Student Publications

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2016
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr. Opin. Cell Biol.. 2016;38:38-44.
Conway AE, Van Nostrand EL, Pratt GA, et al. "Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival." Cell Rep. 2016;15(3):666-79.
Brandler WM, Antaki D, Gujral M, et al. "Frequency and Complexity of De Novo Structural Mutation in Autism." Am. J. Hum. Genet.. 2016;98(4):667-79.
Baker CW, Miller CR, Thaweethai T, et al. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55.
Utrilla J, O'Brien EJ, Chen K, et al. "Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution." Cell Syst. 2016;2(4):260-71.
Gross AM, Jaeger PA, Kreisberg JF, et al. "Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA." Mol. Cell. 2016;62(2):157-68.
Rentas S, Holzapfel NT, Belew MS, et al. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11.
Van Nostrand EL, Pratt GA, Shishkin AA, et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat. Methods. 2016;13(6):508-14.
Yurkovich JT, Palsson BO. "Solving Puzzles With Missing Pieces: The Power of Systems Biology." Proceedings of the IEEE. 2016;104(1):2-7.
Brunk E, Mih N, Monk J, et al. "Systems biology of the structural proteome." BMC Syst Biol. 2016;10:26.
2015
Wu J, Okamura D, Li M, et al. "An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21.
Gross AM, Kreisberg JF, Ideker T. "Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS ONE. 2015;10(11):e0142618.
Shen JPaul, Srivas R, Gross A, et al. "Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69.
Singh G, Pratt G, Yeo GW, Moore MJ. "The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu. Rev. Biochem.. 2015;84:325-54.
Raju SC, Hauff SJ, Lemieux AJ, et al. "Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma." Oral Oncol.. 2015;51(5):470-5.
O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34.
Mukund K, Subramaniam S. "Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis." BMC Res Notes. 2015;8:182.
Choueiri MB, Shen JPaul, Gross AM, Huang JK, Ideker T, Fanta P. "ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS ONE. 2015;10(6):e0126898.
Murrell B, Weaver S, Smith MD, et al. "Gene-wide identification of episodic selection." Mol. Biol. Evol.. 2015;32(5):1365-71.
Schultz MD, He Y, Whitaker JW, et al. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6.
Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
Gross AM, Ideker T. "Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1.
He Y, Ecker JR. "Non-CG Methylation in the Human Genome." Annu Rev Genomics Hum Genet. 2015.
Hung T, Pratt GA, Sundararaman B, et al. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9.
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42.

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