The New York Genome Center Publications

• Publications

  • 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

    
    

    Scientific Reports. 2019 Dec. 13.

  • 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.

    
    

    Cell. 2019 Dec. 12.

  • 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.

    
    

    Nature Neuroscience. 2019 Nov. 25.

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

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

    
    

    Genome Biology. 2019 Nov. 21.

  • 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

    
    

    PNAS. 2019 Nov. 20.

  • 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

    
    

    Journal of Heredity. 2019 Nov. 14.

     

  • 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

    
    

    Molecular Biology and Evolution. 2019 Nov. 8.

  • 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.

     

    
    

    Genome Biology. 2019 Nov. 4.

  • Sequencing two Tyr::CreERT2 transgenic mouse lines.

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

    
    

    Pigment Cell & Melanoma Research. 2019 Nov. 2.

  • 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.

    
    

    Stem Cell Research. 2019 Nov. 1.

  • 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

    
    

    Cell Reports. 2019 Oct. 29.

  • 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

    
    

    Cell Systems. 2019 Oct. 23.
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• Preprints

  • ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data.

    Egor Dolzhenko, Mark F Bennett, Phillip A Richmond, Brett Trost, Sai Chen, Joke JFA van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G Gainullin, Andrew Gross, Bryan Lajoie, Ryan J Taft, Wyeth W Wasserman, Stephen W Scherer, Jan H Veldink, David R Bentley, Ryan KC Yuen, Melanie Bahlo, Michael A Eberle

    
    

    bioRxiv. 2019 Dec. 3.

  • 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

    
    

    bioRxiv. 2019 Nov. 18.

  • Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx.

    Nicole R Gay, Michael Gloudemans, Margaret L. L. Antonio, Brunilda Balliu, YoSon Park, Alicia R. Martin, Shaila Musharoff, Abhiram Rao, François Aguet, Alvaro Barbeira, Rodrigo Bonazzola, Farhad Hormozdiari, GTEx Consortium, Kristin G. Ardlie, Christopher D. Brown, Hae Kyung Im, Tuuli Lappalainen, Xiaoquan Wen, Stephen B. Montgomery

    
    

    bioRxiv. 2019 Nov. 9.

  • Novel patterns of complex structural variation revealed across thousands of cancer genome graphs.

    Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Joel Rosiene, Madison Darmofal, Huasong Tian, Joseph DeRose, Rick Mortensen, Emily Adney, Zoran Gajic, Kenneth Eng, Jeremiah Anthony Wala, Kazimierz O. Wrzeszczyński, Kanika Arora, Minita Shah, Anne-Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert Darnell, Mahmoud Ghandi, Franklin Huang, John Maciejowski, Titia De Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David Knowles, Ed Reznik, Bhubaneswar Mishra, Rameen Beroukhim, Michael Zody, Nicolas Robine, Kenji Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid, Xiaohong Li, David Wilkes, Andrea Sboner, Juan Miguel Mosquera, Olivier Elemento, Marcin Imielinski

    
    

    bioRxiv. 2019 November 9.

  • 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

    
    

    bioRxiv. 2019 Nov. 7.

  • Cell type specific genetic regulation of gene expression across human tissues.

    Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz Aguirre, Valentin Wucher, Silva Kasela, Stephane E. Castel, Andrew R. Hamel, Ana Viñuela, Amy L. Roberts, Serghei Mangul, Xiaoquan Wen, Gao Wang, Alvaro N. Barbeira, Diego Garrido-Martín, Brian Nadel, Yuxin Zou, Rodrigo Bonazzola, Jie Quan, Andrew Brown, Angel Martinez-Perez, José Manuel Soria, GTEx Consortium, Gad Getz, Emmanouil T. Dermitzakis, Kerrin S. Small, Matthew Stephens, Hualin S. Xi, Hae Kyung Im,
    Roderic Guigó, Ayellet V. Segrè, Barbara E., Stranger, Kristin G. Ardlie, Tuuli Lappalainen.

    
    

    bioRxiv. 2019 Oct. 17.

  • A polyclonal allelic expression assay for detecting regulatory effects of transcript variants

    Margot Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen.

    
    

    bioRxiv. 2019 Oct. 7.

  • 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

    
    

    bioRxiv. 2019 Oct. 3

  • Diverse transcriptomic signatures across human tissues identify functional rare genetic variation.

    Nicole M. Ferraro, Benjamin J. Strober, Jonah Einson, Xin Li, Francois Aguet, Alvaro N. Barbeira, Stephane E. Castel, Joe R. Davis, Austin T. Hilliard, Bence Kotis, YoSon Park, Alexandra J. Scott, Craig Smail, Emily K. Tsang, Kristin G. Ardlie, Themistocles L. Assimes, Ira Hall, Hae Kyung Im, GTEx Consortium, Tuuli Lappalainen, Pejman Mohammadi, Stephen B. Montgomery, Alexis Battle

    
    

    bioRxiv. 2019 Oct. 3.

  • A vast resource of allelic expression data spanning human tissues

    Stephane E. Castel, François Aguet, Pejman Mohammadi, GTEx Consortium, Kristin G. Ardlie, Tuuli Lappalainen

    
    

    bioRxiv. 2019 Oct. 3.

  • The GTEx Consortium atlas of genetic regulatory effects across human tissues

    François Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Meritxell Oliva, Princy E Parsana, Elise Flynn, Laure Fresard, Eric R Gaamzon, Andrew R Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Muñoz-Aguirre, YoSon Park, Ashis Saha, Ayellet V Segrć, Benjamin J Strober, Xiaoquan Wen, Valentin Wucher, Sayantan Das, Diego Garrido-Martín, Nicole R Gay, Robert E Handsaker, Paul J Hoffman, Seva Kashin, Alan Kwong, Xiao Li, Daniel MacArthur, John M Rouhana, Matthew Stephens, Ellen Todres, Ana Viñuela, Gao Wang, Yuxin Zou, The GTEx Consortium, Christopher D Brown, Nancy Cox, Emmanouil Dermitzakis, Barbara E Engelhardt, Gad Getz, Roderic Guigo, Stephen B Montgomery, Barbara E Stranger, Hae Kyung Im, Alexis Battle, Kristin G Ardlie, Tuuli Lappalainen

    
    

    bioRxiv. 2019 Oct. 3

  • 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

    
    

    bioRxiv. Sept. 5.

  • SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome.

    Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook.

    
    

    bioRxiv. 2019 Mar 25.

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

    Hafemeister C, Satija R.

    
    

    bioRxiv. 2019 March 14.

  • Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients.

    Farhan SMK, Howrigan DP, Abbott L, Byrnes A, Churchhouse C, Phatnani H, Smith B, Topp S, Rampersaud E, Wu G, Wuu J, Gubitz A, Kilm J, Mordes D, Ghosh S, CReATe Consortium, FALS Consortium, ALSGENS Consortium, Eggan K, Rademakers R, McCauley J, Schule R, Zuchner S, Benatar M, Taylor JP, Nalls M, Traynor B, Shaw C, Goldstein D, Harms M, Daly M, Neale B.

    
    

    bioRxiv. 2018 Apr. 25.

  • The evolutionary history of 2,658 cancers.

    PCAWG Evolution and Heterogeneity Working Group, PCAWG network (includes Imielinski M)

    
    

    bioRxiv. 2017 July 11.