Student Publications

Export 18 results:
Filters: Keyword is Evolution, Molecular  [Clear All Filters]
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.
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.
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.
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.
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.
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.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
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.