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2015 (2)

Crowgey EL, Stabley DL, Chen C, Huang H, Robbins KM, Polson SW, Sol-Church K, Wu CH. An Integrated Approach for Analyzing Clinical Genomic Variant Data from Next-Generation Sequencing. J Biomol Tech. 2015 Jan 29. pii: jbt.15-2601-002. [Epub ahead of print] PubMed PMID: 25649353; PubMed Central PMCID: PMC4310222. [PMCID:PMC4310222]
Smith SA, Krasucki SP, McDowell JV, Balke VL. Complete genome sequence of Sphingobacterium sp. strain ML3W, isolated from wings of Myotis lucifugus infected with white nose syndrome. Genome Announcements. 2015 3(1):e01477-14. (PubMed pending)

2014 (17)

Chen C, Khaleel SS, Huang H, Wu CH. Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014. PubMed PMID: 24955109; PubMed Central PMCID: PMC4064128. [PMCID:PMC4064128]
Debruyn JM, Radosevich M, Wommack KE, Polson SW, Hauser LJ, Fawaz MN, Korlach J, Tsai YC. Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum. Genome Announc. 2014 Apr 3;2(2). pii: e00226-14. doi: 10.1128/genomeA.00226-14. PubMed PMID: 24699952; PubMed Central PMCID: PMC3974934. [PMCID:PMC3974934]
Famiglietti ML, Estreicher A, Gos A, Bolleman J, G�hant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium. Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. Hum Mutat. 2014 Aug;35(8):927-35. doi: 10.1002/humu.22594. Epub 2014 Jun 24. PubMed PMID: 24848695; PubMed Central PMCID: PMC4107114. [PMCID:PMC4107114]
Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, Green PJ. Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol. 2013 Dec 24;14(12):R145. doi: 10.1186/gb-2013-14-12-r145. PubMed PMID: 24367943; PubMed Central PMCID: PMC4053937. [PMCID:PMC4053937]
Kalburge SS, Polson SW, Boyd Crotty K, Katz L, Turnsek M, Tarr CL, Martinez-Urtaza J, Boyd EF. Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493. Genome Announc. 2014 Mar 13;2(2). pii: e00159-14. doi: 10.1128/genomeA.00159-14. PubMed PMID: 24625868; PubMed Central PMCID: PMC3953189. [PMCID:PMC3953189]
Kirchman DL, Hanson TE, Cottrell MT, Hamdan LJ. Metagenomic analysis of organic matter degradation in methane-rich Arctic Ocean sediments. Limnol. Oceanogr. 2014, 59: 548-559. doi:10.4319/lo.2014.59.2.0548 [link]
Maeda M, Harris AW, Kingham BF, Lumpkin CJ, Opdenaker LM, McCahan SM, Wang W, Butchbach ME. Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells. PLoS One. 2014 Sep 5;9(9):e106818. doi: 10.1371/journal.pone.0106818. eCollection 2014. PubMed PMID: 25191843; PubMed Central PMCID: PMC4156416. [PMCID:PMC4156416]
Manthey AL, Lachke SA, FitzGerald PG, Mason RW, Scheiblin DA, McDonald JH, Duncan MK. Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development. Mech Dev. 2014 Feb;131:86-110. doi: 10.1016/j.mod.2013.09.005. Epub 2013 Oct 23. PubMed PMID: 24161570; PubMed Central PMCID: PMC4144920. [PMCID:PMC4144920]
Manthey AL, Terrell AM, Lachke SA, Polson SW, Duncan MK. Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis. Genom Data. 2014 Dec 1;2:369-374. PubMed PMID: 25478318; PubMed Central PMCID: PMC4248573. [PMCID:PMC4248573]
Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, Wommack KE. Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome. 2014 Jan 30;2(1):3. doi: 10.1186/2049-2618-2-3. PubMed PMID: 24475755; PubMed Central PMCID: PMC3937105. [PMCID:PMC3937105]
Poux S, Magrane M, Arighi CN, Bridge A, O’Donovan C, Laiho K; UniProt Consortium. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016. Print 2014. PubMed PMID: 24622611; PubMed Central PMCID: PMC3950660. [PMCID:PMC3950660]
Sakowski EG, Munsell EV, Hyatt M, Kress W, Williamson SJ, Nasko DJ, Polson SW, Wommack KE. Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses. Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15786-91. doi: 10.1073/pnas.1401322111. Epub 2014 Oct 13. PubMed PMID: 25313075; PubMed Central PMCID: PMC4226130. [PMCID:PMC4226130]
Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME J. 2014 Jan;8(1):103-14. doi: 10.1038/ismej.2013.124. Epub 2013 Aug 29. PubMed PMID: 23985748; PubMed Central PMCID: PMC3869006. [PMCID:PMC3869006]
Schmidt SA, Foley PL, Jeong DH, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG, Green PJ. Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. Nucleic Acids Res. 2014 Nov 27. pii: gku1258. [Epub ahead of print] PubMed PMID: 25429978. PMC pending [PMID:25429978]
Schulz MD, Atay C, Heringer J, Romrig FK, Schwitalla S, Aydin B, Ziegler PK, Varga J, Reindl W, Pommerenke C, Salinas-Riester G, Bock A, Alpert C, Blaut M, Polson SC, Brandl L, Kirchner T, Greten FR, Polson SW, Arkan MC. High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature. 2014 Oct 23;514(7523):508-12. doi: 10.1038/nature13398. Epub 2014 Aug 31. PubMed PMID: 25174708; PubMed Central PMCID: PMC4233209. [PMCID:PMC4233209]
UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8. doi: 10.1093/nar/gkt1140. Epub 2013 Nov 18. PubMed PMID: 24253303; PubMed Central PMCID: PMC3965022. [PMCID:PMC3965022]
Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res. 2014 Aug 12;3:191. doi: 10.12688/f1000research.4996.1. eCollection 2014. PubMed PMID: 25309735; PubMed Central PMCID: PMC4184313. [PMCID:PMC4184313]

2013 (13)

Campbell BJ, Polson SW, Zeigler Allen L, Williamson SJ, Lee CK, Wommack KE, Cary SC. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities. Front Microbiol. 2013;4:182. doi: 10.3389/fmicb.2013.00182. eCollection 2013. [PMCID:PMC3721025]
D’Souza MJ, Alabed GJ, Earley M, Roberts N, Gerges FJ. Manipulating In-House Designed Drug Databases For The Prediction of pH-Dependent Aqueous Drug Solubility. Am J Health Sci. 2013 Summer;4(3):137-150. PubMed PMID: 24478935; PubMed Central PMCID: PMC3903345. [PMCID:PMC3903345]
Gonzalez AJ, Liao L, Wu CH. Prediction of contact matrix for protein-protein interaction. Bioinformatics. 2013 Apr 15;29(8):1018-25. doi: 10.1093/bioinformatics/btt076. Epub 2013 Feb 15. PubMed PMID: 23418186; PubMed Central PMCID: PMC3624801. [PMCID:PMC3624801]
Huang X, Bruce B, Buchan A, Congdon CB, Cramer CL, Jennings SF, Jiang H, Li Z, McClure G, McMullen R, Moore JH, Nanduri B, Peckham J, Perkins A, Polson SW, Rekepalli B, Salem S, Specker J, Wunsch D, Xiong D, Zhang S, Zhao Z. No-boundary thinking in bioinformatics research. BioData Min. 2013 Nov 6;6(1):19. doi:10.1186/1756-0381-6-19. PubMed PMID: 24192339; PubMed Central PMCID: PMC3827872. [PMCID:PMC3827872]
Kern C, Gonzalez AJ, Liao L, Vijay-Shanker K. Predicting interacting residues using long-distance information and novel decoding in hidden Markov models. IEEE Trans Nanobioscience. 2013 Sep;12(3):158-64. doi: 10.1109/TNB.2013.2263810. Epub 2013 Aug 15. PubMed PMID: 23955776. [PMID:23955776]
Kuhn, K. L., J. J. Duan, and K. R. Hopper. Next-generation genome sequencing and assembly provides tools for phylogenetics and identification of closely related species of Spathius, parasitoids of Agrilus planipennis (emerald ash borer). 2013. Biological Control: 66 77-82. [link]
Manthey, A.L., Lachke, S.A., Fitzgerald, P.G., Mason, R., Scheiblin D.A., Duncan, M.K. Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development. (2013) Mechanisms of Development, in press [link]
Oppenheim SJ, Gould F, Hopper KR. The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa. Evolution. 2012 Nov;66(11):3336-51. doi: 10.1111/j.1558-5646.2012.01712.x. Epub 2012 Jul 12. [PMCID:PMC3490447]
Orsi W, Biddle JF, Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces. PLoS One. 2013;8(2):e56335. doi: 10.1371/journal.pone.0056335. Epub 2013 Feb 13. [PMCID:PMC3572030]
Orsi WD, Edgcomb VP, Christman GD, Biddle JF. Gene expression in the deep biosphere. Nature. 2013 Jul 11;499(7457):205-8. doi: 10.1038/nature12230. Epub 2013 Jun 12. [PMID:23760485]
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A; UniProt Consortium. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2013 Jan;41(Database issue):D584-9. doi: 10.1093/nar/gks1157. Epub 2012 Nov 27. PubMed PMID: 23193261; PubMed Central PMCID: PMC3531088. [PMCID:PMC3531088]
Srinivasiah S, Lovett J, Polson S, Bhavsar J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE. Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Appl Environ Microbiol. 2013 Sep;79(18):5450-7. doi: 10.1128/AEM.00268-13. Epub 2013 Jun 21. [PMCID:PMC3754152]
UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. doi: 10.1093/nar/gks1068. Epub 2012 Nov 17. PubMed PMID: 23161681; PubMed Central PMCID: PMC3531094. [PMCID:PMC3531094]

2012 (13)

Campbell BJ, Kirchman DL. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J. 2013 Jan;7(1):210-20. doi: 10.1038/ismej.2012.93. Epub 2012 Aug 16. [PMCID:PMC3526181]
Campbell BJ, Yu L, Heidelberg JF, Kirchman DL (2012). Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12776-81. Epub 2011 Jul 18. [PMCID:PMC3150899]
Hammond S, Kaplarevic M, Borth N, Betenbaugh M, Lee KH (2012). Chinese Hamster Genome Database: An Online Resource for the CHO Community at , Biotechnology and Bioengineering. 109:1353-1356. [PMID:22105744]
Hammond S, Swanberg J, Polson S, Lee KH (2012). Profiling Conserved MicroRNA Expression in Recombinant CHO Cell Lines Using Illumina Sequencing, Biotechnology and Bioengineering 109: 1353-1356. [PMCID:PMC3330154]
Hopper, K. R., J. B. Woolley, K. Hoelmer, K. Wu, G. Qiao, and S. Lee. 2012. An identification key to species in the mali complex of Aphelinus (Hymenoptera, Chalcidoidea) with descriptions of three new species. Journal of Hymenoptera Research 26:73-96. [link]
Jamindar S, Polson SW, Srinivasiah S, Waidner L, Wommack KE. Evaluation of two approaches for assessing the genetic similarity of virioplankton populations as defined by genome size. Appl Environ Microbiol. 2012 Dec;78(24):8773-83. doi: 10.1128/AEM.02432-12. Epub 2012 Oct 12. [PMCID:PMC3502916]
Kern C, Gonzalez A, Liao L, & V Shankar (2012). Improving Interacting Residue Prediction Using Long Distance Information in Hidden Markov Models. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM12) . pp. 179-184.
Lachke SA, Ho JW, Kryukov GV, O’Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, & RL Maas. (2012). iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci. 53(3):1617-1627. [PMCID:PMC3339920]
Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, & SC Cary (2012). Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 7(9):e44224. Epub 2012 Sep 6. [PMCID:PMC3435322]
Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E. High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol. 2012 Nov;86(22):12161-75. doi:10.1128/JVI.00869-12. Epub 2012 Aug 29. [PMCID:PMC3486453]
Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K. The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database (Oxford). 2012 Dec 5;2012:bas044. doi: 10.1093/database/bas044. Print 2012. [PMCID:PMC3514748]
Wang, Q.*, C.N. Arighi*, B.L. King*, S.W. Polson*, J. Vincent*, C. Chen, H. Huang, B. Kingham, S.T. Page, M.F. Rendino, W.K. Thomas, D.W. Udwary, C.H. Wu, and the North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert – Little skate genome annotation workshops and jamborees. Database, doi: 10.1093/database/bar064. * authors contributed equally [PMCID:PMC3308154]
Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci. 2012 Jul 30;6(3):427-39. doi:10.4056/sigs.2945050. Epub 2012 Jul 27. [PMCID:PMC3558967]

2011 (10)

Dumas, M.D., S.W. Polson, D. Ritter, J. Ravel, J. Gelb Jr., R. Morgan, and K.E. Wommack (2011). Impacts of poultry house environment on poultry litter bacterial community composition. PLOS One, 6(9):e24785 [PMCID:PMC3174962]
Gonzalez AJ, Liao L & CH Wu (2011). Predicting ligand binding residues and functional sites using multi-positional correlations with graph theoretic clustering and kernel CCA. IEEE/ACM Transaction on Computational Biology and Bioinformaics, 9(4):992-1001. [PMID:22025754]
Hammond S, Swanberg JC, Kaplarevic M, and Lee KH (2011). Genomic sequencing and analysis of a Chinese Hamster ovary cell line using Illumina sequencing technology, BMC Genomics, 12: 67. [PMCID:PMC3038171]
King B.L., J.A. Gillis, H.R. Carlisle, R.D. Dahn. A natural deletion of the HoxC cluster in elasmobranch fishes. Science. 2011 Dec 16;334(6062):1517. [PMCID:PMC3264428 ]
Marine, R., S.W. Polson, J. Ravel, G. Hatfull, D. Russell, M. Sullivan, F. Syed, N. Caruccio, M. Dumas, and K.E. Wommack (2011). Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied and Environmental Microbiology, 77:8071-8079. [PMCID:PMC3209006]
Polson SW, Wilhelm SW, Wommack KE. (2011) Unraveling the viral tapestry (from inside the capsid out). The ISME Journal 5:165-8. [PMCID:PMC3105704]
Schneider, I., I. Aneas, A.R. Gehrke, R.D. Dahn, M.A. Nobrega, N.H. Shubin. (2011) Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A. 108(31):12782-6. [PMCID:PMC3150877]
Williamson, K.E., J. Kan, S.W. Polson, S.J. Williamson (2011). Optimizing the Indirect Extraction of Prokaryotic DNA from Soils. Soil Biology and Biochemistry. 43:736-748. [link]
Wommack, K. E., Srinivasiah, S., Liles, M. R., Bhavsar, J., Bench, S., Williamson, K. E. and Polson, S. W. (2011) Metagenomic Contrasts of Viruses in Soil and Aquatic Environments, in Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (ed F. J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118010549.ch4 [link]
Xu X, Nagarajan H, Lewis NE, Pan Shengkai, Liu X, Chen W, Xie M, Wang W, Hammond S, AndersenM, Neff N, Passarelli B, Koh W, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J (2011). The Genomic Sequence of the Chinese Hamster Ovary (CHO) K1 Cell Line, Nature Biotechnology 29: 735-741. [PMCID:PMC3164356]

2010 (14)

Campbell BJ, Polson SW, Hanson TE, Mack MC, & EAG Schuur (2010). The effect of nutrient deposition on Arctic tundra bacterial communities. Environ. Microbiol. 12, 1842-1854 [PMID:20236166]
Chen C, McGarvey PB, Huang H, & CH Wu. (2010) Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput omics data. Advances in Bioinformatics 2010, 423589. [PMCID:PMC2847380]
Gomez-Pereira PR, Fuchs BM, Alonso C, Oliver MJ, Beusekom, JEE, & R. Amann (2010). Distinct flavobacterial commuities in contrasting water masses of the North Atlantic Ocean. The ISME Journal, 4:472-87. [PMID:20054356]
Gonzalez AJ & L Liao (2010). Predicting Domain-Domain Interaction Based on Domain Profiles with Feature Selection and Support Vector Machines. BMC Bioinformatics, 11:53. [PMCID:PMC2989984]
Gonzalez AJ, Liao L, & C Wu (2010). Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine. [PMID:22025754]
Gonzalez AJ, Liao L, & C. Wu (2010). Predicting Functional Sites in Biological Sequences Using Canonical Correlation Analysis. Proceedings of The International Conference on Bioinformatics and Computational Biology (BioComp10), pp.269-273 [link]
Kirchman DL, Cottrell MT, and C Lovejoy (2010). The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol. 12: 1132 – 1143. [PMID:20132284]
Oliver MJ, Schofield O, & K Bidle (2010). Density dependent expression of a diatom retrotransposon. Marine Genomics, 3:145-150. [PMID:21798208]
Parsley LC, Consuegra EJ, Thomas SJ, Bhavsar J, Land AM, Bhuiyan NN, Mazher MA, Waters RJ, Wommack KE, Harper WF Jr, Liles MR. Census of the viral metagenome within an activated sludge microbial assemblage. Appl Environ Microbiol. 2010 Apr;76(8):2673-7. doi: 10.1128/AEM.02520-09. Epub 2010 Feb 12. [PMCID:PMC2849206]
Schofield O, Glenn S, Orcutt J, Arrott M, Messinger M, Gangopadhyay A, Brown W, Signell R, Moline M, Chao Y, Chien S, Thompson D, Balasuriya A, Lermusaiux P, & M Oliver (2010). Automated sensor networks to advance ocean science. EOS, 91(39). [link]
Schofield O, Kohut J, Glenn G, Morell J, Capella J, Corredor J, Orcutt J, Arrott M, Krueger I, Meisinger M, Peach C, Vernon F, Chave A, Chao Y, Chien S, Thompson D, Brown W, Oliver M, & WA Boicourt. Regional Slocum Glider Network in the Mid-Atlantic Bight leverages broad community engagement. Marine Technology Society Journal[link]
Wenter R, Hutz K, Dibbern D, Li T, Reisinger V, Ploscher M, Eichacker L, Eddie B, Hanson T, Bryant DA, J Overmann. Expression-based identification of genetic determinants of the bacterial symbiosis ‘Chlorochromatium aggregatum’. Environmental Microbiology[PMID:21966918]
Zhu M, Ginder-Vogel M & DL Sparks (2010). Ni(II) Sorption on biogenic Mn-oxides with varying Mn octahedral layer structure. Environ. Sci. Technol. 44:4472-4478. [PMID:20469849]
Zhu M, Ginder-Vogel M, Parikh SJ, Feng X, & DL Sparks (2010). Cation effects on the layer structure of biogenic Mn-oxides. Environ. Sci. Technol. 44: 4465-4471. [PMID:20469850]

2009 (6)

Domagal-Goldman SD, Paul KW, Sparks DL, & JD Kubicki (2009). Quantum chemical study of the Fe(III)-desferrioxamine B siderophore complex – Electronic structure, vibrational frequencies, and equilibrium Fe-isotope fractionation. Geochim. Cosmochim. Acta 73(1):1-12. [link]
Gonzalez A and L Liao (2009). Constrained Fisher Scores Derived From Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Prediction. Proceedings of The 1st International Conference on Bioinformatics and Computational Biology (BICoB)}. pp. 236-247. [link]
Helton RR, Wommack KE. Seasonal dynamics and metagenomic characterization of estuarine viriobenthos assemblages by randomly amplified polymorphic DNA PCR. Appl Environ Microbiol. 2009 Apr;75(8):2259-65. doi: 10.1128/AEM.02551-08. Epub 2009 Feb 13. [PMCID:PMC2675235]
Irwin AJ & MJ Oliver (2009). Are ocean deserts getting larger? Geophysical Research Letters, Vol. 36, L18706, doi:10.1029/2009GL039414 [link]
Waidner L, Morgan RW, Anderson AS, Bernberg EL, Kamboj S, Garcia M, Riblet S, Ouyang M, Isaacs GK, Markis M, Meyers BC, Green PJ, & J Burnside (2009). Novel ILTV and HVT microRNAs have conserved genomic locations with those of other Gallid and Meleagrid herpesvirus microRNAs. Virology 338:128-136. [PMID:19328516]
Zhu M, Paul KW, Kubicki JD, & DL Sparks (2009). Quantum chemical study of arsenic (III, V) adsorption on Mn-oxides: Implications for arsenic(III) oxidation. Environ. Sci. Technol. 43: 6655-6661. [PMID:19764231]

2008 (9)

Burnside J, Ouyang M, Anderson AS, Bernberg EL, Cheng L, Meyers BC, Green PJ, Markis M, Isaacs GK, Huang E, & RW Morgan (2008). Deep Sequencing of Chicken microRNAs. BMC Genomics 9:185. [PMCID:PMC2375912]
Gonzalez A & L Liao (2008). Clustering Exact Matches of Pairwise Sequence Alignments by Weighted Linear Regression. BMC Bioinformatics, 9:102. [PMCID:PMC2263025]
Grzymski JJ, Murray AE, Campbell BJ, Kaplarevic M, Gao GR, Lee C, Daniel R, Ghadiri A, Feldman R, & SC Cary (2008). Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proceedings of the National Academy of Sciences USA. 105: 17516-17521. [PMCID:PMC2579889]
Kubicki JD, Paul KP, & DL Sparks (2008). Periodic density functional theory calculations of bulk and the (010) surface of goethite. Geochemical Transactions 9:4. [link]
Morgan RW, Anderson AS, Bernberg EL, Kamboj S, Huang E, Lagasse G, Isaacs GK, Parcells M, Meyers BC, Green PJ, & J Burnside (2008). Sequence conservation and differential expression of Marek’s disease virus microRNAs. J. Virology 82:12213-12220. [PMCID:PMC2593341]
Oliver MJ & AJ Irwin (2008). Objective Global Ocean Biogeographic Provinces. Geophysical Research Letters, Vol. 35, L15601, doi:10.1029/2008GL034238. [link]
Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, & D Mead (2008). Assembly of Viral Metagenomes from Yellowstone Hot Springs. Applied and Environmental Microbiology, vol. 74 (13) pp. 4164-4174 [PMCID:PMC2446518]
Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, Wommack KE. Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Res Microbiol. 2008 Jun;159(5):349-57. doi: 10.1016/j.resmic.2008.04.010. Epub 2008 May 8. Review. [PMID:18565737]
Wommack KE, Bhavsar J, Ravel J. Metagenomics: read length matters. Appl Environ Microbiol. 2008 Mar;74(5):1453-63. doi: 10.1128/AEM.02181-07. Epub 2008 Jan 11. [PMCID:PMC2258652]

2007 (3)

Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K, & KE Wommack (2007). Metagenomic characterization of Chesapeake Bay virioplankton. Applied and Environmental Microbiology, vol. 73 (23) pp. 7629-7641 [PMCID:PMC2168038]
Kubicki JD, Kwon KD, Paul KP, & DL Sparks (2007). Surface complex structures modelled with quantum chemical calculations: carbonate, phosphate, sulphate, arsenate and arsenite. European J Soil Sci. 58:932-944. [link]
Paul KW, Kubicki JD, & DL Sparks (2007). Sulphate adsorption at the Fe (hydr)oxide-H2O interface: comparison of cluster and periodic slab DFT predictions, European J Soil Sci. 58:978-988. [link]

2006 (3)

Lu C, Kulkarni K, Souret FF, Valliappan RM, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, PJ Green* & BC Meyers* (2006). microRNAs and other small RNAs enriched in the Arabidopsis RNA-DEPENDENT RNA POLYMERASE-2 mutant. Genome Research. 16: 1276-1288. * indicates co-corresponding authors. [PMCID:PMC1581437]
Paul KW, Kubick JD, Sparks DL. Quantum chemical calculations of sulfate adsorption at the Al- and Fe-(hydr)oxide-H20 interface-estimation of gibbs free energies. Environ Sci Technol. 2006 Dec 15;40(24):7717-24. [PMCID:PMC17256518]
Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, & J Jiang (2006). Genomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere. Plant Cell. 18: 2123-2133. [PMCID:PMC1560911]

2005 (1)

Paul KW, Borda MJ, Kubicki JD, Sparks DL. Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation. Langmuir. 2005 Nov 22;21(24):11071-8 [PMID:16285773]

2004 (1)

Meyers BC, Vu TH, Tej SS, Matvienko M, Ghazal H, Agrawal V, & CD Haudenschild (2004). Analysis of the transcriptional complexity of Arabidopsis by massively parallel signature sequencing. Nature Biotechnology. 22: 1006-1011. [PMID:15247925]


The Core is generously supported by grants from the NIH National Institute of General Medical Sciences (8 P20 GM103446-14), and National Science Foundation EPSCoR (EPS-081425). Please acknowledge this contribution in any publications supported by Core resources.