• Annals of Neurology  ·  August 4, 2015

    A destructive feedback loop mediated by CXCL10 in CNS inflammatory disease.

    Wendy K. Roberts, Ph.D., Nathalie E. Blachère, Ph.D., Mayu O. Frank, M.S., Athanasios Dousmanis, M.D., Ph.D., Richard M. Ransohoff, M.D., Robert B. Darnell, M.D., Ph.D.

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  • Nat Methods  ·  July 6, 2015

    G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

    Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T.

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  • Cell  ·  July 1, 2015

    Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

    Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA.

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  • JAMA Oncology  ·  July 1, 2015

    Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

    Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Paul C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic VEmde AKOschwald D, Tan AY, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Robinson BD, Nanus DM, Tagawa ST, Campagne F, Xiang JZ, Smogorzewska A, Demichelis F, Rickman D, Sboner A, Elemento O, Rubin MA.

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  • PLoS ONE  ·  June 23, 2015

    Gut Microbiota and Tacrolimus Dosing in Kidney Transplantation.

    Lee JR, Muthukumar T, Dadhania D, Taur Y, Jenq RR, Toussaint NC, Ling L, Pamer EG, Suthanthiran M.

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  • The Journal of Infectious Diseases  ·  June 23, 2015

    Loss of Microbiota-Mediated Colonization Resistance to Clostridium difficile Infection With Oral Vancomycin Compared With Metronidazole.

    Lewis BB, Buffie CG, Carter RA, Leiner I, Toussaint NC, Miller LC, Gobourne A, Ling L, Pamer EG.

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  • Science  ·  May 27, 2015

    The human transcriptome across tissues and individuals

    Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, The GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R.

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  • Science  ·  May 27, 2015

    Impact of predicted protein-truncating genetic variants on the human transcriptome.

    Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca D, Fromer M, Ferreira P, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer D, Stenson PD, Cooper DN, Consortium TG, Consortium TG, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.

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  • Genome Research  ·  May 27, 2015

    The landscape of genomic imprinting across diverse adult human tissues

    Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T.

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  • Cold Spring Harb Perspect Biol  ·  May 21, 2015

    Astrocytes in Neurodegenerative Disease.

    Phatnani H, Maniatis T.

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  • Bioinformatics  ·  May 21, 2015

    Assessing allele-specific expression across multiple tissues from RNA-seq read data

    Pirinen M, Lappalainen T, Zaitlen NA; GTEx Consortium, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA.

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  • Proc Natl Acad Sci USA  ·  May 21, 2015

    Structural insights into mis-regulation of protein kinase A in human tumors

    Cheung J, Ginter C, Cassidy M, Franklin MC, Rudolph MJ, Robine N, Darnell RB, Hendrickson WA.

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  • Cell  ·  May 21, 2015

    Hepatitis C virus RNA functionally sequesters miR-122

    Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB.

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  • Science  ·  May 21, 2015

    Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens

    Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A.

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  • Nature Biotechnology  ·  May 20, 2015

    Spatial reconstruction of single-cell gene expression data

    Satija R, Farrell JA, Gennert D, Schier AF, Regev A

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  • Genetics 193: 911-28  ·  February 8, 2015

    The variance of identity-by-descent sharing in the Wright-Fisher model.

    Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe’er I.

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  • Journal of Translational Medicine  ·  February 2, 2015

    Dendritic cell vaccines containing lymphocytes produce improved immunogenicity in patients with cancer.

    Frank, M. O., Kaufman, J., Parveen, S., Blachère, N. E., Orange, D. E., Darnell, R. B.

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  • PLoS Computational Biology 8: e1002709  ·  February 2, 2015

    Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

    Vacic V, Markwick PRL, Oldfield CJ, Zhao X, Haynes C, Uversky VN, Iakoucheva LM.

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  • Science 344: 921-5  ·  February 2, 2015

    The cellular and molecular origin of tumor-associated macrophages.

    Franklin RA, Liao W, Sarkar A, Kim MV, Bivona MR, Liu K, Pamer EG, Li MO.

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  • Nature Methods 11: 1033-6  ·  February 2, 2015

    Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

    Narzisi G, O’Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.

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  • Cell 158: 705-21  ·  February 2, 2015

    Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

    Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D,Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ.

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