Student Publications

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Bean GJ, Jaeger PA, Bahr S, Ideker T. "Development of ultra-high-density screening tools for microbial "omics"." PLoS ONE. 2014;9(1):e85177.
Buganim Y, Markoulaki S, van Wietmarschen N, et al. "The developmental potential of iPSCs is greatly influenced by reprogramming factor selection." Cell Stem Cell. 2014;15(3):295-309.
Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61.
Chaillon A, Wagner GA, Hepler LN, et al. "Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection." J. Virol.. 2013;87(23):12737-44.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ. "Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat. Chem. Biol.. 2012;8(1):65-71.
Bean GJ, Ideker T. "Differential analysis of high-throughput quantitative genetic interaction data." Genome Biol.. 2012;13(12):R123.
Lagier-Tourenne C, Polymenidou M, Hutt KR, et al. "Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs." Nat. Neurosci.. 2012;15(11):1488-97.
Nagarajan H, Butler JE, Klimes A, et al. "De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads." PLoS ONE. 2010;5(6):e10922.
Chang RL, Luo F, Johnson S, Scheuermann RH. "Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks." Int J Bioinform Res Appl. 2010;6(2):101-19.
Hawkins DR, Hon GC, Lee LK, et al. "Distinct epigenomic landscapes of pluripotent and lineage-committed human cells." Cell Stem Cell. 2010;6(5):479-91.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938.
Chaisson MJ, Brinza D, Pevzner PA. "De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res.. 2009;19(2):336-46.
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30.
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9.
Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566.
Abdulla M-H, Ruelas DS, Wolff B, et al. "Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening." PLoS Negl Trop Dis. 2009;3(7):e478.
Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. "A dynamic network of transcription in LPS-treated human subjects." BMC Syst Biol. 2009;3:78.
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc. Natl. Acad. Sci. U.S.A.. 2008;105(52):21034-8.
Rodriguez J, Gupta N, Smith RD, Pevzner PA. "Does trypsin cut before proline?" J. Proteome Res.. 2008;7(1):300-5.