Publications

Our Scientific Publications

  • 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.

    Landau Lab Cancer
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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.

    Sanjana Lab Satija Lab Technology Innovation
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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.

    Cancer Computational Biology Lab
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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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  • Genes & Development  ·  April 11, 2019

    The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells.

    Charles Ng, Martin Aichinger, Tung Nguyen, Christy Au, Tariq Najar, Lin Wu, Kai R. Mesa, Will Liao, Jean-Pierre Quivy, Benjamin Hubert, Genevieve Almouzni, Johannes Zuber and Dan R. Littman.
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    Cancer Technology Innovation Computational Biology Lab
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  • Nature  ·  April 10, 2019

    The bone marrow microenvironment at single-cell resolution

    Anastasia N. Tikhonova, Igor Dolgalev, Hai Hu, Kishor K. Sivaraj, Edlira Hoxha, Álvaro Cuesta-Domínguez, Sandra Pinho, Ilseyar Akhmetzyanova , Jie Gao, Matthew Witkowski, Maria Guillamot, Michael C. Gutkin, Yutong Zhang, Christian Marier, Catherine Diefenbach, Stavroula Kousteni, Adriana Heguy, Hua Zhong, David R. Fooksman , Jason M. Butler, Aris Economides, Paul S. Frenette, Ralf H. Adams, Rahul Satija, Aristotelis Tsirigos & Iannis Aifantis.

    Satija Lab Technology Innovation
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  • Methods Mol Biol  ·  April 4, 2019

    De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads.

    Kerr SC, Gaiti F, Tanurdzic M.
    Landau Lab Technology Innovation
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  • Science  ·  April 4, 2019

    Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis.

    Maniatis S, Tarmo Äijö, Sanja Vickovic, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää,Gonzalo Saiz-Castro, Miguel Cuevas, Aaron Watters, Joakim Lundeberg, Richard Bonneau, and Phatnani H.

    Phatnani Lab Neurodegenerative Disease
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  • Cell  ·  April 4, 2019

    Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice.

    Daniele Canzio, Chiamaka L. Nwakeze, Adan Horta, Sandy M. Rajkumar, Eliot L. Coffey, Erin E. Duffy, Rachel Duffié, Kevin Monahan, Sean O’Keeffe, Matthew D. Simon, Stavros Lomvardas, Tom Maniatis.

    Maniatis Lab Neurodegenerative Disease
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  • Genome Res  ·  April 2, 2019

    A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS.

    Gelfman S, Dugger SA, Araujo Martins Moreno C, Ren Z, Wolock CJ, Shneider N, Phatnani H, Cirulli ET, Lasseigne BN, Harris T, Maniatis T, Rouleau G, Brown RH, Gitler AD, Myers RM, Petrovski S, Allen A, Goldstein DB, Harms MB.

    Phatnani Lab Neurodegenerative Disease
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  • Nat Genet  ·  March 29, 2019

    Opportunities and challenges for transcriptome-wide association studies.

    Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A.

    Knowles Lab Technology Innovation
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  • Leukemia  ·  March 25, 2019

    Short telomeres are associated with inferior outcome, genomic complexity, and clonal evolution in chronic lymphocytic leukemia.

    Jebaraj BMC, Tausch E, Landau DA, Bahlo J, Robrecht S, Taylor-Weiner AN, Bloehdorn J, Scheffold A, Mertens D, Böttcher S, Kneba M, Jäger U, Zenz T, Wenger MK, Fingerle-Rowson G, Wendtner C, Fink AM, Wu CJ, Eichhorst B, Fischer K, Hallek M, Döhner H, Stilgenbauer S.

    Landau Lab Cancer
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  • Nat Neurosci  ·  February 22, 2019

    Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus-CA3 projection.

    Zhou W, He Y, Rehman AU, Kong Y, Hong S, Ding G, Yalamanchili HK, Wan YW, Paul B, Wang C, Gong Y, Zhou W, Liu H, Dean J, Scalais E, O’Driscoll M, Morton JEV; DDD study, Hou X, Wu Q, Tong Q, Liu Z, Liu P, Xu Y, Sun Z.

    Clinical Genetics
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  • Scientific Reports  ·  March 14, 2019

    Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator.

    Oh BY, Shin HT, Yun JW, Kim KT, Kim J, Bae JS, Cho YB, Lee WY, Yun SH, Park YA, Park YH, Im YH, Lee J, Joung JG, Kim HC, Park WY.

    Landau Lab Cancer Technology Innovation
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  • Genome Biology  ·  December 23, 2019

    Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.

    Hafemeister C, Satija R.

    Satija Lab Technology Innovation
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  • Arthritis & rheumatology (Hoboken, N.J.)  ·  March 5, 2019

    Histologic and transcriptional evidence of subclinical synovial inflammation in rheumatoid arthritis patients in clinical remission.

    Orange DE, Agius P, DiCarlo EF, Mirza S, Pannellini T, Szymonifka J, Jiang CS, Figgie MP, Frank MO, Robinson WH, Donlin LT, Rozo C, Gravallese EM, Bykerk VP, Goodman SM.

    Computational Biology Lab
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  • Bioinformatics  ·  May 27, 2019

    ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions.

    Dolzhenko E, Deshpande V, Schlesinger F, Krusche P, Petrovski R, Chen S, Emig-Agius D, Gross A, Narzisi G, Bowman B, Scheffler K, van Vugt JJFA, French C, Sanchis-Juan A, Ibanez K, Tucci A, Lajoie B, Veldink JH, Raymond L, Taft RJ, Bentley DR, Eberle MA.
    Computational Biology Lab
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  • Leukemia  ·  February 13, 2019

    Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia.

    McNeer NA, Philip J, Geiger H, Ries RE, Lavallée VP, Walsh M, Shah M, Arora K, Emde AK, Robine N, Alonzo TA, Kolb EA, Gamis AS, Smith M, Gerhard DS, Guidry-Auvil J, Meshinchi S, Kentsis A.

    Cancer Computational Biology Lab
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