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Y

Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E. 2014. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3

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.

S

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

Selengut J., Rusch DB, Haft DH. 2010. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. BMC bioinformaticsBMC Bioinformatics. 11

Selengut JD, Rusch DB, Haft DH. 2010. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.. BMC Bioinformatics. 11:52.

R

Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. 2004. Reducing storage requirements for biological sequence comparison.. Bioinformatics. 20(18):3363-9.

P

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.

K

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.

Khan Z, Balch T, Dellaert F. 2005. MCMC-based particle filtering for tracking a variable number of interacting targets.. IEEE Trans Pattern Anal Mach Intell. 27(11):1805-19.

Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L. 2009. Protein quantification across hundreds of experimental conditions.. Proc Natl Acad Sci U S A. 106(37):15544-8.

Khan Z, Balch T, Dellaert F. 2006. MCMC data association and sparse factorization updating for real time multitarget tracking with merged and multiple measurements.. IEEE Trans Pattern Anal Mach Intell. 28(12):1960-72.

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.

H

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.

C

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

B

Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. 2009. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.. BMC Genomics. 10:221.

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

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.

A

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.