Student Publications

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. "Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment." Genome Biol. 2017;18(1):57. PubMed PMC DOI

Wolf DP, Morey R, Kang E, Ma H, Hayama T, Laurent LC, Mitalipov S. "Concise Review: Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer: A Horse in the Race?." Stem Cells. 2017;35(1):26-34. PubMed DOI

Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L. "Strain Level Streptococcus Colonization Patterns during the First Year of Life." Front Microbiol. 2017;8:1661. PubMed PMC DOI

Xiao S, Lu J, Sridhar B, Cao X, Yu P, Zhao T, Chen CC, McDee D, Sloofman L, Wang Y, Rivas-Astroza M, Telugu BPVL, Levasseur D, Zhang K, Liang H, Zhao JC, Tanaka TS, Stormo G, Zhong S. "SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination." Cell Rep. 2017;18(13):3117-3128. PubMed PMC DOI

Yang F, Ma Q, Liu Z, Li W, Tan Y, Jin C, Ma W, Hu Y, Shen J, Ohgi KA, Telese F, Liu W, Rosenfeld MG. "Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program." Mol Cell. 2017;66(3):321-331.e6. PubMed PMC DOI

Yu B, Zhang K, Milner JJ, Toma C, Chen R, Scott-Browne JP, Pereira RM, Crotty S, Chang JT, Pipkin ME, Wang W, Goldrath AW. "Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation." Nat Immunol. 2017;18(5):573-582. PubMed PMC DOI

Yurkovich JT, Yang L, Palsson BO. "Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells." PLoS Comput Biol. 2017;13(3):e1005424. PubMed PMC DOI

Yurkovich JT, Yang L, Palsson BO. "Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells." Proc. IEEE Conference on Control Technology and Applications. 2017. DOI

Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. "A Padawan Programmer's Guide to Developing Software Libraries." Cell Syst. 2017;5(5):431-437. PubMed DOI

Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. "Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks." J Biol Chem. 2017;292(48):19556-19564. PubMed PMC DOI

Zare F, Dow M, Monteleone N, Hosny A, Nabavi S. "An evaluation of copy number variation detection tools for cancer using whole exome sequencing data." BMC Bioinformatics. 2017;18(1):286. PubMed PMC DOI

Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, Weinreich DM. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55. PubMed PMC DOI

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, Gadomski TE, Hong O, Fajardo KV, Bhandari A, Owen R, Baughn M, Yuan J, Solomon T, Moyzis AG, Maile MS, Sanders SJ, Reiner GE, Vaux KK, Strom CM, Zhang K, Muotri AR, Akshoomoff N, Leal SM, Pierce K, Courchesne E, Iakoucheva LM, Corsello C, Sebat J. "Frequency and Complexity of De Novo Structural Mutation in Autism." Am J Hum Genet. 2016;98(4):667-79. PubMed PMC DOI

Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO. "Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis." Proc Natl Acad Sci U S A. 2016;113(51):E8344-E8353. PubMed PMC DOI

Brooks RA, Blansit K, Young-Lin N, Usach I, Chen LM, Yu X, Kapp DS, Chan JK. "The economic impact of surgical care for morbidly obese endometrial cancer patients: a nationwide study." Am J Obstet Gynecol. 2016;214(4):498.e1-498.e6. PubMed DOI

Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. "Systems biology of the structural proteome." BMC Syst Biol. 2016;10:26. PubMed PMC DOI

Chen F, Dow M, Ding S, Lu Y, Jiang X, Tang H, Wang S. "PREMIX: PRivacy-preserving EstiMation of Individual admiXture." AMIA Annu Symp Proc. 2016;2016:1747-1755. PubMed PMC

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW. "Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival." Cell Rep. 2016;15(3):666-679. PubMed PMC DOI

Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT, Zhang Z, Gutierrez E, Groisman A, Hwa T. "Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel." Proc Natl Acad Sci U S A. 2016;113(41):11414-11419. PubMed PMC DOI

Crews LA, Balaian L, Delos Santos NP, Leu HS, Court AC, Lazzari E, Sadarangani A, Zipeto MA, La Clair JJ, Villa R, Kulidjian A, Storb R, Morris SR, Ball ED, Burkart MD, Jamieson CHM. "RNA Splicing Modulation Selectively Impairs Leukemia Stem Cell Maintenance in Secondary Human AML." Cell Stem Cell. 2016;19(5):599-612. PubMed PMC DOI

Fan S, Huang K, Ai R, Wang M, Wang W. "Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data." Genomics. 2016;107(4):132-7. PubMed DOI

Fan S, Li C, Ai R, Wang M, Firestein GS, Wang W. "Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis." Bioinformatics. 2016;32(12):1773-8. PubMed PMC DOI

Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B. "Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq." Cell Res. 2016;26(12):1345-1348. PubMed PMC DOI

Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2016;35(5):608-20. PubMed PMC DOI

Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. "Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA." Mol Cell. 2016;62(2):157-168. PubMed PMC DOI