Twelve years of SAMtools and BCFtools
Danecek, Petr, Bonfield, James K, Liddle, Jennifer, Marshall, John, Ohan, Valeriu, Pollard, Martin O, Whitwham, Andrew, Keane, Thomas, McCarthy, Shane A, Davies, Robert M, Li, Heng
Published in Gigascience (16.02.2021)
Published in Gigascience (16.02.2021)
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Cuomo, Anna S E, Seaton, Daniel D, McCarthy, Davis J, Martinez, Iker, Bonder, Marc Jan, Garcia-Bernardo, Jose, Amatya, Shradha, Madrigal, Pedro, Isaacson, Abigail, Buettner, Florian, Knights, Andrew, Natarajan, Kedar Nath, Vallier, Ludovic, Marioni, John C, Chhatriwala, Mariya, Stegle, Oliver
Published in Nature communications (10.02.2020)
Published in Nature communications (10.02.2020)
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Reference-based phasing using the Haplotype Reference Consortium panel
Loh, Po-Ru, Danecek, Petr, Palamara, Pier Francesco, Fuchsberger, Christian, A Reshef, Yakir, K Finucane, Hilary, Schoenherr, Sebastian, Forer, Lukas, McCarthy, Shane, Abecasis, Goncalo R, Durbin, Richard, L Price, Alkes
Published in Nature genetics (01.11.2016)
Published in Nature genetics (01.11.2016)
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The variant call format and VCFtools
Danecek, Petr, Auton, Adam, Abecasis, Goncalo, Albers, Cornelis A., Banks, Eric, DePristo, Mark A., Handsaker, Robert E., Lunter, Gerton, Marth, Gabor T., Sherry, Stephen T., McVean, Gilean, Durbin, Richard
Published in Bioinformatics (01.08.2011)
Published in Bioinformatics (01.08.2011)
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Ancient human parallel lineages within North America contributed to a coastal expansion
Scheib, C L, Li, Hongjie, Desai, Tariq, Link, Vivian, Kendall, Christopher, Dewar, Genevieve, Griffith, Peter William, Mörseburg, Alexander, Johnson, John R, Potter, Amiee, Kerr, Susan L, Endicott, Phillip, Lindo, John, Haber, Marc, Xue, Yali, Tyler-Smith, Chris, Sandhu, Manjinder S, Lorenz, Joseph G, Randall, Tori D, Faltyskova, Zuzana, Pagani, Luca, Danecek, Petr, O'Connell, Tamsin C, Martz, Patricia, Boraas, Alan S, Byrd, Brian F, Leventhal, Alan, Cambra, Rosemary, Williamson, Ronald, Lesage, Louis, Holguin, Brian, Ygnacio-De Soto, Ernestine, Rosas, JohnTommy, Metspalu, Mait, Stock, Jay T, Manica, Andrea, Scally, Aylwyn, Wegmann, Daniel, Malhi, Ripan S, Kivisild, Toomas
Published in Science (American Association for the Advancement of Science) (01.06.2018)
Published in Science (American Association for the Advancement of Science) (01.06.2018)
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HTSlib: C library for reading/writing high-throughput sequencing data
Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M
Published in Gigascience (16.02.2021)
Published in Gigascience (16.02.2021)
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
Lilue, Jingtao, Doran, Anthony G, Fiddes, Ian T, Abrudan, Monica, Armstrong, Joel, Bennett, Ruth, Chow, William, Collins, Joanna, Collins, Stephan, Czechanski, Anne, Danecek, Petr, Diekhans, Mark, Dolle, Dirk-Dominik, Dunn, Matt, Durbin, Richard, Earl, Dent, Ferguson-Smith, Anne, Flicek, Paul, Flint, Jonathan, Frankish, Adam, Fu, Beiyuan, Gerstein, Mark, Gilbert, James, Goodstadt, Leo, Harrow, Jennifer, Howe, Kerstin, Ibarra-Soria, Ximena, Kolmogorov, Mikhail, Lelliott, Chris J, Logan, Darren W, Loveland, Jane, Mathews, Clayton E, Mott, Richard, Muir, Paul, Nachtweide, Stefanie, Navarro, Fabio C P, Odom, Duncan T, Park, Naomi, Pelan, Sarah, Pham, Son K, Quail, Mike, Reinholdt, Laura, Romoth, Lars, Shirley, Lesley, Sisu, Cristina, Sjoberg-Herrera, Marcela, Stanke, Mario, Steward, Charles, Thomas, Mark, Threadgold, Glen, Thybert, David, Torrance, James, Wong, Kim, Wood, Jonathan, Yalcin, Binnaz, Yang, Fengtang, Adams, David J, Paten, Benedict, Keane, Thomas M
Published in Nature genetics (01.11.2018)
Published in Nature genetics (01.11.2018)
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Mouse genomic variation and its effect on phenotypes and gene regulation
KEANE, Thomas M, GOODSTADT, Leo, FURLOTTE, Nicholas A, ESKIN, Eleazar, NELLAKER, Christoffer, WHITLEY, Helen, CLEAK, James, JANOWITZ, Deborah, HERNANDEZ-PLIEGO, Polinka, EDWARD, Andrew, GRANT BELGARD, T, OLIVER, Peter L, DANECEKL, Petr, MCINTYRE, Rebecca E, BHOMRA, Amarjit, NICOD, Jérôme, GAN, Xiangchao, WEI YUAN, DER WEYDEN, Louise Van, STEWARD, Charles A, BALA, Sendu, STALKER, Jim, MOTT, Richard, WHITE, Michael A, DURBIN, Richard, JACKSON, Ian J, CZECHANSKI, Anne, AFONSO GUERRA-ASSUNCAO, Jose, RAE DONAHUE, Leah, REINHOLDT, Laura G, PAYSEUR, Bret A, PONTING, Chris P, BIRNEY, Ewan, FLINT, Jonathan, WONG, Kim, ADAMS, David J, YALCIN, Binnaz, HEGER, Andreas, AGAM, Avigail, SLATER, Guy, GOODSON, Martin
Published in Nature (London) (15.09.2011)
Published in Nature (London) (15.09.2011)
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An organelle-specific protein landscape identifies novel diseases and molecular mechanisms
Boldt, Karsten, van Reeuwijk, Jeroen, Lu, Qianhao, Koutroumpas, Konstantinos, Nguyen, Thanh-Minh T, Texier, Yves, van Beersum, Sylvia E C, Horn, Nicola, Willer, Jason R, Mans, Dorus A, Dougherty, Gerard, Lamers, Ideke J C, Coene, Karlien L M, Arts, Heleen H, Betts, Matthew J, Beyer, Tina, Bolat, Emine, Gloeckner, Christian Johannes, Haidari, Khatera, Hetterschijt, Lisette, Iaconis, Daniela, Jenkins, Dagan, Klose, Franziska, Knapp, Barbara, Latour, Brooke, Letteboer, Stef J F, Marcelis, Carlo L, Mitic, Dragana, Morleo, Manuela, Oud, Machteld M, Riemersma, Moniek, Rix, Susan, Terhal, Paulien A, Toedt, Grischa, van Dam, Teunis J P, de Vrieze, Erik, Wissinger, Yasmin, Wu, Ka Man, Apic, Gordana, Beales, Philip L, Blacque, Oliver E, Gibson, Toby J, Huynen, Martijn A, Katsanis, Nicholas, Kremer, Hannie, Omran, Heymut, van Wijk, Erwin, Wolfrum, Uwe, Kepes, François, Davis, Erica E, Franco, Brunella, Giles, Rachel H, Ueffing, Marius, Russell, Robert B, Roepman, Ronald
Published in Nature communications (13.05.2016)
Published in Nature communications (13.05.2016)
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Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians
Pagani, Luca, Schiffels, Stephan, Gurdasani, Deepti, Danecek, Petr, Scally, Aylwyn, Chen, Yuan, Xue, Yali, Haber, Marc, Ekong, Rosemary, Oljira, Tamiru, Mekonnen, Ephrem, Luiselli, Donata, Bradman, Neil, Bekele, Endashaw, Zalloua, Pierre, Durbin, Richard, Kivisild, Toomas, Tyler-Smith, Chris
Published in American journal of human genetics (04.06.2015)
Published in American journal of human genetics (04.06.2015)
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Contribution of retrotransposition to developmental disorders
Gardner, Eugene J, Prigmore, Elena, Gallone, Giuseppe, Danecek, Petr, Samocha, Kaitlin E, Handsaker, Juliet, Gerety, Sebastian S, Ironfield, Holly, Short, Patrick J, Sifrim, Alejandro, Singh, Tarjinder, Chandler, Kate E, Clement, Emma, Lachlan, Katherine L, Prescott, Katrina, Rosser, Elisabeth, FitzPatrick, David R, Firth, Helen V, Hurles, Matthew E
Published in Nature communications (11.10.2019)
Published in Nature communications (11.10.2019)
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Population-scale proteome variation in human induced pluripotent stem cells
Mirauta, Bogdan Andrei, Seaton, Daniel D, Bensaddek, Dalila, Brenes, Alejandro, Bonder, Marc Jan, Kilpinen, Helena, Stegle, Oliver, Lamond, Angus I
Published in eLife (10.08.2020)
Published in eLife (10.08.2020)
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Low-frequency variation in TP53 has large effects on head circumference and intracranial volume
Haworth, Simon, Shapland, Chin Yang, Hayward, Caroline, Prins, Bram P, Felix, Janine F, Medina-Gomez, Carolina, Rivadeneira, Fernando, Wang, Carol, Ahluwalia, Tarunveer S, Vrijheid, Martine, Guxens, Mònica, Sunyer, Jordi, Tachmazidou, Ioanna, Walter, Klaudia, Iotchkova, Valentina, Jackson, Andrew, Cleal, Louise, Huffmann, Jennifer, Min, Josine L, Sass, Lærke, Timmers, Paul R H J, Davey Smith, George, Fisher, Simon E, Wilson, James F, Cole, Tim J, Fernandez-Orth, Dietmar, Bønnelykke, Klaus, Bisgaard, Hans, Pennell, Craig E, Jaddoe, Vincent W V, Dedoussis, George, Timpson, Nicholas, Zeggini, Eleftheria, Vitart, Veronique, St Pourcain, Beate
Published in Nature communications (21.01.2019)
Published in Nature communications (21.01.2019)
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Journal Article
Detection and characterization of copy-number variants from exome sequencing in the DDD study
Danecek, Petr, Gardner, Eugene J., Fitzgerald, Tomas W., Gallone, Giuseppe, Kaplanis, Joanna, Eberhardt, Ruth Y., Wright, Caroline F., Firth, Helen V., Hurles, Matthew E.
Published in Genetics in Medicine Open (2024)
Published in Genetics in Medicine Open (2024)
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Insights into human genetic variation and population history from 929 diverse genomes
Bergström, Anders, McCarthy, Shane A, Hui, Ruoyun, Almarri, Mohamed A, Ayub, Qasim, Danecek, Petr, Chen, Yuan, Felkel, Sabine, Hallast, Pille, Kamm, Jack, Blanché, Hélène, Deleuze, Jean-François, Cann, Howard, Mallick, Swapan, Reich, David, Sandhu, Manjinder S, Skoglund, Pontus, Scally, Aylwyn, Xue, Yali, Durbin, Richard, Tyler-Smith, Chris
Published in Science (American Association for the Advancement of Science) (20.03.2020)
Published in Science (American Association for the Advancement of Science) (20.03.2020)
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A reference panel of 64,976 haplotypes for genotype imputation
Das, Sayantan, Delaneau, Olivier, Wood, Andrew R, Teumer, Alexander, Kang, Hyun Min, Danecek, Petr, Luo, Yang, Sidore, Carlo, Kwong, Alan, Timpson, Nicholas, Koskinen, Seppo, Vrieze, Scott, Scott, Laura J, Zhang, He, Mahajan, Anubha, Veldink, Jan, Peters, Ulrike, Pato, Carlos, van Duijn, Cornelia M, Gillies, Christopher E, Gandin, Ilaria, Mezzavilla, Massimo, Gilly, Arthur, Cocca, Massimiliano, Traglia, Michela, Angius, Andrea, Barrett, Jeffrey C, Boomsma, Dorrett, Branham, Kari, Breen, Gerome, Brummett, Chad M, Busonero, Fabio, Campbell, Harry, Chen, Sai, Chew, Emily, Collins, Francis S, Corbin, Laura J, Smith, George Davey, Dedoussis, George, Dorr, Marcus, Farmaki, Aliki-Eleni, Ferrucci, Luigi, Forer, Lukas, Fraser, Ross M, Gabriel, Stacey, Levy, Shawn, Groop, Leif, Harrison, Tabitha, Hattersley, Andrew, Holmen, Oddgeir L, Hveem, Kristian, Kretzler, Matthias, Lee, James C, McGue, Matt, Meitinger, Thomas, Vincent, John B, Nauck, Matthias, Nickerson, Deborah, Palotie, Aarno, Pato, Michele, Pirastu, Nicola, McInnis, Melvin, Richards, J Brent, Sala, Cinzia, Salomaa, Veikko, Schlessinger, David, Schoenherr, Sebastian, Slagboom, P Eline, Small, Kerrin, Spector, Timothy, Tuke, Marcus, Tuomilehto, Jaakko, Van den Berg, Leonard H, Van Rheenen, Wouter, Volker, Uwe, Wijmenga, Cisca, Toniolo, Daniela, Zeggini, Eleftheria, Gasparini, Paolo, Sampson, Matthew G, Wilson, James F, Frayling, Timothy, de Bakker, Paul I W, Swertz, Morris A, McCarroll, Steven, Kooperberg, Charles, Dekker, Annelot, Altshuler, David, Willer, Cristen, Iacono, William, Ripatti, Samuli, Soranzo, Nicole, Walter, Klaudia, Swaroop, Anand, Cucca, Francesco, Anderson, Carl A, Myers, Richard M, Boehnke, Michael, McCarthy, Mark I, Durbin, Richard
Published in Nature genetics (01.10.2016)
Published in Nature genetics (01.10.2016)
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