Light Reading

A selection of review articles and interesting research that should not be missed.  If you are working with NGS or proteomics data for the first time, many of these will be invaluable.

Genome Assembly, Alignment, and Annotation

Year Title Journal
2015 Annual Review Genomics
2015 Nucleic Acids Research
2015 Briefings in Bioinformatics
2014 Decade in Review – genomics: A decade of discovery in cancer genomics Nature Reviews Clinical Oncology
2014 Single cell genomics: advancements and future perspectives Plos Genetics
2013 Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species Giga Science
2013 Scaffolding DNA Assemblies by 3D Proximity Nature Reviews Genetics
2012 A beginner’s guide to eukaryotic genome annotation Nature Reviews Genetics
2011 Microbial Metagenomics: Beyond the Genome Annual Review of Marine Science

Metagenomics

Year Title Journal
2016

Databases of the marine metagenomics

Gene
2016

Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments

Microbial Ecology
2016

Metagenome-wide association studies: fine-mining the microbiome

Nature Reviews Microbiology
2016

Metagenomic Assembly: Overview, Challenges and Applications

Yale Journal of Biology and Medicine
2015 EpiRADSeq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing Methods in Ecology and Evolution
2015

Web Resources for Metagenomics Studies

Genomics, Proteomics, & Bioinformatics
2014 Current challenges in the bioinformatics of single-cell genomics Frontiers in Oncology
2013 Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data Microbial Informatics & Experimentation
2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing Nature Reviews Genetics
2011 Repetitive DNA and next-generation sequencing: computational challenges and solutions Nature Review Genetics
 2011 Limitations of next-generation genome sequence assembly Nature Methods

Next Generation Sequencing

Year Title Journal
2016

Coming of age: ten years of next-generation sequencing technologies

Nature Review Genetics
2013 Next Generation Sequencing Platforms Analytical Chemistry
2013 The next-generation sequencing revolution and its impact on genomics Cell
2011 Field guide to next-generation DNA sequencers Molecular Ecology Resources

Proteomics

Year Title Journal
2016 Annual Review of Analytical Chemistry
2015 Nature Reviews Molecular Cell Biology
2014 Analytical Chemistry
2014 Journal of Theoretical Biology
2014 Nature Methods
2013

Next-generation proteomics: towards an integrative view of proteome dynamics

Nature Reviews Genetics
2013

Open source libraries and frameworks for mass spectrometry based proteomics: A developer’s perspective

Biochimica et Biophysica Acta
2012 Next-generation proteomics: towards an integrative view of proteome dynamics Nature Review Genetics
2012 Computational and Statistical Analysis of Protein Mass Spectrometry Data Plos Computational Biology

Transcriptomics

Year Title Journal
2016 A Survey of Best Practices for RNA-Seq Analysis Genome Biology
2016

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

PLOS ONE
2015

Computational and analytical challenges in single-cell transcriptomics

Nature Reviews Genetics
2015

Spatially resolved transcriptomics and beyond

Nature Reviews Genetics
2015

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

Genome Research
2013 Assessment of Transcript Reconstruction Methods Nature Methods
2013 Genomics: The State of the Art in RNA-Seq analysis Nature Methods
2013 Single-Cell Sequencing-Based Technologies will Revolutionize Whole-Organism Science  Nature Reviews Genetics
2012 Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach Plos One
2011 Next Generation Transcriptome Assembly Nature Reviews Genetics

Variation Detection and Characterization

Year Title Journal
2016 Next-generation biology: Sequencing and data analysis approaches for non-model organisms Marine Genomics
2016 Conservation genomics of natural and managed populations: building a conceptual and practical framework Molecular Ecology
2016 Harnessing the power of RADseq for ecological and evolutionary genomics Nature Reviews Genetics
2016 Review of alignment and SNP calling algorithms for next-generation sequencing data Journal of Applied Genetics
2016 Structural variation detection using next-generation sequencing data: A comparative technical review Methods
2015

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

 GENETICS
2015 EpiRADSeq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing Methods in Ecology and Evolution
2015 Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations Molecular Plant
2014 Current challenges in the bioinformatics of single-cell genomics Frontiers in Oncology
2014 Sequencing pools of individuals — mining genome-wide polymorphism data without big funding Nature Reviews Genetics
2014 Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples  Bioinformatics
2013 Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data Microbial Informatics & Experimentation
2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing Nature Reviews Genetics
2011 Repetitive DNA and next-generation sequencing: computational challenges and solutions Nature Reviews Genetics
2011 Limitations of next-generation genome sequence assembly Nature Methods