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 […]






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 […]






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 […]






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 […]






The expanding scope of DNA sequencing




The expanding scope of DNA sequencing. by Jay Shendure and Erez Lieberman Aiden from U.Washington published in Nat Biotechnol. 2012 Nov;30(11):1084-94. Abstract In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. […]






Global gene disruption in human cells to assign genes to phenotypes




Global gene disruption in human cells to assign genes to phenotypes by Jan E. Carette, et. al. published in Nat Biotechnol. 2011 May 29; 29(6): 542–546. Abstract Insertional mutagenesis in a haploid background can lead to complete disruption of gene function1. Here we generate a population of human cells that contain insertions in >98% of […]






High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment




High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment by Aaron C. Logan et. al. published in Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9. Abstract The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease […]






High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis




High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis by Rupali P Patwardhan et. al. published in Nat Biotechnol. 2009 December; 27(12): 1173–1175. We present a method that harnesses massively parallel DNA synthesis and sequencing for the high-throughput functional analysis of regulatory sequences at single-nucleotide resolution. As a proof of concept, we quantitatively assayed […]






Genome-wide measurement of RNA secondary structure in yeast.




Genome-wide measurement of RNA secondary structure in yeast. by Kertesz, M. et. al. published in Nature 2010 Sep 2;467(7311):103-7. Abstract The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here we describe a novel strategy termed parallel analysis of […]






Development of a BACarray translational profiling approach for the molecular characterization of CNS cell types




Development of a BACarray translational profiling approach for the molecular characterization of CNS cell types by Myriam Heiman et. al. published in Cell, 2008 November 14; 135(4): 738–748. Abstract The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations. We have now developed a new ‘BACarray’ methodology, based […]