• Elife  ·  December 5, 2017

    Science Forum: The Human Cell Atlas.

    Regev A, Teichmann SA ,Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe’er D, Phillipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Schumacher TN, Shalek AK, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton MR, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold BJ, Xavier RJ, Yosef N; Human Cell Atlas Meeting Participants.

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  • Science  ·  December 7, 2017

    Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

    Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM.

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  • Cell  ·  November 16, 2017

    Cancer Evolution: No Room for Negative Selection.

    Bakhoum SF, Landau DA.
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  • Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1016). Chapter First Online: 2017  ·  November 13, 2017

    Target Discovery for Precision Medicine Using High-Throughput Genome Engineering.

    Guo X, Chitale P, Sanjana NE.

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  • Cell  ·  November 2, 2017

    SnapShot: Discovering Genetic Regulatory Variants by QTL Analysis.

    Brandt M, Lappalainen T.

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  • Nature Communications  ·  October 26, 2017

    Resistance to checkpoint blockade therapy through inactivation of antigen presentation.

    Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA, Van Seventer EE, Shukla SA, Yizhak K, Ray JP, Rosebrock D, Livitz D, Adalsteinsson V, Getz G, Duncan LM, Li B, Corcoran RB, Lawrence DP, Stemmer-Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ, Hacohen N.

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  • Nature  ·  October 11, 2017

    Landscape of X chromosome inactivation across human tissues.

    Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG.

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  • Genome Research  ·  October 11, 2017

    Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.

    Mohammadi P, Castel SE, Brown AA, Lappalainen T.

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  • Molecular Cell  ·  October 5, 2017

    High-Throughput Approaches to Pinpoint Function within the Noncoding Genome.

    Montalbano A, Canver, MC and Sanjana NE.

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  • Nature  ·  March 5, 2018

    Developmental diversification of cortical inhibitory interneurons.

    Mayer C, Hafemeister C, Bandler RC, Machold R, Allaway K, Jaglin X, Brito RB, Butler A, Fishell G, Satija R.
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  • Communications Biology  ·  March 22, 2018

    Lancet: genome-wide somatic variant calling using localized colored DeBruijn graphs.

    Narzisi G, Corvelo A, Arora K, Bergmann E, Shah M, Musunuri R, Emde, A-K, Robine N, Vacic V, Zody MC.
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  • Nature Genetics  ·  September 11, 2017

    Interpreting short tandem repeat variations in humans using mutational constraint.

    Gymrek M, Willems T, Reich D, Erlich Y.

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  • Cell  ·  September 28, 2017

    Genomic Patterns of De Novo Mutation in Simplex Autism.

    Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB,
    Eichler EE.

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  • Genome Research  ·  August 9, 2018

    Whole-Genome Bisulphite Sequencing With Improved Accuracy and Cost

    Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM.

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  • PLOS Biology  ·  December 30, 2018

    Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results.

    Alterovitz G, Dean DA II, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, King CHS IV, Johanson E, Thompson EE, Donaldson E, Tsang HS, Goecks J, Almeida JS, Guo L, Walderhaug M, Walsh P, Kahsay R, Bloom T, Lai Y, Simonyan V, Mazumder R.

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  • Nature Genetics  ·  August 20, 2018

    Modified penetrance of coding variants by cis-regulatory variation shapes human traits.

    Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Vasileva A, Lappalainen T.
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  • Nature Reviews Clinical Oncology  ·  February 14, 2017

    Genomic complexity of multiple myeloma and its clinical implications.

    Manier S, Salem KZ, Park J, Landau DA, Getz G, Ghobrial IM.

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  • Current Opinion in Systems Biology  ·  December 9, 2016

    Modeling cancer rearrangement landscapes.

    Maciejowski J, Imielinski M.

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  • Cold Spring Harbor Perspectives in Medicine  ·  June 1, 2017

    Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution.

    Bakhoum SF, Landau DA.

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  • Immunity  ·  September 7, 2017

    An NF-kB Transcription-Factor-Dependent Lineage Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

    Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U Rabadan R, Ghosh S.

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