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 […]






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 […]






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 […]






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 […]