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2015
Okrah K, Bravo HCorrada.  2015.  Shape analysis of high-throughput transcriptomics experiment data.. Biostatistics. 16(4):627-40.
Dillon LAL, Suresh R, Okrah K, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions.. BMC Genomics. 16(1):1108.
Megchelenbrink W, Katzir R, Lu X, Ruppin E, Notebaart RA.  2015.  Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival.. Proc Natl Acad Sci U S A.
Goodheart J, Camacho-García Y, Padula V, Schrödl M, Cervera JL, Gosliner TM, Valdés Á.  2015.  Systematics and biogeography of Pleurobranchus  Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae). Zoological Journal of the Linnean Society. :n/a-n/a.
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.
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.
Pop M, Salzberg SL.  2015.  Use and mis-use of supplementary material in science publications. BMC Bioinformatics. 1632733845166(1)
2014
Koren S, Treangen T, Hill CM, Pop M, Phillippy AM.  2014.  Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126.
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.
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.
Mendelowitz L, Pop M.  2014.  Computational methods for optical mapping. GigaScienceGigaScience. 3:33.
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.
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.
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.
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.
Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S..  2014.  Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.
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.
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.
Chelaru F, Smith L, Goldstein N, Bravo HCorrada.  2014.  Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.
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.
Bazinet AL, Zwickl DJ, Cummings MP.  2014.  A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Syst Biol.
Eilam O., Zarecki R., Oberhardt M., Ursell L.K, Kupiec M., Knight R., Gophna U., Ruppin E..  2014.  Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14.
Treangen T, Ondov BD, Koren S, Phillippy AM.  2014.  The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. 15:524.
Stempler S, Yizhak K, Ruppin E.  2014.  Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.  2014.  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.

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