Publications

2017

  1. Cuevas, D.A. and Edwards, R.A. (2017). PMAnalyzer: a new web interface for bacterial growth curve analysis. Bioinformatics. (doi: 10.1093/bioinformatics/btx084). [Funding: NSF grants CNS-1305112 and MCB-1330800]

2016

  1. Cuevas, D.A., Edirisinghe, J., Henry, C.S., Overbeek, R., O’Connell, T.G., and Edwards, R.A. (2016). From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. Front. Microbiol. 907. (doi: 10.3389/fmicb.2016.00907). [Funding: NSF grants CNS-1305112 and MCB-1330800, and DUE-1259951]
  2. Mart Krupovic, Bas E Dutilh, Evelien M Adriaenssens, Johannes Wittmann, Finn K Vogensen, Mathew B Sullivan, Janis Rumnieks, David Prangishvili, Rob Lavigne, Andrew M Kropinski, Jochen Klumpp, Annika Gillis, Francois Enault, Rob A Edwards, Siobain Duffy, Martha RC Clokie, Jakub Barylski, Hans-Wolfgang Ackermann, Jens H Kuhn. Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome. Arch Virol. 2016 Jan 5. [Epub ahead of print]
  3. Fabyano Alvares Cardoso Lopes, Elisa Caldeira Pires Catão, Renata Henrique Santana, Anderson de Souza Cabral, Rodolfo Paranhos, Thiago Pessanha Rangel, Carlos Eduardo de Rezende, Robert A Edwards, Cristiane C Thompson, Fabiano L Thompson, Ricardo Henrique Kruger. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. PLoS One. 2016 Feb 16;11(2):e0148296. doi: 10.1371/journal.pone.0148296. eCollection 2016.
  4. B Knowles, CB Silveira, BA Bailey, K Barott, VA Cantu, AG Cobián-Güemes, FH Coutinho, EA Dinsdale, B Felts, KA Furby, EE George, KT Green, GB Gregoracci, AF Haas, JM Haggerty, ER Hester, N Hisakawa, LW Kelly, YW Lim, M Little, A Luque, T McDole-Somera, K McNair, LS de Oliveira, SD Quistad, NL Robinett, E Sala, P Salamon, SE Sanchez, S Sandin, GGZ Silva, J Smith, C Sullivan, C Thompson, MJA Vermeij, M Youle, C Young, B Zgliczynski, R Brainard, RA Edwards, J Nulton, F Thompson, F Rohwer. Lytic to temperate switching of viral communities. Nature. 2016 Mar 24;531(7595):466-70. doi: 10.1038/nature17193. Epub 2016 Mar 16.
  5. Silva, G. G. Z., Alvares, F. & Edwards, R. A. An agile functional analysis of metagenomic data using SUPER-FOCUS. Springer Book chapter – Methods in Mol. Biol. (2016) (accepted)
  6. Robert Edwards Genivaldo Gueiros Z. Silva, Bas Dutilh. FOCUS2: agile and sensitive classification of metagenomics data using a reduced database, biorxiv 2016
  7.  Adriana Sturion Lorenzi, Genivaldo Gueiros Z. Silva, Fabyano Alvares Cardoso Lopes, Mathias Ahii Chia, Robert A. Edwards, and Maria do Carmo Bittencourt-Oliveira: Draft genome sequence of the saxitoxin-producing cyanobacteria Cylindrospermopsis raciborskii ITEP A1 from a Brazilian semi-arid freshwater body revealing cylindrospermopsin synthetase Genes. (accepted;Genome Announcements)
  8. Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai. Using metagenomics to connect microbial community biodiversity and functions. Book chapter (accepted)
  9. Using viromes to predict novel immune proteins in non-model organisms. Steven D. Quistad, Yan Wei Lim, Genivaldo Gueiros Z. Silva, Craig E. Nelson, Andreas F. Haas, Linda Wegley Kelly, Robert A. Edwards, Forest L. Rohwer. Using viromes to predict novel immune proteins in non-model organisms. Proc Biol Sci. 2016 Aug 31;283(1837). pii: 20161200. doi: 10.1098/rspb.2016.1200.

2015

  1. Thomas Brettin, James J Davis, Terry Disz, Robert A Edwards, Svetlana Gerdes, Gary J Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, James A Thomason III, Rick Stevens, Veronika Vonstein, Alice R Wattam, Fangfang Xia. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365.
  2. Ramy K. Aziz1, Bhakti Dwivedi, Sajia Akhter, Mya Breitbart and Robert A. Edwards. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.  Front. Microbiol. | doi: 10.3389/fmicb.2015.00381
  3. Acacio A. Navarrete, Tatiana R. Diniz, Lucas P. P. Braga, Genivaldo G. Z. Silva, Julio C. Franchinic, Raffaella Rossettod, Robert A. Edwards, Siu M. Tsai. Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems PLoS One. 2015 Jun 9;10(6):e0129765. doi: 10.1371/journal.pone.0129765.
  4. Edmundo Calva, Claudia Silva, Mussaret Zaidi, Alejandro Sanchéz-Flores, Karel Estrada, Genivaldo Silva, Mayela Soto-Jiménez, Magdalena Wiesner, Marcos Fernández-Mora, Rob Edwards, and Pablo Vinuesa. Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella enterica serovar Typhimurium strain of the emerging ST213 genotype  (Genome Announcements accepted)
  5. T. David Matthews, Robert Schmieder, Genivaldo G. Z. Silva, Julia Busch, Noriko Cassman, Matthew Doherty, Dawn Green, Brian Matlock, Brian Heffernan, Gary Olsen, Leigh Farris Hanna, Dieter Schifferli, Stanley Maloy, Elizabeth A. Dinsdale, and Robert A. Edwards. Comparison of the Closely-related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum. PLoS One. 2015 Jun 3;10(6):e0126883. doi: 10.1371/journal.pone.0126883. eCollection 2015.
  6. Pedro M. Meirelles, Gilberto M. Amado-Filho, Guilherme H. Pereira-Filho, Hudson T. Pinheiro, Rodrigo L. de Moura, Jean-Christophe Joyeux, Eric F. Mazzei, Alex C. Bastos, Robert A. Edwards, Elizabeth Dinsdale, Rodolfo Paranhos, Eidy O. Santos, Tetsuya Iida, Kazuyoshi Gotoh, Shota Nakamura, Tomoo Sawabe, Carlos E. Rezende, Luiz M. R. Gadelha Jr, Ronaldo B. Francini-Filho, Cristiane Thompson, Fabiano L. Thompson. Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data Published: June 19, 2015DOI: 10.1371/journal.pone.0130084
  7. Savannah E Sanchez, Daniel A Cuevas, Jason E Rostron, Tiffany Y Liang, Cullen G Pivaroff, Matthew R Haynes, Jim Nulton, Ben Felts, Barbara A Bailey, Peter Salamon, Robert A Edwards, Alex B Burgin, Anca M Segall, Forest Rohwer. Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins. J. Vis. Exp. 2015. (100), e52854. (doi: 10.3791/52854) [Funding: NSF funding from DEB-1046413 as part of the Dimensions: Shedding Light on Viral Dark Matter project]
  8. Adriaenssens EM, Edwards R, Nash JH, Mahadevan P, Seto D, Ackermann HW, Lavigne R, Kropinski AM. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology. 2015 Mar;477:144-54. doi: 10.1016/j.virol.2014.10.016. Epub 2014 Nov 14.
  9. Katelyn McNair, Robert A. Edwards. GenomePeek—an online tool for prokaryotic genome and metagenome analysis.  PeerJ
  10. Genivaldo G. Z. Silva, Green K., B. E. Dutilh, and R. A. Edwards: SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. Bioinformatics. 2015 Oct 9. pii: btv584.
  11. Andriy Kryshtafovych, John Moult, Arnaud Baslé, Alex Burgin, Timothy K Craig, Robert A Edwards, Deborah Fass, Marcus D Hartmann, Mateusz Korycinski, Richard J Lewis, Donald Lorimer, Andrei N Lupas, Janet Newman, Thomas S Peat, Kurt H Piepenbrink, Janani Prahlad, Mark J van Raaij, Forest Rohwer, Anca M Segall, Victor Seguritan, Eric J Sundberg, Abhimanyu K Singh, Mark A Wilson, Torsten Schwede. Some of the most interesting CASP11 targets through the eyes of their authors. Proteins. 2015 Oct 16. doi: 10.1002/prot.24942.
  12. Min Yue, Xiangan Han, Leon De Masi, Chunhong Zhu, Xun Ma, Junjie Zhang, Renwei Wu, Robert Schmieder, Radhey S Kaushik, George P Fraser, Shaohua Zhao, Patrick F McDermott, François-Xavier Weill, Jacques G Mainil, Cesar Arze, W Florian Fricke, Robert A Edwards, Dustin Brisson, Nancy R Zhang, Shelley C Rankin, Dieter M Schifferli. Allelic variation contributes to bacterial host specificity. Nat Commun. 2015 Oct 30;6:8754. doi: 10.1038/ncomms9754.
  13.   Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, Bas E. Dutilh. Computational approaches to predict bacteriophage–host relationships. http://dx.doi.org/10.1093/femsre/fuv048 fuv048 First published online: 9 December 2015

2014

  1. Ross Overbeek, Robert Olson, Gordon D Pusch, Gary J Olsen, James J Davis, Terry Disz, Robert A Edwards, Svetlana Gerdes, Bruce Parrello, Maulik Shukla, Veronika Vonstein, Alice R Wattam, Fangfang Xia, Rick Stevens. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014 Jan;42. [PMID: 24293654] [Funding: NSF DBI-0850356 and the PhAnToMe project]
  2. Yan Wei Lim, Jose S Evangelista, Robert Schmieder, Barbara Bailey, Matthew Haynes, Mike Furlan, Heather Maughan, Robert Edwards, Forest Rohwer, Douglas Conrad. Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis J Clin Microbiol. 2014 Feb;52(2):425-37. doi: 10.1128/JCM.02204-13. Epub 2013 Nov 20.
  3. Genivaldo Gueiros Z. Silva, Daniel Cuevas, Bas E. Dutilh, Robert Edwards. FOCUS: an Alignment-free Model to Identify Organisms in Metagenomes Using Non-negative Least Squares.PeerJ 2014 Jun 5;2:e425. [Funding: NSF DEB-1046413 and CNS-1305112 ]
  4. Linda W Kelly, Gareth J Williams, Katie L Barott, Craig A Carlson, Elizabeth A Dinsdale, Robert A Edwards, Andreas F Haas, Matthew Haynes, Yan Wei Lim, Tracey McDole, Craig E Nelson, Enric Sala, Stuart A Sandin, Jennifer E Smith, Mark JA Vermeij, Merry Youle, Forest Rohwer. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. PNAS 2014.  [Funding: Viral Dark Matter]
  5. Yan Wei Lim, Daniel Cuevas, Genivaldo G.Z. Silva, Kristen Aguinaldo, Elizabeth Dinsdale, Andreas Haas, Mark Hatay, Savannah Sanchez, Linda Wegley-Kelly, Bas E. Dutilh, Timothy Harkins, Clarence Lee, Warren Tom, Stuart Sandin, Jennifer E. Smith, Brian Zgliczynski, Mark J.A. Vermeij, Forest Rohwer, Robert A. Edwards (2014), “Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands research expedition”, . Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands research expedition. PeerJ preprints: e433. [Funding: Viral Dark Matter]
  6. Yan Wei Lim, Daniel Cuevas, Genivaldo G.Z. Silva, Kristen Aguinaldo, Elizabeth Dinsdale, Andreas Haas, Mark Hatay, Savannah Sanchez, Linda Wegley-Kelly, Bas E. Dutilh, Timothy Harkins, Clarence Lee, Warren Tom, Stuart Sandin, Jennifer E. Smith, Brian Zgliczynski, Mark J.A. Vermeij, Forest Rohwer, Robert A. Edwards (2014), “Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands research expedition”, . Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands research expedition. PeerJ [Funding: Viral Dark Matter]
  7. Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah Sanchez, Genivaldo G.Z. Silva, Lance Boling, Jeremy J. Barr, Daan R. Speth, Victor Seguritan, Ramy K. Aziz, Ben Felts, Elizabeth A. Dinsdale, John L. Mokili & Robert A. Edwards. Unknown sequences in faecal metagenomes reveal a widely distributed and highly abundant bacteriophage. Nature communications. [Funding: Viral Dark Matter]
  8. Bas E Dutilh, Cristiane C Thompson, Ana CP Vicente, Michel A Marin, Clarence Lee, Genivaldo GZ Silva, Robert Schmieder, Bruno GN Andrade, Luciane Chimetto, Daniel Cuevas, Daniel Garza, Iruka N Okeke, A. Oladipo Aboderin, Jessica Spangler, Tristen Ross, Elizabeth A Dinsdale, Fabiano L Thompson, Timothy T Harkins and Robert A Edwards
    Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions [BMC Genomics] [Funding: DBI: 0850356 and DEB:1046413]
  9. Nelson Alves Junior, Pedro Milet Meirelles, Eidy de Oliveira Santos, Bas Dutilh, Genivaldo G. Z. Silva, Rodolfo Paranhos, Anderson S. Cabral, Carlos Rezende,Tetsuya Iida, Rodrigo L. de Moura, Ricardo Henrique Kruger, Renato C. Pereira, Rogério Valle, Tomoo Sawabe, Cristiane Thompson,Fabiano Thompson. Microbial community diversity and physical–chemical features of the Southwestern Atlantic Ocean. [Archives of Microbiology]
  10.  Silva GGZ, Dutilh BE, Edwards RA: FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation. bioRxiv 2014:010801.
  11. Cristiane C. Thompson, Gilda R. Amaral, Mariana Campeão, Robert A. Edwards, Martin F. Polz, Bas E. Dutilh, David W. Ussery, Tomoo Sawabe, Jean Swings, Fabiano L. Thompson. Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Archives of Microbiology, 2014
  12. Daniel A Cuevas, Daniel Garza, Savannah E Sanchez, Jason Rostron, Chris S Henry, Veronika Vonstein, Ross A Overbeek, Anca Segall, Forest Rohwer, Elizabeth A Dinsdale, Robert A Edwards. Elucidating genomic gaps using phenotypic profiles. F1000Research 2014, 3:210 (doi: 10.12688/f1000research.5140.1) [Funding: NSF funding from CNS-1305112, MCB-1330800, DUE-132809, DEB-1046413, DUE-1259951]

2013

  1. Akhter S,Bailey BA,Salamon P, Aziz RK and Edwards RA. Applying Shannon’s information theory to bacterial and phage genomes and metagenomes.Nature Sci. Rep. 3, Article number:1033. 2013 [Link] [Funding: PhAnToME]
  2. Gizele D. Garcia, Gustavo B. Gregoracci, Eidy de O. Santos, Pedro M. Meirelles, Genivaldo GZ Silva, Rob Edwards,, Tomoo Sawabe, Kazuyoshi Gotoh, Shota Nakamura, Tetsuya Iida, Rodrigo L. de Moura, and Fabiano L. Thompson. Metagenomic analysis of healthy and White-plague affected Mussismilia braziliensis corals. Microb Ecol. 2013 May;65(4):1076-86 [PMID: 23314124] [Funding FIPSE-CAPES]
  3. Dwivedi B, Xue B, Lundin D, Edwards RA, Breitbart M. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol. 2013 Feb 7;13(1):33. doi:10.1186/1471-2148-13-33 [PMID: 23391036] [Funding: PhAnToME]
  4. Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB Jr. Structure and function of a cyanophage-encoded peptide deformylase. ISME J. 2013 Jun;7(6):1150-60 [PMID: 23407310] [Funding: Viral Dark Matter]
  5. Dutilh, B.E., Backus, L., Edwards, R.A., Wels, M., Bayjanov, J.R., and S.A.F.T. van Hijum. Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Briefings in Functional Genomics. Brief Funct Genomics. 2013 Jul;12(4):366-80. [PMID 23625995] [Funding: PhAnToME and Viral Dark Matter]
  6. Peter M. Letcher mail, Salvador Lopez, Robert Schmieder, Philip A. Lee, Craig Behnke, Martha J. Powell, Robert C. McBride. Characterization of Amoeboaphelidium protococcarum, an Algal Parasite New to the Cryptomycota Isolated from an Outdoor Algal Pond Used for the Production of Biofuel. PLoS One. 2013;8(2):e56232. [PMID: 23437098]
  7. Dinsdale EA, Edwards RA, Bailey B, Tuba I, Akhter S, McNair K, Schmieder R, Apkarian N, Creek M, Guan E, Hernandez M, Isaacs K, Peterson C, Regh T and Ponomarenko V (2013). Multivariate analysis of functional metagenomes. Front. Genet. 4:41. doi:10.3389/fgene.2013.00041[Link] [Funding: Microbes, Metagenomes and Marine Mammals; and PhAnToME]
  8. Ward R.M, Schmieder R, Highnam G, Mittelman D. Big data challenges and opportunities in high-throughput sequencing. Systems Biomedicine Review Volume 1 Issue 1 2013 [Link]
  9. Cristiane C Thompson, Genivaldo GZ Silva, Nayra M Vieira, Robert Edwards, Ana Carolina P Vicente, Fabiano L Thompson. Genomic Taxonomy of the Genus Prochlorococcus. Microbial ecology 2013, 66:752-762 [Link] [PMID: 23963220] [Funding: CAPES, FAPERJ, and CNPq]
  10. R. A. Edwards, John Matthew Haggerty, Noriko Cassman, Julia Christine Busch, Kristen Aguinaldo, Sowmya Chinta, Meredith Houle Vaughn, Robert Morey, Timothy T Harkins, Clotilde Teiling, Karin Fredrikson, Elizabeth Ann Dinsdale. Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics. 2013 Sep 4;14:600 [Link] [PMID 24007365]
  11. Bhakti Dwivedi, Bingjie Xue, Daniel Lundin, Robert A Edwards, Mya Breitbart. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomesBMC Evol Biol. 2013 Feb 7;13:33 [Link] [PMID 23391036] [funding DBI-0850356]
  12. Genivaldo G. Z. Silva, Bas E. Dutilh,T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale and Robert A. Edwards. Combining de novo and reference-guided assembly with Scaffold_builderSource Code Biol Med. 2013 Nov 22;8(1):23 [ PMID:24267787] [Funding FIPSE-CAPES and NSF DBI 0850356 and TUES:1044453]
  13. Mark Eppinger, Katelyn McNair, Xhavit Zogaj, Elizabeth A. Dinsdale, Robert A.Edwards, and Karl E. Klose. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis. Genome Announc. 2013 Nov 7;1(6). pii: e00926-13 [PMID 24201203]

2012

  1. RA Edwards, R Olson, T Disz, GD Pusch, V Vonstein, R Stevens, R Overbeek. Real Time Metagenomics: Using k-mers to annotate metagenomes. Bioinformatics 28 (24), 3316-3317. 2012. [PMID: 23047562] [Funding: PhAnToME and Viral Dark Matter]
  2. Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, Edwards RA, Mokili JL. Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics. 2012 Dec 15;28(24):3225-31. doi: 10.1093/bioinformatics/bts613. [PMID: 23074261] [Funding: PhAnToME and Viral Dark Matter]
  3. Hanna LF, Matthews TD, Dinsdale EA, Hasty D, Edwards RA. Characterization of the ELPhiS Prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol. 2012 Mar;78(6):1785-93. [PMID: 22247173] [Funding: Microbes, Metagenomes and Marine Mammals; and PhAnToME]
  4. McNair K, Bailey BA, Edwards RA. PHACTS, a computational approach to classifying the lifestyle of phages.Bioinformatics. 2012 Mar 1;28(5):614-8. [PMID: 22238260] [Funding: PhAnToME]
  5. Schmieder R and Edwards R. Insights into antibiotic resistance through metagenomic approaches. Future Microbiol. 2012 Jan;7(1):73-89. [PMID: 22191448] [Funding: PhAnToME and Viral Dark Matter]
  6. Schmieder R, Lim YW, Edwards R. Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics. 2012 Feb 1;28(3):433-5. [PMID: 22155869] [Funding: PhAnToME]
  7. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.Environ Microbiol. 2012 Jan;14(1):207-27 [PMID: 22004549]
  8. Espinoza-Valles I, Soto-Rodríguez S, Edwards RA, Wang Z, Vora GJ, Gómez-Gil B. Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792.J Bacteriol. 2012 Apr;194(8):2104 [PMID: 22461546][Funding: PhAnToME]
  9. Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M. PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.BMC Bioinformatics. 2012 Mar 4;13:37 [PMID: 22385976][Funding: PhAnToME]
  10. Li JW, Schmieder R, Ward RM, Delenick J, Olivares EC, Mittelman D. SEQanswers: An open access community for collaboratively decoding genomes.Bioinformatics. 2012 May 1;28(9):1272-3 [PMID: 22419780]
  11. Luckwu de Lucena BT, Silva GG, Manoel Dos Santos B, Dias GM, Amaral GR, Moreira AP, de Morais Júnior MA, Dutilh BE, Edwards RA, Balbino V, Thompson CC, Thompson FL. Genome sequence of the ethanol tolerant Lactobacillus vini strains LMG23202T and JP7.8.9.J Bacteriol. 2012 Jun;194(11):3018 [PMID: 22582376] [Funding: PhAnToME and FIPSE-CAPES]
  12. Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.Nucleic Acids Research 2012 40: e126 [PMID: 22584627] [Funding: PhAnToME]
  13. Garza DR, Thompson CC, Loureiro EC B, Dutilh BE, Inada DT, Junior ECS, Cardoso JF, Nunes MRT, de Lima CPS, Vellasco RS, Nunes KNB, Santos ECO, Edwards RA, Vicente ACP, Morais LLCS. Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic.PLoS One. 2012;7(5):e37283 [PMID: 22662140]
  14. Amaral GRS, Silva BSO, Santos EO, Dias GM, Lopes RM, Edwards RA, Thompson CC, Thompson FL. Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank. J Bacteriol. 2012 May;194(10):2759-60. [PMID: 22535939][Funding: PhAnToME and FIPSE-CAPES]
  15. Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RG, Thompson FL. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis.PLoS One. 2012;7(7):e39905. [PMID: 22768320]
  16. Hedin M, Starrett J, Akhter S, Schönhofer AL, Shultz JW. Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data.PLoS One. 2012;7(8):e42888. [PMID: 22936998]
  17. YW Lim, R Schmieder, M Haynes, D Willner, M Furlan, M Youle, K Abbott, R Edwards, J. Evangelista, D. Conrad, F. Rohwer. Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities. J Cyst Fibros. 2012 Aug 28 [Link]
  18. M Yue, R Schmieder, RA Edwards, SC Rankin, DM Schifferli. Microfluidic PCR combined with pyrosequencing identify allelic variants with phenotypic associations in targeted Salmonella genes. Appl Environ Microbiol. 2012 Oct;78(20):7480-2 [PMID: 22885744]
  19. Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS One. 2012;7(7):e41389. [PMID: 22848480]
  20. M Yue, SC Rankin, RT Blanchet, JD Nulton, RA Edwards, DM Schifferli. Diversification of the Salmonella Fimbriae: A Model of Macro-and Microevolution. PLoS One. 2012;7(6):e38596. [PMID: 22701679] [Funding: PhAnToME]
  21. Bruce T, Meirelles PM, Garcia G, Paranhos R, Rezende CE, de Moura RL, Filho RF, Coni EO, Vasconcelos AT, Amado Filho G, Hatay M, Schmieder R, Edwards R, Dinsdale E, Thompson FL. Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data. PLoS One. 2012;7(6):e36687. [PMID: 22679480]
  22. N. Cassman, A. Prieto-Davó, K. Walsh, G. G. Z. Silva, F. Angly, S. Akhter, K. Barott, J. Busch, T. McDole, J. M. Haggerty, D. Willner, G. Alarcón, O. Ulloa, E F. DeLong, B. Dulith, F. Rohwer, E A. Dinsdale. Oxygen minimum zones harbor novel viral communities with low diversity. Environ Microbiol. 2012 Nov;14(11):3043-65.[PMID: 23039259]
  23. A. E Trindade-Silva, C. PJ Rua, B. GN Andrade, A.C. Paulo Vicente, G. G. Z Silva, RGS Berlinck, FL Thompson. Polyketide synthase gene diversity within the endemic sponge Arenosclera brasiliensis microbiome. Appl Environ Microbiol. 2013 Mar;79(5):1598-605 [PMID:23275501].
  24. R. K. Aziz, S. Devoid, T. Disz, R. A. Edwards, C. S. Henry, G. J. Olsen, R. Olson, R. Overbeek,B. Parrello, G. D. Pusch, R. L. Stevens, V. Vonstein, F. Xia. SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models PLoS One. 2012;7(10):e48053 [PMID: 23110173] [Funding: PhAnToME and Viral Dark Matter]

2011

  1. C. C. Thompson, M. Abanto Marin, G. Maria Dias, B. E. Dutilh, R. Edwards, T. Iida, F. L. Thompson. Genome sequence of the human pathogen Vibrio cholerae Amazonia. J Bacteriol. 2011 Oct;193(20):5877-8. [PMID: 21952545] [Funding: PhAnToME andFIPSE-CAPES]
  2. Schmieder, R and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011 Mar 15;27(6):863-4. [PMID: 21278185] [Funding: PhAnToME]
  3. Julian R. Marchesi, Bas E. Dutilh, Neil Hall, Wilbert H. M. Peters, Rian Roelofs, Annemarie Boleij, Harold Tjalsma. Towards the Human Colorectal Cancer Microbiome. PLoS ONE 2011. [PMID: 21647227]
  4. Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One. 2011 Mar 9;6(3):e17288. [PMID: 21408061] [Funding: PhAnToME]
  5. Matthews TD, Rabsch W, Maloy S. Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers. MBio. 2011 Jun 7;2(3):e00060-11. [PMID: 21652779]
  6. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol. 2012 Jan;14(1):207-27 [PMID: 22004549]
  7. Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D, Rohwer F. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol. 2012 Feb;46(2):127-31. [PMID: 21980056]
  8. Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, Rohwer F, Conrad D. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J. 2012 Feb;6(2):471-4. [PMID: 21796216]
  9. Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M. Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes.PLoS One. 2011;6(6):e20579. [PMID: 21674005]
  10. Maartje A.H.J. van Kessel, Bas E. Dutilh, Kornelia Neveling, Michael P. Kwint, Joris A. Veltman, Gert Flik, Mike S.M. Jetten, Peter H.M. Klaren and Huub J.M. Op den Camp Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express. 2011 Nov 18;1:41. [PMID 22093413]
  11. R. K Aziz , B. Dwivedi, M. Breitbart, R. A Edwards Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets.BMC Bioinformatics 12(Suppl 7):A9 2011. [Link] [Funding: PhAnToME]

2010

  1. Mobberley J, Authement RN, Segall AM, Edwards RA, Slepecky RA, Paul JH: Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico. Appl Environ Microbiol. 2010 Feb;76(3):829-42. [PMID: 20008174]
  2. Aziz RK, Breitbart M, Edwards RA: Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 2010 Jul;38(13):4207-17. [PMID: 20215432] [Funding: PhAnToME]
  3. Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, Felts B, Haynes M, Liu H, Lipson D, Mahaffy J, Martin-Cuadrado AB, Mira A, Nulton J, Pašic L, Rayhawk S, Rodriguez-Mueller J, Rodriguez-Valera F, Salamon P, Srinagesh S, Thingstad TF, Tran T, Thurber RV, Willner D, Youle M, Rohwer F: Viral and microbial community dynamics in four aquatic environments. ISME J. 2010 Jun;4(6):739-51. [PMID: 20147985]
  4. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP, Rohwer F, Haynes M: Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity.Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4547-53. [PMID: 20547834]
  5. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA: Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics. 2010 Jun 14;11:319.[PMID: 20546611]
  6. Schmieder R, Lim YW, Rohwer F, Edwards R: TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics. 2010 Jun 23;11:341. [PMID: 20573248] [Funding: PhAnToME]
  7. F.L. Thompson, Rodrigues, T.B., Gonzalez, A., Cardoso, A. Clementino, M., Costagliola, M., Hozbor, C., Otero, E., Paranhos, R., Piccini, C., Peressutti, S., Schmieder, R., Edwards, R., Smith, M., Takiyama, L.R., Vieira, R., Artigas, L.F. 2010. Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6-tag pyrosequencing. Arch Microbiol. 2011 Feb;193(2):105-14. [PMID: 21076816]
  8. Matthews TD, Edwards R, Maloy S. Chromosomal rearrangements formed by rrn recombination do not improve rep