Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

Autor: Mir Henglin, Maryam Ghareghani, William T. Harvey, David Porubsky, Sergey Koren, Evan E. Eichler, Peter Ebert, Tobias Marschall

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-26 (2024)

Abstract Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haploty

Externí odkaz: https://doaj.org/article/3512fe7340b944e4bcccd787429f9cff

Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51

Autor: Anne Margriet Heijink, Colin Stok, David Porubsky, Eleni Maria Manolika, Jurrian K. de Kanter, Yannick P. Kok, Marieke Everts, H. Rudolf de Boer, Anastasia Audrey, Femke J. Bakker, Elles Wierenga, Marcel Tijsterman, Victor Guryev, Diana C. J. Spierings, Puck Knipscheer, Ruben van Boxtel, Arnab Ray Chaudhuri, Peter M. Lansdorp, Marcel A. T. M. van Vugt

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-16 (2022)

Sister chromatid exchanges (SCEs) are considered to be products of homologous recombination repair. The authors show that SCEs can arise independently of homologous recombination due to processing of replication intermediates during mitosis.

Externí odkaz: https://doaj.org/article/6a7ed7595d2b4f12a042a1aaa930abc6

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Autor: Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, David Porubsky, Kristen Kuhn, Kathryn A. Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J. Hall, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan, Sarah B. Kingan

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)

Methods to produce haplotype-resolved genome assemblies often rely on access to family trios. The authors present FALCON-Phase, a tool that combines ultra-long range Hi-C chromatin interaction data with a long read de novo assembly to extend haplotyp

Externí odkaz: https://doaj.org/article/36f8c0b7e92d40fdb0d367dee6cfc462

A draft human pangenome reference

Autor: Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten

Publikováno v: Nature. 617:312-324

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce56c54eebc15371aabecb5595f996d0
https://doi.org/10.1038/s41586-023-05896-x

Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects

Autor: Athel Cornish-Bowden, David Rasnick, Henry H. Heng, Steven Horne, Batoul Abdallah, Guo Liu, Christine J. Ye, Mathew Bloomfield, Mark D. Vincent, C. Marcelo Aldaz, Jenny Karlsson, Anders Valind, Caroline Jansson, David Gisselsson, Jennifer A. Marshall Graves, Aleksei A. Stepanenko, Svitlana V. Andreieva, Kateryna V. Korets, Dmytro O. Mykytenko, Nataliya L. Huleyuk, Vladimir P. Baklaushev, Oksana A. Kovaleva, Vladimir P. Chekhonin, Yegor S. Vassetzky, Stanislav S. Avdieiev, Bjorn Bakker, Aaron S. Taudt, Mirjam E. Belderbos, David Porubsky, Diana C. J. Spierings, Tristan V. de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S. J. M. de Bont, Anke van den Berg, Victor Guryev, Peter M. Lansdorp, Maria Colomé Tatché, Floris Foijer, Thomas Liehr, Nicolaas C. Baudoin, Joshua M. Nicholson, Kimberly Soto, Isabel Quintanilla, Jordi Camps, Daniela Cimini, M. Dürrbaum, N. Donnelly, V. Passerini, C. Kruse, B. Habermann, Z. Storchová, Daniele Mandrioli, Fiorella Belpoggi, Ellen K Silbergeld, Melissa J Perry, Rolf I. Skotheim, Marthe Løvf, Bjarne Johannessen, Andreas M. Hoff, Sen Zhao, Jonas M. SveeStrømme, Anita Sveen, Ragnhild A. Lothe, R. Hehlmann, A. Voskanyan, A. Fabarius, Alfred Böcking, Stefan Biesterfeld, Leonid Berynskyy, Christof Börgermann, Rainer Engers, Josef Dietz, A. Fritz, N. Sehgal, J. Vecerova, B. Stojkovicz, H. Ding, N. Page, C. Tye, S. Bhattacharya, J. Xu, G. Stein, J. Stein, R. Berezney, Xue Gong, Sarah Grasedieck, Julian Swoboda, Frank G. Rücker, Lars Bullinger, Jonathan R. Pollack, Fani-Marlen Roumelioti, Maria Chiourea, Christina Raftopoulou, Sarantis Gagos, Peter Duesberg, Mat Bloomfield, Sunyoung Hwang, Hans Tobias Gustafsson, Ciara O’Sullivan, Aracelli Acevedo-Colina, Xinhe Huang, Christian Klose, Andrej Schevchenko, Robert C. Dickson, Paola Cavaliere, Noah Dephoure, Eduardo M. Torres, Martha R. Stampfer, Lukas Vrba, Mark A. LaBarge, Bernard Futscher, James C. Garbe, Yi-Hong Zhou, Andrew L. Trinh, Michelle Digman

Publikováno v: Molecular Cytogenetics, Vol 10, Iss S2, Pp 77-94 (2017)

Externí odkaz: https://doaj.org/article/b6866d4289674f288bf6c946e8f882e4