Publications

Our Scientific Publications

  • 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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  • FASEB Journal  ·  January 30, 2019

    Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons.

    Lu C, Shi X, Allen A, Baez-Nieto D, Nikish A, Sanjana NE, Pan JQ.

    Sanjana Lab Neuropsychiatric Disease
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  • The Lancet  ·  January 31, 2019

    Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study.

    Petrovski S, Aggarwal, V, Giordano, JL, Stosic, M, Wou, K, Bier L, Spiegel E, Brennan K, Stong N, Jobanputra V, Ren Z, Zhu X, Mebane C, Nahum O, Wang Q, Kamalakaran S, Malone C, Anyane-Yeboa K, MD, Miller R, Levy B, Goldstein DB, Wapner RJ.

    Clinical Genetics
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  • European journal of human genetics: EJHG  ·  January 24, 2019

    De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms.

    Jansen S, van der Werf IM, Innes AM, Afenjar A, Agrawal PB, Anderson IJ, Atwal PS, van Binsbergen E, van den Boogaard MJ, Castiglia L, Coban-Akdemir ZH, van Dijck A, Doummar D, van Eerde AM, van Essen AJ, van Gassen KL, Guillen Sacoto MJ, van Haelst MM, Iossifov I, Jackson JL, Judd E, Kaiwar C, Keren B, Klee EW, Klein Wassink-Ruiter JS, Meuwissen ME, Monaghan KG, de Munnik SA, Nava C, Ockeloen CW, Pettinato R, Racher H, Rinne T, Romano C, Sanders VR, Schnur RE, Smeets EJ, Stegmann APA, Stray-Pedersen A, Sweetser DA, Terhal PA, Tveten K, VanNoy GE, de Vries PF, Waxler JL, Willing M, Pfundt R, Veltman JA, Kooy RF, Vissers LELM, de Vries BBA.

    Iossifov Lab Neuropsychiatric Disease
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  • Nature Methods  ·  July 1, 2018

    DeTiN: overcoming tumor-in-normal contamination.

    Taylor-Weiner A, Stewart C, Giordano T, Miller M, Rosenberg M, Macbeth A, Lennon N, Rheinbay E, Landau DA, Wu CJ, Getz G.

    Landau Lab
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  • Frontiers in immunology  ·  June 27, 2018

    CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency.

    Requena D, Maffucci P, Bigio B, Shang L, Abhyankar A, Boisson B, Stenson PD, Cooper DN, Cunningham-Rundles C, Casanova JL, Abel L, Itan Y.

    Clinical Genetics
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  • Elife  ·  July 13, 2018

    Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism.

    Conlon EG, Fagegaltier D, Agius P, Davis-Porada J, Gregory J, Hubbard I, Kang K, Kim D; New York Genome Center ALS Consortium, Phatnani H, Kwan J, Sareen D, Broach JR, Simmons Z, Arcila-Londono X, Lee EB, Van Deerlin VM, Shneider NA, Fraenkel E, Ostrow LW, Baas F, Zaitlen N, Berry JD, Malaspina A, Fratta P, Cox GA, Thompson LM, Finkbeiner S, Dardiotis E, Miller TM, Chandran S, Pal S, Hornstein E, MacGowan DJ, Heiman-Patterson T, Hammell MG, Patsopoulos NA, Dubnau J, Nath A, Phatnani H, Shneider NA, Manley JL.

    Phatnani Lab
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  • American journal of human genetics  ·  August 2, 2018

    Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles.

    Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C; Baylor-Hopkins Center for Mendelian Genomics, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CMB.

    Lappalainen Lab
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  • Brain: a journal of neurology  ·  September 1, 2018

    The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target.

    Petyuk VA, Chang R, Ramirez-Restrepo M, Beckmann ND, Henrion MYR, Piehowski PD, Zhu K, Wang S, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, De Jager P, Schneider JA, Morris CM, McKeith IG, Perry RH, Lovestone S, Woltjer RL, Beach TG, Sue LI, Serrano GE, Lieberman AP, Albin RL, Ferrer I, Mash DC, Hulette CM, Ervin JF, Reiman EM, Hardy JA, Bennett DA, Schadt E, Smith RD, Myers AJ.

    Phatnani Lab
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  • Methods in Molecular Biology  ·  December 1, 2018

    Prenatal Diagnosis by Whole Exome Sequencing in Fetuses with Ultrasound Abnormalities.

    Felice V, Abhyankar A, Jobanputra V

    Clinical Genetics
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  • Genome Biology  ·  December 19, 2018

    Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.

    Stoeckius M, Zheng S, Houck-Loomis, B, Hao S, Yeung B, Smibert P, Satija R.

    Satija Lab Technology Innovation
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  • Genome Research  ·  December 18, 2018

    Human papillomavirus and the landscape of secondary genetic alterations in oral cancers.

    Gillison ML, Akagi K, Xiao W, Jiang B, Pickard RKL, Li J, Swanson BJ, Agrawal AD, Zucker M, Stache-Crain B, Emde A-K, Geiger HM, Robine R, Coombes KR and Symer DE.

    Computational Biology Lab
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  • Nucleic Acids Research  ·  November 30, 2018

    Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.

    Ruf-Zamojski F, Ge Y, Nair V, Zamojski M, Pincas H, Toufaily C, Tome-Garcia J, Stoeckius M, Stephenson W, Smith GR, Bernard DJ, Tsankova NM, Hartmann BM, Fribourg M, Smibert P, Swerdlow H, Turgeon JL, Sealfon SC.

    Technology Innovation
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