Literature DB >> 30684131

Big data challenges in genome informatics.

Ka-Chun Wong1.   

Abstract

In recent years, we have witnessed a big data explosion in genomics, thanks to the improvement in high-throughput technologies at drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in gigabytes (GBs). It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years.

Year:  2019        PMID: 30684131      PMCID: PMC6381353          DOI: 10.1007/s12551-018-0493-5

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  28 in total

Review 1.  A window into third-generation sequencing.

Authors:  Eric E Schadt; Steve Turner; Andrew Kasarskis
Journal:  Hum Mol Genet       Date:  2010-09-21       Impact factor: 6.150

2.  The ENCODE (ENCyclopedia Of DNA Elements) Project.

Authors: 
Journal:  Science       Date:  2004-10-22       Impact factor: 47.728

3.  BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

Authors:  Christoph Bock; Sabine Reither; Thomas Mikeska; Martina Paulsen; Jörn Walter; Thomas Lengauer
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

Review 4.  The impact of next-generation sequencing technology on genetics.

Authors:  Elaine R Mardis
Journal:  Trends Genet       Date:  2008-02-11       Impact factor: 11.639

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

7.  ChIP-seq accurately predicts tissue-specific activity of enhancers.

Authors:  Axel Visel; Matthew J Blow; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; Bing Ren; Edward M Rubin; Len A Pennacchio
Journal:  Nature       Date:  2009-02-12       Impact factor: 49.962

8.  An oestrogen-receptor-alpha-bound human chromatin interactome.

Authors:  Melissa J Fullwood; Mei Hui Liu; You Fu Pan; Jun Liu; Han Xu; Yusoff Bin Mohamed; Yuriy L Orlov; Stoyan Velkov; Andrea Ho; Poh Huay Mei; Elaine G Y Chew; Phillips Yao Hui Huang; Willem-Jan Welboren; Yuyuan Han; Hong Sain Ooi; Pramila N Ariyaratne; Vinsensius B Vega; Yanquan Luo; Peck Yean Tan; Pei Ye Choy; K D Senali Abayratna Wansa; Bing Zhao; Kar Sian Lim; Shi Chi Leow; Jit Sin Yow; Roy Joseph; Haixia Li; Kartiki V Desai; Jane S Thomsen; Yew Kok Lee; R Krishna Murthy Karuturi; Thoreau Herve; Guillaume Bourque; Hendrik G Stunnenberg; Xiaoan Ruan; Valere Cacheux-Rataboul; Wing-Kin Sung; Edison T Liu; Chia-Lin Wei; Edwin Cheung; Yijun Ruan
Journal:  Nature       Date:  2009-11-05       Impact factor: 49.962

9.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

10.  Model-based analysis of ChIP-Seq (MACS).

Authors:  Yong Zhang; Tao Liu; Clifford A Meyer; Jérôme Eeckhoute; David S Johnson; Bradley E Bernstein; Chad Nusbaum; Richard M Myers; Myles Brown; Wei Li; X Shirley Liu
Journal:  Genome Biol       Date:  2008-09-17       Impact factor: 13.583

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  3 in total

1.  Big data: the elements of good questions, open data, and powerful software.

Authors:  Joshua W K Ho; Eleni Giannoulatou
Journal:  Biophys Rev       Date:  2019-01-25

2.  An information-theoretical analysis of gene nucleotide sequence structuredness for a selection of aging and cancer-related genes.

Authors:  David Blokh; Joseph Gitarts; Ilia Stambler
Journal:  Genomics Inform       Date:  2020-12-08

Review 3.  Phytosterol Profiles, Genomes and Enzymes - An Overview.

Authors:  Sylvain Darnet; Aurélien Blary; Quentin Chevalier; Hubert Schaller
Journal:  Front Plant Sci       Date:  2021-05-19       Impact factor: 5.753

  3 in total

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