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2015

Goodheart J, Bazinet AL, Collins AG, CUMMINGS MICHAELP. 2015. Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. Royal Society Open Science. 23547143619757560685451171766(9):150196.

Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WHWilson, Moravec CS, Margulies KB, Cappola TP et al.. 2015. RNA-Seq identifies novel myocardial gene expression signatures of heart failure.. Genomics. 105(2):83-9.

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.

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.

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.

2014

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.

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.

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.

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.

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.

Bazinet AL, Zwickl DJ, Cummings MP. 2014. A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Syst Biol.

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.

Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al.. 2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.

Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al.. 2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.

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.

Parker HS, Bravo HCorrada, Leek JT. 2014. Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561.

Paulson JN, Bravo éctorCorrada, Pop M. 2014. Reply to: "A fair comparison". Nature Methods. 11(4):359-360.

Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DTW, Laje G, Johnson K et al.. 2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.. Mol Psychiatry. 19(11):1179-85.

Akula N., Barb J., Jiang X., Wendland J.R, Choi K.H, Sen S.K, Hou L., Chen D.TW, Laje G., Johnson K. et al.. 2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry.

Akula N., Barb J., Jiang X., Wendland J.R, Choi K.H, Sen S.K, Hou L., Chen D.TW, Laje G., Johnson K. et al.. 2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry.

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