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Author Title [ Type(Desc)] Year
Journal Article
Balch T., Dellaert F., Feldman A., Guillory A., Isbell C.L., Khan Z., Pratt S.C., Stein A.N., Wilde H..  2006.  How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior. Proceedings of the IEEE. 94(7):1445-1463.
Battle A., Khan Z., Wang S.H, Mitrano A., Ford M.J, Pritchard J.K, Gilad Y..  2015.  Impact of regulatory variation from RNA to protein. Science. 347(6222):664-667.
Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS.  2015.  Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.
Pal LR, Yu C-H, Mount SM, Moult J.  2015.  Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease.. BMC Genomics. 16 Suppl 8:S4.
Stempler S, Yizhak K, Ruppin E.  2014.  Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.  2014.  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Segal EShtifman, Freilich S, Henry CS, Gophna U, Ruppin E.  2014.  Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.
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, 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, 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.
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.
Yizhak K., Chaneton B., Gottlieb E., Ruppin E..  2015.  Modeling cancer metabolism on a genome scale. Molecular Systems Biology. 11(6):817-817.
Jerby-Arnon L, Ruppin E.  2015.  Moving ahead on harnessing synthetic lethality to fight cancer. Molecular & Cellular Oncology. 2(2):e977150.
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.
Wang K, Das A, Xiong Z-M, Cao K, Hannenhalli S.  2015.  Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12(1):30-39.
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., Ford M.J, Cusanovich D.A, Mitrano A., Pritchard J.K, Gilad Y..  2013.  Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures. Science. 342(6162):1100-1104.
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.
Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, Avanzato D, Maione F, Hernandez-Fernaud JR, Mackay G, Zheng L et al..  2015.  Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.
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.

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