Samuel V Angiuoli

26. Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 2008 Oct 9;455(7214):757-63.

25. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O. Toward a standards-compliant genomic and metagenomic publication record. OMICS 2008 Jun;12(2):157-60.

24. Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L; and the Genomic Standards Consortium. Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop. OMICS 2008 Jun;12(2):109-13.

23. Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T. Meeting Report: The Fourth Genomic Standards Consortium (GSC) Workshop. OMICS 2008 Jun;12(2):101-8.

22. Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 26, 541 - 547 (2008).

21. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation. OMICS 2008 Apr 16.

20. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus.PLoS Genetics. 2008 Apr 11;4(4)

19. Lynn M. Schriml, Aaron Gussman, Kathy Phillippy, Sam Angiuoli, Kumar Hari, Alan Goates, Ravi Jain, Tanja Davidsen, Anurhada Ganapathy, Elodie Ghedin, Steven Salzberg, Owen White, Neil Hall. Gemina: A Web-Based Epidemiology and Genomic Metadata System Designed to Identify Infectious Agents. Intelligence and Security Informatics: Biosurveillance. Springer Berlin, 2007: 228-229

18. Jonathan Crabtree, Samuel V. Angiuoli, Jennifer R. Wortman, Owen R. White. Sybil: Methods and Software for Multiple Genome Comparison and Visualization. Gene Function Analysis (Methods in Molecular Biology). Humana Press, 2007: 93-108.

17.   Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, PeregríAlvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science Sep 21;317(5845):1756-60

16.   Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K. (2007) The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.PLoS ONE Aug 22;2(1):e766.

15.   Wortman JR, Fedorova N, Crabtree J, Joardar V, Maiti R, Haas BJ, Amedeo P, Lee E, Angiuoli SV, Jiang B, Anderson MJ, Denning DW, White OR, Nierman WC. (2006) Whole genome comparison of the A. fumigatus family. Med Mycol. Sep;44

14.   Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H.  (2006) Comparative Genomics of Emerging Human Ehrlichiosis Agents. PLoS Genetics 2(2):e21

13.   Filliol I, Motiwala AS, Cavatore M, Qi W, Hernando Hazbon M, Bobadilla Del Valle M, Fyfe J, Garcia-Garcia L, Rastogi N, Sola C, Zozio T, Guerrero MI, Leon CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendon A, Sifuentes-Osornio J, Ponce de Leon A, Cave MD, Fleischmann R, Whittam TS, Alland D.   (2006). Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set. J Bacteriology 188(2):759-72.

12.   Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM.  (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". PNAS 102(39):13950-5.

11.   El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N.  (2005). Comparative genomics of trypanosomatid parasitic protozoa. Science 309(5733):404-9.

10.   Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V.  (2005). Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309(5731):134-7.

9.   Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Angiuoli SV, Durkin AS, Haft DF, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.  (2005). Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriology 187(7): 2426-38.

8.   Ghedin, E., Bringaud, F., Peterson, J., Myler, P., Berriman, M., Ivens, A., Andersson, B., Bontempi, E., Eisen, J., Angiuoli, S., Wanless, D., Von Arx, A., Murphy, L., Lennard, N., Salzberg, S., Adams, M.D., White, O., Hall, N., Stuart, K., Fraser, C.M. and El-Sayed, N.M.  (2004). Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 134(2): 183-91.

7.   Nelson, K.E., Fouts, D.E., Mongodin, E.F., Ravel, J., DeBoy, R.T., Kolonay, J.F., Rasko, D.A., Angiuoli, S.V., Gill, S.R., Paulsen, I.T., Peterson, J., White, O., Nelson, W.C., Nierman, W., Beanan, M.J., Brinkac, L.M., Daugherty, S.C., Dodson, R.J., Durkin, A.S., Madupu, R., Haft, D.H., Selengut, J., Van Aken, S., Khouri, H., Fedorova, N., Forberger, H., Tran, B., Kathariou, S., Wonderling, L.D., Uhlich, G.A., Bayles, D.O., Luchansky, J.B. and Fraser, C.M.  (2004). Whole genome comparisons of serotype 4b and 1\/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res 32(8): 2386-95.

6.   Rasko, D.A., Ravel, J., OA, O.K., Helgason, E., Cer, R.Z., Jiang, L., Shores, K.A., Fouts, D.E., Tourasse, N.J., Angiuoli, S.V., Kolonay, J., Nelson, W.C., Kolsto, A.B., Fraser, C.M. and Read, T.D.  (2004). The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 32(3): 977-988.

5.   Carlton, J.M., Angiuoli, S.V., Suh, B.B., Kooij, T.W., Pertea, M., Silva, J.C., Ermolaeva, M.D., Allen, J.E., Selengut, J.D., Koo, H.L., Peterson, J.D., Pop, M., Kosack, D.S., Shumway, M.F., Bidwell, S.L., Shallom, S.J., van Aken, S.E., Riedmuller, S.B., Feldblyum, T.V., Cho, J.K., Quackenbush, J., Sedegah, M., Shoaibi, A., Cummings, L.M., Florens, L., Yates, J.R., Raine, J.D., Sinden, R.E., Harris, M.A., Cunningham, D.A., Preiser, P.R., Bergman, L.W., Vaidya, A.B., van Lin, L.H., Janse, C.J., Waters, A.P., Smith, H.O., White, O.R., Salzberg, S.L., Venter, J.C., Fraser, C.M., Hoffman, S.L., Gardner, M.J. and Carucci, D.J.  (2002). Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419(6906): 512-9.

Top 3 hot paper in Microbiology 2002-2004

4.   Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., Salzberg, S.L., Craig, A., Kyes, S., Chan, M.S., Nene, V., Shallom, S.J., Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., Haft, D., Mather, M.W., Vaidya, A.B., Martin, D.M., Fairlamb, A.H., Fraunholz, M.J., Roos, D.S., Ralph, S.A., McFadden, G.I., Cummings, L.M., Subramanian, G.M., Mungall, C., Venter, J.C., Carucci, D.J., Hoffman, S.L., Newbold, C., Davis, R.W., Fraser, C.M. and Barrell, B.  (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419(6906): 498-511.

3.   Gardner, M.J., Shallom, S.J., Carlton, J.M., Salzberg, S.L., Nene, V., Shoaibi, A., Ciecko, A., Lynn, J., Rizzo, M., Weaver, B., Jarrahi, B., Brenner, M., Parvizi, B., Tallon, L., Moazzez, A., Granger, D., Fujii, C., Hansen, C., Pederson, J., Feldblyum, T., Peterson, J., Suh, B., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., White, O., Cummings, L.M., Smith, H.O., Adams, M.D., Venter, J.C., Carucci, D.J., Hoffman, S.L. and Fraser, C.M.  (2002). Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419(6906): 531-4.

2.   Tettelin, H., Nelson, K.E., Paulsen, I.T., Eisen, J.A., Read, T.D., Peterson, S., Heidelberg, J., DeBoy, R.T., Haft, D.H., Dodson, R.J., Durkin, A.S., Gwinn, M., Kolonay, J.F., Nelson, W.C., Peterson, J.D., Umayam, L.A., White, O., Salzberg, S.L., Lewis, M.R., Radune, D., Holtzapple, E., Khouri, H., Wolf, A.M., Utterback, T.R., Hansen, C.L., McDonald, L.A., Feldblyum, T.V., Angiuoli, S., Dickinson, T., Hickey, E.K., Holt, I.E., Loftus, B.J., Yang, F., Smith, H.O., Venter, J.C., Dougherty, B.A., Morrison, D.A., Hollingshead, S.K. and Fraser, C.M.  (2001). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293(5529): 498-506.

1.   Angiuoli, S.V., Prisant M.G. (2000). Atom Size and Packing in Proteins: A Delaunay Graph Analysis Approach. Citeseer