH Corton, A Cronin, RM Davies, J Doggett, A Djikeng, T Feldblyum, MC Field, A Fraser, I Goodhead, Z Hance, D Harper, BR Harris, H Hauser, J Hostetler, A Ivens, K Jagels, D Johnson, J Johnson, K Jones, AX Kerhornou, H Koo, N Larke, S Landfear, C Larkin, V Leech, A Line, A Lord, A Macleod, PJ Mooney, S Moule, DM Martin, GW Morgan, K Mungall, H Norbertczak, D Ormond, G Pai, CS Peacock, J Peterson, MA Quail, E Rabbinowitsch, MA Rajandream, C Reitter, SL Salzberg, M Sanders, S Schobel, S Sharp, M Simmonds, AJ Simpson, L Tallon, CM Turner, A Tait, AR Tivey, S Van Aken, D Walker, D Wanless, S Wang, B White, O White, S Whitehead, J Woodward, J Wortman, MD Adams, TM Embley, K Gull, E Ullu, JD Barry, AH Fairlamb, F Opperdoes, BG Barrell, JE Donelson, N Hall, CM Fraser, SE Melville, NM El-Sayed The genome of the African trypanosome Trypanosoma brucei. Science, 309:416-22 2005 More details »
MJ Gardner, R Bishop, T Shah, EP de Villiers, JM Carlton, N Hall, Q Ren, IT Paulsen, A Pain, M Berriman, RJ Wilson, S Sato, SA Ralph, DJ Mann, Z Xiong, SJ Shallom, J Weidman, L Jiang, J Lynn, B Weaver, A Shoaibi, AR Domingo, D Wasawo, J Crabtree, JR Wortman, B Haas, SV Angiuoli, TH Creasy, C Lu, B Suh, JC Silva, TR Utterback, TV Feldblyum, M Pertea, J Allen, WC Nierman, EL Taracha, SL Salzberg, OR White, HA Fitzhugh, S Morzaria, JC Venter, CM Fraser, V Nene Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science, 309:134-7 2005 More details »
B Loftus, I Anderson, R Davies, UC Alsmark, J Samuelson, P Amedeo, P Roncaglia, M Berriman, RP Hirt, BJ Mann, T Nozaki, B Suh, M Pop, M Duchene, J Ackers, E Tannich, M Leippe, M Hofer, I Bruchhaus, U Willhoeft, A Bhattacharya, T Chillingworth, C Churcher, Z Hance, B Harris, D Harris, K Jagels, S Moule, K Mungall, D Ormond, R Squares, S Whitehead, MA Quail, E Rabbinowitsch, H Norbertczak, C Price, Z Wang, N Guillén, C Gilchrist, SE Stroup, S Bhattacharya, A Lohia, PG Foster, T Sicheritz-Ponten, C Weber, U Singh, C Mukherjee, NM El-Sayed, WA Petri, CG Clark, TM Embley, B Barrell, CM Fraser, N Hall The genome of the protist parasite Entamoeba histolytica. Nature, 433:865-8 2005 More details »
WH Majoros, M Pertea, SL Salzberg Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics, 21:1782-8 2005 More details »
BJ Loftus, E Fung, P Roncaglia, D Rowley, P Amedeo, D Bruno, J Vamathevan, M Miranda, IJ Anderson, JA Fraser, JE Allen, IE Bosdet, MR Brent, R Chiu, TL Doering, MJ Donlin, CA D'Souza, DS Fox, V Grinberg, J Fu, M Fukushima, BJ Haas, JC Huang, G Janbon, SJ Jones, HL Koo, MI Krzywinski, JK Kwon-Chung, KB Lengeler, R Maiti, MA Marra, RE Marra, CA Mathewson, TG Mitchell, M Pertea, FR Riggs, SL Salzberg, JE Schein, A Shvartsbeyn, H Shin, M Shumway, CA Specht, BB Suh, A Tenney, TR Utterback, BL Wickes, JR Wortman, NH Wye, JW Kronstad, JK Lodge, J Heitman, RW Davis, CM Fraser, RW Hyman The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science, 307:1321-4 2005 More details »
DE Fouts, EF Mongodin, RE Mandrell, WG Miller, DA Rasko, J Ravel, LM Brinkac, RT Deboy, CT Parker, SC Daugherty, RJ Dodson, AS Durkin, R Madupu, SA Sullivan, JU Shetty, MA Ayodeji, A Shvartsbeyn, MC Schatz, JH Badger, CM Fraser, KE Nelson Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol, 3:e15 2005 More details »
2004
WH Majoros, SL Salzberg An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics, 5:206 2004 More details »
B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, S. Istrail A Survey of Computational Methods for Determining Haplotypes. Computational Methods for SNPs and Haplotype Inference DIMACS/RECOMB Satellite Workshop, LNCS, 2983:26-47 2004 More details »
N. Hashmi, S. Lee, M.P. Cummings Abstracting workflows: unifying bioinformatics task conceptualization and specification through semantic web services. W3C Workshop on Semantic Web for Life Sciences, Cambridge, Massachusetts USA, 2004 More details »
N Ward, Ø Larsen, J Sakwa, L Bruseth, H Khouri, AS Durkin, G Dimitrov, L Jiang, D Scanlan, KH Kang, M Lewis, KE Nelson, B Methé, M Wu, JF Heidelberg, IT Paulsen, D Fouts, J Ravel, H Tettelin, Q Ren, T Read, RT Deboy, R Seshadri, SL Salzberg, HB Jensen, NK Birkeland, WC Nelson, RJ Dodson, SH Grindhaug, I Holt, I Eidhammer, I Jonasen, S Vanaken, T Utterback, TV Feldblyum, CM Fraser, JR Lillehaug, JA Eisen Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol, 2:e303 2004 More details »
MP Cummings, MR Segal Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. BMC Bioinformatics, 5:137 2004 More details »
N Edwards, R. Lippert Sequence database compression for peptide identification from tandem mass spectra. 4th Workshop on Algorithms in Bioinformatics (WABI 2004), 2004 More details »
MP Cummings, DS Myers Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics, 5:132 2004 More details »
SL Salzberg, D Church, M DiCuccio, E Yaschenko, J Ostell The genome Assembly Archive: a new public resource. PLoS Biol, 2:E285 2004 More details »
M Pop, A Phillippy, AL Delcher, SL Salzberg Comparative genome assembly. Brief Bioinform, 5:237-48 2004 More details »
BP Berman, BD Pfeiffer, TR Laverty, SL Salzberg, GM Rubin, MB Eisen, SE Celniker Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology, 5:R61 2004 More details »
M Roberts, BR Hunt, JA Yorke, RA Bolanos, AL Delcher A preprocessor for shotgun assembly of large genomes. J Comput Biology, 11:734-52 2004 More details »
M Roberts, W Hayes, BR Hunt, SM Mount, JA Yorke Reducing storage requirements for biological sequence comparison. Bioinformatics, 20:3363-9 2004 More details »
BJ Haas, AL Delcher, JR Wortman, SL Salzberg DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics, 20:3643-6 2004 More details »
MC Neel, MP Cummings Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions. BMC Evolutionary Biology, 4:15 2004 More details »
WH Majoros, M Pertea, SL Salzberg TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics, 20:2878-9 2004 More details »
E Ghedin, F Bringaud, J Peterson, P Myler, M Berriman, A Ivens, B Andersson, E Bontempi, J Eisen, S Angiuoli, D Wanless, A Von Arx, L Murphy, N Lennard, S Salzberg, MD Adams, O White, N Hall, K Stuart, CM Fraser, NM El-Sayed Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol, 134:183-91 2004 More details »
A Pain, J Woodward, MA Quail, MJ Anderson, R Clark, M Collins, N Fosker, A Fraser, D Harris, N Larke, L Murphy, S Humphray, S O'Neil, M Pertea, C Price, E Rabbinowitsch, MA Rajandream, S Salzberg, D Saunders, K Seeger, S Sharp, T Warren, DW Denning, B Barrell, N Hall Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genet Biol, 41:443-53 2004 More details »
M Pop, D Kosack Using the TIGR assembler in shotgun sequencing projects. Methods Mol Biol, 255:279-94 2004 More details »
DB Mark Welch, MP Cummings, DM Hillis, M Meselson Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc Natl Acad Sci U S A, 101:1622-5 2004 More details »
S Istrail, GG Sutton, L Florea, AL Halpern, CM Mobarry, R Lippert, B Walenz, H Shatkay, I Dew, JR Miller, MJ Flanigan, NJ Edwards, R Bolanos, D Fasulo, BV Halldorsson, S Hannenhalli, R Turner, S Yooseph, F Lu, DR Nusskern, BC Shue, XH Zheng, F Zhong, AL Delcher, DH Huson, SA Kravitz, L Mouchard, K Reinert, KA Remington, AG Clark, MS Waterman, EE Eichler, MD Adams, MW Hunkapiller, EW Myers, JC Venter Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A, 101:1916-21 2004 More details »
S Kurtz, A Phillippy, AL Delcher, M Smoot, M Shumway, C Antonescu, SL Salzberg Versatile and open software for comparing large genomes. Genome Biology, 5:R12 2004 More details »
P Gajer, M Schatz, SL Salzberg Automated correction of genome sequence errors. Nucleic Acids Res, 32:562-9 2004 More details »
JE Allen, M Pertea, SL Salzberg Computational gene prediction using multiple sources of evidence. Genome Res, 14:142-8 2004 More details »
M Pop, DS Kosack, SL Salzberg Hierarchical scaffolding with Bambus. Genome Res, 14:149-59 2004 More details »
M. Pop Shotgun Sequence Assembly Advances in Computers. Elsevier, Academic Press, 193-248 2004 More details »
S.L. Salzberg, A.L. Delcher Tools for gene finding and whole genome comparison. Microbial Genomes. Humana Press, 19-32 2004 More details »
M. P. Cummings Sixteen entries on molecular evolution software packages: BAMBE pgs. 39-40, DnaSP pgs. 123-124, ENCprime/SeqCount pg. 146, LAMARC pgs. 288-289, MacClade pg. 305, MEGA pg. 318, Modeltest pg. 337, MrBayes pg. 352, PAML pg. 388, PAUP* pg. 392, PHYLIP pgs. 39 In Hancock, J. M. and M. J. Zvelebil (Eds.) Dictionary of Bioinformatics. John Wiley & Sons, New York, 2004 More details »
M. P. Cummings A book like its cover - The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny Cummings M. P. , D. S. Myers, and M. Mangelson. 2004. Applying Permutation Tests to Tree-Based Statistical Models: Extending the R Package rpart. Tehnical Report CS-TR-4581, UMIACS-TR-2004-24, Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland., 2004 More details »
2003
BJ Haas, AL Delcher, SM Mount, JR Wortman, RK Smith, LI Hannick, R Maiti, CM Ronning, DB Rusch, CD Town, SL Salzberg, O White Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res, 31:5654-66 2003 More details »
EF Kirkness, V Bafna, AL Halpern, S Levy, K Remington, DB Rusch, AL Delcher, M Pop, W Wang, CM Fraser, JC Venter The dog genome: survey sequencing and comparative analysis. Science, 301:1898-903 2003 More details »
NM El-Sayed, E Ghedin, J Song, A Macleod, F Bringaud, C Larkin, D Wanless, J Peterson, L Hou, S Taylor, A Tweedie, N Biteau, HG Khalak, X Lin, T Mason, L Hannick, E Caler, G Blandin, D Bartholomeu, AJ Simpson, S Kaul, H Zhao, G Pai, S Van Aken, T Utterback, B Haas, HL Koo, L Umayam, B Suh, C Gerrard, V Leech, R Qi, S Zhou, D Schwartz, T Feldblyum, S Salzberg, A Tait, CM Turner, E Ullu, O White, S Melville, MD Adams, CM Fraser, JE Donelson The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res, 31:4856-63 2003 More details »
WH Majoros, M Pertea, C Antonescu, SL Salzberg GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res, 31:3601-4 2003 More details »
N Volfovsky, BJ Haas, SL Salzberg Computational discovery of internal micro-exons. Genome Res, 13:1216-21 2003 More details »
SL Salzberg Genomics: Yeast rises again. Nature, 423:233-4 2003 More details »
TD Read, SN Peterson, N Tourasse, LW Baillie, IT Paulsen, KE Nelson, H Tettelin, DE Fouts, JA Eisen, SR Gill, EK Holtzapple, OA Okstad, E Helgason, J Rilstone, M Wu, JF Kolonay, MJ Beanan, RJ Dodson, LM Brinkac, M Gwinn, RT Deboy, R Madpu, SC Daugherty, AS Durkin, DH Haft, WC Nelson, JD Peterson, M Pop, HM Khouri, D Radune, JL Benton, Y Mahamoud, L Jiang, IR Hance, JF Weidman, KJ Berry, RD Plaut, AM Wolf, KL Watkins, WC Nierman, A Hazen, R Cline, C Redmond, JE Thwaite, O White, SL Salzberg, B Thomason, AM Friedlander, TM Koehler, PC Hanna, AB Kolstø, CM Fraser The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature, 423:81-6 2003 More details »
MD Ermolaeva, M Wu, JA Eisen, SL Salzberg The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol, 51:859-66 2003 More details »
S Salzberg, E Birney, S Eddy, O White Unrestricted free access works and must continue. Nature, 422:801 2003 More details »
TD Read, GS Myers, RC Brunham, WC Nelson, IT Paulsen, J Heidelberg, E Holtzapple, H Khouri, NB Federova, HA Carty, LA Umayam, DH Haft, J Peterson, MJ Beanan, O White, SL Salzberg, RC Hsia, G McClarty, RG Rank, PM Bavoil, CM Fraser Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res, 31:2134-47 2003 More details »
B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, S Istrail Combinatorial problems arising in SNP and haplotype analysis Fourth International Conference on Discrete Mathematics and Theoretical Computer Science (DMTCS 2003), LNCS, 2731:26-47 2003 More details »
V. Bafna, N. Edwards On de novo interpretation of tandem mass spectra for peptide identification. Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003), 2003 More details »
MP Cummings, SA Handley, DS Myers, DL Reed, A Rokas, K Winka Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol, 52:477-87 2003 More details »
M. C. Neel, M. P. Cummings Genetic consequences of ecological reserve design guidelines: an empirical investigation Conservation Genetics, 4:427-439 2003 More details »
D. S. Myers, M. P. Cummings Necessity is the mother of invention: a simple Grid computing system using commodity tools Journal of Parallel and Distributed Computing, 63:578-589 2003 More details »
MP Cummings, JM Nugent, RG Olmstead, JD Palmer Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Current Genetics, 43:131-8 2003 More details »
M. C. Neel, M. P. Cummings Effectiveness of conservation targets in capturing genetic diversity. Conservation Biology, 17:219-229 2003 More details »
2002 and earlier
CM Fraser, JA Eisen, KE Nelson, IT Paulsen, SL Salzberg The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol, 184:6403-5; discusion 6405 2002 More details »
KE Nelson, C Weinel, IT Paulsen, RJ Dodson, H Hilbert, VA Martins dos Santos, DE Fouts, SR Gill, M Pop, M Holmes, L Brinkac, M Beanan, RT Deboy, S Daugherty, J Kolonay, R Madupu, W Nelson, O White, J Peterson, H Khouri, I Hance, P Chris Lee, E Holtzapple, D Scanlan, K Tran, A Moazzez, T Utterback, M Rizzo, K Lee, D Kosack, D Moestl, H Wedler, J Lauber, D Stjepandic, J Hoheisel, M Straetz, S Heim, C Kiewitz, JA Eisen, KN Timmis, A Düsterhöft, B Tümmler, CM Fraser Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol, 4:799-808 2002 More details »
RA Holt, GM Subramanian, A Halpern, GG Sutton, R Charlab, DR Nusskern, P Wincker, AG Clark, JM Ribeiro, R Wides, SL Salzberg, B Loftus, M Yandell, WH Majoros, DB Rusch, Z Lai, CL Kraft, JF Abril, V Anthouard, P Arensburger, PW Atkinson, H Baden, V de Berardinis, D Baldwin, V Benes, J Biedler, C Blass, R Bolanos, D Boscus, M Barnstead, S Cai, A Center, K Chaturverdi, GK Christophides, MA Chrystal, M Clamp, A Cravchik, V Curwen, A Dana, A Delcher, I Dew, CA Evans, M Flanigan, A Grundschober-Freimoser, L Friedli, Z Gu, P Guan, R Guigo, ME Hillenmeyer, SL Hladun, JR Hogan, YS Hong, J Hoover, O Jaillon, Z Ke, C Kodira, E Kokoza, A Koutsos, I Letunic, A Levitsky, Y Liang, JJ Lin, NF Lobo, JR Lopez, JA Malek, TC McIntosh, S Meister, J Miller, C Mobarry, E Mongin, SD Murphy, DA O'Brochta, C Pfannkoch, R Qi, MA Regier, K Remington, H Shao, MV Sharakhova, CD Sitter, J Shetty, TJ Smith, R Strong, J Sun, D Thomasova, LQ Ton, P Topalis, Z Tu, MF Unger, B Walenz, A Wang, J Wang, M Wang, X Wang, KJ Woodford, JR Wortman, M Wu, A Yao, EM Zdobnov, H Zhang, Q Zhao, S Zhao, SC Zhu, I Zhimulev, M Coluzzi, A della Torre, CW Roth, C Louis, F Kalush, RJ Mural, EW Myers, MD Adams, HO Smith, S Broder, MJ Gardner, CM Fraser, E Birney, P Bork, PT Brey, JC Venter, J Weissenbach, FC Kafatos, FH Collins, SL Hoffman The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298:129-49 2002 More details »
EM Zdobnov, C von Mering, I Letunic, D Torrents, M Suyama, RR Copley, GK Christophides, D Thomasova, RA Holt, GM Subramanian, HM Mueller, G Dimopoulos, JH Law, MA Wells, E Birney, R Charlab, AL Halpern, E Kokoza, CL Kraft, Z Lai, S Lewis, C Louis, C Barillas-Mury, D Nusskern, GM Rubin, SL Salzberg, GG Sutton, P Topalis, R Wides, P Wincker, M Yandell, FH Collins, J Ribeiro, WM Gelbart, FC Kafatos, P Bork Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science, 298:149-59 2002 More details »
JM Carlton, SV Angiuoli, BB Suh, TW Kooij, M Pertea, JC Silva, MD Ermolaeva, JE Allen, JD Selengut, HL Koo, JD Peterson, M Pop, DS Kosack, MF Shumway, SL Bidwell, SJ Shallom, SE van Aken, SB Riedmuller, TV Feldblyum, JK Cho, J Quackenbush, M Sedegah, A Shoaibi, LM Cummings, L Florens, JR Yates, JD Raine, RE Sinden, MA Harris, DA Cunningham, PR Preiser, LW Bergman, AB Vaidya, LH van Lin, CJ Janse, AP Waters, HO Smith, OR White, SL Salzberg, JC Venter, CM Fraser, SL Hoffman, MJ Gardner, DJ Carucci Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature, 419:512-9 2002 More details »
MJ Gardner, N Hall, E Fung, O White, M Berriman, RW Hyman, JM Carlton, A Pain, KE Nelson, S Bowman, IT Paulsen, K James, JA Eisen, K Rutherford, SL Salzberg, A Craig, S Kyes, MS Chan, V Nene, SJ Shallom, B Suh, J Peterson, S Angiuoli, M Pertea, J Allen, J Selengut, D Haft, MW Mather, AB Vaidya, DM Martin, AH Fairlamb, MJ Fraunholz, DS Roos, SA Ralph, GI McFadden, LM Cummings, GM Subramanian, C Mungall, JC Venter, DJ Carucci, SL Hoffman, C Newbold, RW Davis, CM Fraser, B Barrell Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419:498-511 2002 More details »
MJ Gardner, SJ Shallom, JM Carlton, SL Salzberg, V Nene, A Shoaibi, A Ciecko, J Lynn, M Rizzo, B Weaver, B Jarrahi, M Brenner, B Parvizi, L Tallon, A Moazzez, D Granger, C Fujii, C Hansen, J Pederson, T Feldblyum, J Peterson, B Suh, S Angiuoli, M Pertea, J Allen, J Selengut, O White, LM Cummings, HO Smith, MD Adams, JC Venter, DJ Carucci, SL Hoffman, CM Fraser Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature, 419:531-4 2002 More details »
IT Paulsen, R Seshadri, KE Nelson, JA Eisen, JF Heidelberg, TD Read, RJ Dodson, L Umayam, LM Brinkac, MJ Beanan, SC Daugherty, RT Deboy, AS Durkin, JF Kolonay, R Madupu, WC Nelson, B Ayodeji, M Kraul, J Shetty, J Malek, SE van Aken, S Riedmuller, H Tettelin, SR Gill, O White, SL Salzberg, DL Hoover, LE Lindler, SM Halling, SM Boyle, CM Fraser The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A, 99:13148-53 2002 More details »
RD Fleischmann, D Alland, JA Eisen, L Carpenter, O White, J Peterson, R DeBoy, R Dodson, M Gwinn, D Haft, E Hickey, JF Kolonay, WC Nelson, LA Umayam, M Ermolaeva, SL Salzberg, A Delcher, T Utterback, J Weidman, H Khouri, J Gill, A Mikula, W Bishai, WR Jacobs Jr, JC Venter, CM Fraser Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol, 184:5479-90 2002 More details »
N.J. Edwards, R.A. Lippert Generating peptide candidates from amino-acid sequence databases for protein identification via mass spectrometry 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), 2002 More details »
AL Delcher, A Phillippy, J Carlton, SL Salzberg Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res, 30:2478-83 2002 More details »
RJ Mural, MD Adams, EW Myers, HO Smith, GL Miklos, R Wides, A Halpern, PW Li, GG Sutton, J Nadeau, SL Salzberg, RA Holt, CD Kodira, F Lu, L Chen, Z Deng, CC Evangelista, W Gan, TJ Heiman, J Li, Z Li, GV Merkulov, NV Milshina, AK Naik, R Qi, BC Shue, A Wang, J Wang, X Wang, X Yan, J Ye, S Yooseph, Q Zhao, L Zheng, SC Zhu, K Biddick, R Bolanos, AL Delcher, IM Dew, D Fasulo, MJ Flanigan, DH Huson, SA Kravitz, JR Miller, CM Mobarry, K Reinert, KA Remington, Q Zhang, XH Zheng, DR Nusskern, Z Lai, Y Lei, W Zhong, A Yao, P Guan, RR Ji, Z Gu, ZY Wang, F Zhong, C Xiao, CC Chiang, M Yandell, JR Wortman, PG Amanatides, SL Hladun, EC Pratts, JE Johnson, KL Dodson, KJ Woodford, CA Evans, B Gropman, DB Rusch, E Venter, M Wang, TJ Smith, JT Houck, DE Tompkins, C Haynes, D Jacob, SH Chin, DR Allen, CE Dahlke, R Sanders, K Li, X Liu, AA Levitsky, WH Majoros, Q Chen, AC Xia, JR Lopez, MT Donnelly, MH Newman, A Glodek, CL Kraft, M Nodell, F Ali, HJ An, D Baldwin-Pitts, KY Beeson, S Cai, M Carnes, A Carver, PM Caulk, A Center, YH Chen, ML Cheng, MD Coyne, M Crowder, S Danaher, LB Davenport, R Desilets, SM Dietz, L Doup, P Dullaghan, S Ferriera, CR Fosler, HC Gire, A Gluecksmann, JD Gocayne, J Gray, B Hart, J Haynes, J Hoover, T Howland, C Ibegwam, M Jalali, D Johns, L Kline, DS Ma, S MacCawley, A Magoon, F Mann, D May, TC McIntosh, S Mehta, L Moy, MC Moy, BJ Murphy, SD Murphy, KA Nelson, Z Nuri, KA Parker, AC Prudhomme, VN Puri, H Qureshi, JC Raley, MS Reardon, MA Regier, YH Rogers, DL Romblad, J Schutz, JL Scott, R Scott, CD Sitter, M Smallwood, AC Sprague, E Stewart, RV Strong, E Suh, K Sylvester, R Thomas, NN Tint, C Tsonis, G Wang, G Wang, MS Williams, SM Williams, SM Windsor, K Wolfe, MM Wu, J Zaveri, K Chaturvedi, AE Gabrielian, Z Ke, J Sun, G Subramanian, JC Venter, CM Pfannkoch, M Barnstead, LD Stephenson A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science, 296:1661-71 2002 More details »
BJ Haas, N Volfovsky, CD Town, M Troukhan, N Alexandrov, KA Feldmann, RB Flavell, O White, SL Salzberg Full-length messenger RNA sequences greatly improve genome annotation. Genome Biology, 3:RESEARCH0029 2002 More details »
TD Read, SL Salzberg, M Pop, M Shumway, L Umayam, L Jiang, E Holtzapple, JD Busch, KL Smith, JM Schupp, D Solomon, P Keim, CM Fraser Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science, 296:2028-33 2002 More details »
M Pertea, SL Salzberg Computational gene finding in plants. Plant Mol Biol, 48:39-48 2002 More details »
M García-Varela, MP Cummings, G Pérez-Ponce de León, SL Gardner, JP Laclette Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class polyacanthocephala (acanthocephala). Mol Phylogenet Evol, 23:288-92 2002 More details »
M. Pertea, S.L. Salzberg A method to improve the performance of translation start site detection and its application for gene finding Algorithms in Bioinformatics, Proceedings, 2452:210-219 2002 More details »
M. Pop, S.L. Salzberg, M. Shumway Genome sequence assembly: Algorithms and issues Computer, 35:47-54 2002 More details »
BE Suzek, MD Ermolaeva, M Schreiber, SL Salzberg A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics, 17:1123-30 2001 More details »
SP Kennedy, WV Ng, SL Salzberg, L Hood, S DasSarma Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res, 11:1641-50 2001 More details »
SL Salzberg, JA Eisen Lateral gene transfer or viral colonization? Science, 293:1048 2001 More details »
N Volfovsky, BJ Haas, SL Salzberg A clustering method for repeat analysis in DNA sequences. Genome Biology, 2:RESEARCH0027 2001 More details »
H Tettelin, KE Nelson, IT Paulsen, JA Eisen, TD Read, S Peterson, J Heidelberg, RT Deboy, DH Haft, RJ Dodson, AS Durkin, M Gwinn, JF Kolonay, WC Nelson, JD Peterson, LA Umayam, O White, SL Salzberg, MR Lewis, D Radune, E Holtzapple, H Khouri, AM Wolf, TR Utterback, CL Hansen, LA McDonald, TV Feldblyum, S Angiuoli, T Dickinson, EK Hickey, IE Holt, BJ Loftus, F Yang, HO Smith, JC Venter, BA Dougherty, DA Morrison, SK Hollingshead, CM Fraser Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science, 293:498-506 2001 More details »
SL Salzberg, O White, J Peterson, JA Eisen Microbial genes in the human genome: lateral transfer or gene loss? Science, 292:1903-6 2001 More details »
V Bafna, N Edwards SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics, 17 Suppl 1:S13-21 2001 More details »
M Bevan, K Mayer, O White, JA Eisen, D Preuss, T Bureau, SL Salzberg, HW Mewes Sequence and analysis of the Arabidopsis genome. Curr Opin Plant Biol, 4:105-10 2001 More details »
WC Nierman, TV Feldblyum, MT Laub, IT Paulsen, KE Nelson, JA Eisen, JF Heidelberg, MR Alley, N Ohta, JR Maddock, I Potocka, WC Nelson, A Newton, C Stephens, ND Phadke, B Ely, RT Deboy, RJ Dodson, AS Durkin, ML Gwinn, DH Haft, JF Kolonay, J Smit, MB Craven, H Khouri, J Shetty, K Berry, T Utterback, K Tran, A Wolf, J Vamathevan, M Ermolaeva, O White, SL Salzberg, JC Venter, L Shapiro, CM Fraser, J Eisen Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A, 98:4136-41 2001 More details »
MD Ermolaeva, O White, SL Salzberg Prediction of operons in microbial genomes. Nucleic Acids Res, 29:1216-21 2001 More details »
M Pertea, X Lin, SL Salzberg GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res, 29:1185-90 2001 More details »
Q Yuan, J Quackenbush, R Sultana, M Pertea, SL Salzberg, CR Buell Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol, 125:1166-74 2001 More details »
JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, GG Sutton, HO Smith, M Yandell, CA Evans, RA Holt, JD Gocayne, P Amanatides, RM Ballew, DH Huson, JR Wortman, Q Zhang, CD Kodira, XH Zheng, L Chen, M Skupski, G Subramanian, PD Thomas, J Zhang, GL Gabor Miklos, C Nelson, S Broder, AG Clark, J Nadeau, VA McKusick, N Zinder, AJ Levine, RJ Roberts, M Simon, C Slayman, M Hunkapiller, R Bolanos, A Delcher, I Dew, D Fasulo, M Flanigan, L Florea, A Halpern, S Hannenhalli, S Kravitz, S Levy, C Mobarry, K Reinert, K Remington, J Abu-Threideh, E Beasley, K Biddick, V Bonazzi, R Brandon, M Cargill, I Chandramouliswaran, R Charlab, K Chaturvedi, Z Deng, V Di Francesco, P Dunn, K Eilbeck, C Evangelista, AE Gabrielian, W Gan, W Ge, F Gong, Z Gu, P Guan, TJ Heiman, ME Higgins, RR Ji, Z Ke, KA Ketchum, Z Lai, Y Lei, Z Li, J Li, Y Liang, X Lin, F Lu, GV Merkulov, N Milshina, HM Moore, AK Naik, VA Narayan, B Neelam, D Nusskern, DB Rusch, S Salzberg, W Shao, B Shue, J Sun, Z Wang, A Wang, X Wang, J Wang, M Wei, R Wides, C Xiao, C Yan, A Yao, J Ye, M Zhan, W Zhang, H Zhang, Q Zhao, L Zheng, F Zhong, W Zhong, S Zhu, S Zhao, D Gilbert, S Baumhueter, G Spier, C Carter, A Cravchik, T Woodage, F Ali, H An, A Awe, D Baldwin, H Baden, M Barnstead, I Barrow, K Beeson, D Busam, A Carver, A Center, ML Cheng, L Curry, S Danaher, L Davenport, R Desilets, S Dietz, K Dodson, L Doup, S Ferriera, N Garg, A Gluecksmann, B Hart, J Haynes, C Haynes, C Heiner, S Hladun, D Hostin, J Houck, T Howland, C Ibegwam, J Johnson, F Kalush, L Kline, S Koduru, A Love, F Mann, D May, S McCawley, T McIntosh, I McMullen, M Moy, L Moy, B Murphy, K Nelson, C Pfannkoch, E Pratts, V Puri, H Qureshi, M Reardon, R Rodriguez, YH Rogers, D Romblad, B Ruhfel, R Scott, C Sitter, M Smallwood, E Stewart, R Strong, E Suh, R Thomas, NN Tint, S Tse, C Vech, G Wang, J Wetter, S Williams, M Williams, S Windsor, E Winn-Deen, K Wolfe, J Zaveri, K Zaveri, JF Abril, R Guigo, MJ Campbell, KV Sjolander, B Karlak, A Kejariwal, H Mi, B Lazareva, T Hatton, A Narechania, K Diemer, A Muruganujan, N Guo, S Sato, V Bafna, S Istrail, R Lippert, R Schwartz, B Walenz, S Yooseph, D Allen, A Basu, J Baxendale, L Blick, M Caminha, J Carnes-Stine, P Caulk, YH Chiang, M Coyne, C Dahlke, A Mays, M Dombroski, M Donnelly, D Ely, S Esparham, C Fosler, H Gire, S Glanowski, K Glasser, A Glodek, M Gorokhov, K Graham, B Gropman, M Harris, J Heil, S Henderson, J Hoover, D Jennings, C Jordan, J Jordan, J Kasha, L Kagan, C Kraft, A Levitsky, M Lewis, X Liu, J Lopez, D Ma, W Majoros, J McDaniel, S Murphy, M Newman, T Nguyen, N Nguyen, M Nodell, S Pan, J Peck, M Peterson, W Rowe, R Sanders, J Scott, M Simpson, T Smith, A Sprague, T Stockwell, R Turner, E Venter, M Wang, M Wen, D Wu, M Wu, A Xia, A Zandieh, X Zhu The sequence of the human genome. Science, 291:1304-51 2001 More details »
MR Segal, MP Cummings, AE Hubbard Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics, 57:632-42 2001 More details »
M Salanoubat, K Lemcke, M Rieger, W Ansorge, M Unseld, B Fartmann, G Valle, H Blöcker, M Perez-Alonso, B Obermaier, M Delseny, M Boutry, LA Grivell, R Mache, P Puigdomènech, V De Simone, N Choisne, F Artiguenave, C Robert, P Brottier, P Wincker, L Cattolico, J Weissenbach, W Saurin, F Quétier, M Schäfer, S Müller-Auer, C Gabel, M Fuchs, V Benes, E Wurmbach, H Drzonek, H Erfle, N Jordan, S Bangert, R Wiedelmann, H Kranz, H Voss, R Holland, P Brandt, G Nyakatura, A Vezzi, M D'Angelo, A Pallavicini, S Toppo, B Simionati, A Conrad, K Hornischer, G Kauer, TH Löhnert, G Nordsiek, J Reichelt, M Scharfe, O Schön, M Bargues, J Terol, J Climent, P Navarro, C Collado, A Perez-Perez, B Ottenwälder, D Duchemin, R Cooke, M Laudie, C Berger-Llauro, B Purnelle, D Masuy, M de Haan, AC Maarse, JP Alcaraz, A Cottet, E Casacuberta, A Monfort, A Argiriou, M flores, R Liguori, D Vitale, G Mannhaupt, D Haase, H Schoof, S Rudd, P Zaccaria, HW Mewes, KF Mayer, S Kaul, CD Town, HL Koo, LJ Tallon, J Jenkins, T Rooney, M Rizzo, A Walts, T Utterback, CY Fujii, TP Shea, TH Creasy, B Haas, R Maiti, D Wu, J Peterson, S Van Aken, G Pai, J Militscher, P Sellers, JE Gill, TV Feldblyum, D Preuss, X Lin, WC Nierman, SL Salzberg, O White, JC Venter, CM Fraser, T Kaneko, Y Nakamura, S Sato, T Kato, E Asamizu, S Sasamoto, T Kimura, K Idesawa, K Kawashima, Y Kishida, C Kiyokawa, M Kohara, M Matsumoto, A Matsuno, A Muraki, S Nakayama, N Nakazaki, S Shinpo, C Takeuchi, T Wada, A Watanabe, M Yamada, M Yasuda, S Tabata Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature, 408:820-2 2000 More details »
A Theologis, JR Ecker, CJ Palm, NA Federspiel, S Kaul, O White, J Alonso, H Altafi, R Araujo, CL Bowman, SY Brooks, E Buehler, A Chan, Q Chao, H Chen, RF Cheuk, CW Chin, MK Chung, L Conn, AB Conway, AR Conway, TH Creasy, K Dewar, P Dunn, P Etgu, TV Feldblyum, J Feng, B Fong, CY Fujii, JE Gill, AD Goldsmith, B Haas, NF Hansen, B Hughes, L Huizar, JL Hunter, J Jenkins, C Johnson-Hopson, S Khan, E Khaykin, CJ Kim, HL Koo, I Kremenetskaia, DB Kurtz, A Kwan, B Lam, S Langin-Hooper, A Lee, JM Lee, CA Lenz, JH Li, Y Li, X Lin, SX Liu, ZA Liu, JS Luros, R Maiti, A Marziali, J Militscher, M Miranda, M Nguyen, WC Nierman, BI Osborne, G Pai, J Peterson, PK Pham, M Rizzo, T Rooney, D Rowley, H Sakano, SL Salzberg, JR Schwartz, P Shinn, AM Southwick, H Sun, LJ Tallon, G Tambunga, MJ Toriumi, CD Town, T Utterback, S Van Aken, M Vaysberg, VS Vysotskaia, M Walker, D Wu, G Yu, CM Fraser, JC Venter, RW Davis Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature, 408:816-20 2000 More details »
JA Eisen, JF Heidelberg, O White, SL Salzberg Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology, 1:RESEARCH0011 2000 More details »
F Liang, I Holt, G Pertea, S Karamycheva, SL Salzberg, J Quackenbush An optimized protocol for analysis of EST sequences. Nucleic Acids Res, 28:3657-65 2000 More details »
H. Forster, M.P. Cummings, M. D. Coffey Phylogenetic relationships of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycological Research, 104:1055-1061 2000 More details »
DD Pollock, JA Eisen, NA Doggett, MP Cummings A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol, 17:1776-88 2000 More details »
CM Fraser, JA Eisen, SL Salzberg Microbial genome sequencing. Nature, 406:799-803 2000 More details »
MD Ermolaeva, HG Khalak, O White, HO Smith, SL Salzberg Prediction of transcription terminators in bacterial genomes. J Mol Biol, 301:27-33 2000 More details »
JF Heidelberg, JA Eisen, WC Nelson, RA Clayton, ML Gwinn, RJ Dodson, DH Haft, EK Hickey, JD Peterson, L Umayam, SR Gill, KE Nelson, TD Read, H Tettelin, D Richardson, MD Ermolaeva, J Vamathevan, S Bass, H Qin, I Dragoi, P Sellers, L McDonald, T Utterback, RD Fleishmann, WC Nierman, O White, SL Salzberg, HO Smith, RR Colwell, JJ Mekalanos, JC Venter, CM Fraser DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature, 406:477-83 2000 More details »
F Liang, I Holt, G Pertea, S Karamycheva, SL Salzberg, J Quackenbush Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet, 25:239-40 2000 More details »
TD Read, RC Brunham, C Shen, SR Gill, JF Heidelberg, O White, EK Hickey, J Peterson, T Utterback, K Berry, S Bass, K Linher, J Weidman, H Khouri, B Craven, C Bowman, R Dodson, M Gwinn, W Nelson, R DeBoy, J Kolonay, G McClarty, SL Salzberg, J Eisen, CM Fraser Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res, 28:1397-406 2000 More details »
H Tettelin, NJ Saunders, J Heidelberg, AC Jeffries, KE Nelson, JA Eisen, KA Ketchum, DW Hood, JF Peden, RJ Dodson, WC Nelson, ML Gwinn, R DeBoy, JD Peterson, EK Hickey, DH Haft, SL Salzberg, O White, RD Fleischmann, BA Dougherty, T Mason, A Ciecko, DS Parksey, E Blair, H Cittone, EB Clark, MD Cotton, TR Utterback, H Khouri, H Qin, J Vamathevan, J Gill, V Scarlato, V Masignani, M Pizza, G Grandi, L Sun, HO Smith, CM Fraser, ER Moxon, R Rappuoli, JC Venter Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science, 287:1809-15 2000 More details »
M Pertea, SL Salzberg, MJ Gardner Finding genes in Plasmodium falciparum. Nature, 404:34; discussion 34-5 2000 More details »
M García-Varela, G Pérez-Ponce de León, P de la Torre, MP Cummings, SS Sarma, JP Laclette Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol Evol, 50:532-40 2000 More details »
X Lin, S Kaul, S Rounsley, TP Shea, MI Benito, CD Town, CY Fujii, T Mason, CL Bowman, M Barnstead, TV Feldblyum, CR Buell, KA Ketchum, J Lee, CM Ronning, HL Koo, KS Moffat, LA Cronin, M Shen, G Pai, S Van Aken, L Umayam, LJ Tallon, JE Gill, MD Adams, AJ Carrera, TH Creasy, HM Goodman, CR Somerville, GP Copenhaver, D Preuss, WC Nierman, O White, JA Eisen, SL Salzberg, CM Fraser, JC Venter Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 402:761-8 1999 More details »
H Tettelin, D Radune, S Kasif, H Khouri, SL Salzberg Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics, 62:500-7 1999 More details »
AL Delcher, D Harmon, S Kasif, O White, SL Salzberg Improved microbial gene identification with GLIMMER. Nucleic Acids Res, 27:4636-41 1999 More details »
HO Smith, ML Gwinn, SL Salzberg DNA uptake signal sequences in naturally transformable bacteria. Res Microbiol, 150:603-16 1999 More details »
O White, JA Eisen, JF Heidelberg, EK Hickey, JD Peterson, RJ Dodson, DH Haft, ML Gwinn, WC Nelson, DL Richardson, KS Moffat, H Qin, L Jiang, W Pamphile, M Crosby, M Shen, JJ Vamathevan, P Lam, L McDonald, T Utterback, C Zalewski, KS Makarova, L Aravind, MJ Daly, KW Minton, RD Fleischmann, KA Ketchum, KE Nelson, S Salzberg, HO Smith, JC Venter, CM Fraser Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science, 286:1571-7 1999 More details »
AL Delcher, S Kasif, RD Fleischmann, J Peterson, O White, SL Salzberg Alignment of whole genomes. Nucleic Acids Res, 27:2369-76 1999 More details »
SL Salzberg, M Pertea, AL Delcher, MJ Gardner, H Tettelin Interpolated Markov models for eukaryotic gene finding. Genomics, 59:24-31 1999 More details »
KE Nelson, RA Clayton, SR Gill, ML Gwinn, RJ Dodson, DH Haft, EK Hickey, JD Peterson, WC Nelson, KA Ketchum, L McDonald, TR Utterback, JA Malek, KD Linher, MM Garrett, AM Stewart, MD Cotton, MS Pratt, CA Phillips, D Richardson, J Heidelberg, GG Sutton, RD Fleischmann, JA Eisen, O White, SL Salzberg, HO Smith, JC Venter, CM Fraser Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature, 399:323-9 1999 More details »
S.L. Salzberg Gene discovery in DNA sequences Ieee Intelligent Systems & Their Applications, 14:44-48 1999 More details »
MP Cummings, SP Otto, J Wakeley Genes and other samples of DNA sequence data for phylogenetic inference. Biol Bull, 196:345-50 1999 More details »
S. Tilghman, H. S. Astin, W. Brinkley, M. D. Chilton, M. P. Cummings, R. G. Ehrenberg, M. F. Fox, K. Glenn, P. J. Green, S. Hans, A. Kelman, J. LaPidus, B Levin, J. R. McIntosh, H. Riecken, P. E. Stephans Trends in the early careers of life scientists. Committee on Dimensions, Causes, and Implications of Recent Trends in the Careers of Life Scientists. Mol Biol Cell, 9:3007-15 1998 More details »
MJ Gardner, H Tettelin, DJ Carucci, LM Cummings, L Aravind, EV Koonin, S Shallom, T Mason, K Yu, C Fujii, J Pederson, K Shen, J Jing, C Aston, Z Lai, DC Schwartz, M Pertea, S Salzberg, L Zhou, GG Sutton, R Clayton, O White, HO Smith, CM Fraser, MD Adams, JC Venter, SL Hoffman Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science, 282:1126-32 1998 More details »
A Campos, MP Cummings, JL Reyes, JP Laclette Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences. Mol Phylogenet Evol, 10:1-10 1998 More details »
SL Salzberg, AJ Salzberg, AR Kerlavage, JF Tomb Skewed oligomers and origins of replication. Gene, 217:57-67 1998 More details »
MP Cummings, MT Clegg Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci U S A, 95:5637-42 1998 More details »
S. Tilghman, H. S. Astin, W. Brinkley, M. D. Chilton, M. P. Cummings, R. G. Ehrenberg, M. F. Fox, K. Glenn, P. J. Green, S. Hans, A. Kelman, J. LaPidus, B. Levin, J. R. McIntosh, H. Riecken, P. E. Stephans Trends in the early careers of life scientists National Academy Press, Washington, DC., 178 1998 More details »
CM Fraser, SJ Norris, GM Weinstock, O White, GG Sutton, R Dodson, M Gwinn, EK Hickey, R Clayton, KA Ketchum, E Sodergren, JM Hardham, MP McLeod, S Salzberg, J Peterson, H Khalak, D Richardson, JK Howell, M Chidambaram, T Utterback, L McDonald, P Artiach, C Bowman, MD Cotton, C Fujii, S Garland, B Hatch, K Horst, K Roberts, M Sandusky, J Weidman, HO Smith, JC Venter Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science, 281:375-88 1998 More details »
SL Salzberg, AL Delcher, S Kasif, O White Microbial gene identification using interpolated Markov models. Nucleic Acids Res, 26:544-8 1998 More details »
S Salzberg, AL Delcher, KH Fasman, J Henderson A decision tree system for finding genes in DNA. J Comput Biology, 5:667-80 1998 More details »
M. P. Cummings, N. Welschmeyer Pigment composition of putatively achlorophyllous angiosperms Plant Systematics and Evolution, 210:105-111 1998 More details »
S. L. Salzberg, D. B. Searls, S. Kasif A Tutorial introduction to computation for biologists. Computational Methods in Molecular Biology, 11-27 1998 More details »
S. L. Salzberg, D. B. Searls, S. Kasif Decision trees and markov chains for gene finding Computational Methods in Molecular Biology, 187-203 1998 More details »
LM King, MP Cummings Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae). Mol Biol Evol, 14:1088-95 1997 More details »
MT Clegg, MP Cummings, ML Durbin The evolution of plant nuclear genes. Proc Natl Acad Sci U S A, 94:7791-8 1997 More details »
CM Fraser, S Casjens, WM Huang, GG Sutton, R Clayton, R Lathigra, O White, KA Ketchum, R Dodson, EK Hickey, M Gwinn, B Dougherty, JF Tomb, RD Fleischmann, D Richardson, J Peterson, AR Kerlavage, J Quackenbush, S Salzberg, M Hanson, R van Vugt, N Palmer, MD Adams, J Gocayne, J Weidman, T Utterback, L Watthey, L McDonald, P Artiach, C Bowman, S Garland, C Fuji, MD Cotton, K Horst, K Roberts, B Hatch, HO Smith, JC Venter Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature, 390:580-6 1997 More details »
J. C. Marks, M. P. Cummings DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater Cladophora (Chlorophyta) Journal of Phycology, 32:1035-1042 1996 More details »
D. Blair, A. Campos, M. P. Cummings, J. P. Laclette Evolutionary biology of platyhelminths comes of age: the role of molecular phylogenetics Parasitology Today, 12:66-71 1996 More details »
S. P. Otto, M. P. Cummings, J. Wakeley Inferring phylogenies from DNA sequence data: The effects of sampling. In Harvey, P. H., A. J. Leigh Brown, J. Maynard Smith and S. Nee (Eds.) New Uses for New Phylogenies. Oxford University Press, 103-115 1996 More details »
MP Cummings, SP Otto, J Wakeley Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol, 12:814-22 1995 More details »
M. P. Cummings Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer Trends in Ecology and Evolution, 9:141-148 1994 More details »
MP Cummings, LM King, EA Kellogg Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol Biol Evol, 11:1-8 1994 More details »
DF Voytas, MP Cummings, A Koniczny, FM Ausubel, SR Rodermel copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci U S A, 89:7124-8 1992 More details »
M. P. Cummings Copia-like retrotransposons in plants: a brief introduction The Plant Genetics Newsletter, 8:38-41 1992 More details »
A Konieczny, DF Voytas, MP Cummings, FM Ausubel A superfamily of Arabidopsis thaliana retrotransposons. Genetics, 127:801-9 1991 More details »
M. P. Cummings Review of Fundamentals of Molecular Evolution, by Li, W.-H. and D. Graur Cladistics, 7:310-312 1991 More details »
G. R. Furnier, M. P. Cummings, M. T. Clegg Evolution of the avocados as revealed by DNA restriction site variation. Journal of Heredity, 81:183-188 1990 More details »
DF Voytas, A Konieczny, MP Cummings, FM Ausubel The structure, distribution and evolution of the Ta1 retrotransposable element family of Arabidopsis thaliana. Genetics, 126:713-21 1990 More details »