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2014
Ye C, Hsiao C, Bravo H C.  2014.  BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics (Oxford, England).
Alemu EY, Carl JW, Bravo H C, Hannenhalli S.  2014.  Determinants of expression variability.. Nucleic acids research.
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.  2014.  Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.. Bioinformatics (Oxford, England).
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.. Molecular psychiatry.
2013
Cummings MP.  2013.  AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite .... Dictionary of Bioinformatics.
Mukherjee R, Singh LNS, Evans P, Hannenhalli S.  2013.  Correlated evolution of positions within mammalian cis elements PLoS ONE. PLoS ONE. in press:126.
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.  2013.  De novo likelihood-based measures for comparing genome assemblies. BMC research notes. 6:334.
Boca SM, Bravo H C, Caffo B, Leek JT, Parmigiani G.  2013.  A decision-theory approach to interpretable set analysis for high-dimensional data.. Biometrics. 69(3):614-23.
Paulson JN, Stine CO, Bravo H C, Pop M.  2013.  Differential abundance analysis for microbial marker-gene surveys. Nature methods.
Nijkamp JF, Pop M, Reinders MJT, de Ridder D.  2013.  Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.. Bioinformatics (Oxford, England). 29(22):2826-34.
Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al..  2013.  Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia.. Proceedings of the National Academy of Sciences of the United States of America. 110:240-5.
Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M, Read TD, Richards AL.  2013.  Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate. Genome announcements. 1(3):e00399-13.
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.  2013.  Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in bioinformatics. 14:213–224.
Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P.  2013.  Intrinsically disordered proteins and conformational noise: Implications in cancer. Cell Cycle. 12(1):26-31.
Hill CM, Albach CH, Angel S, Pop M.  2013.  K-mulus: Strategies for BLAST in the cloud. 10th International Conference on Parallel Processing and Applied Mathematics (PPAM).
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.  2013.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 14:R2.
Sohn J-C, Regier JC, Mitter C, Davis D, Landry J-\ F, Zwick A, Cummings MP.  2013.  A molecular phylogeny for Yponomeutoidea (Insecta, Lepido\ ptera, Ditrysia) and its implications for classification, biogeography and\ the evolution of host plant use.. PLoS One.
Lindsay B, Ochieng JB, Ikumapayi UN, Toure A, Ahmed D, Li S, Panchalingam S, Levine MM, Kotloff K, Rasko DA.  2013.  Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries. Journal of Clinical Microbiology. 51(6):1740-1746.
Nagarajan N, Pop M.  2013.  Sequence assembly demystified. Nature Reviews Genetics. 14(3):157-167.
Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Corrada Bravo H, Fredrikson KM, Harkins TT et al..  2013.  Somatic alterations contributing to metastasis of a castration-resistant prostate cancer.. Human mutation. 34(9):1231-41.
Lindsay B, Pop M, Antonio M, Walker AW, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine MM.  2013.  Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. Journal of Clinical Microbiology. 51(10):3263-3269.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013.. Nucleic acids research. 41(Database issue):D387-95.
2012
Memon AM.  2012.  Advances in Computers.
Lin HC, Goldstein S, Mendelowitz L, Zhou S, Wetzel J, Schwartz DC, Pop M.  2012.  AGORA: Assembly Guided by Optical Restriction Alignment. BMC bioinformatics. 13:189.
Haft DH, Payne SH, Selengut JD.  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.. Journal of bacteriology. 194(1):36-48.

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