Recent Publications:
Schrenk M,O.,
Huber, J.A., and
K.J. Edwards.
2010.
Microbial Provinces in the Subseafloor.
Annual Review of Marine Science.
2: 279-304.
William J. Brazelton, Kristin A. Ludwiga, Mitchell L. Sogin, Ekaterina N. Andreishcheva, Deborah S. Kelley, Chuan-Chou Shen, R. Lawrence Edwards and John A. Baross; Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. PNAS January 11, 2010, doi: 10.1073/pnas.0905369107
Jennifer J. Wernegreen, Seth N. Kauppinen, Sean G. Brady and Philip S. Ward. 2009. One nutritional symbiosis begat another: Phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects. BMC Evolutionary Biology 9:292.
Egija Zaura, Bart JF Keijser, Susan Huse and Wim Crielaard.
Defining the healthy "core microbiome" of oral microbial communities; BMC Microbiology 2009, 9:259doi:10.1186/1471-2180-9-259
Slip into something more functional: Selection maintains ancient frameshifts in homopolymeric sequences
Jennifer J. Wernegreen;
Seth N. Kauppinen;
Patrick H. Degnan
Molecular Biology and Evolution 2009;
doi: 10.1093/molbev/msp290 (MBE Advance Access published online on December 2, 2009 )
Mark Welch, D.B.,
C. Ricci
and M. Meselson, 2009.
Bdelloid rotifers: progress in understanding the success of an evolutionary scandal.
pp 259-279 In: I. Schön, K. Martens, and P. van Dijk (eds.)
Lost Sex: The Evolutionary Biology of Parthenogenesis,
Springer, 615 p.
Witek, A.,
H. Herlyn,
I. Ebersberger,
D. B Mark Welch,
and T. Hankeln, 2009.
Support for the monophyletic origin of Gnathifera from phylogenomics. Mol. Phylogenet. Evol. 53: 1037-1041.
doi:10.1016/j.ympev.2009.07.031
Lasek-Nesselquist, E.,
D. B. Mark Welch,
R.C.A. Thompson, R.F. Steuart, and
M.L. Sogin.
2008.
Genetic exchange within and between assemblages of Giardia intestinalis
J. Eukar. Microbiol. 56: 504-518.
doi: 10.1111/j.1550-7408.2009.00443.x
Hasegawa, Yuko,
Jessica L. Mark Welch,
Alex Valm,
Christopher Rieken,
Mitchell Sogin, and
Gary Borisy
(in press).
Imaging marine bacteria with unique 16S rRNA V6 sequences by fluorescence in
situ hybridization and spectral analysis.
Geomicrobiology Journal,
accepted for publication.
Alliegro, M.C. and P. Satir,
2009.
Origin of the Cilium: Novel approaches to examine a centriolar evolution hypothesis.
Meth. Cell Biol. 94:51-63
Lazarevic V,
Whiteson K,
Huse S,
Hernandez D,
Farinelli L,
Osteras M,
Schrenzel J, &
Francois P
(in press)
Metagenomic study of the oral microbiota by Illumina high throughput sequencing
Journal of Microbiological Methods.
Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield PJ,
Huse S, & Joint I (2009 prerelease)
The seasonal structure of microbial communities in the Western English Channel
Environmental Microbiology 9999
Wernegreen, J. J., and D. E. Wheeler. 2009. Remaining flexible in old alliances: functional plasticity in constrained mutualisms. DNA Cell Biol 28:371-382.
Van Doninck, K., M. Mandigo, J. Hur , P. Wang , J. Guglielmini , M. Milinkovitch , W. Lane, M Meselson. (2009). Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers. PLoS Genetics, 5(3): e1000401.
Hur, J., K. Van Doninck, M. Mandigo, M Meselson. (2009). Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged. Molecular Biology and Evolution 26:375-383.
Kozul CD, Horvath RJ, Bomberger JM, Hamilton JW. Arsenic decreases chemotaxis of bone marrow derived dendritic cells. In Review, 2009.
Kozul CD, Ely KH, Enelow RI, Hamilton JW. Low-dose arsenic compromises the immune response to influenza A infection in vivo. Environ Hlth Perspect 117:1441-1447, 2009.
Barr FD, Krohmer LJ, Hamilton JW, Sheldon LA. Disruption of histone modification and CARM1 recruitment by arsenic represses transcription atglucocorticoid receptor-regulated promoters. PLoS ONE 4(8): e6766. doi:10.1371/journal.pone.0006766, 2009.
Kozul CD, Hampton TH, Davey JC, Gosse JA, Nomikos AP, Eisenhauer PL, WeissDJ, Thorpe JE, Ihnat MA, Hamilton JW. Chronic exposure to arsenic in the drinking water alters the expression of immune response genes in mouse lung.Environ Hlth Perspect 117:1108-1115, 2009.
Serres, MH, Kerr, AR, McCormack TJ, Riley, M. 2009. Evolution by leaps: gene duplication in bacteria. Biol. Direct 4(1):46.
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. Funct. Integr. Genomics (epub online)
Gillor O., Hadas O., Post A.F. and Belkin S. 2009. Phosphorus and nitrogen in a monomictic fresh water lake: a new insight into nutrient bioavailability. Freshwater Biol., doi:10.1111/j.1365-2427.2009.02342.x.
Claessens M., Wickham S.A., Post A.F. and Reuter M. 2009. A paradox of the ciliates? High cilate diversity in a resource-poor environment. Mar. Biol., doi 10.1007/s00227-009-1334-7.
Aberle N., Hansen T., Böttger-Schnack R., Holzman R., Post A.F. and Sommer U. 2009. Trophodynamic interactions of zooplankton communities in the northern Gulf of Aqaba. Mar. Biol., doi 10.1007/s00227-009-1306-y.
Gladyshev E.A., Arkhipova I.R. (2010).
Bdelloid rotifers.
McGraw Hill Yearbook of Science and Technology, McGraw Hill, New York, NY (in press).
Gladyshev E.A., and
Arkhipova I.R. (2009)
Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally
long target site duplication upon insertion. Gene 448(2):145-150.
Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L. A.,
Rodriguez-Mora, M., Chistoserdov, A., Orsi, W. & Edgcomb, V. 2009,
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities, BMC Biology, vol. 7, no. 1, p. 72.
Snell, T.W., Shearer T.L., Smith H.A., Kubanek J., Gribble, K.E., and Mark Welch D.B. 2009.
Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera). BMC Biology 7:60.
Konstantinos T. Konstantinidis, Margrethe H. Serres, Margaret F. Romine, Jorge L. M. Rodrigues, Jennifer Auchtung, Lee-Ann McCue, Mary S. Lipton, Anna Obraztsova, Carol S. Giometti, Kenneth H. Nealson, James K. Fredrickson, and James M. Tiedje.
Comparative systems biology across an evolutionary gradient within the Shewanella genus
PNAS 2009 : Published online before print September 1, 2009, doi: 10.1073/pnas.0902000106
Nahum LA, Goswami S, Serres MH.
Protein families reflect the metabolic diversity of organisms and provide support for functional prediction. Physiol Genomics. 2009 Aug 7;38(3):250-60. PMID: 19491149
Amaral-Zettler L.A., McCliment E.A., Ducklow H.W., Huse S.M. (2009)
A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable
Regions of Small-Subunit Ribosomal RNA Genes.
PLoS ONE 4(7): e6372. doi:10.1371/journal.pone.0006372
Eugene A. Gladyshev and
Irina R. Arkhipova.
A single-copy IS5-like transposon in the genome of a bdelloid rotifer
Molecular Biology and Evolution, 26(8): 1921-1929.
Huber, J. A., H. G. Morrison, S. M. Huse,
P. R. Neal, M. L. Sogin, and D. B. Mark Welch. 2009.
Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology 11:1292-1302.
Dionysios A. Antonopoulos, Susan M. Huse, Hilary G. Morrison, Thomas M. Schmidt,
Mitchell L. Sogin, and Vincent B. Young. 2009.
Reproducible Community Dynamics of the Gastrointestinal Microbiota Following Antibiotic Perturbation.
Infect. Immun doi:10.1128/IAI.01520-08
Gribble, K.E., D.M. Anderson, D.W. Coats. 2009.
Sexual and Asexual Processes in Protoperidinium steidingerae Balech (Dinophyceae), with Observations on Life-History Stages of Protoperidinium depressum (Bailey) Balech (Dinophyceae). Journal of Eukaryotic Microbiology 56(1): 88-103.
Turnbaugh, P.J., M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J.Jones, B.A. Roe, J.P. Affourtit, M.Egholm, B. Henrissat, A.C. Heath, R. Knight and J.I. Gordon. A core gut microbiome in obese and lean twins. Nature 457:480-484 (2009).
Donna E. Akiyoshi, Hilary G. Morrison, Shi Lei, Xiaochuan Feng, Quanshun Zhang, Nicolas
Corradi, Harriet Mayanja, James K. Tumwine, Patrick J. Keeling, Louis M. Weiss, Saul Tzipori.
(2009) Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen. Enterocytozoon bieneusi.
PLoS Pathog 5(1): e1000261. doi:10.1371/journal.ppat.1000261
Anton A. Turanov, Alexey V. Lobanov, Dmitri E. Fomenko, Hilary G. Morrison,
Mitchell L. Sogin, Lawrence A. Klobutcher,
Dolph L. Hatfield, Vadim N. Gladyshev. (2009).
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon.
Science 323 no. 5911. pp. 259-261 DOI:10.1126/science.1164748
