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2012

Salzberg S.L, Phillippy A.M, Zimin A., Puiu D., Magoc T., Koren S., Treangen T, Schatz M.C, Delcher A.L, Roberts M. et al.. 2012. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome researchGenome Research. 22

Blanco MAndres, LeRoy G, Khan Z, Alečković M, Zee BM, Garcia BA, Kang Y. 2012. Global secretome analysis identifies novel mediators of bone metastasis.. Cell Res. 22(9):1339-55.

Blanco MAndres, LeRoy G, Khan Z, ković šač, Zee BM, Garcia BA, Kang Y. 2012. Global secretome analysis identifies novel mediators of bone metastasis. Cell Research. 22(9):1339-1355.

Regier JC, Brown JW, Mitter C, Baixeras J, Cho S, Cummings MP, Zwick A. 2012. A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution.. PloS one. 7:e35574.

Regier JC, Mitter C, M. SOLIS ALMA, HAYDEN JAMESE, LANDRY BERNARD, NUSS MATTHIAS, Simonsen TJ, Yen S-H, Zwick A, Cummings MP. 2012. A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification. Systematic Entomology. 37(4):635-656.

2013

Cummings MP. 2013. AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite. Dictionary of Bioinformatics.

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

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

Sohn J.C, Regier J.C, Mitter C., Davis D., Landry J.F, Zwick A., Cummings MP. 2013. A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and\ the evolution of host plant use. PLoS One.

Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HCorrada, Fredrikson KM, Harkins TT et al.. 2013. Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Human mutationHuman mutation. 34

2014

Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY. 2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.

Bazinet AL, Zwickl DJ, Cummings MP. 2014. A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Syst Biol.

Eilam O., Zarecki R., Oberhardt M., Ursell L.K, Kupiec M., Knight R., Gophna U., Ruppin E.. 2014. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14.

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.

Regier JC, Mitter C, Davis DR, HARRISON TERRYL, Sohn J-C, Cummings MP, Zwick A, Mitter KT. 2014. A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Systematic Entomology. 40:409-432.

Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP et al.. 2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20.

Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP et al.. 2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20.

Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. 2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726.

2015

Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, T Johnson I, Gaude E, King A, Leach JDG, Edrada-Ebel RA et al.. 2015. Fumarate induces redox-dependent senescence by modifying glutathione metabolism.. Nat Commun. 6:6001.

Tardito S, Oudin ïs, Ahmed SU, Fack F, Keunen O, Zheng L, Miletic H, Sakariassen Ø, Weinstock A, Wagner A et al.. 2015. Glutamine synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restricted glioblastoma. Nature Cell Biology. 17(12):1556-1568.

Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk H-P, Gophna U, Ruppin E. 2015. Harnessing the landscape of microbial culture media to predict new organism-media pairings.. Nat Commun. 6:8493.

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.

Regier JC, Mitter C, KRISTENSEN NIELSP, Davis DR, VAN NIEUKERKEN ERIKJ, ROTA JADRANKA, Simonsen TJ, Mitter KT, Kawahara AY, Yen S-H et al.. 2015. A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Systematic Entomology. :n/a-n/a.

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.

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