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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

Shan L, Yang H-C, S. Rabi A, Bravo HCorrada, Shroff NS, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF. 2011. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. Journal of virologyJournal of virology. 85

Severance S, Rajagopal A, Rao AU, Cerqueira GC, Mitreva M, El-Sayed NM, Krause M, Hamza I. 2010. Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans.. PLoS Genet. 6(7):e1001044.

Selengut J., Haft DH. 2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Journal of bacteriologyJournal of bacteriology. 192

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.

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, Haft DH. 2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.. J Bacteriol. 192(21):5788-98.

Savage AF, Cerqueira GC, Regmi S, Wu Y, Sayed NMEl, Aksoy S. 2012. Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts.. PLoS Negl Trop Dis. 6(6):e1708.

K

Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celià-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y et al.. 2011. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.. Nat Med. 17(9):1101-8.

Kim R., Kulkarni P., Hannenhalli S. 2013. Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC CancerBMC CancerBMC Cancer. 13:144.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. 2012. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.. Mol Syst Biol. 8:602.

H

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.

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

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Diehl S, Diehl F, El-Sayed NM, Clayton C, Hoheisel JD. 2002. Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray.. Mol Biochem Parasitol. 123(2):115-23.

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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

Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, el-Sayed NMA, Clark DS. 2005. Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock.. Environ Microbiol. 7(6):789-97.

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.

Bartholomeu DC, Cerqueira GC, Leão ACarolina A, daRocha WD, Pais FS, Macedo C, Djikeng A, Teixeira SMR, El-Sayed NM. 2009. Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi.. Nucleic Acids Res. 37(10):3407-17.

A

Attardo GM, Strickler-Dinglasan P, Perkin SAH, Caler E, Bonaldo MF, Soares MB, El-Sayeed N, Aksoy S. 2006. Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans morsitans.. Insect Mol Biol. 15(4):411-24.