• Nature  ·  October 9, 2019

    Mapping the Human Body at Cellular Resolution — The NIH Human BioMolecular Atlas

    Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis.

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  • bioRxiv  ·  October 3, 2019  ·  Preprint

    Long non-coding RNA gene regulation and trait associations across human tissues.

    O. M. de Goede, N. M. Ferraro, D. C. Nachun, A. S. Rao, F. Aguet, A. N. Barbeira, S. E. Castel, S. Kim-Hellmuth, Y. Park, A. J. Scott, B. J. Strober, GTEx Consortium, C. D. Brown, X. Wen, I. M. Hall, A. Battle, T. Lappalainen, H. K. Im, K. G. Ardlie, T. Quertermous, K. Kirkegaard, S. B. Montgomery

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  • Nature Genetics  ·  September 23, 2019

    Synergistic effects of common schizophrenia risk variants.

    Schrode N, Ho SM, Yamamuro K, Dobbyn A, Huckins L, Matos MR, Cheng E, Deans PJM, Flaherty E, Barretto N, Topol A, Alganem K, Abadali S, Gregory J, Hoelzli E, Phatnani H, Singh V, Girish D, Aronow B, Mccullumsmith R, Hoffman GE, Stahl EA, Morishita H, Sklar P, Brennand KJ.

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  • Molecular Case Studies  ·  September 13, 2019

    Identification of targetable BRAF ΔN486_P490 variant by whole genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma.

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  • bioRxiv  ·  September 5, 2019  ·  Preprint

    Splotch: Robust estimation of aligned spatial temporal gene expression data.

    Tarmo Aijo, Silas Maniatis, Sanja Vickovic, Kristy Kang, Miguel Cuevas, Catherine Braine, Hemali Phatnani, Joakim Lundeberg, Richard Bonneau

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  • Haematologica  ·  August 29, 2019

    Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1 regulated transcription.

    Edelmann J, Holzmann K, Tausch E, Saunderson EA, Jebaraj BMC, Steinbrecher D, Dolnik A, Blätte TJ, Landau DA, Saub J, Estenfelder S, Ibach S, Cymbalista F, Leblond V, Delmer A, Bahlo J, Robrecht S, Fischer K, Goede V, Bullinger L, Wu CJ, Mertens D, Ficz G, Gribben JG, Hallek M, Döhner H, Stilgenbauer S.

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  • Journal of Investigative Dermatology  ·  August 26, 2019

    Low SATB1 expression promotes IL-5 and IL-9 expression in Sezary Syndrome.

    Herrera A, Fredholm S, Cheng A, Mimitou EP, Seffens A, Bar-Natan M, Sun A, Latkowski J, Willerslew-Olsen A, Buus TB, Gluud M, Krejsgaard T, Torres-Rusillo S, Bonefeld CM, Woetmann A, Geisler C, Geskin LJ, Ouyang Z, Smibert P, Ødum N, Koralov SB.

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  • Cell Reports  ·  August 13, 2019

    m6A RNA Methylation Maintains Hematopoietic Stem Cell Identity and Symmetric Commitment.

    Yuanming Cheng, Hanzhi Luo, Franco Izzo, Brian F. Pickering, Diu Nguyen, Robert Myers, Alexandra Schurer,Saroj Gourkanti, Jens C. Brüning, Ly P. Vu, Samie R. Jaffrey, Dan A. Landau and Michael G. Kharas.

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  • Neurobiology of disease  ·  August 2, 2019

    Examining the relationship between astrocyte dysfunction and neurodegeneration in ALS using hiPSCs.

    Halpern M, Brennand KJ, Gregory J.

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  • The Journal of experimental medicine  ·  June 24, 2019

    Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses.

    Spencer S, Köstel Bal S, Egner W, Lango Allen H, Raza SI, Ma CA, Gürel M, Zhang Y, Sun G, Sabroe RA, Greene D, Rae W, Shahin T, Kania K, Ardy RC, Thian M, Staples E, Pecchia-Bekkum A, Worrall WPM, Stephens J, Brown M, Tuna S, York M, Shackley F, Kerrin D, Sargur R, Condliffe A, Tipu HN, Kuehn HS, Rosenzweig SD, Turro E, Tavaré S, Thrasher AJ, Jodrell DI, Smith KGC, Boztug K, Milner JD, Thaventhiran JED.

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  • Cell  ·  June 6, 2019

    Comprehensive Integration of Single-Cell Data.

    Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WH, Hao Y, Stoeckius M, Smibert P, Satija R.
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  • Nature  ·  May 15, 2019

    Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

    Federico Gaiti, Ronan Chaligne, Hongcang Gu, Ryan M. Brand, Steven Kothen-Hill, Rafael C. Schulman, Kirill Grigorev , Davide Risso, Kyu-Tae Kim, Alessandro Pastore, Kevin Y. Huang, Alicia Alonso, Caroline Sheridan, Nathaniel D. Omans, Evan Biederstedt, Kendell Clement, Lili Wang, Joshua A. Felsenfeld, Erica B. Bhavsar, Martin J. Aryee, John N. Allan, Richard Furman , Andreas Gnirke, Catherine J. Wu, Alexander Meissner & Dan A. Landau.

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  • Nature  ·  May 8, 2019

    Next-generation characterization of the Cancer Cell Line Encyclopedia.

    Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov , Christopher C. Lo, E. Robert McDonald III, Jordi Barretina, Ellen T. Gelfand, Craig M. Bielski, Haoxin Li, Kevin Hu , Alexander Y. Andreev-Drakhlin , Jaegil Kim, Julian M. Hess, Brian J. Haas, François Aguet, Barbara A. Weir, Michael V. Rothberg, Brenton R. Paolella, Michael S. Lawrence, Rehan Akbani, Yiling Lu, Hong L. Tiv, Prafulla C. Gokhale, Antoine de Weck, Ali Amin Mansour, Coyin Oh, Juliann Shih, Kevin Hadi, Yanay Rosen, Jonathan Bistline, Kavitha Venkatesan, Anupama Reddy, Dmitriy Sonkin, Manway Liu, Joseph Lehar, Joshua M. Korn, Dale A. Porter, Michael D. Jones, Javad Golji, Giordano Caponigro, Jordan E. Taylor , Caitlin M. Dunning, Amanda L. Creech, Allison C. Warren, James M. McFarland, Mahdi Zamanighomi, Audrey Kauffmann, Nicolas Stransky, Marcin Imielinski, Yosef E. Maruvka, Andrew D. Cherniack, Aviad Tsherniak, Francisca Vazquez , Jacob D. Jaffe, Andrew A. Lane, David M. Weinstock, Cory M. Johannessen, Michael P. Morrissey, Frank Stegmeier, Robert Schlegel, William C. Hahn, Gad Getz, Gordon B. Mills , Jesse S. Boehm, Todd R. Golub, Levi A. Garraway & William R. Sellers.

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  • Cell Systems  ·  2019

    Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.

    Eric Minwei Liu, Alexander Martinez-Fundichely, Bianca Jay Diaz, Boaz Aronson, Tawny Cuykendall, Matthew MacKay
    Priyanka Dhingra, Elissa W.P. Wong, Ping Chi, Effie Apostolou, Neville E. Sanjana, Ekta Khurana

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  • BMC Med Genomics  ·  April 25, 2019

    Sequencing and curation strategies for identifying candidate glioblastoma treatments.

    Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB.

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  • Scientific Reports  ·  December 13, 2019

    Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

    Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M Oschwald, Michael C Zody, Soren Germer, Vaidehi Jobanputra, Jade Carter, Nicolas Robine
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  • Nature Communications  ·  April 23, 2019

    Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL.

    Alessandro Pastore, Federico Gaiti, Sydney X. Lu, Ryan M. Brand, Scott Kulm, Ronan Chaligne, Hongcang Gu, Kevin Y. Huang, Elena K. Stamenova, Wendy Béguelin, Yanwen Jiang, Rafael C. Schulman, Kyu-Tae Kim, Alicia Alonso, John N. Allan, Richard R. Furman, Andreas Gnirke, Catherine J. Wu, Ari M. Melnick, Alexander Meissner, Bradley E. Bernstein, Omar Abdel-Wahab & Dan A. Landau.

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  • Nature Methods  ·  April 22, 2019

    Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.

    Eleni P. Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengqing Ouyang, Rahul Satija, Neville E. Sanjana, Sergei B. Koralov & Peter Smibert.

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  • Nature Medicine  ·  April 22, 2019

    Immunogenic neoantigens derived from gene fusions stimulate T cell responses.

    Wei Yang, Ken-Wing Lee, Raghvendra M. Srivastava, Fengshen Kuo, Chirag Krishna, Diego Chowell, Vladimir Makarov, Douglas Hoen, Martin G. Dalin, Leonard Wexler, Ronald Ghossein, Nora Katabi, Zaineb Nadeem, Marc A. Cohen, S. Ken Tian, Nicolas Robine, Kanika Arora, Heather Geiger, Phaedra Agius, Nancy Bouvier, Kety Huberman, Katelynd Vanness, Jonathan J. Havel, Jennifer S. Sims, Robert M. Samstein, Rajarsi Mandal, Justin Tepe, Ian Ganly, Alan L. Ho, Nadeem Riaz, Richard J. Wong, Neerav Shukla, Timothy A. Chan & Luc G. T. Morris.

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  • Cell Rep  ·  April 16, 2019

    lncRNA Spehd Regulates Hematopoietic Stem and Progenitor Cells and Is Required for Multilineage Differentiation.

    Delás MJ, Jackson BT, Kovacevic T, Vangelisti S, Munera Maravilla E, Wild SA, Stork EM, Erard N, Knott SRV, Hannon GJ

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