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Journal Article
Khan Z, Balch T, Dellaert F.  2005.  MCMC-Based Particle Filtering for Tracking a Variable Number of Interacting Targets. IEEE Transactions on Pattern Analysis and Machine Intelligence. 27(11):1805-1918.
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(1):221.
Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al..  2014.  Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.
Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al..  2014.  Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.
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.
Khan Z, Herman RA, Wallen K, Balch T.  2005.  An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys.. Behav Res Methods. 37(3):453-63.
Waisberg M, Cerqueira GC, Yager SB, Francischetti IMB, Lu J, Gera N, Srinivasan P, Miura K, Rada B, Lukszo J et al..  2012.  Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.. Proc Natl Acad Sci U S A. 109(14):5429-34.
Khan Z., Bloom J.S, Kruglyak L., Singh M..  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616.
Khan Z., Bloom J.S, Garcia B.A, Singh M., Kruglyak L..  2009.  Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences. 106(37):15544-15548.
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.
Parker HS, Bravo HCorrada, Leek JT.  2014.  Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561.
Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WHWilson, Moravec CS, Margulies KB, Cappola TP et al..  2015.  RNA-Seq identifies novel myocardial gene expression signatures of heart failure.. Genomics. 105(2):83-9.
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.. Mol Psychiatry. 19(11):1179-85.
Okrah K, Bravo HCorrada.  2015.  Shape analysis of high-throughput transcriptomics experiment data.. Biostatistics. 16(4):627-40.
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
Journal Articles
Berman P., Hannenhalli S, Karpinski M..  2002.  1.375-approximation algorithm for sorting by reversals. Algorithms—ESA 2002Algorithms—ESA 2002.
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.
El‐Sayed NM, Bartholomeu D, Ivens A, Johnston DA, LoVerde PT.  2004.  Advances in schistosome genomics. Trends in ParasitologyTrends in Parasitology. 20
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.
Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA.  1980.  Are snRNPs involved in splicing? Nature. 283(5743):220-4.
Marbach-Ad G., Briken V., El-Sayed N.M., Frauwirth K., Fredericksen B., Hutcheson S., Gao L.-Y., Joseph S., Lee V., McIver K.S. et al..  2009.  Assessing Student Understanding of Host Pathogen Interactions Using a Concept Inventory. J. Microbiol. Biol. Ed.. 10:43-50.
Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al..  2011.  Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108
Das A, Morley M, Moravec CS, Tang W.HW, Hakonarson H, Ashley EA, Brandimarto J, Hu R, Li M, Li H et al..  2015.  Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6:8555.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61

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