Skip to content

Publications

In reverse order

Skoog EJ, Huber JA, Serres MH, Levesque A, Zeigler Allen L. Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent. Microbiol Resour Announc. 2021 Aug 26;10(34):e0061521. doi: 10.1128/MRA.00615-21.Epub 2021 Aug 26. PMID: 34435861; PMCID: PMC8388535.

Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Makillie LM, Isern NG, Chrisler WB, Kucek LA, Hill EA, Pinchuk GE, Bryant DA, Wiley SH, Fredrickson JK, Konopka A. 2014. Inference of interactons in cyanobacteial-heterotrophic co-cultures via transcriptome sequencing. ISME Journal 8:2243-2255. PubMed PMID: 24781900; PubMed Central PMCID: PMC4992078; DOI: 10.1038/ismej.2014.69.

Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, Reed JL. Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. 2014. BMC Systems Biology 8: 31. PubMed PMID: 24621294; PubMed Central PMCID: PMC4007644; DOI: 10.1186/1752-0509-8-31.

Sadler NC, Melnicki M, Serres MH, Merkley E, Chrisler WB, Hill, EA, Romine, MF, Kim S, Zink EM, Datta S, Smith RD, Beliaev AS, Konopka, A, Wright, AT. 2014. Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS Chemical Biology 9:291-300. PubMed PMID: 24168666; DOI: 10.1021/cb400769v.

Taylor RC, Webb Robertson BM, Markillie LM, Serres MH, Linggi BE, Aldrich JT, Hill EA, Romine MF, Lipton MS, Wiley HS. 2013. Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria. Integrative Biology (Cambr) 5:1393-406. PubMed PMID: 24081429; PMCID: PMC3968953; DOI: 10.1039/c3ib40120k.

Beg, QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segre, D. 2012. Detection of transcriptional triggers in the dynamics of microbial growth: applications to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Research 40:7132-49. PubMed PMID: 22638572; PubMed Central PMCID: PMC3424579; DOI: 10.1093/nar/gks467.

Rodrigues, JL, Serres, MH, Tiedje, JM. 2011. Large scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at genus level. Applied and Environmental Microbiology. 77:5352-60. PubMed PMID: 21642407; PubMed Central PMCID: PMC3147445; DOI: 10.1128/AEM.00097-11.

Karpinets, TV, Romine, MF, Schmoyer, D.D, Kora, GH, Syed, MH, Leuze, MR, Serres, MH, Park, BH, Samatova, NF, and Uberbacher, EC. 2010. Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database Vol. 2010. PubMed PMID: 20627862; PubMed Central PMCID: PMC2911847; DOI: 10.1093/database/baq012.

Karpinets TV, Obraztsova AY, Wang Y, Schmoyer DD, Kora GH, Park BH, Serres MH, Romine MF, Land ML, Kothe TB, Fredrickson JK, Nealson KH, Uberbacher EC. 2009. Conserved synteny at the protein family level reveals genes underlying Shewanella species cold tolerance and predicts their novel phenotypes. Functional Integrated Genomics 10:97-110. PubMed PMID: 19802638; PubMed Central PMCID: PMC2834769; DOI: 10.1007/s10142-009-0142-y.

Serres MH, Kerr AR, McCormack TJ, Riley M. 2009. Evolution by leaps: gene duplication in bacteria. Biology Direct 4:46. PubMed PMID: 19930658; PubMed Central PMCID: PMC2787491; DOI: 10.1186/1745-6150-4-46.

Konstantinidis KT, Serres MH, Romine MF, Rodrigues JLM, Auchtung, J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. 2009. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proceedings of the National Academy of Sciences USA 106:15909-14.
PubMed PMID: 19805231; PubMed Central PMCID: PMC2747217; DOI: 10.1073/pnas.0902000106

Nahum LA, Goswami S, Serres MH. 2009. Protein families reflect the metabolic diversity of organisms and provide support for functional prediction. Physiological Genomics 38:250-260. PubMed PMID: 19491149; DOI: 10.1152/physiolgenomics.90244.2008.

Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. 2008. Towards environmental systems biology in Shewanella. Nature Reviev of Microbiol. 6:592-603. PubMed PMID: 18604222; DOI: 10.1038/nrmicro1947.

Driscoll ME, Romine MF, Juhn FS, Serres MH, McCue LA, Beliaev AS, Fredrickson JK, Gardner TS. 2007. Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling. Genome Informatics 18:287-298. PubMed PMID: 18546496.

Serres, MH, Riley M. 2006. Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions vs. experiments. Journal of Bacteriology 188:4601-9. PubMed PMID: 16788168; PubMed Central PMCID: PMC1482980; DOI: 10.1128/JB.01787-05.

Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett III G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005. Nucleic Acids Research 34:1-9. PubMed PMID: 16397293; PMCID: PMC1325200; DOI: 10.1093/nar/gkj405.

Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JF, Tiedje JM. 2005. Global profiling of Shewanella oneidensis MR-1: Expression of ‘hypothetical’ genes and improved functional annotations. Proceedings of the National Academy of Sciences USA 102:2099-104. PubMed PMID: 15684069; PMCID: PMC548307; DOI: 10.1073/pnas.0409111102.

Serres, MH, Riley M. 2005. Gene fusions and gene duplications; relevance to genomic annotation and functional analysis. BMC Genomics: 6:33. PubMed PMID: 15757509; PubMed Central PMCID: PMC555942; DOI: 10.1186/1471-2164-6-33.

Serres, MH, Riley M. 2004. Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome. OMICS A Journal of Integrative Biology 8:306-21. PubMed PMID: 15703478; DOI: 10.1089/omi.2004.8.306.

Serres, MH, Goswami S, Riley M. 2004. GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Research 32 Database issue: D300-2. PubMed PMID: 14681418; PubMed Central PMCID: PMC308821; DOI: 10.1093/nar/gkh087.

Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M. 2001. A functional update of the Escherichia coli K-12 genome. Genome Biology 2:RESEARCH0035. PubMed PMID: 11574054; PubMed Central PMCID: PMC56896; DOI: 10.1186/gb-2001-2-9-research0035.

Serres, MH, Riley M. 2000. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microbial and Comparative Genomics 5:205-22. PubMed PMID: 11574054; PubMed Central PMCID: PMC56896; DOI: 10.1186/gb-2001-2-9-research0035.

Riley, M, Serres MH. 2000. Interim report on genomics of Escherichia coli. Annual Review of Microbiology 54:341-411. PubMed PMID: 11018132; DOI: 10.1146/annurev.micro.54.1.341

Serres, MH, Riley, M. 2000. Genomics and metabolism in Escherichia coli. In M. Dworkin et al., eds. The Prokaryotes: An Evolving Electronic Database for the Microbiological Community, 3rd edition (release 3.2), New York, Springer-Verlag [www.prokaryotes.com]

Serres, MH, Fladmark, KE, Døskeland, SO. 2000. An ultrasensitive competitive binding assay for the detection of toxins affecting protein phosphatases. Toxicon 38:347-60. PubMed PMID: 10669024; DOI: 10.1016/s0041-0101(99)00163-4.

Fladmark, KE, Serres, MH, Larsen, NL, Yasumoto, T, Aune, T, Døskeland, SO. 1998. Sensitive detection of apoptogenic toxins in suspension cultures of rat and salmon hepatocytes. Toxicon 36:1101-14. PubMed PMID: 9690778; DOI: 10.1016/s0041-0101(98)00083-x.

Serres MH, Ensign JC. 1996. Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis. Journal of Bacteriology 178:6074-7. PubMed PMID: 8830711; PubMed Central PMCID: PMC178471; DOI: 10.1128/jb.178.20.6074-6077.1996.