Uncovering the complexity of transcriptomes with RNA-Seq.

Journal of Biomedicine & Biotechnology
Valerio CostaAlfredo Ciccodicola

Abstract

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data fil...Continue Reading

References

Feb 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·A M Maxam, W Gilbert
Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Apr 17, 1980·Nature·W F Doolittle, C Sapienza
Jan 24, 1997·Cell·V E VelculescuK W Kinzler
Oct 23, 1997·Genome Research·S Audic, J M Claverie
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Oct 22, 2004·Nature·UNKNOWN International Human Genome Sequencing Consortium
Apr 23, 2005·Nature Methods·Rafael A IrizarryWayne Yu
Jun 24, 2005·Nature Methods·Matthias Harbers, Piero Carninci
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Katy L Simonsen, Lauren M McIntyre
Feb 14, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ryan J TaftJohn S Mattick
Nov 23, 2007·Genome Research·Tatiana Teixeira TorresChristian Schlötterer
Jan 22, 2008·Nature Methods·LaDeana W HillierElaine R Mardis
Jan 30, 2008·Bioinformatics·Ruiqiang LiJun Wang
Feb 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·David J SugarbakerRaphael Bueno
Mar 1, 2008·BMC Bioinformatics·Andrew D SmithMichael Q Zhang
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Mar 22, 2008·Genome Génome / Conseil National De Recherches Canada·Cesar A SommerFlavio Henrique-Silva
Apr 5, 2008·Science·Timothy D HarrisZheng Xie
May 3, 2008·Science·Ugrappa NagalakshmiMichael Snyder
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jun 3, 2008·Nature Methods·Nicole CloonanSean M Grimmond
Jun 14, 2008·Genome Research·Weichun Huang, Gabor Marth
Jun 26, 2008·Annual Review of Genomics and Human Genetics·Elaine R Mardis
Jul 8, 2008·Genomics·Ruben RosenkranzHeinz Himmelbauer
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Aug 8, 2008·Bioinformatics·Hao LinMing Li
Aug 12, 2008·Bioinformatics·Fabio De BonaGunnar Rätsch
Aug 14, 2008·Bioinformatics·Hui Jiang, Wing Hung Wong
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Oct 16, 2008·Current Pharmaceutical Biotechnology·Toshinari TakamuraShuichi Kaneko
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Dec 6, 2008·Science·Yiping HeKenneth W Kinzler

❮ Previous
Next ❯

Citations

May 18, 2011·Genetica·Pedro Martínez-GómezManuel Rubio
Dec 25, 2012·Journal of Molecular Neuroscience : MN·Tomas KavanaghMichael Janitz
Jun 24, 2011·Journal of Applied Genetics·Chandra Shekhar PareekAndrzej Tretyn
Jun 29, 2012·European Journal of Human Genetics : EJHG·Valerio CostaAlfredo Ciccodicola
Jun 2, 2011·Briefings in Functional Genomics·Chandra S PareekAndrzej Tretyn
Jan 19, 2013·Database : the Journal of Biological Databases and Curation·Verena WeissJulio Collado-Vides
Feb 28, 2014·Database : the Journal of Biological Databases and Curation·Margherita ScarpatoValerio Costa
Dec 27, 2011·Nucleic Acids Research·Leslie Y ChenLeroy E Hood
Nov 13, 2012·Nucleic Acids Research·Milana Frenkel-MorgensternAlfonso Valencia
Nov 16, 2013·The Journal of Clinical Investigation·Yu ChenKrzysztof Palczewski
Nov 17, 2012·BMC Genomics·Sunitha KogenaruNian Wang
Mar 2, 2012·BMC Genomics·Neil R HackettRonald G Crystal
Mar 16, 2012·BMC Genomics·Nicole GruenheitPeter Lockhart
Nov 28, 2013·BMC Genomics·Nikolai V RavinKonstantin G Skryabin
Jan 8, 2014·BMC Plant Biology·Aditi RambaniJoshua A Udall
Sep 22, 2011·BMC Systems Biology·Luigi BuonaguroFrancesco M Marincola
May 3, 2011·PloS One·Valerio CostaAlfredo Ciccodicola
Dec 7, 2013·Plant Molecular Biology·Sukhwinder S AulakhBarry S Flinn
Jan 25, 2014·Acta Biochimica Et Biophysica Sinica·Cheng ZhanQun Wang
Jan 2, 2014·Omics : a Journal of Integrative Biology·Xi QianGuofang Zhong
Jan 16, 2015·International Journal of Molecular Sciences·Margherita ScarpatoValerio Costa
Jun 2, 2012·Expert Opinion on Biological Therapy·Maria Ines AlmeidaGeorge Adrian Calin
Mar 16, 2016·BioMed Research International·Francesco RussoClaudia Angelini
Feb 5, 2013·Biochimica Et Biophysica Acta·Paromita Mukherjee, Sridhar Mani

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
nucleic acid sequencing
PCR
feature extraction

Software Mentioned

mate
ENCODE
MapView
ERANGE
PASS
R
EagleView
Illumina
SAM ( Sequencing Alignment / Map
Integrative Genomics Viewer ( IGV

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.