Student Publications

2016

Rentas S, Holzapfel N, Belew MS, Pratt G, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-511. PubMed PMC DOI
Sancho-Martinez I, Nivet E, Xia Y, Hishida T, Aguirre A, Ocampo A, Ma L, Morey R, Krause MN, Zembrzycki A, Ansorge O, Vazquez-Ferrer E, Dubova I, Reddy P, Lam D, Hishida Y, Wu MZ, Esteban CR, O'Leary D, Wahl GM, Verma IM, Laurent LC, Izpisua Belmonte JC. "Establishment of human iPSC-based models for the study and targeting of glioma initiating cells." Nat Commun. 2016;7:10743. PubMed PMC DOI
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. PubMed PMC DOI
Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, Clark AG, Greater Middle East Variome Consortium, Alkuraya FS, Casanova JL, Gleeson JG. "Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery." Nat Genet. 2016;48(9):1071-6. PubMed PMC DOI
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. "A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy." Mol Cell. 2016;63(3):514-25. PubMed PMC DOI
Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R. "Molecular Criteria for Defining the Naive Human Pluripotent State." Cell Stem Cell. 2016;19(4):502-515. PubMed PMC DOI
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. "Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution." Cell Syst. 2016;2(4):260-71. PubMed PMC DOI
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

2015

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