Research Publications

Pages

2015
Simpson J.T, Pop M.. 2015. The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum GenetAnnu Rev Genomics Hum Genet. 16:153-72. Google Scholar BibTeX EndNote XML RIS
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM. 2015. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Pop M, Salzberg SL. 2015. Use and mis-use of supplementary material in science publications. BMC Bioinformatics. 1632733845166(1) DOI Google Scholar BibTeX EndNote XML RIS

2014
Yizhak K, Le Dévédec SE, Rogkoti VMaria, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E. 2014. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Bazinet AL, Zwickl DJ, Cummings MP. 2014. A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Syst Biol. Google Scholar BibTeX EndNote XML RIS
Regier JC, Mitter C, Davis DR, HARRISON TERRYL, Sohn J-C, Cummings MP, Zwick A, Mitter KT. 2014. A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Systematic Entomology. 40:409-432. DOI Google Scholar BibTeX EndNote XML RIS
Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP et al.. 2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20. Google Scholar BibTeX EndNote XML RIS
Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. 2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726. DOI Google Scholar BibTeX EndNote XML RIS
Lu Y, Hannenhalli S, Cappola T, Putt M. 2014. An evaluation of Monte-Carlo logic and logicFS motivated by a study of the regulation of gene expression in heart failure. Journal of Applied Statistics. 41(9):1956-1975. DOI Google Scholar BibTeX EndNote XML RIS
Koren S, Treangen T, Hill CM, Pop M, Phillippy AM. 2014. Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Ye C, Hsiao C, Bravo HCorrada. 2014. BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics. 30(9):1214-9. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Treangen TJ, Maybank RA, Enke S, Friss MBeth, Diviak LF, Karaolis DKR, Koren S, Ondov B, Phillippy AM, Bergman NH. 2014. Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome announcements. 2:e01110–14. Google Scholar BibTeX EndNote XML RIS
Mendelowitz L, Pop M. 2014. Computational methods for optical mapping. GigaScienceGigaScience. 3:33. Google Scholar BibTeX EndNote XML RIS
Park S, Hannenhalli S, Choi S. 2014. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 15(1):526. DOI Google Scholar BibTeX EndNote XML RIS
Almeida M, Hebert A, Abraham A-L, Rasmussen S, Monnet C, Pons N, Delbes C, Loux V, Batto J-M, Leonard P et al.. 2014. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101. Google Scholar BibTeX EndNote XML RIS
Plasschaert R.N, Vigneau S., Tempera I., Gupta R., Maksimoska J., Everett L., Davuluri R., Mamorstein R., Lieberman P.M, Schultz D. et al.. 2014. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids ResNucleic Acids ResNucleic Acids Res. 42:774-89. Google Scholar BibTeX EndNote XML RIS
Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S.. 2014. Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514. DOI Google Scholar BibTeX EndNote XML RIS
Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY. 2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76. PubMed DOI Google Scholar BibTeX EndNote XML RIS
Chelaru F, Smith L, Goldstein N, Bravo HCorrada. 2014. Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40. PubMed DOI Google Scholar BibTeX EndNote XML RIS

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