• The Journal of Molecular Diagnostics  ·  October 23, 2020

    Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies.

    Vaidehi Jobanputra, Peter Andrews, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Dino Robinson, Ferrah London, Inessa Hakker, Kazimierz Wrzeszczynski, Michael Ronemus

    link out icon
  • Nature  ·  October 23, 2020

    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

    link out icon
  • Journal of Investigative Dermatology  ·  October 19, 2020

    Targeted knockout of β-catenin in adult melanocyte stem cells using a mouse line, Dct::CreERT2, results in disrupted stem cell renewal and pigmentation defects.

    Madeleine Le. Coz, Zackie Aktary, Natsuki Watanabe, Ichiro Yajima, Marie Pouteaux, Nisamanee Charoenchon, Tsutomu Motohashi, Takahiro Kunisada, André Corvelo, Lionel Larue

    link out icon
  • Nature Communications  ·  October 14, 2020

    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.

    link out icon
  • Nature Communications  ·  October 12, 2020

    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

    link out icon
  • Cell  ·  October 9, 2020

    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

    link out icon
  • Annals of the Rheumatic Diseases  ·  October 7, 2020

    Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement.

    Showalter K, Spiera R, Magro C, Agius P, Martyanov V, Franks JM, Sharma R, Geiger H, Wood TA, Zhang Y, Hale CR, Finik J, Whitfield ML, Orange DE, Gordon JK.

    link out icon
  • 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

    link out icon
  • 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

    link out icon
  • 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.

    link out icon
  • 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.

    link out icon
  • 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

    link out icon
  • 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)
    link out icon
  • 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
    link out icon
  • 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.

    link out icon
  • 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

    link out icon
  • 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

    link out icon
  • 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

    link out icon
  • 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

    link out icon
Decorative image color fade left Decorative image color fade right Decorative image color fade