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Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.
Hu B, Canon S, Eloe-Fadrosh EA, Anubhav, Babinski M, Corilo Y, Davenport K, Duncan WD, Fagnan K, Flynn M, Foster B, Hays D, Huntemann M, Jackson EKP, Kelliher J, Li PE, Lo CC, Mans D, McCue LA, Mouncey N, Mungall CJ, Piehowski PD, Purvine SO, Smith M, Varghese NJ, Winston D, Xu Y, Chain PSG. Hu B, et al. Among authors: davenport k. Front Bioinform. 2022 Jan 17;1:826370. doi: 10.3389/fbinf.2021.826370. eCollection 2021. Front Bioinform. 2022. PMID: 36303775 Free PMC article. Review.
Genomics for key players in the N cycle from guinea pigs to the next frontier.
Chain PS, Xie G, Starkenburg SR, Scholz MB, Beckloff N, Lo CC, Davenport KW, Reitenga KG, Daligault HE, Detter JC, Freitas TA, Gleasner CD, Green LD, Han CS, McMurry KK, Meincke LJ, Shen X, Zeytun A. Chain PS, et al. Among authors: davenport kw. Methods Enzymol. 2011;496:289-318. doi: 10.1016/B978-0-12-386489-5.00012-9. Methods Enzymol. 2011. PMID: 21514469 Review.
Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2.
Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PS, Chertkov O, Chokoshvili O, Coyne S, Davenport K, Detter JC, Dorman W, Erkkila TH, Folster JP, Frey KG, George M, Gleasner C, Henry M, Hill KK, Hubbard K, Insalaco J, Johnson S, Kitzmiller A, Krepps M, Lo CC, Luu T, McNew LA, Minogue T, Munk CA, Osborne B, Patel M, Reitenga KG, Rosenzweig CN, Shea A, Shen X, Strockbine N, Tarr C, Teshima H, van Gieson E, Verratti K, Wolcott M, Xie G, Sozhamannan S, Gibbons HS; Threat Characterization Consortium. Ahmed SA, et al. Among authors: davenport k. PLoS One. 2012;7(11):e48228. doi: 10.1371/journal.pone.0048228. Epub 2012 Nov 1. PLoS One. 2012. PMID: 23133618 Free PMC article.
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS. Fitzsimons MS, et al. Among authors: davenport kw. Genome Res. 2013 May;23(5):878-88. doi: 10.1101/gr.142208.112. Epub 2013 Mar 14. Genome Res. 2013. PMID: 23493677 Free PMC article.
Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.
Davenport KW, Daligault HE, Minogue TD, Bruce DC, Chain PS, Coyne SR, Jaissle JG, Koroleva GI, Ladner JT, Li PE, Palacios GF, Scholz MB, Teshima H, Johnson SL. Davenport KW, et al. Genome Announc. 2014 Aug 21;2(4):e00832-14. doi: 10.1128/genomeA.00832-14. Genome Announc. 2014. PMID: 25146140 Free PMC article.
Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece.
Reeve W, Ballard R, Howieson J, Drew E, Tian R, Bräu L, Munk C, Davenport K, Chain P, Goodwin L, Pagani I, Huntemann M, Mavrommatis K, Pati A, Markowitz V, Ivanova N, Woyke T, Kyrpides N. Reeve W, et al. Among authors: davenport k. Stand Genomic Sci. 2013 Dec 31;9(3):514-26. doi: 10.4056/sigs.4938652. eCollection 2014 Jun 15. Stand Genomic Sci. 2013. PMID: 25197437 Free PMC article.
Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B.
Reeve W, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Goodwin L, Chain P, Woyke T, Lobos E, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N. Reeve W, et al. Among authors: davenport k. Stand Genomic Sci. 2014 Dec 8;9:3. doi: 10.1186/1944-3277-9-3. eCollection 2014. Stand Genomic Sci. 2014. PMID: 25780496 Free PMC article.
336 results