• Cell  ·  October 1, 2020

    Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.

    Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Huasong Tian,Sarah Kudman, Joel Rosiene, Madison Darmofal, Joseph DeRose, Rick Mortensen, Emily M. Adney, Alon Shaiber, Zoran Gajic, Michael Sigouros, Kenneth Eng, Jeremiah A. Wala, Kazimierz O. Wrzeszczynski Kanika Arora, Minita Shah, Anne-Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert B. Darnell, Mahmoud Ghandi, Franklin Huang, Sally Dewhurst, John Maciejowski,Titia de Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David A. Knowles, Ed Reznik, Bud Mishra, Rameen Beroukhim, Michael C. Zody, Nicolas Robine, Kenji M. 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, and Marcin Imielinski

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  • bioRxiv  ·  September 29, 2020  ·  Preprint

    The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.

    Kazuya Masuda, Adam Kornberg, Sijie Lin, Patricia Ho, Kerim Secener, Nathan Suek, Alyssa M Bacarella, Matthew Ingham, Vilma Rosario, Ahmed M Al-Masrou, Steven A Lee-Kong, P.Ravi Kiran, Kelley S Yan, Marlon Stoeckius, Peter Smibert, Paul E Oberstein, Peter A Sims, Arnold Han

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  • Science  ·  September 24, 2020

    Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

    Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C, Rosain J, Bilguvar K, Ye J, Bolze A, Bigio B, Yang R, Arias AA, Zhou Q, Zhang Y, Onodi F, Korniotis S, Karpf L, Philippot Q, Chbihi M, Bonnet-Madin L, Dorgham K, Smith N, Schneider WM, Razooky BS, Hoffmann HH, Michailidis E, Moens L, Han JE, Lorenzo L, Bizien L, Meade P, Neehus AL, Ugurbil AC, Corneau A, Kerner G, Zhang P, Rapaport F, Seeleuthner Y, Manry J, Masson C, Schmitt Y, Schlüter A, Le Voyer T, Khan T, Li J, Fellay J, Roussel L, Shahrooei M, Alosaimi MF, Mansouri D, Al-Saud H, Al-Mulla F, Almourfi F, Al-Muhsen SZ, Alsohime F, Al Turki S, Hasanato R, van de Beek D, Biondi A, Bettini LR, D’Angio M, Bonfanti P, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Oler AJ, Tompkins MF, Alba C, Vandernoot I, Goffard JC, Smits G, Migeotte I, Haerynck F, Soler-Palacin P, Martin-Nalda A, Colobran R, Morange PE, Keles S, Çölkesen F, Ozcelik T, Yasar KK, Senoglu S, Karabela ŞN, Gallego CR, Novelli G, Hraiech S, Tandjaoui-Lambiotte Y, Duval X, Laouénan C; COVID-STORM Clinicians; COVID Clinicians; Imagine COVID Group; French COVID Cohort Study Group; CoV-Contact Cohort; Amsterdam UMC Covid-19; Biobank; COVID Human Genetic Effort; NIAID-USUHS; TAGC COVID Immunity Group, Snow AL, Dalgard CL, Milner J, Vinh DC, Mogensen TH, Marr N, Spaan AN, Boisson B, Boisson-Dupuis S, Bustamante J, Puel A, Ciancanelli M, Meyts I, Maniatis T, Soumelis V, Amara A, Nussenzweig M, García-Sastre A, Krammer F, Pujol A, Duffy D, Lifton R, Zhang SY, Gorochov G, Béziat V, Jouanguy E, Sancho-Shimizu V, Rice CM, Abel L, Notarangelo LD, Cobat A, Su HC, Casanova JL.

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  • Am J Respir Crit Care Med  ·  September 23, 2020

    Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans.

    Gui H, Levin AM, Hu D, Sleiman P, Xiao S, Mak AC, Yang M, Barczak AJ, Huntsman S, Eng C, Hochstadt S, Zhang E, Whitehouse K, Simons S, Cabral W, Takriti S, Abecasis G, Blackwell TW, Kang HM, Nickerson DA, Germer S, Lanfear DE, Gilliland F, Gauderman WJ, Kumar R, Erle DJ, Martinez FD, Hakonarson H, Burchard EG, Williams LK.

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  • Science  ·  September 11, 2020

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

    Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E. Castel, Andrew R. Hamel, Ana Viñuela, Amy L. Roberts, Serghei Mangul, Xiaoquan Wen, Gao Wang, Alvaro N. Barbeira, Diego Garrido-Martín, Brian B. 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

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  • Science  ·  September 11, 2020

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

    The GTEx Consortium (Corresponding authors: François Aguet, Kristin G. Ardlie, Tuuli Lappalainen)
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  • Genome Biology  ·  September 11, 2020

    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
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  • Genome Medicine  ·  September 11, 2020

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

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

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  • Science  ·  September 11, 2020

    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

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  • Genome Biology  ·  September 11, 2020

    A vast resource of allelic expression data spanning human tissues.

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

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  • bioRxiv  ·  September 8, 2020  ·  Preprint

    Scalable, multimodal profiling of chromatin accessibility and protein levels in single cells.

    Eleni P Mimitou, Caleb A Lareau, Kelvin Y Chen, Andre L Zorzetto-Fernandes, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Yeung, Pratiksha I Thakore, James Badger Wing, Kristopher L Nazor, Shimon Sakaguchi, Leif S Ludwig, Vijay

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  • The International Journal of Biochemistry & Cell Biology  ·  August 28, 2020

    Toll-like Receptor (TLR)-induced Rasgef1b expression in macrophages is regulated by NF-κB through its proximal promoter.

    Felipe B Leão, Lauren S Vaughn, Dev Bhatt, Will Liao, Dillon Maloney, Brener C Carvalho, Leonardo Oliveira, Sankar Ghosh, Aristóbolo M Silva

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  • bioRxiv  ·  August 28, 2020  ·  Preprint

    De Novo Mutation in an Enhancer of EBF3 in simplex autism.

    Evin M. Padhi, Tristan J. Hayeck, Brandon Mannion, Sumantra Chatterjee, Marta Byrska-Bishop, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Zhang Cheng, Riana D. Hunter, Jennifer Akiyama, Lauren E. Fries, Jeffrey Ng, Nick Stong, Andrew S. Allen, Diane E. Dickel, Raphael A. Bernier, David U. Gorkin, Len A. Pennacchio, Michael C. Zody, Tychele N. Turner

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  • bioRxiv  ·  August 19, 2020  ·  Preprint

    CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens.

    Anders West Rasmussen, Tarmo Äijö, Mariano Ignacio Gabitto, Nick Carriero, Neville Sanjana, Jane Skok, Richard Bonneau

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  • The Journal of Clinical Investigation  ·  August 13, 2020

    Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.

    Mercedes Prudencio, Jack Humphrey, Sarah Pickles, Anna-Leigh Brown, Sarah E. Hill, Jennifer Kachergus, Ji Shi, Michael Heckman, Matthew Spiegel, Casey Cook, Yuping Song, Mei Yue, Lillian Daughrity, Yari Carlomagno, Karen Jansen-West, Cristhoper Fernandez De Castro, Michael DeTure, Shunsuke Koga, Ying-Chih Wang, Prasanth Sivakumar, Cristian Bodo, Ana Candalija, Kevin Talbot, Bhuvaneish T. Selvaraj, Karen Burr, Siddharthan Chandran, Jia Newcombe, Tammaryn Lashley, Isabel Hubbard, Demetra Catalano, Duyang Kim, Nadia Propp, Samantha Fennessey, Delphine Fagegaltier, Hemali Phatnani, Maria Secrier, Elizabeth M.C. Fisher, Björn Oskarsson, Marka van Blitterswijk, Rosa Rademakers, Neill R. Graff-Radford, Bradley Boeve, David S. Knopman, Ronald Petersen, Keith Josephs, E. Aubrey Thompson, Towfique Raj, Michael E. Ward, Dennis Dickson, Tania F. Gendron, Pietro Fratta, and Leonard Petrucelli

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  • bioRxiv  ·  July 30, 2020  ·  Preprint

    EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments.

    Alexandre Yahi, Paul Hoffman, Margot Brandt, Pejman Mohammadi, Nicholas P. Tatonetti, Tuuli Lappalainen

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  • bioRxiv  ·  July 24, 2020  ·  Preprint

    Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study.

    Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Gary P. Schroth, Fritz J. Sedlazeck, Giuseppe Narzisi, William Farmerie, Don A. Baldwin, Christopher E. Mason

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  • Current Opinion in Genetics & Development  ·  July 14, 2020

    The role of clustered protocadherins in neurodevelopment and neuropsychiatric diseases.

    Flaherty E, Maniatis T.

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  • Cell  ·  June 24, 2020

    Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy.

    Wu L, Hollinshead KER, Hao Y, Au C, Kroehling L, Ng C, Lin WY, Li D, Silva HM, Shin J, Lafaille JJ, Possemato R, Pacold ME, Papagiannakopoulos T, Kimmelman AC, Satija R, Littman DR.

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