Student Publications

Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K. "Library-free methylation sequencing with bisulfite padlock probes." Nat Methods. 2012;9(3):270-2. PubMed PMC DOI

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80. PubMed PMC DOI

Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78. PubMed PMC DOI

Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc Natl Acad Sci U S A. 2012;109(8):3167-72. PubMed PMC DOI

He Y, Zhang Y, Zheng G, Wei C. "CTF: a CRF-based transcription factor binding sites finding system." BMC Genomics. 2012;13 Suppl 8:S18. PubMed PMC DOI

Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FS. "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int J Antimicrob Agents. 2012;40(3):246-51. PubMed PMC DOI

Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3. PubMed PMC DOI

Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M Jr, Yeo GW. "Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins." Cell Rep. 2012;1(2):167-78. PubMed PMC DOI

Huelga SC, Yeo GW. "Genomics of Alternative Splicing in Stem Cells." Computational Biology of Embryonic Stem Cells. 2012:147-160. DOI

Human Microbiome Project Consortium. "Structure, function and diversity of the healthy human microbiome." Nature. 2012;486(7402):207-14. PubMed PMC DOI

Human Microbiome Project Consortium. "A framework for human microbiome research." Nature. 2012;486(7402):215-21. PubMed PMC DOI

Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. "Release factor one is nonessential in Escherichia coli." ACS Chem Biol. 2012;7(8):1337-44. PubMed PMC DOI

Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet. 2012;8(8):e1002867. PubMed PMC DOI

Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH. "Human-specific transcriptional networks in the brain." Neuron. 2012;75(4):601-17. PubMed PMC DOI

Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. "Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis." G3 (Bethesda). 2012;2(4):487-98. PubMed PMC DOI

Lagier-Tourenne C, Polymenidou M, Hutt KR, Vu AQ, Baughn M, Huelga SC, Clutario KM, Ling SC, Liang TY, Mazur C, Wancewicz E, Kim AS, Watt A, Freier S, Hicks GG, Donohue JP, Shiue L, Bennett CF, Ravits J, Cleveland DW, Yeo GW. "Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs." Nat Neurosci. 2012;15(11):1488-97. PubMed PMC DOI

Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. "In silico method for modelling metabolism and gene product expression at genome scale." Nat Commun. 2012;3:929. PubMed PMC DOI

Lewis NE, Nagarajan H, Palsson BO. "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods." Nat Rev Microbiol. 2012;10(4):291-305. PubMed PMC DOI

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