Research Publications

Pages

2010
Leek JT, Scharpf RB, Bravo HCorrada, Simcha D, Langmead B, W. Johnson E, Geman D, Baggerly K, Irizarry RA. 2010. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature reviews. GeneticsNature reviews. Genetics. 11 Google Scholar BibTeX EndNote XML RIS
Joseph SJ, Fernández-Robledo JA, Gardner MJ, El-Sayed NM, Kuo C-H, Schott EJ, Wang H, Kissinger JC, Vasta GR. 2010. The Alveolate Perkinsus marinus: biological insights from EST gene discovery.. BMC Genomics. 11:228. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Navlakha S., Kingsford C. 2010. The power of protein interaction networks for associating genes with diseases. BioinformaticsBioinformatics. 26 Google Scholar BibTeX EndNote XML RIS
Haley BJ, Grim CJ, Hasan NA, Taviani E, Jongsik C, Brettin TS, Bruce DC, Challacombe JF, J. Detter C, Han CS et al.. 2010. The pre‐seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2 Google Scholar BibTeX EndNote XML RIS
Selengut J., Haft DH. 2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Journal of bacteriologyJournal of bacteriology. 192 Google Scholar BibTeX EndNote XML RIS
Selengut JD, Haft DH. 2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.. J Bacteriol. 192(21):5788-98. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Reyna-Fabian M.E, Laclette J.P, Cummings MP, García-Varela M.. 2010. Validating the systematic position of ıt Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase. HydrobiologiaHydrobiologia. 644 Google Scholar BibTeX EndNote XML RIS
Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB. 2010. Young Proteins Experience More Variable Selection Pressures Than Old Proteins. Genome ResearchGenome Res.Genome ResearchGenome Res.. 20 Google Scholar BibTeX EndNote XML RIS

2009
Kingsford C, Nagarajan N, Salzberg SL. 2009. 2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates. PLoS ONEPLoS ONEPLoS ONEPLoS ONE. 4 Google Scholar BibTeX EndNote XML RIS
Lapizco-Encinas G., Kingsford C, Reggia JA. 2009. A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing. IEEE Swarm Intelligence Symposium, 2009. SIS '09. Google Scholar BibTeX EndNote XML RIS
Treangen T, Darling A.E., Achaz G., Ragan M.A., Messeguer X., Rocha E.P.C.. 2009. A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6(2):180-189. DOI Google Scholar BibTeX EndNote XML RIS
Treangen T, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EPC. 2009. A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 6:180–189. Google Scholar BibTeX EndNote XML RIS
Eng K.H, Bravo HCorrada, Keles S.. 2009. A phylogenetic mixture model for the evolution of gene expression. Molecular biology and evolutionMolecular biology and evolution. 26 Google Scholar BibTeX EndNote XML RIS
Khan Z., Bloom J.S, Kruglyak L., Singh M.. 2009. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616. DOI Google Scholar BibTeX EndNote XML RIS
Khan Z, Bloom JS, Kruglyak L, Singh M. 2009. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.. Bioinformatics. 25(13):1609-16. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Kingsford C, Marçais G.. 2009. A synthesis for exactly 3-edge-connected graphs. Arxiv preprint arXiv:0905.1053Arxiv preprint arXiv:0905.1053. Google Scholar BibTeX EndNote XML RIS
Mohapatra SS, Mantri CK, Mohapatra H, Colwell RR, Singh DV. 2009. Analysis of clonally related environmental Vibrio cholerae O1 El Tor isolated before 1992 from Varanasi, India reveals origin of SXT‐ICEs belonging to O139 and O1 serogroups. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2 Google Scholar BibTeX EndNote XML RIS
Liu B., Pop M.. 2009. ARDB--Antibiotic Resistance Genes Database. Nucleic Acids ResearchNucleic Acids Research. 37 Google Scholar BibTeX EndNote XML RIS
Marbach-Ad G., Briken V., El-Sayed N.M., Frauwirth K., Fredericksen B., Hutcheson S., Gao L.-Y., Joseph S., Lee V., McIver K.S. et al.. 2009. Assessing Student Understanding of Host Pathogen Interactions Using a Concept Inventory. J. Microbiol. Biol. Ed.. 10:43-50. Google Scholar BibTeX EndNote XML RIS
Acevedo MA, Corrada-Bravo CJ, Corrada-Bravo H, Villanueva-Rivera LJ, T. Aide M. 2009. Automated classification of bird and amphibian calls using machine learning: A comparison of methods. Ecological Informatics. 4(4):206-214. DOI Google Scholar BibTeX EndNote XML RIS

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