Publications - New York Genome Center

Neurochem Res. · February 4, 2020

Dynamic Lamin B1-Gene Association During Oligodendrocyte Progenitor Differentiation.

Yattah C, Hernandez M, Huang D, Park H, Liao W, Casaccia P.

Neurodegenerative Disease

Neuropsychiatric Disease

Technology Innovation

Computational Biology Lab

Genome Biology · December 23, 2019

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

Hafemeister C, Satija R.

Science Translational Medicine · December 18, 2019

Human genetics and neuropathology suggest a link between miR-218 and amyotrophic lateral sclerosis pathophysiology.

Irit Reichenstein,*, Chen Eitan, Sandra Diaz-Garcia, Guy Haim, Iddo Magen, Aviad Siany, Mariah L. Hoye, Natali Rivkin, Tsviya Olender, Beata Toth, Revital Ravid, Amitai D. Mandelbaum, Eran Yanowski, Jing Liang, Jeffrey K. Rymer, Rivka Levy, Gilad Beck, Elena Ainbinder, Sali M. K. Farhan, Kimberly A. Lennox, Nicole M. Bode, Mark A. Behlke, Thomas Möller, Smita Saxena, Cristiane A. M. Moreno, Giancarlo Costaguta, Kristel R. van Eijk, Hemali Phatnani, Ammar Al-Chalabi, A. Nazli Başak, Leonard H. van den Berg, Orla Hardiman, John E. Landers, Jesus S. Mora, Karen E. Morrison, Pamela J. Shaw, Jan H. Veldink, Samuel L. Pfaff, Ofer Yizhar, Christina Gross, Robert H. Brown Jr., John M. Ravits, Matthew B. Harms, Timothy M. Miller and Eran Hornstein

Phatnani Lab

Neurodegenerative Disease

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.

PLoS Genet · December 13, 2019

Leveraging allelic imbalance to refine fine-mapping for eQTL studies.

Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E.

Lappalainen Lab

Technology Innovation

Cell · December 12, 2019

Toward a Common Coordinate Framework for the Human Body.

Jennifer E. Rood, Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William Mauck, Gökçen Eraslan, John C. Marioni, Aviv Regev, Rahul Satija.

Satija Lab

Technology Innovation

Nature Neuroscience · November 25, 2019

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein.

Farhan SMK, Howrigan DP, Abbott LE, Klim JR, Topp SD, Byrnes AE, Churchhouse C, Phatnani H, Smith BN, Rampersaud E, Wu G, Wuu J, Shatunov A, Iacoangeli A, Al Khleifat A, Mordes DA, Ghosh S; ALSGENS Consortium; FALS Consortium; Project MinE Consortium; CReATe Consortium, Eggan K, Rademakers R, McCauley JL, Schüle R, Züchner S, Benatar M, Taylor JP, Nalls M, Gotkine M, Shaw PJ, Morrison KE, Al-Chalabi A, Traynor B, Shaw CE, Goldstein DB, Harms MB, Daly MJ, Neale BM.

Phatnani Lab

Neurodegenerative Disease

Genome Biology · November 21, 2019

EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation.

, Gunjan Sethia, Izzo F, Sana Badri, MacIntosh Cornwell, Kim K-T, Landau D, Jane Skok

Landau Lab

Technology Innovation

PNAS · November 20, 2019

Effects of ALS-associated TANK binding kinase 1 mutations on protein–protein interactions and kinase activity

Junqiang Ye, Jonah Cheung, Valeria Gerbino, Göran Ahlsén, Christina Zimanyi, David Hirsh, and Tom Maniatis

Maniatis Lab

Neurodegenerative Disease

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

Our Scientific Publications

Dynamic Lamin B1-Gene Association During Oligodendrocyte Progenitor Differentiation.

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

Human genetics and neuropathology suggest a link between miR-218 and amyotrophic lateral sclerosis pathophysiology.

Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

Leveraging allelic imbalance to refine fine-mapping for eQTL studies.

Toward a Common Coordinate Framework for the Human Body.

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein.

EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation.

Effects of ALS-associated TANK binding kinase 1 mutations on protein–protein interactions and kinase activity

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.