Literature DB >> 24316648

Genome assembly and haplotyping with Hi-C.

Jan O Korbel1, Charles Lee.   

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Year:  2013        PMID: 24316648     DOI: 10.1038/nbt.2764

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  13 in total

1.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Authors:  Sante Gnerre; Iain Maccallum; Dariusz Przybylski; Filipe J Ribeiro; Joshua N Burton; Bruce J Walker; Ted Sharpe; Giles Hall; Terrance P Shea; Sean Sykes; Aaron M Berlin; Daniel Aird; Maura Costello; Riza Daza; Louise Williams; Robert Nicol; Andreas Gnirke; Chad Nusbaum; Eric S Lander; David B Jaffe
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-27       Impact factor: 11.205

2.  The complete genome of an individual by massively parallel DNA sequencing.

Authors:  David A Wheeler; Maithreyan Srinivasan; Michael Egholm; Yufeng Shen; Lei Chen; Amy McGuire; Wen He; Yi-Ju Chen; Vinod Makhijani; G Thomas Roth; Xavier Gomes; Karrie Tartaro; Faheem Niazi; Cynthia L Turcotte; Gerard P Irzyk; James R Lupski; Craig Chinault; Xing-zhi Song; Yue Liu; Ye Yuan; Lynne Nazareth; Xiang Qin; Donna M Muzny; Marcel Margulies; George M Weinstock; Richard A Gibbs; Jonathan M Rothberg
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

3.  High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology.

Authors:  Marieke Simonis; Petra Klous; Irene Homminga; Robert-Jan Galjaard; Erik-Jan Rijkers; Frank Grosveld; Jules P P Meijerink; Wouter de Laat
Journal:  Nat Methods       Date:  2009-10-11       Impact factor: 28.547

4.  Finishing the euchromatic sequence of the human genome.

Authors: 
Journal:  Nature       Date:  2004-10-21       Impact factor: 49.962

Review 5.  The importance of phase information for human genomics.

Authors:  Ryan Tewhey; Vikas Bansal; Ali Torkamani; Eric J Topol; Nicholas J Schork
Journal:  Nat Rev Genet       Date:  2011-02-08       Impact factor: 53.242

6.  International network of cancer genome projects.

Authors:  Thomas J Hudson; Warwick Anderson; Axel Artez; Anna D Barker; Cindy Bell; Rosa R Bernabé; M K Bhan; Fabien Calvo; Iiro Eerola; Daniela S Gerhard; Alan Guttmacher; Mark Guyer; Fiona M Hemsley; Jennifer L Jennings; David Kerr; Peter Klatt; Patrik Kolar; Jun Kusada; David P Lane; Frank Laplace; Lu Youyong; Gerd Nettekoven; Brad Ozenberger; Jane Peterson; T S Rao; Jacques Remacle; Alan J Schafer; Tatsuhiro Shibata; Michael R Stratton; Joseph G Vockley; Koichi Watanabe; Huanming Yang; Matthew M F Yuen; Bartha M Knoppers; Martin Bobrow; Anne Cambon-Thomsen; Lynn G Dressler; Stephanie O M Dyke; Yann Joly; Kazuto Kato; Karen L Kennedy; Pilar Nicolás; Michael J Parker; Emmanuelle Rial-Sebbag; Carlos M Romeo-Casabona; Kenna M Shaw; Susan Wallace; Georgia L Wiesner; Nikolajs Zeps; Peter Lichter; Andrew V Biankin; Christian Chabannon; Lynda Chin; Bruno Clément; Enrique de Alava; Françoise Degos; Martin L Ferguson; Peter Geary; D Neil Hayes; Thomas J Hudson; Amber L Johns; Arek Kasprzyk; Hidewaki Nakagawa; Robert Penny; Miguel A Piris; Rajiv Sarin; Aldo Scarpa; Tatsuhiro Shibata; Marc van de Vijver; P Andrew Futreal; Hiroyuki Aburatani; Mónica Bayés; David D L Botwell; Peter J Campbell; Xavier Estivill; Daniela S Gerhard; Sean M Grimmond; Ivo Gut; Martin Hirst; Carlos López-Otín; Partha Majumder; Marco Marra; John D McPherson; Hidewaki Nakagawa; Zemin Ning; Xose S Puente; Yijun Ruan; Tatsuhiro Shibata; Michael R Stratton; Hendrik G Stunnenberg; Harold Swerdlow; Victor E Velculescu; Richard K Wilson; Hong H Xue; Liu Yang; Paul T Spellman; Gary D Bader; Paul C Boutros; Peter J Campbell; Paul Flicek; Gad Getz; Roderic Guigó; Guangwu Guo; David Haussler; Simon Heath; Tim J Hubbard; Tao Jiang; Steven M Jones; Qibin Li; Nuria López-Bigas; Ruibang Luo; Lakshmi Muthuswamy; B F Francis Ouellette; John V Pearson; Xose S Puente; Victor Quesada; Benjamin J Raphael; Chris Sander; Tatsuhiro Shibata; Terence P Speed; Lincoln D Stein; Joshua M Stuart; Jon W Teague; Yasushi Totoki; Tatsuhiko Tsunoda; Alfonso Valencia; David A Wheeler; Honglong Wu; Shancen Zhao; Guangyu Zhou; Lincoln D Stein; Roderic Guigó; Tim J Hubbard; Yann Joly; Steven M Jones; Arek Kasprzyk; Mark Lathrop; Nuria López-Bigas; B F Francis Ouellette; Paul T Spellman; Jon W Teague; Gilles Thomas; Alfonso Valencia; Teruhiko Yoshida; Karen L Kennedy; Myles Axton; Stephanie O M Dyke; P Andrew Futreal; Daniela S Gerhard; Chris Gunter; Mark Guyer; Thomas J Hudson; John D McPherson; Linda J Miller; Brad Ozenberger; Kenna M Shaw; Arek Kasprzyk; Lincoln D Stein; Junjun Zhang; Syed A Haider; Jianxin Wang; Christina K Yung; Anthony Cros; Anthony Cross; Yong Liang; Saravanamuttu Gnaneshan; Jonathan Guberman; Jack Hsu; Martin Bobrow; Don R C Chalmers; Karl W Hasel; Yann Joly; Terry S H Kaan; Karen L Kennedy; Bartha M Knoppers; William W Lowrance; Tohru Masui; Pilar Nicolás; Emmanuelle Rial-Sebbag; Laura Lyman Rodriguez; Catherine Vergely; Teruhiko Yoshida; Sean M Grimmond; Andrew V Biankin; David D L Bowtell; Nicole Cloonan; Anna deFazio; James R Eshleman; Dariush Etemadmoghadam; Brooke B Gardiner; Brooke A Gardiner; James G Kench; Aldo Scarpa; Robert L Sutherland; Margaret A Tempero; Nicola J Waddell; Peter J Wilson; John D McPherson; Steve Gallinger; Ming-Sound Tsao; Patricia A Shaw; Gloria M Petersen; Debabrata Mukhopadhyay; Lynda Chin; Ronald A DePinho; Sarah Thayer; Lakshmi Muthuswamy; Kamran Shazand; Timothy Beck; Michelle Sam; Lee Timms; Vanessa Ballin; Youyong Lu; Jiafu Ji; Xiuqing Zhang; Feng Chen; Xueda Hu; Guangyu Zhou; Qi Yang; Geng Tian; Lianhai Zhang; Xiaofang Xing; Xianghong Li; Zhenggang Zhu; Yingyan Yu; Jun Yu; Huanming Yang; Mark Lathrop; Jörg Tost; Paul Brennan; Ivana Holcatova; David Zaridze; Alvis Brazma; Lars Egevard; Egor Prokhortchouk; Rosamonde Elizabeth Banks; Mathias Uhlén; Anne Cambon-Thomsen; Juris Viksna; Fredrik Ponten; Konstantin Skryabin; Michael R Stratton; P Andrew Futreal; Ewan Birney; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Sancha Martin; Jorge S Reis-Filho; Andrea L Richardson; Christos Sotiriou; Hendrik G Stunnenberg; Giles Thoms; Marc van de Vijver; Laura van't Veer; Fabien Calvo; Daniel Birnbaum; Hélène Blanche; Pascal Boucher; Sandrine Boyault; Christian Chabannon; Ivo Gut; Jocelyne D Masson-Jacquemier; Mark Lathrop; Iris Pauporté; Xavier Pivot; Anne Vincent-Salomon; Eric Tabone; Charles Theillet; Gilles Thomas; Jörg Tost; Isabelle Treilleux; Fabien Calvo; Paulette Bioulac-Sage; Bruno Clément; Thomas Decaens; Françoise Degos; Dominique Franco; Ivo Gut; Marta Gut; Simon Heath; Mark Lathrop; Didier Samuel; Gilles Thomas; Jessica Zucman-Rossi; Peter Lichter; Roland Eils; Benedikt Brors; Jan O Korbel; Andrey Korshunov; Pablo Landgraf; Hans Lehrach; Stefan Pfister; Bernhard Radlwimmer; Guido Reifenberger; Michael D Taylor; Christof von Kalle; Partha P Majumder; Rajiv Sarin; T S Rao; M K Bhan; Aldo Scarpa; Paolo Pederzoli; Rita A Lawlor; Massimo Delledonne; Alberto Bardelli; Andrew V Biankin; Sean M Grimmond; Thomas Gress; David Klimstra; Giuseppe Zamboni; Tatsuhiro Shibata; Yusuke Nakamura; Hidewaki Nakagawa; Jun Kusada; Tatsuhiko Tsunoda; Satoru Miyano; Hiroyuki Aburatani; Kazuto Kato; Akihiro Fujimoto; Teruhiko Yoshida; Elias Campo; Carlos López-Otín; Xavier Estivill; Roderic Guigó; Silvia de Sanjosé; Miguel A Piris; Emili Montserrat; Marcos González-Díaz; Xose S Puente; Pedro Jares; Alfonso Valencia; Heinz Himmelbauer; Heinz Himmelbaue; Victor Quesada; Silvia Bea; Michael R Stratton; P Andrew Futreal; Peter J Campbell; Anne Vincent-Salomon; Andrea L Richardson; Jorge S Reis-Filho; Marc van de Vijver; Gilles Thomas; Jocelyne D Masson-Jacquemier; Samuel Aparicio; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Hendrik G Stunnenberg; Laura van't Veer; Douglas F Easton; Paul T Spellman; Sancha Martin; Anna D Barker; Lynda Chin; Francis S Collins; Carolyn C Compton; Martin L Ferguson; Daniela S Gerhard; Gad Getz; Chris Gunter; Alan Guttmacher; Mark Guyer; D Neil Hayes; Eric S Lander; Brad Ozenberger; Robert Penny; Jane Peterson; Chris Sander; Kenna M Shaw; Terence P Speed; Paul T Spellman; Joseph G Vockley; David A Wheeler; Richard K Wilson; Thomas J Hudson; Lynda Chin; Bartha M Knoppers; Eric S Lander; Peter Lichter; Lincoln D Stein; Michael R Stratton; Warwick Anderson; Anna D Barker; Cindy Bell; Martin Bobrow; Wylie Burke; Francis S Collins; Carolyn C Compton; Ronald A DePinho; Douglas F Easton; P Andrew Futreal; Daniela S Gerhard; Anthony R Green; Mark Guyer; Stanley R Hamilton; Tim J Hubbard; Olli P Kallioniemi; Karen L Kennedy; Timothy J Ley; Edison T Liu; Youyong Lu; Partha Majumder; Marco Marra; Brad Ozenberger; Jane Peterson; Alan J Schafer; Paul T Spellman; Hendrik G Stunnenberg; Brandon J Wainwright; Richard K Wilson; Huanming Yang
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

7.  Paired-end mapping reveals extensive structural variation in the human genome.

Authors:  Jan O Korbel; Alexander Eckehart Urban; Jason P Affourtit; Brian Godwin; Fabian Grubert; Jan Fredrik Simons; Philip M Kim; Dean Palejev; Nicholas J Carriero; Lei Du; Bruce E Taillon; Zhoutao Chen; Andrea Tanzer; A C Eugenia Saunders; Jianxiang Chi; Fengtang Yang; Nigel P Carter; Matthew E Hurles; Sherman M Weissman; Timothy T Harkins; Mark B Gerstein; Michael Egholm; Michael Snyder
Journal:  Science       Date:  2007-09-27       Impact factor: 47.728

8.  Limitations of next-generation genome sequence assembly.

Authors:  Can Alkan; Saba Sajjadian; Evan E Eichler
Journal:  Nat Methods       Date:  2010-11-21       Impact factor: 28.547

9.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962

10.  A high-resolution map of the three-dimensional chromatin interactome in human cells.

Authors:  Fulai Jin; Yan Li; Jesse R Dixon; Siddarth Selvaraj; Zhen Ye; Ah Young Lee; Chia-An Yen; Anthony D Schmitt; Celso A Espinoza; Bing Ren
Journal:  Nature       Date:  2013-10-20       Impact factor: 49.962

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  24 in total

1.  Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

Authors:  Matthew Z DeMaere; Aaron E Darling
Journal:  Gigascience       Date:  2018-02-01       Impact factor: 6.524

Review 2.  Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping.

Authors:  Joshua A Udall; R Kelly Dawe
Journal:  Plant Cell       Date:  2017-12-20       Impact factor: 11.277

3.  OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Authors:  Enrique Vidal; François le Dily; Javier Quilez; Ralph Stadhouders; Yasmina Cuartero; Thomas Graf; Marc A Marti-Renom; Miguel Beato; Guillaume J Filion
Journal:  Nucleic Acids Res       Date:  2018-05-04       Impact factor: 16.971

Review 4.  An Overview of Genome Organization and How We Got There: from FISH to Hi-C.

Authors:  James Fraser; Iain Williamson; Wendy A Bickmore; Josée Dostie
Journal:  Microbiol Mol Biol Rev       Date:  2015-09       Impact factor: 11.056

5.  Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal.

Authors:  Graham J Etherington; Darren Heavens; David Baker; Ashleigh Lister; Rose McNelly; Gonzalo Garcia; Bernardo Clavijo; Iain Macaulay; Wilfried Haerty; Federica Di Palma
Journal:  Gigascience       Date:  2020-05-01       Impact factor: 6.524

Review 6.  A molecular toolkit for superorganisms.

Authors:  Bogdan Sieriebriennikov; Danny Reinberg; Claude Desplan
Journal:  Trends Genet       Date:  2021-06-08       Impact factor: 11.821

7.  Whole-genome haplotyping approaches and genomic medicine.

Authors:  Gustavo Glusman; Hannah C Cox; Jared C Roach
Journal:  Genome Med       Date:  2014-09-25       Impact factor: 11.117

8.  The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer.

Authors:  Fabio Tordini; Marco Aldinucci; Luciano Milanesi; Pietro Liò; Ivan Merelli
Journal:  Front Genet       Date:  2016-11-15       Impact factor: 4.599

9.  PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.

Authors:  S A Lapp; J A Geraldo; J-T Chien; F Ay; S B Pakala; G Batugedara; J Humphrey; J D DeBARRY; K G Le Roch; M R Galinski; J C Kissinger
Journal:  Parasitology       Date:  2017-07-19       Impact factor: 3.234

Review 10.  The Current State of Cephalopod Science and Perspectives on the Most Critical Challenges Ahead From Three Early-Career Researchers.

Authors:  Caitlin E O'Brien; Katina Roumbedakis; Inger E Winkelmann
Journal:  Front Physiol       Date:  2018-06-06       Impact factor: 4.566

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