Student Publications

Loriaux PM, Hoffmann A. "A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness." Methods Cell Biol. 2012;110:81-109. PubMed PMC DOI

Ma Q, Liu W, Rosenfeld MG. "mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release." Proc ACM Conf Bioinf Comp Biol Biomed. 2012:515. DOI

Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4. PubMed PMC DOI

Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, Richman DD, Little SJ, Smith DM. "Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men." AIDS. 2012;26(2):157-65. PubMed PMC DOI

Panopoulos AD, Yanes O, Ruiz S, Kida YS, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua Belmonte JC. "The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming." Cell Res. 2012;22(1):168-77. PubMed PMC DOI

Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5. PubMed PMC DOI

Ronen R, Boucher C, Chitsaz H, Pevzner P. "SEQuel: improving the accuracy of genome assemblies." Bioinformatics. 2012;28(12):i188-96. PubMed PMC DOI

Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, Plongthongkum N, Kumar S, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Kan NG, Schöler HR, Mercola M, Zhang K, Izpisua Belmonte JC. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc Natl Acad Sci U S A. 2012;109(40):16196-201. PubMed PMC DOI

Schultz MD, Schmitz RJ, Ecker JR. "Leveling' the playing field for analyses of single-base resolution DNA methylomes." Trends Genet. 2012;28(12):583-5. PubMed PMC DOI

Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A. "Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways." Nat Immunol. 2012;13(12):1162-70. PubMed PMC DOI

Szpankowski L, Encalada SE, Goldstein LS. "Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesicles." Proc Natl Acad Sci U S A. 2012;109(22):8582-7. PubMed PMC DOI

Thiele I, Fleming RM, 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. PubMed PMC DOI

Wilbert ML, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, Massirer KB, Morris Q, Hoon S, Yeo GW. "LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance." Mol Cell. 2012;48(2):195-206. PubMed PMC DOI

Yamaguchi S, Hong K, Liu R, Shen L, Inoue A, Diep D, Zhang K, Zhang Y. "Tet1 controls meiosis by regulating meiotic gene expression." Nature. 2012;492(7429):443-7. PubMed PMC DOI

Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA. "Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens." Nucleic Acids Res. 2012;40(14):e107. PubMed PMC DOI

Chan JE, Kolodner RD. "A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements." PLoS Genet. 2011;7(5):e1002089. PubMed PMC DOI

Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA. "Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism." Mol Syst Biol. 2011;7:518. PubMed PMC DOI

Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. "An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92." BMC Syst Biol. 2011;5:163. PubMed PMC DOI

Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. "Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat Chem Biol. 2011;8(1):65-71. PubMed PMC DOI

Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BØ. "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res. 2011;39(15):6456-64. PubMed PMC DOI

Cuív PÓ, Klaassens ES, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M. "Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces." J Bacteriol. 2011;193(15):4025-6. PubMed PMC DOI

Cuív PÓ, Klaassens ES, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M. "Draft genome sequence of Turicibacter sanguinis PC909, isolated from human feces." J Bacteriol. 2011;193(5):1288-9. PubMed PMC DOI

Diep D, Zhang K. "Genome-wide mapping of the sixth base." Genome Biol. 2011;12(6):116. PubMed PMC DOI

Encalada SE, Szpankowski L, Xia CH, Goldstein LS. "Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles." Cell. 2011;144(4):551-65. PubMed PMC DOI

Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD. "A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation." Genomics. 2011;98(4):266-71. PubMed PMC DOI