Seq Papers

One of the goals of this blog is to frequently write blog posts on interesting papers on sequencing, be it a new sequencing technology/assay or a new computational method to analyze sequencing data. Although have not really managed to do that to my satisfaction, here is an attempt to summarize what is done so far. Hope this will help increase more posts on interesting papers.

Seq Papers, the new page, collate all the blog-posts written in this blog NextGenSeek.com. Ideally, these posts should be a good summary posts with enough details on recent papers, which caught the attention, passed the inertia tests to read and write.  However, only a few are that detailed. Therefore, papers mentioned even peripherally in a post has made it in to the list now.  Hope it will be useful to other sequencing enthusiasts even in a smallest way.

Seq Papers in 2016

  1. Fast and accurate single-cell RNA-seq analysis using equivalence class counts

Seq Papers in 2015

  1. HISAT: A Fast and Memory Lean RNA-seq aligner,
  2. Three papers on new RNA-seq methods offer a new way to do RNA-seq analysis
  3. Inferring Cellular Localization from Single Cell RNA-seq
  4. An Atlas of Genomic Imprinting in Mouse and Human Using RNA-seq data
  5. kallisto, a new ultra fast RNA-seq quantitation method
  6. kallisto paper summary: Near-optimal RNA-seq quantification

Seq Papers in 2014

  1. Personal Allele-Specific Transcriptomics by PacBio Long Reads
  2. Platypus: A New Variant Caller that Integrates Mapping, Assembly and Haplotype-based approaches
  3. RNA-Skim: new RNA-seq quantitation method that is faster than Sailfish
  4. Two Single-Cell RNA-seq Papers This Week

  5. Bayesian Approach to Single-Cell RNA-Seq Differential Expression Analysis

  6. Papers on Grappling With Technical Variation in Single Cell RNA-seq Analysis

  7. RNA-seq on Identical Twins Discordant for Down’s Syndrome Reveal Genome-Wide Expression Dysregulation

  8. Sailfish: Alignment-free isoform quantification from RNA-seq reads

  9. Hacking Illumina GA IIx to Study RNA-Protein Interaction

  10. Ballgown for estimating differential expression of genes, transcripts, or exons from RNA-seq

  11. The first published paper on RNA-seq: Setting the record straight

  12. Multiple Papers on Random Monoallelic Expression by RNA-seq

  13. Moleculo Long-reads in action for haplotyping whole human genome

  14. Paper Summary: Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression

Seq Papers in 2013

  1. Digital DNA Storage Moves Towards Scalable and Practical

  2. Yeast Genomics Helps Explaining Missing Heritability

  3. HeLa Cell Line Genome Sequencing Raises Ethical/Privacy Concerns

  4. The Trouble with Discordant SNP/Indel Calling

  5. Illumina Announces Moleculo Long Read Technology and Phasing As Service

  6. Tophat/RNA-seq Analysis Nostalgia

  7. Sailfish: Isoform Quantitation at the Speed of Making a Cup of Coffee

  8. Large Scale Sequencing Efforts Go Beyond Genetic Variations Towards Function

  9. IDP: Isoform Detection and Prediction Using Second Generation Sequencing and PacBio Sequencing

  10. How Replicates Can Help With Experimental Sources of Errors in Next-gen sequencing?
  11. Long reads of the year 2013

Seq Papers in 2012

  1. The Best Benchtop Next-Gen High-Throughput Sequencer: MiSeq or Ion Torrent PGM or 454 GS Junior?

  2. All Things GWAS at Nature Genetics

  3. Complete Genomics’ New Technology to Produce Accurate Sequencing With Small Amount of DNA

  4. Comparing the Performance of Three Next-Gen Sequencers; Illumina MiSeq, Ion Torrent PGM and PacBio RS

  5. Comparing Price and Tech. Specs. of Illumina MiSeq, Ion Torrent PGM, 454 GS Junior, and PacBio RS

  6. Next-Gen Digital Data Storage Goes DNA

  7. The Add-On Costs of Setting Up a Sequencing Lab

  8. ENCODE By The Numbers & ENCODE Coverage Round Up: Press, Blogs, and Tweets

  9. 10 Tips To Be A Better Programmer for Analyzing Next Gen Sequence Data

  10. Tips for Next-Gen Sequencing Experiment Design: Randomization

  11. Did You Know There Are (At Least) 20 Applications of Next-generation DNA Sequencing?

  12. Detecting chromosomal aberrations in cancer patients using Whole Genome Sequencing

  13. Five Massive Next-Gen Sequencing Projects Published in 2012

  14. Genomes That Got Sequenced: Class of 2012