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A

Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S. 2011. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.. Genome Biol. 12(12):R122.

Koren S, Treangen T, Hill CM, Pop M, Phillippy AM. 2014. Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126.

B

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.

C

Bazinet AL, Cummings MP. 2011. Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids. Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on.

E

Chelaru F, Smith L, Goldstein N, Bravo HCorrada. 2014. Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.

G

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

I

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al.. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.. Nucleic Acids Res. 31(19):5654-66.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database.. Nucleic Acids Res. 40(Database issue):D306-12.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40

M

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. 30(10):1363-9.

O

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.

P

Basu MK, Selengut JD, Haft DH. 2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.. BMC Bioinformatics. 12:434.

Basu MK, Selengut J., Haft DH. 2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC bioinformaticsBMC Bioinformatics. 12

Q

Khan Z, Wang Y-C, Wieschaus EF, Kaschube M. 2014. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.. Development. 141(14):2895-900.

S

Patro R, Mount SM, Kingsford C. 2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.. Nat Biotechnol. 32(5):462-4.

Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C. 1992. Splicing signals in Drosophila: intron size, information content, and consensus sequences.. Nucleic Acids Res. 20(16):4255-62.

T

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