Literature DB >> 24727769

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

Jessica Severin1, Marina Lizio1, Jayson Harshbarger1, Hideya Kawaji2, Carsten O Daub1, Yoshihide Hayashizaki3, Nicolas Bertin4, Alistair R R Forrest1.   

Abstract

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Year:  2014        PMID: 24727769     DOI: 10.1038/nbt.2840

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


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  19 in total

1.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

Review 2.  Visualizing genomes: techniques and challenges.

Authors:  Cydney B Nielsen; Michael Cantor; Inna Dubchak; David Gordon; Ting Wang
Journal:  Nat Methods       Date:  2010-02-25       Impact factor: 28.547

3.  Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types.

Authors:  Gang Wei; Brian J Abraham; Ryoji Yagi; Raja Jothi; Kairong Cui; Suveena Sharma; Leelavati Narlikar; Daniel L Northrup; Qingsong Tang; William E Paul; Jinfang Zhu; Keji Zhao
Journal:  Immunity       Date:  2011-08-26       Impact factor: 31.745

4.  The NIH Roadmap Epigenomics Program data resource.

Authors:  Lisa Helbling Chadwick
Journal:  Epigenomics       Date:  2012-06       Impact factor: 4.778

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

7.  The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors:  Thomas Derrien; Rory Johnson; Giovanni Bussotti; Andrea Tanzer; Sarah Djebali; Hagen Tilgner; Gregory Guernec; David Martin; Angelika Merkel; David G Knowles; Julien Lagarde; Lavanya Veeravalli; Xiaoan Ruan; Yijun Ruan; Timo Lassmann; Piero Carninci; James B Brown; Leonard Lipovich; Jose M Gonzalez; Mark Thomas; Carrie A Davis; Ramin Shiekhattar; Thomas R Gingeras; Tim J Hubbard; Cedric Notredame; Jennifer Harrow; Roderic Guigó
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

8.  BioMart: a data federation framework for large collaborative projects.

Authors:  Junjun Zhang; Syed Haider; Joachim Baran; Anthony Cros; Jonathan M Guberman; Jack Hsu; Yong Liang; Long Yao; Arek Kasprzyk
Journal:  Database (Oxford)       Date:  2011-09-19       Impact factor: 3.451

9.  modMine: flexible access to modENCODE data.

Authors:  Sergio Contrino; Richard N Smith; Daniela Butano; Adrian Carr; Fengyuan Hu; Rachel Lyne; Kim Rutherford; Alex Kalderimis; Julie Sullivan; Seth Carbon; Ellen T Kephart; Paul Lloyd; E O Stinson; Nicole L Washington; Marc D Perry; Peter Ruzanov; Zheng Zha; Suzanna E Lewis; Lincoln D Stein; Gos Micklem
Journal:  Nucleic Acids Res       Date:  2011-11-12       Impact factor: 16.971

10.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

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  88 in total

1.  mRNA 5' ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced.

Authors:  Mikaela R Berger; Rolando Alvarado; Daniel L Kiss
Journal:  FEBS Lett       Date:  2019-03-09       Impact factor: 4.124

2.  A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists.

Authors:  Camilla Fagorzi; Alice Checcucci
Journal:  Methods Mol Biol       Date:  2021

3.  LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.

Authors:  Luca Ducoli; Saumya Agrawal; Eliane Sibler; Tsukasa Kouno; Carlotta Tacconi; Chung-Chao Hon; Simone D Berger; Daniela Müllhaupt; Yuliang He; Jihye Kim; Marco D'Addio; Lothar C Dieterich; Piero Carninci; Michiel J L de Hoon; Jay W Shin; Michael Detmar
Journal:  Nat Commun       Date:  2021-02-10       Impact factor: 14.919

4.  An atlas of human long non-coding RNAs with accurate 5' ends.

Authors:  Chung-Chau Hon; Jordan A Ramilowski; Jayson Harshbarger; Nicolas Bertin; Owen J L Rackham; Julian Gough; Elena Denisenko; Sebastian Schmeier; Thomas M Poulsen; Jessica Severin; Marina Lizio; Hideya Kawaji; Takeya Kasukawa; Masayoshi Itoh; A Maxwell Burroughs; Shohei Noma; Sarah Djebali; Tanvir Alam; Yulia A Medvedeva; Alison C Testa; Leonard Lipovich; Chi-Wai Yip; Imad Abugessaisa; Mickaël Mendez; Akira Hasegawa; Dave Tang; Timo Lassmann; Peter Heutink; Magda Babina; Christine A Wells; Soichi Kojima; Yukio Nakamura; Harukazu Suzuki; Carsten O Daub; Michiel J L de Hoon; Erik Arner; Yoshihide Hayashizaki; Piero Carninci; Alistair R R Forrest
Journal:  Nature       Date:  2017-03-01       Impact factor: 49.962

5.  Genome-Wide Interaction Analysis of Air Pollution Exposure and Childhood Asthma with Functional Follow-up.

Authors:  Anna Gref; Simon K Merid; Olena Gruzieva; Stéphane Ballereau; Allan Becker; Tom Bellander; Anna Bergström; Yohan Bossé; Matteo Bottai; Moira Chan-Yeung; Elaine Fuertes; Despo Ierodiakonou; Ruiwei Jiang; Stéphane Joly; Meaghan Jones; Michael S Kobor; Michal Korek; Anita L Kozyrskyj; Ashish Kumar; Nathanaël Lemonnier; Elaina MacIntyre; Camille Ménard; David Nickle; Ma'en Obeidat; Johann Pellet; Marie Standl; Annika Sääf; Cilla Söderhäll; Carla M T Tiesler; Maarten van den Berge; Judith M Vonk; Hita Vora; Cheng-Jian Xu; Josep M Antó; Charles Auffray; Michael Brauer; Jean Bousquet; Bert Brunekreef; W James Gauderman; Joachim Heinrich; Juha Kere; Gerard H Koppelman; Dirkje Postma; Christopher Carlsten; Göran Pershagen; Erik Melén
Journal:  Am J Respir Crit Care Med       Date:  2017-05-15       Impact factor: 21.405

6.  FVIII expression by its native promoter sustains long-term correction avoiding immune response in hemophilic mice.

Authors:  Simone Merlin; Rosella Famà; Ester Borroni; Diego Zanolini; Valentina Bruscaggin; Silvia Zucchelli; Antonia Follenzi
Journal:  Blood Adv       Date:  2019-03-12

7.  Genetic algorithm-based personalized models of human cardiac action potential.

Authors:  Dmitrii Smirnov; Andrey Pikunov; Roman Syunyaev; Ruslan Deviatiiarov; Oleg Gusev; Kedar Aras; Anna Gams; Aaron Koppel; Igor R Efimov
Journal:  PLoS One       Date:  2020-05-11       Impact factor: 3.240

8.  Expression of mouse Dab2ip transcript variants and gene methylation during brain development.

Authors:  Farimah Salami; Shuhong Qiao; Ramin Homayouni
Journal:  Gene       Date:  2015-05-07       Impact factor: 3.688

9.  A promoter-level mammalian expression atlas.

Authors:  Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassmann; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C Clevers; Emiliano Dalla; Carrie A Davis; Michael Detmar; Alexander D Diehl; Taeko Dohi; Finn Drabløs; Albert S B Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C Farach-Carson; Geoffrey J Faulkner; Alexander V Favorov; Malcolm E Fisher; Martin C Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furino; Jun-ichi Furusawa; Teunis B Geijtenbeek; Andrew P Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J Hitchens; Shannan J Ho Sui; Oliver M Hofmann; Ilka Hoof; Furni Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; Artem S Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I Kawamura; Tsugumi Kawashima; Judith S Kempfle; Tony J Kenna; Juha Kere; Levon M Khachigian; Toshio Kitamura; S Peter Klinken; Alan J Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T Kwon; Jeroen F J Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-Sim; Ri-ichiroh Manabe; Jessica C Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Shohei Noma; Tadasuke Noazaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohimiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G D Prendergast; Owen J L Rackham; Jordan A Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A Schultes; Gundula G Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W Shin; Christophe Simon; Daisuke Sugiyama; Takaai Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K Swoboda; Peter A C 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyodo; Tetsuro Toyoda; Elvind Valen; Marc van de Wetering; Linda M van den Berg; Roberto Verado; Dipti Vijayan; Ilya E Vorontsov; Wyeth W Wasserman; Shoko Watanabe; Christine A Wells; Louise N Winteringham; Ernst Wolvetang; Emily J Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E Zabierowski; Peter G Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M Summers; Harukazu Suzuki; Carsten O Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C Freeman; Boris Lenhard; Vladimir B Bajic; Martin S Taylor; Vsevolod J Makeev; Albin Sandelin; David A Hume; Piero Carninci; Yoshihide Hayashizaki
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

10.  Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Authors:  Mathys Grapotte; Manu Saraswat; Chloé Bessière; Christophe Menichelli; Jordan A Ramilowski; Jessica Severin; Yoshihide Hayashizaki; Masayoshi Itoh; Michihira Tagami; Mitsuyoshi Murata; Miki Kojima-Ishiyama; Shohei Noma; Shuhei Noguchi; Takeya Kasukawa; Akira Hasegawa; Harukazu Suzuki; Hiromi Nishiyori-Sueki; Martin C Frith; Clément Chatelain; Piero Carninci; Michiel J L de Hoon; Wyeth W Wasserman; Laurent Bréhélin; Charles-Henri Lecellier
Journal:  Nat Commun       Date:  2021-06-02       Impact factor: 14.919

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