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Author Title [ Type(Asc)] Year
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Journal Articles
Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT et al..  2004.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32
Selengut J., Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, R. Richter A, White O.  2007.  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013.. Nucleic Acids Res. 41(Database issue):D387-95.
Haft DH, Selengut J., Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013. Nucleic acids researchNucleic Acids Research. 41
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
LoVerde PT, Hirai H, Merrick JM, Lee NH, El‐Sayed NM.  2004.  Schistosoma mansoni genome project: an update. Parasitology InternationalParasitology International. 53
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.
Shi W, Wahba G, Irizarry RA, Bravo HCorrada, Wright SJ.  2012.  The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC bioinformaticsBMC Bioinformatics. 13
Bowler C, Karl DM, Colwell RR.  2009.  Microbial oceanography in a sea of opportunity. NatureNature. 459
Mount SM.  2000.  Genomic sequence, splicing, and gene annotation.. Am J Hum Genet. 67(4):788-92.
Haft DH, Selengut J., Brinkac LM, Zafar N, White O.  2005.  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 21
Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S et al..  2004.  Gene synteny and evolution of genome architecture in trypanosomatids.. Mol Biochem Parasitol. 134(2):183-91.
Bravo HCorrada, Pihur V, McCall M, Irizarry RA, Leek JT.  2012.  Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC bioinformaticsBMC Bioinformatics. 13
Choi J, El-Sayed NM.  2012.  Functional genomics of trypanosomatids.. Parasite Immunol. 34(2-3):72-9.
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN et al..  2007.  Evolution of genes and genomes on the Drosophila phylogeny.. Nature. 450(7167):203-18.
Hotopp JCDunning, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M et al..  2006.  Comparative genomics of emerging human ehrlichiosis agents. PLoS geneticsPLoS genetics. 2
Cummings MP.  2004.  A book like its cover. HeredityHeredity. 93
Koren S, Treangen T, Hill CM, Pop M, Phillippy AM.  2014.  Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126.
Journal Article
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al..  2015.  Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.
Smircich P, Forteza D, El-Sayed NM, Garat B.  2013.  Genomic analysis of sequence-dependent DNA curvature in Leishmania.. PLoS One. 8(4):e63068.
Chelaru F, Smith L, Goldstein N, Bravo HCorrada.  2014.  Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.
Conference Proceedings
Nagarajan N., Kingsford C.  2008.  Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08.
Liu B, Gibbons T., Ghodsi M., Pop M..  2010.  MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
Ghodsi M., Pop M..  2009.  Inexact Local Alignment Search over Suffix Arrays. IEEE International Conference on Bioinformatics and Biomedicine, 2009. BIBM '09.
Hochheiser H., Baehrecke E.H, Mount SM, Shneiderman B.  2003.  Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3

Publications