Search Results - "Danecek, Petr"

BCFtools/csq: haplotype-aware variant consequences by Danecek, Petr, McCarthy, Shane A

“…Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants…”
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BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data by Narasimhan, Vagheesh, Danecek, Petr, Scally, Aylwyn, Xue, Yali, Tyler-Smith, Chris, Durbin, Richard

“…Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen…”
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Twelve years of SAMtools and BCFtools by 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

“…SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and…”
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression by 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

“…Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo…”
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Reference-based phasing using the Haplotype Reference Consortium panel by 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

“…Po-Ru Loh, Alkes Price and colleagues present Eagle2, a reference-based phasing algorithm that allows for highly accurate and efficient phasing of genotypes…”
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The variant call format and VCFtools by 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

“…The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with…”
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Ancient human parallel lineages within North America contributed to a coastal expansion by 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

“…Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas…”
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HTSlib: C library for reading/writing high-throughput sequencing data by Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M

“…Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a…”
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci by 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.

“…We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We…”
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Mouse genomic variation and its effect on phenotypes and gene regulation by Keane, Thomas M., Goodstadt, Leo, Danecek, Petr, White, Michael A., Wong, Kim, Yalcin, Binnaz, Heger, Andreas, Agam, Avigail, Slater, Guy, Goodson, Martin, Furlotte, Nicholas A., Eskin, Eleazar, Nellåker, Christoffer, Whitley, Helen, Cleak, James, Janowitz, Deborah, Hernandez-Pliego, Polinka, Edwards, Andrew, Belgard, T. Grant, Oliver, Peter L., McIntyre, Rebecca E., Bhomra, Amarjit, Nicod, Jérôme, Gan, Xiangchao, Yuan, Wei, van der Weyden, Louise, Steward, Charles A., Bala, Sendu, Stalker, Jim, Mott, Richard, Durbin, Richard, Jackson, Ian J., Czechanski, Anne, Guerra-Assunção, José Afonso, Donahue, Leah Rae, Reinholdt, Laura G., Payseur, Bret A., Ponting, Chris P., Birney, Ewan, Flint, Jonathan, Adams, David J.

“…We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to…”
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An organelle-specific protein landscape identifies novel diseases and molecular mechanisms by 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

“…Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate…”
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Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians by 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

“…The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative…”
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Contribution of retrotransposition to developmental disorders by 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.

“…Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In…”
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A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data by Danecek, Petr, McCarthy, Shane A, Durbin, Richard

“…Genomic screening for chromosomal abnormalities is an important part of quality control when establishing and maintaining stem cell lines. We present a new…”
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Population-scale proteome variation in human induced pluripotent stem cells by Mirauta, Bogdan Andrei, Seaton, Daniel D, Bensaddek, Dalila, Brenes, Alejandro, Bonder, Marc Jan, Kilpinen, Helena, Stegle, Oliver, Lamond, Angus I

“…Human disease phenotypes are driven primarily by alterations in protein expression and/or function. To date, relatively little is known about the variability…”
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Low-frequency variation in TP53 has large effects on head circumference and intracranial volume by 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

“…Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The…”
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Detection and characterization of copy-number variants from exome sequencing in the DDD study by Danecek, Petr, Gardner, Eugene J., Fitzgerald, Tomas W., Gallone, Giuseppe, Kaplanis, Joanna, Eberhardt, Ruth Y., Wright, Caroline F., Firth, Helen V., Hurles, Matthew E.

“…Structural variants such as multiexon deletions and duplications are an important cause of disease but are often overlooked in standard exome/genome sequencing…”
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Insights into human genetic variation and population history from 929 diverse genomes by 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

“…Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships…”
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Comparison of the numerical stability of methods for anharmonic calculations of vibrational molecular energies by Danecek, Petr, Bour, Petr

“…On model examples, we compare the performance of the vibrational self‐consistent field, variational, and four perturbational schemes used for computations of…”
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Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells by Rouhani, Foad J., Zou, Xueqing, Danecek, Petr, Badja, Cherif, Amarante, Tauanne Dias, Koh, Gene, Wu, Qianxin, Memari, Yasin, Durbin, Richard, Martincorena, Inigo, Bassett, Andrew R., Gaffney, Daniel, Nik-Zainal, Serena

“…We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide…”
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