Towards practical, high-capacity, low-maintenance information storage in synthesized DNA




Towards practical, high-capacity, low-maintenance information storage in synthesized DNA, by Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos & Ewan Birney published in Nature (2013) doi:10.1038/nature11875. Abstract Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that […]






Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants




Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants by Wenqing Fu et. al. published in Nature (2012) doi:10.1038/nature11690. Abstract Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for […]






Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes




Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes by Jacob A. Tennessen, et. al. published in Science 6 July 2012, Vol. 337 no. 6090 pp. 64-69 DOI: 10.1126/science.1219240 Abstract As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding […]






De novo mutations revealed by whole-exome sequencing are strongly associated with autism




De novo mutations revealed by whole-exome sequencing are strongly associated with autism by Stephan J. Sanders et. al.. published in Nature 485, 237–241 (10 May 2012) doi:10.1038/nature10945. Abstract Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants […]






Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations




Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations by Brian J. O’Roak et. al. published in Nature 485, 246–250 (10 May 2012) doi:10.1038/nature10989. Abstract It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is […]






ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.




ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions by Furey, Terrence S published in Nature reviews. Genetics. 2012 13(12):840-52 Abstract Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as […]






Differential analysis of gene regulation at transcript resolution with RNA-seq




Differential analysis of gene regulation at transcript resolution with RNA-seq by Cole Trapnell, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn & Lior Pachter published in Nature Biotechnology (2012) doi:10.1038/nbt.2450 Abstract Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses […]






Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets




Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets by Adina Chuang Howe et. al. published in the open preprint server arXiv on 1st Dec 2012. Find the paper repository at github https://github.com/ged-lab/2012-assembly-artifacts. Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity […]






Compression of structured high-throughput sequencing data




Compression of structured high-throughput sequencing data by Fabien Campagne et. al. published in the preprint server arXiv.org on 28th November 2012. Abstract Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of highthroughput sequencing (HTS). Most approaches currently used to store HTS data are either […]






Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing




Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing by Rebecca J. Leary et. al. from JHU published in Sci. Transl. Med. 28 November 2012: Vol. 4, Issue 162. Abstract Clinical management of cancer patients could be improved through the development of noninvasive approaches for the detection of incipient, residual, and […]