Journal ArticleDOI
Next-generation DNA sequencing.
Jay Shendure,Hanlee P. Ji +1 more
TLDR
Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.Abstract:
DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.read more
Citations
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Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Journal ArticleDOI
DnaSP v5
Pablo Librado,Julio Rozas +1 more
TL;DR: Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets, including visualizing sliding window results integrated with available genome annotations in the UCSC browser.
Journal ArticleDOI
Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
TL;DR: The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Journal ArticleDOI
The impact of the gut microbiota on human health: an integrative view.
TL;DR: It is suggested that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in the microbiota.
Journal ArticleDOI
The tomato genome sequence provides insights into fleshy fruit evolution
Shusei Sato,Satoshi Tabata,Hideki Hirakawa,Erika Asamizu,Kenta Shirasawa,Sachiko Isobe,Takakazu Kaneko,Yasukazu Nakamura,Daisuke Shibata,Koh Aoki,Michael Egholm,James R. Knight,Robert Bogden,Changbao Li,Yang Shuang,Xun Xu,Shengkai Pan,Shifeng Cheng,Xin Liu,Yuanyuan Ren,Jun Wang,Alessandro Albiero,Francesca Dal Pero,Sara Todesco,Joyce Van Eck,Robert M. Buels,Aureliano Bombarely,Joseph Gosselin,Minyun Huang,Jonathan A. Leto,Naama Menda,Susan R. Strickler,Linyong Mao,Shan Gao,Isaak Y. Tecle,Thomas L. York,Yi Zheng,Julia Vrebalov,Je Min Lee,Silin Zhong,Lukas A. Mueller,Willem J. Stiekema,Paolo Ribeca,Tyler Alioto,Wencai Yang,Sanwen Huang,Yongchen Du,Zhonghua Zhang,Jianchang Gao,Yanmei Guo,Xiaoxuan Wang,Ying Li,Jun He,Chuanyou Li,Zhukuan Cheng,Jianru Zuo,Jianfeng Ren,Jiuhai Zhao,Liuhua Yan,Hongling Jiang,Bao Wang,Hongshuang Li,Zhenjun Li,Fuyou Fu,Bingtang Chen,Bin Han,Qi Feng,Danlin Fan,Ying Wang,Hong-Qing Ling,Yongbiao Xue,Doreen Ware,W. Richard McCombie,Zachary B. Lippman,Jer Ming Chia,Ke Jiang,Shiran Pasternak,Laura Gelley,Melissa Kramer,Lorinda K. Anderson,Song Bin Chang,Suzanne M. Royer,Lindsay A. Shearer,Stephen M. Stack,Jocelyn K. C. Rose,Yimin Xu,Nancy T. Eannetta,Antonio J. Matas,Ryan P. McQuinn,Steven D. Tanksley,Francisco Camara,Roderic Guigó,Stephane Rombauts,Jeffrey A. Fawcett,Yves Van de Peer,Dani Zamir,Chunbo Liang,Manuel Spannagl,Heidrun Gundlach,Rémy Bruggmann,Klaus F. X. Mayer,Zhiqi Jia,Junhong Zhang,Zhibiao Ye,Gerard J. Bishop,Sarah Butcher,Rosa Lopez-Cobollo,Daniel W. A. Buchan,Ioannis Filippis,James Abbott,Manju Singh,Alok Singh,Jitendra Kumar Pal,Awadhesh Pandit,Pradeep Kumar Singh,Ajay Kumar Mahato,Vivek Dogra,Kishor Gaikwad,Tilak Raj Sharma,Trilochan Mohapatra,Nagendra K. Singh,Mathilde Causse,Christophe Rothan,Céline Noirot,Arnaud Bellec,Christophe Klopp,Corinne Delalande,Hélène Bergès,Jérôme Mariette,Pierre Frasse,Sonia Vautrin,Toulouse Mohamed Zouine,Alain Latché,Christine Rousseau,Farid Regad,Jean-Claude Pech,Murielle Philippot,Mondher Bouzayen,Pierre Pericard,Sonia Osorio,Asuncion Fernandez Del Carmen,Antonio J. Monforte,Antonio Granell,Rafael Fernández-Muñoz,Mariana Conte,Gabriel Lichtenstein,Fernando Carrari,Gianluca De Bellis,Fabio Fuligni,Clelia Peano,Silvana Grandillo,Pasquale Termolino,Marco Pietrella,Elio Fantini,Giulia Falcone,Alessia Fiore,Giovanni Giuliano,Loredana Lopez,Paolo Facella,Gaetano Perrotta,Loretta Daddiego,Glenn J. Bryan,Biology Modesto Orozco,Xavier Pastor,David Torrents,Marco G.M. Van Schriek,Richard Feron,Jan van Oeveren,Peter De Heer,Lorena Da Ponte,Saskia Jacobs-Oomen,Mike Cariaso,Marcel Prins,Michael Josephus Theresia Van Eijk,Antoine Janssen,J. J. Van Haaren,Sung HwanJo,Jungeun Kim,Suk-Yoon Kwon,Sangmi Kim,Dal-Hoe Koo,Sanghyeob Lee,Christopher Clouser,Alain Rico,Asis Hallab,Christiane Gebhardt,Kathrin Klee,Anika Jöcker,Jens Warfsmann,Ulrike Göbel,Shingo Kawamura,Kentaro Yano,Jamie D. Sherman,Hiroyuki Fukuoka,Satomi Negoro,Sarita Bhutty,Parul Chowdhury,Debasis Chattopadhyay,Erwin Datema,Sandra Smit,Elio Schijlen,José van de Belt,Jan C. van Haarst,Sander Peters,Marjo J. van Staveren,Marleen H.C. Henkens,Paul Mooyman,Thamara Hesselink,Roeland C. H. J. van Ham,Guoyong Jiang,Marcus Droege,Doil Choi,Byung Cheol Kang,Byung-Dong Kim,Minkyu Park,Seungill Kim,Seon-In Yeom,Yong-Hwan Lee,Yang Do Choi,Guangcun Li,Jianwei Gao,Yongsheng Liu,Shengxiong Huang,Victoria Fernandez-Pedrosa,Carmen Collado,Sheila Zuñ Iga,Guoping Wang,Rebecca Cade,Robert A. Dietrich,Jane Rogers,Sandra Knapp,Zhangjun Fei,Zhangjun Fei,Ruth White,Ruth White,Theodore W. Thannhauser,Theodore W. Thannhauser,James J. Giovannoni,James J. Giovannoni,Miguel A. Botella,Louise Gilbert,Fabra Ramon Gonzalez,Jose Luis Goicoechea,Yeisoo Yu,David Kudrna,Kristi Collura,Marina Wissotski,Rod A. Wing,Blake C. Meyers,Aishwarya Bala Gurazada,Pamela J. Green,Saloni Mathur,Shailendra Vyas,Amolkumar U. Solanke,Rajesh Kumar,Vikrant Gupta,Arun Sharma,Paramjit Khurana,Jitendra P. Khurana,Akhilesh K. Tyagi,Tamas Dalmay,Irina Mohorianu,Brandon Walts,Srikar Chamala,W. Brad Barbazuk,Jingping Li,Hui Guo,Tae-Ho Lee,Yupeng Wang,Dong Zhang,Andrew H. Paterson,Xiyin Wang,Xiyin Wang,Haibao Tang,Haibao Tang,Amalia Barone,Maria Luisa Chiusano,Maria Raffaella Ercolano,Nunzio D’Agostino,Miriam Di Filippo,Alessandra Traini,Walter Sanseverino,Luigi Frusciante,Graham B. Seymour,Mounir Elharam,Ying Fu,Axin Hua,Steven Kenton,Jennifer Lewis,Shaoping Lin,Fares Z. Najar,Hongshing Lai,Baifang Qin,Ruihua Shi,Chunmei Qu,Douglas White,James R. White,Yanbo Xing,Keqin Yang,Jing Yi,Ziyun Yao,Liping Zhou,Bruce A. Roe,Alessandro Vezzi,Michela D'Angelo,Rosanna Zimbello,Riccardo Schiavon,Elisa Caniato,Chiara Rigobello,Davide Campagna,Nicola Vitulo,Giorgio Valle,David R. Nelson,Emanuele De Paoli,Dóra Szinay,Hans H. De Jong,Yuling Bai,Richard G. F. Visser,Reném Klein Lankhorst,Helen Beasley,Karen McLaren,Christine Nicholson,Claire Riddle,Giulio Gianese +323 more
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
References
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Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies,Michael Egholm,William E. Altman,Said Attiya,Joel S. Bader,Lisa A. Bemben,Jan Berka,Michael S. Braverman,Yi-Ju Chen,Zhoutao Chen,Scott Dewell,Lei Du,J. M. Fierro,Xavier V. Gomes,Brian C. Godwin,Wen He,Scott Edward Helgesen,Chun Heen Ho,Gerard P. Irzyk,Szilveszter C. Jando,Maria L. I. Alenquer,Thomas P. Jarvie,Kshama B. Jirage,Jong-Bum Kim,James R. Knight,Janna R. Lanza,John H. Leamon,Steven Lefkowitz,Ming Lei,Jing Li,Kenton Lohman,Hong Lu,Vinod Makhijani,Keith Mcdade,Michael P. McKenna,Eugene W. Myers,Elizabeth Nickerson,John Nobile,Ramona Plant,Bernard P. Puc,Michael T. Ronan,George T. Roth,Gary J. Sarkis,Jan Fredrik Simons,John Simpson,Maithreyan Srinivasan,Karrie R. Tartaro,Alexander Tomasz,Kari A. Vogt,Greg A. Volkmer,Shally H. Wang,Yong Wang,Michael P. Weiner,Pengguang Yu,Richard F. Begley,Jonathan M. Rothberg +55 more