Student Publications

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

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