Student Publications

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat Methods. 2016;13(6):508-14. PubMed PMC DOI

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. "Toward Community Standards and Software for Whole-Cell Modeling." IEEE Trans Biomed Eng. 2016;63(10):2007-14. PubMed PMC DOI

Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO. "Principles of proteome allocation are revealed using proteomic data and genome-scale models." Sci Rep. 2016;6:36734. PubMed PMC DOI

Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. "Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems." Cell Syst. 2016;2(2):77-88. PubMed PMC DOI

Yurkovich JT, Palsson BO. "Solving puzzles with missing pieces: The power of systems biology." Proc. IEEE. 2016. DOI

Zhang K, Li N, Ainsworth RI, Wang W. "Systematic identification of protein combinations mediating chromatin looping." Nat Commun. 2016;7:12249. PubMed PMC DOI

Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W. "Constructing 3D interaction maps from 1D epigenomes." Nat Commun. 2016;7:10812. PubMed PMC DOI

An J, González-Avalos E, Chawla A, Jeong M, López-Moyado IF, Li W, Goodell MA, Chavez L, Ko M, Rao A. "Acute loss of TET function results in aggressive myeloid cancer in mice." Nat Commun. 2015;6:10071. PubMed PMC DOI

Bliven SE, Bourne PE, Prlić A. "Detection of circular permutations within protein structures using CE-CP." Bioinformatics. 2015;31(8):1316-8. PubMed PMC DOI

Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. "Evidence for a common evolutionary rate in metazoan transcriptional networks." eLife. 2015;4:e11615. PubMed PMC DOI

Chan JK, Gardner AB, Taylor K, Blansit K, Thompson CA, Brooks R, Yu X, Kapp DS. "The centralization of robotic surgery in high-volume centers for endometrial cancer patients--a study of 6560 cases in the U.S." Gynecol Oncol. 2015;138(1):128-32. PubMed DOI

Chan JK, Gardner AB, Taylor K, Thompson CA, Blansit K, Yu X, Kapp DS. "Robotic versus laparoscopic versus open surgery in morbidly obese endometrial cancer patients - a comparative analysis of total charges and complication rates." Gynecol Oncol. 2015;139(2):300-5. PubMed DOI

Choueiri MB, Shen JP, 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. PubMed PMC DOI

DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CH, Carson D, Kipps TJ, Frazer KA. "Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers." PLoS Comput Biol. 2015;11(3):e1004105. PubMed PMC DOI

Fang R, Wang C, Skogerbo G, Zhang Z. "Functional diversity of CTCFs is encoded in their binding motifs." BMC Genomics. 2015;16:649. PubMed PMC DOI

Fuh KC, Secord AA, Bevis KS, Huh W, ElNaggar A, Blansit K, Previs R, Tillmanns T, Kapp DS, Chan JK. "Comparison of bevacizumab alone or with chemotherapy in recurrent ovarian cancer patients." Gynecol Oncol. 2015;139(3):413-8. PubMed DOI

Garitaonandia I, Amir H, Boscolo FS, Wambua GK, Schultheisz HL, Sabatini K, Morey R, Waltz S, Wang YC, Tran H, Leonardo TR, Nazor K, Slavin I, Lynch C, Li Y, Coleman R, Gallego Romero I, Altun G, Reynolds D, Dalton S, Parast M, Loring JF, Laurent LC. "Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions." PLoS One. 2015;10(2):e0118307. PubMed PMC DOI

Gonzalez R, Garitaonandia I, Crain A, Poustovoitov M, Abramihina T, Noskov A, Jiang C, Morey R, Laurent LC, Elsworth JD, Snyder EY, Redmond DE Jr, Semechkin R. "Proof of concept studies exploring the safety and functional activity of human parthenogenetic-derived neural stem cells for the treatment of Parkinson's disease." Cell Transplant. 2015;24(4):681-90. PubMed DOI

Gross AM, Cohen EE. "Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015:28-32. PubMed DOI

Gross AM, Ideker T. "Molecular networks in context." Nat Biotechnol. 2015;33(7):720-1. PubMed DOI

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. PubMed PMC DOI

He Y, Ecker JR. "Non-CG Methylation in the Human Genome." Annu Rev Genomics Hum Genet. 2015;16:55-77. PubMed PMC DOI

Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, Behrens TW. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9. PubMed PMC DOI

Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J. "Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity." Mol Cell. 2015;59(3):413-25. PubMed PMC DOI

Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. "Integrative analysis of haplotype-resolved epigenomes across human tissues." Nature. 2015;518(7539):350-354. PubMed PMC DOI