Publications from the MSC and GSCID

2012

David R. Cameron, Doyle Ward, Benjamin P. Howden, Xenia Kostoulias, Robert C. Moellering Jr., George M. Eliopoulos, Anton Y. Peleg. The serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus (2012). Accepted Journal of Infectious Diseases [PubMed]

Georgia Giannoukos, Dawn Ciulla, Katherine Huang, Brian J. Haas, Jacques Izard, Joshua Z. Levin, Jonathan Livny, Ashlee M. Earl, Dirk Gevers, Doyle V. Ward, Chad Nusbaum, Bruce W. Birren and Andreas Gnirke. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biology 2012, 13:R23 [PubMed]

Grad YH, Lipsitch M, Feldgarden M, Arachchi H, Cerqueira GC, Fitzgerald MG, Godfrey P, Haas B, Murphy CI, Russ C, Sykes SM, Walker BJ, Wortman JR, Young SK, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, DeSmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, and Hanage WP. 2012. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci 109:3065-70. [PubMed]

Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, et al. (2012) Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathog 8: e1002529. doi:10.1371/journal.ppat.1002529. [PubMed]

Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, et al. (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8: e1002417. doi:10.1371/journal.pcbi.1002417 [PubMed]

Palmer KL, Godfrey P, Griggs A, Kos VN, Zucker J, Desjardins C, Cerqueira G, Gevers D, Walker S, Wortman J, Feldgarden M, Haas B, Birren B, Gilmore MS. Comparative Genomics of Enterococci: Variation in Enterococcus faecalis, Clade Structure in E. faecium, and Defining Characteristics of E. gallinarum and E. casseliflavus. MBio. 2012 Mar 1;3(1). pii: e00318-11. [PubMed]

Peleg AY, Miyakis S, Ward DV, Earl AM, Rubio A, Cameron DR, Pillai S, Moellering RC Jr, Eliopoulos GM. Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus (2012).
PLoS One. 2012;7(1):e28316. Epub 2012 Jan 6. [PubMed]

Kendra Pesko, Kelly A Fitzpatrick, Elizabeth M Ryan, Pei-Yong Shi, Bo Zhang, Niall J Lennon, Ruchi M Newman, Matthew R Henn, Gregory D Ebel. Internally deleted West Nile virus genomes isolated from exotic birds in New Mexico: Function in cells, mosquitoes, and mice. Virology (2012);427(1):10-7. [PubMed]

Thomas JC, Godfrey PA, Feldgarden M, Robinson DA. 2012. Candidate Targets of Balancing Selection in the Genome of Staphylococcus aureus. Mol. Biol. Evol. 29(4):1175-86. [PubMed]
 

2011
Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biology 12: R18. [PubMed]

Armstrong PM, Vossbrinck CR, Andreadis TG, Anderson JF, Pesko KN, Newman RM, Lennon NJ, Birren BW, Ebel GD, and Henn MR. 2011. Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008. Virology 17: 203-210. [PubMed]

Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira MES, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LVG, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter MEMT, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CMA, Birren BW, Cuomo CA. 2011. “Comparative Genomic Analysis of Human Fungal pathogens causing Paracoccidioidomycosis” PLoS Genet 7(10): e1002345. doi:10.1371/journal.pgen.1002345 [PubMed]

Erlich R.L., Jia, X., Anderson, S., Banks, E., Gao, X., Carrington, M., Gupta, N., DePristo, M.A., Henn, M.R., Lennon, N.J., de Bakker, P.I. 2011. Next-generation sequencing for HLA typing of class I loci. BMC Genomics 12:42. [PubMed]

Grabherr, M.G.,* Haas, B.J.,* Yassour, M.,* Levin, J.Z., Thompson, D.A., Amit., I., Adiconis, Z., Fan, L. Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, W. Nusbaum, Lindblad-Toh, K., Friedman, N., Regev, A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644-652 (2011) [PubMed]
*authors contributed equally

Goldman, S.R., Sharp, J.S., Vvedenskaya, I.O., Livny, J., Dove, S.L., and Nickels, B.E. 2011. NanoRNAs prime transcription initiation in vivo. Molecular Cell. 42(6):817-25. [PubMed]

Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E., Methé, B., DeSantis, T.Z., Human Microbiome Consortium, Petrosino, J.F., Knight, R., Birren, B.W. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. 2011 Genome research, doi:gr.112730.110 [PubMed]

Luo, C., Walk, S.T., Gordon, D.M., Feldgarden, M., Tiedje, J.M., & Konstantinidis, K.T. 2011. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. PNAS 108:7200-5. [PubMed]

Mandlik, A., Livny, J, Robins, W.P., Ritchie, J.M., Mekalanos, J.J., and Waldor, M.K. 2011. RNAseq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host and Microbe. 10(2):165-74. [PubMed]

Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D, Sene PD, Wirth DF, Nusbaum C, Volkman SK, Birren BW, Gnirke A and Neafsey DE. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biology 2011, 12:R73. [PubMed]

Oniangue-Ndza C, Kuntzen T, Kemper M, Berical A, Wang YE, Neumann-Haefelin C, Foote PK, Hills-Evans K, Reyor LL, Kane K, et al. 2011. Compensatory Mutations Restore the Replication Defects Caused by CTL Escape Mutations in HCV Polymerase. Journal of Virology. http://www.ncbi.nlm.nih.gov/pubmed/21880756 85(22):11883-90. [PubMed]

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ., Birren BW., Henn MR., Simmon;s, CP. 2011. Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission. PLoS Pathog 7: e1002064. [PubMed]

Van Tyne, D. Park, D.J., Schaffner, S.F., Neafsey, D.E., Angelino, E., Cortese, J.F., Barnes, K.G., Rosen, D.M., Lukens, A.K., Daniels, R.F., Milner Jr., D.A., Johnson, C.A., Shlyakhter, I., Grossman, S.R., Becker, J.S., Yamins, D., Karlsson, E.K., Ndiaye, D., Sarr, O., Mboup, S., Happi, C., Furlotte, N.A., Eskin, E., Kang, H.M., Hartl, D.L., Birren, B.W., Wiegand, R.C., Lander, E.S., Wirth, D.F., Volkman, S.K., and Sabeti, P.C. Identification and functional validation of the novel malarial resistance locus PF10_0355 in Plasmodium falciparum. In Press, PLOS Genetics. [PubMed]

Yu, Q., Ryan, E.M., Allen, T.M., Birren, B.W., Henn, M.R., Lennon, N,J. 2011 PriSM: A Primer Selection and Matching tool for amplification and sequencing of viral genomes. Bioinformatics 27:2, pages 266–267. [PubMed]

2010
Arensburger P. et al. (2010) Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics. Science 330(6000):86-88. [Pubmed]

Bartholomay L. et al. (2010) Pathogenomics of Culex quinquefasciatus and Meta-Analysis of Infection Responses to Diverse Pathogens. Science 330(6000):88-90. [PubMed]

Balmaseda A. et al. (2010) Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua. J. Infect. Dis. 201:5-14. [Pubmed]

Brister, J.R., Bao, Y.-M., Kuiken, C., Lefkowitz, E.J., Le Mercier, P., Leplae, R. Madupu, R., Scheuermann, R.H., Schobel, S., Seto, D., Shrivastava, S., Sterk, P., Qiandong Zeng, Q., Klimke, W., and Tatusova, T. “Viral genome annotation standards, report from the 2010 NCBI Annotation Workshop”, Viruses 2010, 2(10), 2258-2268; doi:10.3390/v2102258 [PubMed]

Lennon N.J. et al. (2010) A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol. 11:R15. [Pubmed]

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods.
Nat Methods. 2010 Sep;7(9):709-15. PMID: 20711195 [PubMed]

M. Reyes et al., “Index cluster study of dengue virus infection in nicaragua,” The American Journal of Tropical Medicine and Hygiene, vol. 83, no. 3, pp. 683-689, Sep. 2010. [PubMed]

Neafsey et al., “Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control,” Genome Research, vol. 20, no. 7, pp. 938-946, Jul. 2010. [PubMed]

Vu et al., “Emergence of the Asian 1 genotype of dengue virus serotype 2 in Vietnam: in vivo fitness advantage and lineage replacement in South-East Asia,” PLoS Neglected Tropical Diseases, vol. 4, no. 7, p. e757, 2010. [PubMed]


2009
Butler G. et al. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459(7247):657-62 [Pubmed]

Chain P.S. et al. (2009) Genome project standards in a new era of sequencing. Science. 326(5950):236-37 [Pubmed]

Champion M.D. et al. (2009) Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. PLoS Pathog. 5:e1000459 [Pubmed]

Colijn C. et al. (2009) Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol. 5:e1000489. [Pubmed]

Garber M. et al. (2009) Closing gaps in the human genome using sequencing by synthesis. Genome Biol. 10(6):R60 [Pubmed]

Gawronski J.D. et al. (2009) Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci USA. 106:16422-16427. [Pubmed]

Gnirke A. et al. (2009) Solution hybrid selection with ultra-long oligonucleotide probes for massively parallel targeted sequencing. Nat Biotechnol. 27:182-189. [Pubmed]

Hood, H.M. et al. (2009) Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. (2009) Annu Rev Microbiol. 63:385-409. [Pubmed]

Irimia, M. et al. (2009). Complex selection on 5’ splice sites in intron-rich organisms. Genome Res. 19(11):2021-7 [Pubmed]

Lozovsky, E.R. et al. (2009) Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Nat Acad Sci USA. 106:12025-30. [Pubmed]

Neafsey, D.E. (2009) Malaria genomics: New tools to fight an old disease. The Biochemist. 31: 12-15. [Pubmed]

Nusbaum C. et al. (2009) Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nature Methods. 6:67-69. [Pubmed]

Rodrigue S. et al. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS One. 4(9):e6864. [Pubmed]

Sharpton T.J. et al. (2009) Comparative genomic analysis of the human fungal pathogens Coccidioides and their relatives. Genome Res. 19(10):1722-31. [Pubmed]

Yassour M. et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci USA. 106(9):3264-9 [Pubmed]

2008
Brockman, W. et al. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res.18(5): 763-70. [Pubmed]

Butler, J. et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 18(5):810-20. [Pubmed]

Carlton J.M. et al. (2008) Comparative evolutionary genomics of human malaria parasites. Trends Parasitol. 24(12):545-50. [Pubmed]

Chiang D.Y. et al. (2008) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 6(1):99-103. [Pubmed]

Daniels R. et al. (2008) A general SNP-based molecular barcode for P. falciparum identification and tracking. Malaria J. 7(1):223. [Pubmed]

Fierer, N. et al. (2008) Short-term temporal variability in airborne bacterial and fungal populations. Appl Environ Microbiol. 74(1):200-7. [Pubmed]

Kuntzen T. et al. (2008) A set of reference sequences for the hepatitis C genotypes 4d, 4f and 4k covering the full open reading frame. J Med Virol. 80(8):1370–1378. [Pubmed]

Kuntzen T. et al. (2008) Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology. 48(6):1769-78 [Pubmed]

Mathee, K. et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA. 105(8):3100-5. [Pubmed]

McGuire, A.M. et al. (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 9(3):R50. [Pubmed]

McGuire A.M. et al. (2008) Conserved secondary structures in Aspergillus. PLoS ONE. 3(7):e2812 [Pubmed]

Neafsey D.E. et al. (2008) Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol. 9(12):R171. [Pubmed]

Orsi R.H. et al. (2008) Short-term genome evolution of Listeria moncytogenes in a non-controlled environment. BMC Genomics. 9:539. [Pubmed]

White T. et al. (2008) Generating and testing molecular hypotheses in the Dermatophytes. Eukaryot Cell. 7(8):1238–1245. [Pubmed]

2007
Dunlap J.C., et al. (2007) Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet. 57:49-96. [Pubmed]

Decaprio, D. et al. (2007) Conrad: Gene prediction using conditional random fields. Genome Res. 17(9):1389-98 [Pubmed]

Neafsey, D.E. et al. (2007) Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 24(8):1744-51. [Pubmed]

Neafsey, D.E. et al. (2007) Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 7:119. [Pubmed]

Nene, V. et al. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 316(5832):1718-23. [Pubmed]

Volkman, S.K. et al. (2007) A genome-wide map of diversity in Plasmodium falciparum. Nat Genet. 39(1):113-9. [Pubmed]

2006
Yu, Y. et al. (2006) Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. BMC Microbiol. 6:46. [Pubmed]

2005
Galagan, J.E. et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 438(7071):1105-15. [Pubmed]

Nierman, W.C., et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 438(7071):1151-6. [Pubmed]

 

GSCID funding is provided by the National Institute of Allergy and Infectious Diseases