Publications

Our Scientific Publications

  • Nature Communications  ·  February 11, 2022

    Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.

    Sanja Vicković, Denis Schapiro, Konstantin Carlberg, Britta Lötstedt, Ludvig Larsson, Franziska Hildebrandt, Marina Korotkova, Aase H. Hensvold, Anca I. Catrina, Peter K. Sorger, Vivianne Malmström, Aviv Regev & Patrik L. Ståhl

    Vicković Lab Biology, Genomics & Technology Neurodegenerative Disease
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  • Nature Biotechnology  ·  February 7, 2022

    Curated variation benchmarks for challenging medically relevant autosomal genes.

    Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M Wenger, William J Rowell, Ziad M Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E Miller, David Jaspez, Jose M Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A Rubio-Rodriguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E Clarke, Joyce Lee, Christopher E Mason, Stephen E Lincoln, Karen H. Miga, Mark TW Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M Zook, Fritz J Sedlazeck

    Biology, Genomics & Technology Computational Biology Lab
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  • bioRxiv  ·  February 2, 2022  ·  Preprint

    Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq.

    Hans-Hermann Wessels, Alejandro Mendez-Mancilla, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija

    Sanjana Lab Satija Lab Computational Biology Lab
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  • PLoS Genet  ·  January 31, 2022

    Transcription factor regulation of eQTL activity across individuals and tissues.

    Elise Flynn, Athena L. Tsu, Silva Kasela, Sarah Kim-Hellmuth, Francois Aguet, Kristin G. Ardlie, Harmen J. Bussemaker, Pejman Mohammadi, Tuuli Lappalainen

    Lappalainen Lab Biology, Genomics & Technology
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  • bioRxiv  ·  January 20, 2022  ·  Preprint

    Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring.

    Adam J. Widman, Minita Shah, Nadia Ogaard, Cole C. Khamnei, Amanda Frydendahl, Aditya Deshpande, Anushri Arora, Mingxuan Zhang, Daniel Halmos, Jake Bass, Theophile Langanay, Srinivas Rajagopalan, Zoe Steinsnyder, Will Liao, Mads Heilskov Rasmussen, Sarah Ostrup Jensen, Jesper Nors, Christina Therkildsen, Jesus Sotelo, Ryan Brand, Ronak H. Shah, Alexandre Pellan Cheng, Colleen Maher, Lavinia Spain, Kate Krause, Dennie T. Frederick, Murtaza S. Malbari, Melissa Marton, Dina Manaa, Lara Winterkorn, Margaret K. Callahan, Genevieve Boland, Jedd D. Wolchok, Ashish Saxena, Samra Turajlic, Marcin Imielinski, Michael F. Berger, Nasser K. Altorki, Michael A. Postow, Nicolas Robine, Claus Lindbjerg Andersen, Dan A. Landau
    Imieliński Lab Landau Lab Cancer Biology, Genomics & Technology Computational Biology Lab
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  • 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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