Publications

316 Results (Filters Applied)
Nature. 2020 Nov. 11.

Dense sampling of bird diversity increases power of comparative genomics.

Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel-Holger S. Sinding, Lara Puetz, Emily Cavill, Ângela M. Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jønsson, Ian G. Jamieson, Rute R. da Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, André E. R. Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, André Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten & Guojie Zhang

Nature. 2020 Oct. 23.

Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease.

Christian R. Marshall, Shimul Chowdhury, Ryan J. Taft, Mathew S. Lebo, Jillian G. Buchan, Steven M. Harrison, Ross Rowsey, Eric W. Klee, Pengfei Liu, Elizabeth A. Worthey, Vaidehi Jobanputra, David Dimmock, Hutton M. Kearney, David Bick, Shashikant Kulkarni, Stacie L. Taylor, John W. Belmont, Dimitri J. Stavropoulos, Niall J. Lennon & Medical Genome Initiative

Nature Communications. 2020 Oct. 14.

Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants.

Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O’Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lung Working Group, Cho MH, Manichaikul A.

Nature Communications. 2020 Oct. 12..

Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium.

Satria P Sajuthi, Peter DeFord, Nathan D Jackson, Michael T Montgomery, Jamie L Everman, Cydney L Rios, Elmar Pruesse, James D Nolin, Elizabeth G Plender, Michael E Wechsler, Angel CY Mak, Celeste Eng, Sandra Salazar, Vivian Medina, Eric M Wohlford, Scott Huntsman, Deborah A Nickerson, Soren Germer, Michael C Zody, Goncalo Abecasis, Hyun Min Kang, Kenneth M Rice, Rajesh Kumar, Sam Oh, Jose Rodriguez-Santana, Esteban G Burchard, Max A Seibold

Cell. 2020 Oct. 9.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Daniel K. Wells, Marit M. van Buuren, Kristen K. Dang, Vanessa M. Hubbard-Lucey, Kathleen C.F. Sheehan, Katie M. Campbell, Andrew Lamb, Jeffrey P. Ward, John Sidney,Ana B. Blazquez,Andrew J. Rech, Jesse M. Zaretsky, Begonya Comin-Anduix, Alphonsus H.C. Ng, William Chour, Thomas V. Yu, Hira Rizvi, Jia M. Chen, Patrice Manning, Gabriela M. Steiner, Xengie C. Doan, The Tumor Neoantigen Selection Alliance, Taha Merghoub,Justin Guinney, Adam Kolom, Cheryl Selinsky, Antoni Ribas, Matthew D. Hellmann, Nir Hacohen, Alessandro Sette, James R. Heath, Nina Bhardwaj, Fred Ramsdell, Robert D. Schreiber, Ton N. Schumacher, Pia Kvistborg, and Nadine A. Defranoux

Cell 2020 October 1.

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

Science. 2020 Sep 24.

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.

This work was partially supported by a gift from the Simons Foundation.