Literature DB >> 25518043

Cardiovascular transcriptomics and epigenomics using next-generation sequencing: challenges, progress, and opportunities.

Po-Yen Wu1, Raghu Chandramohan1, John H Phan1, William T Mahle1, J William Gaynor1, Kevin O Maher1, May D Wang2.   

Abstract

Entities:  

Keywords:  biomarkers; chromatin immunoprecipitation; computational biology; epigenomics; gene expression profiling; high-throughput nucleotide sequencing; transcriptome

Mesh：

Year:  2014        PMID： 25518043      PMCID： PMC4983435          DOI： 10.1161/CIRCGENETICS.113.000129

Source DB:  PubMed          Journal:  Circ Cardiovasc Genet        ISSN： 1942-3268


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  69 in total

1.  SOAP2: an improved ultrafast tool for short read alignment.

Authors:  Ruiqiang Li; Chang Yu; Yingrui Li; Tak-Wah Lam; Siu-Ming Yiu; Karsten Kristiansen; Jun Wang
Journal:  Bioinformatics       Date:  2009-06-03       Impact factor: 6.937

2.  OSA: a fast and accurate alignment tool for RNA-Seq.

Authors:  Jun Hu; Huanying Ge; Matt Newman; Kejun Liu
Journal:  Bioinformatics       Date:  2012-05-15       Impact factor: 6.937

3.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

4.  Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Authors:  Yarden Katz; Eric T Wang; Edoardo M Airoldi; Christopher B Burge
Journal:  Nat Methods       Date:  2010-11-07       Impact factor: 28.547

5.  Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.

Authors:  Jun Li; Robert Tibshirani
Journal:  Stat Methods Med Res       Date:  2011-11-28       Impact factor: 3.021

6.  F-Seq: a feature density estimator for high-throughput sequence tags.

Authors:  Alan P Boyle; Justin Guinney; Gregory E Crawford; Terrence S Furey
Journal:  Bioinformatics       Date:  2008-09-10       Impact factor: 6.937

7.  rQuant.web: a tool for RNA-Seq-based transcript quantitation.

Authors:  Regina Bohnert; Gunnar Rätsch
Journal:  Nucleic Acids Res       Date:  2010-06-15       Impact factor: 16.971

8.  Association between multiple cardiovascular risk factors and atherosclerosis in children and young adults. The Bogalusa Heart Study.

Authors:  G S Berenson; S R Srinivasan; W Bao; W P Newman; R E Tracy; W A Wattigney
Journal:  N Engl J Med       Date:  1998-06-04       Impact factor: 91.245

9.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

10.  A comparison of methods for differential expression analysis of RNA-seq data.

Authors:  Charlotte Soneson; Mauro Delorenzi
Journal:  BMC Bioinformatics       Date:  2013-03-09       Impact factor: 3.169
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  6 in total

Review 1.  Systems biology in cardiovascular disease: a multiomics approach.

Authors:  Abhishek Joshi; Marieke Rienks; Konstantinos Theofilatos; Manuel Mayr
Journal:  Nat Rev Cardiol       Date:  2020-12-18       Impact factor: 32.419

Review 2.  Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart.

Authors:  Cinzia Perrino; Albert-Laszló Barabási; Gianluigi Condorelli; Sean Michael Davidson; Leon De Windt; Stefanie Dimmeler; Felix Benedikt Engel; Derek John Hausenloy; Joseph Addison Hill; Linda Wilhelmina Van Laake; Sandrine Lecour; Jonathan Leor; Rosalinda Madonna; Manuel Mayr; Fabrice Prunier; Joost Petrus Geradus Sluijter; Rainer Schulz; Thomas Thum; Kirsti Ytrehus; Péter Ferdinandy
Journal:  Cardiovasc Res       Date:  2017-06-01       Impact factor: 10.787

3.  Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study.

Authors:  Chau-Chyun Sheu; Wei-An Chang; Ming-Ju Tsai; Ssu-Hui Liao; Inn-Wen Chong; Po-Lin Kuo
Journal:  J Clin Med       Date:  2019-03-05       Impact factor: 4.241

Review 4.  Systems Medicine as an Emerging Tool for Cardiovascular Genetics.

Authors:  Tina Haase; Daniela Börnigen; Christian Müller; Tanja Zeller
Journal:  Front Cardiovasc Med       Date:  2016-08-30

Review 5.  Big data from electronic health records for early and late translational cardiovascular research: challenges and potential.

Authors:  Harry Hemingway; Folkert W Asselbergs; John Danesh; Richard Dobson; Nikolaos Maniadakis; Aldo Maggioni; Ghislaine J M van Thiel; Maureen Cronin; Gunnar Brobert; Panos Vardas; Stefan D Anker; Diederick E Grobbee; Spiros Denaxas
Journal:  Eur Heart J       Date:  2018-04-21       Impact factor: 29.983

Review 6.  Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology.

Authors:  Shrey Gandhi; Frank Ruehle; Monika Stoll
Journal:  Noncoding RNA       Date:  2019-01-31
  6 in total

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