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 | Gene | |
2016 | Microbial Ecology | |
2016 |
Metagenome-wide association studies: fine-mining the microbiome |
Nature Reviews Microbiology |
2016 | 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 | 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 | 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 |
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown |
Nature Protocols |
2016 | A Survey of Best Practices for RNA-Seq Analysis | Genome Biology |
2016 | PLOS ONE | |
2015 |
Computational and analytical challenges in single-cell transcriptomics |
Nature Reviews Genetics |
2015 | Nature Reviews Genetics | |
2015 | 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 |