Search Results - "Fiume, Marc"

Similarity network fusion for aggregating data types on a genomic scale by Wang, Bo, Mezlini, Aziz M, Demir, Feyyaz, Fiume, Marc, Tu, Zhuowen, Brudno, Michael, Haibe-Kains, Benjamin, Goldenberg, Anna

“…Similarity network fusion (SNF) is an approach to integrate multiple data types on the basis of similarity between biological samples rather than individual…”
Get full text

SHRiMP: accurate mapping of short color-space reads by Rumble, Stephen M, Lacroute, Phil, Dalca, Adrian V, Fiume, Marc, Sidow, Arend, Brudno, Michael

“…The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is…”
Get full text

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data by Mezlini, Aziz M, Smith, Eric J M, Fiume, Marc, Buske, Orion, Savich, Gleb L, Shah, Sohrab, Aparicio, Sam, Chiang, Derek Y, Goldenberg, Anna, Brudno, Michael

“…High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the RNA content…”
Get full text

Consent Codes: Upholding Standard Data Use Conditions by Dyke, Stephanie O M, Philippakis, Anthony A, Rambla De Argila, Jordi, Paltoo, Dina N, Luetkemeier, Erin S, Knoppers, Bartha M, Brookes, Anthony J, Spalding, J Dylan, Thompson, Mark, Roos, Marco, Boycott, Kym M, Brudno, Michael, Hurles, Matthew, Rehm, Heidi L, Matern, Andreas, Fiume, Marc, Sherry, Stephen T

“…A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP…”
Get full text

International federation of genomic medicine databases using GA4GH standards by Thorogood, Adrian, Rehm, Heidi L., Goodhand, Peter, Page, Angela J.H., Joly, Yann, Baudis, Michael, Rambla, Jordi, Navarro, Arcadi, Nyronen, Tommi H., Linden, Mikael, Dove, Edward S., Fiume, Marc, Brudno, Michael, Cline, Melissa S., Birney, Ewan

“…We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across…”
Get full text

Detecting copy number variation with mated short reads by Medvedev, Paul, Fiume, Marc, Dzamba, Misko, Smith, Tim, Brudno, Michael

“…The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human…”
Get full text

Savant: genome browser for high-throughput sequencing data by Fiume, Marc, Williams, Vanessa, Brook, Andrew, Brudno, Michael

“…Motivation: The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the…”
Get full text

Genomic architecture of autism from comprehensive whole-genome sequence annotation by Trost, Brett, Thiruvahindrapuram, Bhooma, Chan, Ada J.S., Engchuan, Worrawat, Higginbotham, Edward J., Howe, Jennifer L., Loureiro, Livia O., Reuter, Miriam S., Roshandel, Delnaz, Whitney, Joe, Zarrei, Mehdi, Bookman, Matthew, Somerville, Cherith, Shaath, Rulan, Abdi, Mona, Aliyev, Elbay, Patel, Rohan V., Pellecchia, Giovanna, Hamdan, Omar, Kaur, Gaganjot, Wang, Zhuozhi, MacDonald, Jeffrey R., Wei, John, Sung, Wilson W.L., Lamoureux, Sylvia, Hoang, Ny, Selvanayagam, Thanuja, Deflaux, Nicole, Geng, Melissa, Ghaffari, Siavash, Bates, John, Young, Edwin J., Ding, Qiliang, Shum, Carole, D'Abate, Lia, Bradley, Clarrisa A., Rutherford, Annabel, Aguda, Vernie, Apresto, Beverly, Chen, Nan, Desai, Sachin, Du, Xiaoyan, Fong, Matthew L.Y., Pullenayegum, Sanjeev, Samler, Kozue, Wang, Ting, Ho, Karen, Paton, Tara, Pereira, Sergio L., Herbrick, Jo-Anne, Fuerth, Jonathan, Noppornpitak, Juti, Ward, Heather, Magee, Patrick, Al Baz, Ayman, Kajendirarajah, Usanthan, Vlasblom, Jim, Valluri, Monica, Green, Joseph, Seifer, Vicki, Quirbach, Morgan, Rennie, Olivia, Kelley, Elizabeth, Masjedi, Nina, Lord, Catherine, Szego, Michael J., Zawati, Ma'n H., Lang, Michael, Strug, Lisa J., Marshall, Christian R., Costain, Gregory, Calli, Kristina, Iaboni, Alana, Yusuf, Afiqah, Ambrozewicz, Patricia, Gallagher, Louise, Amaral, David G., Brian, Jessica, Elsabbagh, Mayada, Georgiades, Stelios, Messinger, Daniel S., Ozonoff, Sally, Sebat, Jonathan, Sjaarda, Calvin, Smith, Isabel M., Szatmari, Peter, Zwaigenbaum, Lonnie, Kushki, Azadeh, Frazier, Thomas W., Vorstman, Jacob A.S., Fakhro, Khalid A., Fernandez, Bridget A., Lewis, M.E. Suzanne, Weksberg, Rosanna, Fiume, Marc, Yuen, Ryan K.C., Anagnostou, Evdokia, Sondheimer, Neal, Glazer, David, Hartley, Dean M.

“…Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG…”
Get full text

PhenoTips: Patient Phenotyping Software for Clinical and Research Use by Girdea, Marta, Dumitriu, Sergiu, Fiume, Marc, Bowdin, Sarah, Boycott, Kym M., Chénier, Sébastien, Chitayat, David, Faghfoury, Hanna, Meyn, M. Stephen, Ray, Peter N., So, Joyce, Stavropoulos, Dimitri J., Brudno, Michael

“…ABSTRACT We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our…”
Get full text

Federated discovery and sharing of genomic data using Beacons by Fiume, Marc, Cupak, Miroslav, Keenan, Stephen, Rambla, Jordi, de la Torre, Sabela, Dyke, Stephanie O. M., Brookes, Anthony J., Carey, Knox, Lloyd, David, Goodhand, Peter, Haeussler, Maximilian, Baudis, Michael, Stockinger, Heinz, Dolman, Lena, Lappalainen, Ilkka, Törnroos, Juha, Linden, Mikael, Spalding, J. Dylan, Ur-Rehman, Saif, Page, Angela, Flicek, Paul, Sherry, Stephen, Haussler, David, Varma, Susheel, Saunders, Gary, Scollen, Serena

Get full text

The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants by Reuter, Miriam S, Walker, Susan, Thiruvahindrapuram, Bhooma, Whitney, Joe, Cohn, Iris, Sondheimer, Neal, Yuen, Ryan K C, Trost, Brett, Paton, Tara A, Pereira, Sergio L, Herbrick, Jo-Anne, Wintle, Richard F, Merico, Daniele, Howe, Jennifer, MacDonald, Jeffrey R, Lu, Chao, Nalpathamkalam, Thomas, Sung, Wilson W L, Wang, Zhuozhi, Patel, Rohan V, Pellecchia, Giovanna, Wei, John, Strug, Lisa J, Bell, Sherilyn, Kellam, Barbara, Mahtani, Melanie M, Bassett, Anne S, Bombard, Yvonne, Weksberg, Rosanna, Shuman, Cheryl, Cohn, Ronald D, Stavropoulos, Dimitri J, Bowdin, Sarah, Hildebrandt, Matthew R, Wei, Wei, Romm, Asli, Pasceri, Peter, Ellis, James, Ray, Peter, Meyn, M Stephen, Monfared, Nasim, Hosseini, S Mohsen, Joseph-George, Ann M, Keeley, Fred W, Cook, Ryan A, Fiume, Marc, Lee, Hin C, Marshall, Christian R, Davies, Jill, Hazell, Allison, Buchanan, Janet A, Szego, Michael J, Scherer, Stephen W

“…The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe…”
Get full text

ClinGen advancing genomic data‐sharing standards as a GA4GH driver project by Dolman, Lena, Page, Angela, Babb, Lawrence, Freimuth, Robert R., Arachchi, Harindra, Bizon, Chris, Brush, Matthew, Fiume, Marc, Haendel, Melissa, Hansen, David P., Milosavljevic, Aleksandar, Patel, Ronak Y., Pawliczek, Piotr, Yates, Andrew D., Rehm, Heidi L.

“…The Clinical Genome Resource (ClinGen)’s work to develop a knowledge base to support the understanding of genes and variants for use in precision medicine and…”
Get full text

Registered access: authorizing data access by Dyke, Stephanie O M, Linden, Mikael, Lappalainen, Ilkka, De Argila, Jordi Rambla, Carey, Knox, Lloyd, David, Spalding, J Dylan, Cabili, Moran N, Kerry, Giselle, Foreman, Julia, Cutts, Tim, Shabani, Mahsa, Rodriguez, Laura L, Haeussler, Maximilian, Walsh, Brian, Jiang, Xiaoqian, Wang, Shuang, Perrett, Daniel, Boughtwood, Tiffany, Matern, Andreas, Brookes, Anthony J, Cupak, Miro, Fiume, Marc, Pandya, Ravi, Tulchinsky, Ilia, Scollen, Serena, Törnroos, Juha, Das, Samir, Evans, Alan C, Malin, Bradley A, Beck, Stephan, Brenner, Steven E, Nyrönen, Tommi, Blomberg, Niklas, Firth, Helen V, Hurles, Matthew, Philippakis, Anthony A, Rätsch, Gunnar, Brudno, Michael, Boycott, Kym M, Rehm, Heidi L, Baudis, Michael, Sherry, Stephen T, Kato, Kazuto, Knoppers, Bartha M, Baker, Dixie, Flicek, Paul

“…The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an…”
Get full text

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2 by Cline, Melissa S, Liao, Rachel G, Parsons, Michael T, Paten, Benedict, Alquaddoomi, Faisal, Antoniou, Antonis, Baxter, Samantha, Brody, Larry, Cook-Deegan, Robert, Coffin, Amy, Couch, Fergus J, Craft, Brian, Currie, Robert, Dlott, Chloe C, Dolman, Lena, den Dunnen, Johan T, Dyke, Stephanie O M, Domchek, Susan M, Easton, Douglas, Fischmann, Zachary, Foulkes, William D, Garber, Judy, Goldgar, David, Goldman, Mary J, Goodhand, Peter, Harrison, Steven, Haussler, David, Kato, Kazuto, Knoppers, Bartha, Markello, Charles, Nussbaum, Robert, Offit, Kenneth, Plon, Sharon E, Rashbass, Jem, Rehm, Heidi L, Robson, Mark, Rubinstein, Wendy S, Stoppa-Lyonnet, Dominique, Tavtigian, Sean, Thorogood, Adrian, Zhang, Can, Zimmermann, Marc, Burn, John, Chanock, Stephen, Rätsch, Gunnar, Spurdle, Amanda B

“…The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data…”
Get full text

Data sharing as a national quality improvement program: reporting on BRCA1 and BRCA2 variant-interpretation comparisons through the Canadian Open Genetics Repository (COGR) by Lebo, Matthew S, Zakoor, Kathleen-Rose, Chun, Kathy, Speevak, Marsha D, Waye, John S, McCready, Elizabeth, Parboosingh, Jillian S, Lamont, Ryan E, Feilotter, Harriet, Bosdet, Ian, Tucker, Tracy, Young, Sean, Karsan, Aly, Charames, George S, Agatep, Ronald, Spriggs, Elizabeth L, Chisholm, Caitlin, Vasli, Nasim, Daoud, Hussein, Jarinova, Olga, Tomaszewski, Robert, Hume, Stacey, Taylor, Sherryl, Akbari, Mohammad R, Lerner-Ellis, Jordan

“…Purpose The purpose of this study was to develop a national program for Canadian diagnostic laboratories to compare DNA-variant interpretations and resolve…”
Get full text

Savant Genome Browser 2: visualization and analysis for population-scale genomics by Fiume, Marc, Smith, Eric J M, Brook, Andrew, Strbenac, Dario, Turner, Brian, Mezlini, Aziz M, Robinson, Mark D, Wodak, Shoshana J, Brudno, Michael

“…High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data…”
Get full text

Publisher Correction: Federated discovery and sharing of genomic data using Beacons by Fiume, Marc, Cupak, Miroslav, Keenan, Stephen, Rambla, Jordi, de la Torre, Sabela, Dyke, Stephanie O. M., Brookes, Anthony J., Carey, Knox, Lloyd, David, Goodhand, Peter, Haeussler, Maximilian, Baudis, Michael, Stockinger, Heinz, Dolman, Lena, Lappalainen, Ilkka, Törnroos, Juha, Linden, Mikael, Spalding, J. Dylan, Ur-Rehman, Saif, Page, Angela, Flicek, Paul, Sherry, Stephen, Haussler, David, Varma, Susheel, Saunders, Gary, Scollen, Serena

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
Get full text

System for Interpretation of Personal Genomes by Fiume, Marc

“…Genomics is undergoing a revolution sparked by higher throughput and cost effective DNA sequencing technologies. Sequencing has become a ubiquitous tool with…”
Get full text

System for Interpretation of Personal Genomes by Fiume, Marc

“…Genomics is undergoing a revolution sparked by higher throughput and cost effective DNA sequencing technologies. Sequencing has become a ubiquitous tool with…”
Get full text

The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology by Gill, Erin E, Jia, Baofeng, Murall, Carmen Lia, Poujol, Raphaël, Anwar, Muhammad Zohaib, John, Nithu Sara, Richardsson, Justin, Hobb, Ashley, Olabode, Abayomi S, Lepsa, Alexandru, Duggan, Ana T, Tyler, Andrea D, N'Guessan, Arnaud, Kachru, Atul, Chan, Brandon, Yoshida, Catherine, Yung, Christina K, Bujold, David, Andric, Dusan, Su, Edmund, Griffiths, Emma J, Van Domselaar, Gary, Jolly, Gordon W, Ward, Heather K E, Feher, Henrich, Baker, Jared, Simpson, Jared T, Uddin, Jaser, Ragoussis, Jiannis, Eubank, Jon, Fritz, Jörg H, Gálvez, José Héctor, Fang, Karen, Cullion, Kim, Rivera, Leonardo, Xiang, Linda, Croxen, Matthew A, Shiell, Mitchell, Prystajecky, Natalie, Quirion, Pierre-Olivier, Bajari, Rosita, Rich, Samantha, Mubareka, Samira, Moreira, Sandrine, Cain, Scott, Sutcliffe, Steven G, Kraemer, Susanne A, Alturmessov, Yelizar, Joly, Yann, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Fiume, Marc, Snutch, Terrance P, Bell, Cindy, Lopez-Correa, Catalina, Hussin, Julie G, Joy, Jeffrey B, Colijn, Caroline, Gordon, Paul M K, Hsiao, William W L, Poon, Art F Y, Knox, Natalie C, Courtot, Mélanie, Stein, Lincoln, Otto, Sarah P, Bourque, Guillaume, Shapiro, B Jesse, Brinkman, Fiona S L

“…The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health…”
Get full text