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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.
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.
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.
Kawahara A.Y, Ohshima I., Kawakita A., Regier J.C, Mitter C., Cummings MP, Davis D.R, Wagner D.L, De Prinis J., Lopez-Vaamonde C..  2011.  Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evol BiolBMC Evol Biol. 11:182
Zwick A, Regier JC, Mitter C, Cummings MP.  2011.  Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera). Systematic EntomologySystematic Entomology. 36
Takala-Harrison S., Jacob C.G, Arze C., Cummings MP, Silva J.C, Dondorp A.M, Fukuda M.M, Hien T.T, Mayxay M., Noedl H. et al..  2015.  Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.
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
Shan L., Yang H.-C., Rabi S.A, Bravo H.C, Shroff N.S, Irizarry R.A, Zhang H., Margolick J.B, Siliciano J.D, Siliciano R.F.  2011.  Influence of Host Gene Transcription Level and Orientation on HIV-1 Latency in a Primary-Cell Model. Journal of Virology. 85(11):5384-5393.
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.
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
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.
Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P.  2013.  Intrinsically disordered proteins and conformational noise: Implications in cancer. Cell CycleCell Cycle. 12
Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P.  2013.  Intrinsically disordered proteins and conformational noise: Implications in cancer. Cell CycleCell Cycle. 12
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Auslander N, Yizhak K, Weinstock A, Budhu A, Tang W, Wang XWei, Ambs S, Ruppin E.  2016.  A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.. Sci Rep. 6:29662.
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Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn J-C, Zwickl DJ, Cho S, Davis DR et al..  2013.  A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS OnePLoS One. 8
Treangen T, Darling AE, Ragan MA, Messeguer X.  2008.  Lecture Notes in Computer ScienceBioinformatics Research and ApplicationsGapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. 4983:74-86.
Khan Z, Balch T, Dellaert F.  2004.  Lecture Notes in Computer ScienceComputer Vision - ECCV 2004An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets. 3024:279-290.
Bafna V, Hannenhalli S, Rice K, Vawter L.  2000.  Ligand-Receptor Pairing Via Tree Comparison. Journal of Computational BiologyJournal of Computational Biology. 7
Vezzulli L, Brettar I, Pezzati E, Reid PC, Colwell RR, Höfle MG, Pruzzo C.  2011.  Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. The ISME JournalThe ISME journal. 6
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Todd GJ, Schwartz A, Rapoport F.  1989.  Management of an enlarging aortic aneurysm in the presence of radiation induced retroperitoneal fibrosis.. J Cardiovasc Surg (Torino). 30(2):233-5.
Colwell RR.  2008.  The marine environment and human health: the cholera model. Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence.
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.
Bringaud F, Müller M, Cerqueira GCoutinho, Smith M, Rochette A, el-Sayed NMA, Papadopoulou B, Ghedin E.  2007.  Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.. PLoS Pathog. 3(9):1291-307.
Shaked I, Oberhardt  A., Atias N, Sharan R, Ruppin E.  2016.  Metabolic Network Prediction of Drug Side Effects. Cell Systems. 2(3):209-213.
Hasan NA, W. Chowdhury B, Rahim N, Sultana M, S. Shabnam A, Mai V, Ali A, Morris GJ, R. Sack B, Huq A et al..  2011.  Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem. Bangladesh Journal of MicrobiologyBangladesh Journal of Microbiology. 27

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