Publications - New York Genome Center

bioRxiv · November 18, 2019 · Preprint

Genome-wide profiling of druggable active tumor defense mechanisms to enhance cancer immunotherapy

Rigel J Kishton, Shashank J Patel, Suman K Vodnala, Amy K Decker, Yogin Patel, Madhusudhanan Sukumar, Tori N Yamamoto, Zhiya Yu, Michelle Ji, Amanda N Henning, Devikala Gurusamy, Douglas C Palmer, Winifred Lo, Anna Pasetto, Parisa Malekzadeh, Drew C Deniger, Kris C Wood, Neville E. Sanjana, Nicholas P Restifo

Sanjana Lab Cancer
Journal of Heredity · November 14, 2019

Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi.

Michael G Campana, André Corvelo, Jennifer Shelton, Taylor E Callicrate, Karen L Bunting, Bridget Riley-Gillis, Frank Wos, Justin DeGrazia, Erich D Jarvis, Robert C Fleischer

Computational Biology Lab
Molecular Biology and Evolution · November 8, 2019

Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha.

Irene Julca, Marina Marcet-Houben, Fernando Cruz, Carlos Vargas-Chavez, J Spencer Johnston, Jèssica Gómez-Garrido, Leonor Frias, André Corvelo, Damian Loska, Francisco Cámara, Marta Gut, Tyler Alioto, Amparo Latorre, Toni Gabaldón

Computational Biology Lab
bioRxiv · November 7, 2019 · Preprint

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Netha Ulahannan, Matthew Pendleton, Aditya S Deshpande, Stefan Schwenk, Julie M Behr, Xiaoguang Dai, Carly Tyer, Priyesh Rughani, Sarah Kudman, Emily Adney, Huasong Tian, David Wilkes, Juan Miguel Mosquera, David Stoddart, Daniel J Turner, Sissel Juul, Eoghan Harrington, Marcin Imielinski

Imieliński Lab Technology Innovation
Genome Biology · November 4, 2019

Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Balliu B, Durrant M, Goede O, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E, Montgomery SB.

Knowles Lab Technology Innovation
Pigment Cell & Melanoma Research · November 2, 2019

Sequencing two Tyr::CreERT2 transgenic mouse lines.

Aktary Z, Corvelo A, Estrin C, Larue L.

Cancer Computational Biology Lab
Stem Cell Research · November 1, 2019

Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1 (NYGCe001-A).

Lu C, Sanjana NE.

Sanjana Lab Technology Innovation
Cell Reports · October 29, 2019

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, The NYGC ALS Consortium, Delphine Fagegaltier, Brent T. Harris, Lyle W. Ostrow, Hemali Phatnani, John Ravits, Josh Dubnau, and Molly Gale Hammell

Phatnani Lab Neurodegenerative Disease
Cell Systems · October 23, 2019

Genotype-Fitness Maps of EGFR-Mutant Lung Adenocarcinoma Chart the Evolutionary Landscape of Resistance for Combination Therapy Optimization

Patrick O. Bolan, Asaf Zviran, Lisa Brenan, Joshua S. Schiffman, Neville Dusaj, Amy Goodale, Federica Piccioni, Cory M. Johannessen, Dan A. Landau

Landau Lab Cancer
Science · October 10, 2019

Genetic regulatory variation in populations informs transcriptome analysis in rare disease.

Pejman Mohammadi, Stephane E. Castel, Beryl B. Cummings, Jonah Einson, Christina Sousa, Paul Hoffman, Sandra Donkervoort, Zhuoxun Jiang, Payam Mohassel, A. Reghan Foley, Heather E. Wheeler, Hae Kyung Im, Carsten G. Bonnemann, Daniel G. MacArthur, Tuuli Lappalainen.

Lappalainen Lab Technology Innovation
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.

Satija Lab Technology Innovation
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

Lappalainen Lab
Nature Biomedical Engineering · September 23, 2019

Immunomagnetic cell sorting.

Legut M, Sanjana NE.

Sanjana Lab Technology Innovation
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.

Phatnani Lab Neuropsychiatric Disease
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.
Kazimierz O Wrzeszczynski, Sadia Rahman, Mayu O Frank, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Dina Manaa, Esra Dikoglu, Depinder Khaira, A Rao Chimpiri, Vanessa V Michelini, Vaidehi Jobanputra, Robert B Darnell, Scott Powers and Minsig Choi.
Cancer Clinical Genetics
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

Phatnani Lab Neurodegenerative Disease Technology Innovation
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.

Landau Lab Cancer
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.

Cancer Technology Innovation
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.

Landau Lab Cancer
Neurobiology of disease · August 2, 2019

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

Halpern M, Brennand KJ, Gregory J.

Phatnani Lab Neurodegenerative Disease
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.

Tavaré Lab

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Our Scientific Publications

Genome-wide profiling of druggable active tumor defense mechanisms to enhance cancer immunotherapy

Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi.

Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha.

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Sequencing two Tyr::CreERT2 transgenic mouse lines.

Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1 (NYGCe001-A).

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

Genotype-Fitness Maps of EGFR-Mutant Lung Adenocarcinoma Chart the Evolutionary Landscape of Resistance for Combination Therapy Optimization

Genetic regulatory variation in populations informs transcriptome analysis in rare disease.

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

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

Immunomagnetic cell sorting.

Synergistic effects of common schizophrenia risk variants.

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

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

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

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

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

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

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