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Reports
Bravo HCorrada, Eng K.H, Keles S., Wahba G., Wright S..  2008.  Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression. 1142
Journal Articles
Takala S.L, Coulibaly D., Thera M.A, Batchelor A.H, Cummings MP, Escalante A.A, Ouattara A., Traoré K., Niangaly A., Djimdé A.A et al..  2009.  Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development. Sci Transl MedSci Transl Med. 1
Kelley D.R, Kingsford C.  2011.  Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. Journal of Computational BiologyJournal of Computational Biology. 18
Stelter K, El‐Sayed NM, Seeber F.  2007.  The Expression of a Plant-type Ferredoxin Redox System provides Molecular Evidence for a Plastid in the Early Dinoflagellate Perkinsus marinus. ProtistProtist. 158
Nijkamp JF, Pop M., Reinders MJT, de Ridder D.  2013.  Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 29
Ye C, Ma Z.S, Cannon C.H, Pop M., Yu D.W.  2012.  Exploiting sparseness in de novo genome assembly. BMC bioinformaticsBMC Bioinformatics. 13
Pop M., Adviser-Kosaraju S.R.  2000.  Exploiting coherence in spatial database queries.
Mount SM, Anderson P.  2000.  Expanding the definition of informational suppression.. Trends Genet. 16(4):157.
Haft DH, Paulsen IT, Ward N, Selengut J..  2006.  Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC biologyBMC biology. 4
Bravo H.C, Lee K.E, Klein B.EK, Klein R., Iyengar S.K, Wahba G..  2009.  Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models. Proceedings of the National Academy of Sciences. 106(20):8128-8133.
Lin C-F, Mount SM, Jarmołowski A, Makałowski W.  2010.  Evolutionary dynamics of U12-type spliceosomal introns.. BMC Evol Biol. 10:47.
Blair D., Campos A., Cummings MP, Laclette J.P.  1996.  Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics. Parasitol TodayParasitol Today. 12
Rangarajan N, Kulkarni P, Hannenhalli S.  2015.  Evolutionarily conserved network properties of intrinsically disordered proteins.. PLoS One. 10(5):e0126729.
Clegg M.T, Cummings MP, Durbin M.L.  1997.  The evolution of plant nuclear genes. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 94
Bringaud F, Ghedin E, Blandin G, Bartholomeu DC, Caler E, Levin MJ, Baltz T, El‐Sayed NM.  2006.  Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology. 145
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN et al..  2007.  Evolution of genes and genomes on the Drosophila phylogeny.. Nature. 450(7167):203-18.
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN et al..  2007.  Evolution of genes and genomes on the Drosophila phylogeny. NatureNature. 450
Hannenhalli S, Kaestner KH.  2009.  The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev GenetNature reviews. GeneticsNat Rev Genet. 10
Furnier G.R, Cummings MP, Clegg M.T.  1990.  Evolution of avocados as revealed by DNA restriction fragment variation. J HeredJ Hered. 81
Putt M.E, Hannenhalli S, Lu Y., Haines P., Chandrupatla H.R, Morrisey E.E, Margulies K.B, Cappola T.P.  2009.  Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart FailureCLINICAL PERSPECTIVE. Circulation: Cardiovascular GeneticsCirculation: Cardiovascular Genetics. 2
Mount SM, Chang C.  2002.  Evidence for a plastid origin of plant ethylene receptor genes.. Plant Physiol. 130(1):10-4.
Hannenhalli S.  2007.  Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational Genomics: Current MethodsComputational Genomics: Current Methods.
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
Bravo HCorrada, Wright S, Eng KH, Keles S, Wahba G.  2009.  Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. J Mach Learn Res. 5:41-48.
Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS.  2015.  Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes.. Sci Rep. 5:9838.

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