Publications

Our Scientific Publications

  • bioRxiv  ·  January 18, 2022  ·  Preprint

    Non-Coding Genetic Analysis Implicates Interleukin 18 Receptor Accessory Protein 3′UTR in Amyotrophic Lateral Sclerosis.

    Chen Eitan, Aviad Siany, Elad Barkan, Tsviya Olender, Kristel R. van Eijk, Matthieu Moisse, Sali M. K. Farhan, Yehuda M. Danino, Eran Yanowski, Hagai Marmor-Kollet, Natalia Rivkin, Nancy Yacovzada, Shu-Ting Hung, Johnathan Cooper-Knock, Chien-Hsiung Yu, Cynthia Louis, Seth L. Masters, Kevin P. Kenna, Rick A. A. van der Spek, William Sproviero, Ahmad Al Khleifat, Alfredo Iacoangeli, Aleksey Shatunov, Ashley R. Jones, Yael Elbaz Alon, Yahel Cohen, Elik Chapnik, Daphna Rothschild, Omer Weissbrod, Gilad Beck, Elena Ainbinder, Shifra Ben-Dor, Sebastian Werneburg, Dorothy P. Schafer, Robert H. Brown Jr, Pamela J. Shaw, Philip Van Damme, Leonard H. van den Berg, Hemali P. Phatnani, Eran Segal, Justin K. Ichida, Ammar Al-Chalabi, Jan H. Veldink, Project MinE ALS Sequencing Consortium, NYGC ALS Consortium, Eran Hornstein
    Phatnani Lab Biology, Genomics & Technology Neurodegenerative Disease
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  • bioRxiv  ·  January 12, 2022  ·  Preprint

    Epigenetic dysregulation from chromosomal transit in micronuclei.

    Albert Agustinus, Ramya Raviram, Bhargavi Dameracharla, Jens Luebeck, Stephanie Stransky, Lorenzo Scipioni, Robert Myers Melody DiBona, Mercedes Duran, Britta Weigelt, Shira Yomtoubian, Eleonore Toufektchan, Paul Mischel, Vivek Mittal, Sohrab Shah, John Maciejowski, Enrico Gratton, Peter Ly, Mathieu Bakhoum, Dan Landau, Vineet Bafna, Simone Sidoli, Yael David, Samuel F Bakhoum

    Landau Lab Cancer Biology, Genomics & Technology
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  • iScience  ·  January 10, 2022

    Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.

    Sahajpal NS, Jill Lai CY, Hastie A, Mondal AK, Dehkordi SR, van der Made CI, Fedrigo O, Al-Ajli F, Jalnapurkar S, Byrska-Bishop M, Kanagal-Shamanna R, Levy B, Schieck M, Illig T, Bacanu SA, Chou JS, Randolph AG, Rojiani AM, Zody MC, Brownstein CA, Beggs AH, Bafna V, Jarvis ED, Hoischen A, Chaubey A, Kolhe R; COVID19hostgenomesv consortium

    Biology, Genomics & Technology Computational Biology Lab
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  • American Journal of Human Genetics  ·  December 20, 2021

    Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes.

    George Hindy et al. including Soren Germer

    Biology, Genomics & Technology
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  • Genome Research  ·  December 13, 2021

    Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers.

    Symer DE, Akagi K, Geiger HM, Song Y, Li G, Emde AK, Xiao W, Jiang B, Corvelo A, Toussaint NC, Li J, Agrawal A, Ozer E, El-Naggar AK, Du Z, Shewale JB, Stache-Crain B, Zucker M, Robine N, Coombes KR, Gillison ML.

    Cancer Computational Biology Lab
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  • Cancers  ·  December 7, 2021

    RNA Sequencing of Primary Cutaneous and Breast-Implant Associated Anaplastic Large Cell Lymphomas Reveals Infrequent Fusion Transcripts and Upregulation of PI3K/AKT Signaling via Neurotrophin Pathway Genes.

    Di Napoli A, Vacca D, Bertolazzi G, Lopez G, Piane M, Germani A, Rogges E, Pepe G, Santanelli Di Pompeo F, Salgarello M, Jobanputra V, Hsiao S, Wrzeszczynski KO, Berti E, Bhagat G.

    Cancer Computational Biology Lab Clinical Genetics
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  • Genome Biology  ·  December 6, 2021

    The SEQC2 epigenomics quality control (EpiQC) study.

    Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE.
    Biology, Genomics & Technology Computational Biology Lab
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  • bioRxiv  ·  November 20, 2021  ·  Preprint

    Antigen presentation by type 3 innate lymphoid cells instructs the differentiation of gut microbiota-specific regulatory T cells.

    Ranit Kedmi, Tariq Najar, Kailin R. Mesa, Allyssa Grayson, Lina Kroehling, Yuhan Hao, Stephanie Hao, Maria Pokrovskii, Mo Xu, Jhimmy Talbot, Jiaxi Wang, Mark S. Anderson, James M. Gardner, Terri M. Laufer, Iannis Aifantis, Juliet M. Bartleson, Paul M. Allen, Marlon Stoeckius, Dan R. Littman

    Biology, Genomics & Technology Computational Biology Lab
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  • Molecular Psychiatry  ·  November 19, 2021

    The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders.

    Alkelai A, Greenbaum L, Docherty AR, Shabalin AA, Povysil G, Malakar A, Hughes D, Delaney SL, Peabody EP, McNamara J, Gelfman S, Baugh EH, Zoghbi AW, Harms MB, Hwang HS, Grossman-Jonish A, Aggarwal V, Heinzen EL, Jobanputra V, Pulver AE, Lerer B, Goldstein DB.
    Biology, Genomics & Technology Neuropsychiatric Disease Computational Biology Lab Clinical Genetics
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  • Microbiology Spectrum  ·  November 17, 2021

    Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study.

    Barun Mathema, Liang Chen, Kar Fai Chow, Yanan Zhao, Michael C Zody, Jose R Mediavilla, Marcus H Cunningham, Kaelea Composto, Annie Lee, Dayna M Oschwald, Soren Germer, Samantha Fennessey, Kishan Patel, David Wilson, Ann Cassell, Lauren Pascual, Andrew Ip, André Corvelo, Sophia Dar, Yael Kramer, Tom Maniatis, David S Perlin, Barry N Kreiswirth

    Maniatis Lab Biology, Genomics & Technology Computational Biology Lab
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  • The Plant Cell  ·  November 15, 2021

    Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.

    Simon C Groen, Zoe Joly-Lopez, Adrian E Platts, Mignon Natividad, Zoe Fresquez, William M Mauck III, Marinell R Quintana, Carlo LU Cabral, Rolando O Torres, Rahul Satija, Michael D Purugganan, Amelia Henry
    Satija Lab Biology, Genomics & Technology
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  • bioRxiv  ·  November 10, 2021  ·  Preprint

    High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

    Marta Byrska-Bishop, Uday S Evani, Xuefang Zhao, Anna O Basile, Haley J Abel, Allison A Regier, André Corvelo, Wayne E Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, The Human Genome Structural Variation Consortium, Paul Flicek, Soren Germer, Harrison Brand, Ira M Hall, Michael E Talkowski, Giuseppe Narzisi, Michael C Zody

    Biology, Genomics & Technology Computational Biology Lab
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  • Genes  ·  October 30, 2021

    Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values.

    Abdul Karim, Zheng Su, Phillip K. West, Matthew Keon, The NYGC ALS Consortium, Jannah Shamsani, Samuel Brennan, Ted Wong, Ognjen Milicevic, Guus Teunisse, Hima Nikafshan Rad and Abdul Sattar

    Phatnani Lab Neurodegenerative Disease
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