Student Publications

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

Jones BW, Deem J, Younts TJ, Weisenhaus M, Sanford CA, Slack MC, Chin J, Nachmanson D, McKennon A, Castillo PE, McKnight GS. "Targeted deletion of AKAP7 in dentate granule cells impairs spatial discrimination." Elife. 2016;5. PubMed PMC DOI

Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O'Neil R, O'Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR. "Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions." Cell. 2016;166(2):492-505. PubMed PMC DOI

Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. "Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons." Nat Protoc. 2016;11(3):499-524. PubMed PMC DOI

Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O. "Immune DNA signature of T-cell infiltration in breast tumor exomes." Sci Rep. 2016;6:30064. PubMed PMC DOI

Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. "Assembly of long error-prone reads using de Bruijn graphs." Proc Natl Acad Sci U S A. 2016;113(52):E8396-E8405. PubMed PMC DOI

Lio CW, Zhang J, González-Avalos E, Hogan PG, Chang X, Rao A. "Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility." Elife. 2016;5. PubMed PMC DOI

Ma H, Marti Gutierrez N, Morey R, Van Dyken C, Kang E, Hayama T, Lee Y, Li Y, Tippner-Hedges R, Wolf DP, Laurent LC, Mitalipov S. "Incompatibility between Nuclear and Mitochondrial Genomes Contributes to an Interspecies Reproductive Barrier." Cell Metab. 2016;24(2):283-94. PubMed PMC DOI

McNamara RP, Guzman C, Reeder JE, D'Orso I. "Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II." Genom Data. 2016;7:250-5. PubMed PMC DOI

Mih N, Brunk E, Bordbar A, Palsson BO. "A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism." PLoS Comput Biol. 2016;12(7):e1005039. PubMed PMC DOI

Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham MC, Levitt P, Nelson S, Amaral DG, Hertz-Picciotto I, Fallin MD, Weiss LA. "Pleiotropic Mechanisms Indicated for Sex Differences in Autism." PLoS Genet. 2016;12(11):e1006425. PubMed PMC DOI

Mora-Castilla S, To C, Vaezeslami S, Morey R, Srinivasan S, Dumdie JN, Cook-Andersen H, Jenkins J, Laurent LC. "Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing." J Lab Autom. 2016;21(4):557-67. PubMed PMC DOI

Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S. "Mapping RNA-RNA interactome and RNA structure in vivo by MARIO." Nat Commun. 2016;7:12023. PubMed PMC DOI

Pineda G, Lennon KM, Delos Santos NP, Lambert-Fliszar F, Riso GL, Lazzari E, Marra MA, Morris S, Sakaue-Sawano A, Miyawaki A, Jamieson CH. "Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche." Sci Rep. 2016;6:23885. PubMed PMC DOI