Student Publications

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Filters: Keyword is Evolution, Molecular  [Clear All Filters]
2012
Konopka G, Friedrich T, Davis-Turak J, et al. "Human-specific transcriptional networks in the brain." Neuron. 2012;75(4):601-17.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO. "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage." PLoS ONE. 2012;7(9):e45635.
Nam H, Lewis NE, Lerman JA, et al. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4.
Dixon JR, Selvaraj S, Yue F, et al. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80.
2010
Lewis NE, Hixson KK, Conrad TM, et al. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390.
2009
Fossum E, Friedel CC, Rajagopala SV, et al. "Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog.. 2009;5(9):e1000570.
Valas RE, Yang S, Bourne PE. "Nothing about protein structure classification makes sense except in the light of evolution." Curr. Opin. Struct. Biol.. 2009;19(3):329-34.
Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. "Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome." PLoS Comput. Biol.. 2009;5(3):e1000315.
2008
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504.
2007
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816.
2006
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56.
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol.. 2006;7(1):R7.
Allen TE, Price ND, Joyce AR, Palsson BØ. "Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization." PLoS Comput. Biol.. 2006;2(1):e2.
2005
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
2004
Bandyopadhyay S, Cookson MR. "Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol. Biol.. 2004;4:6.
Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr. Opin. Biotechnol.. 2004;15(1):70-7.