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 […]






Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling




Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling by Nicholas T. Ingolia et. al. published in Science. 2009 April 10; 324(5924): 218–223. Abstract Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the […]






An Oestrogen Receptor α-bound Human Chromatin Interactome




An Oestrogen Receptor α-bound Human Chromatin Interactome by Melissa J. Fullwood et. al. published in Nature. 2009 November 5; 462(7269): 58–64. Abstract Genomes are organized into high-level 3-dimensional structures, and DNA elements separated by long genomic distances could functionally interact. Many transcription factors bind to regulatory DNA elements distant from gene promoters. While distal binding […]






Comprehensive mapping of long range interactions reveals folding principles of the human genome




Comprehensive mapping of long range interactions reveals folding principles of the human genome by Erez Lieberman-Aiden et. al. Science, 2009 October 9; 326(5950): 289–293. Abstract We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome […]






Nascent transcript sequencing visualizes transcription at nucleotide resolution




Nascent transcript sequencing visualizes transcription at nucleotide resolution by L. Stirling Churchman & Jonathan S. Weissman published in Nature 469, 368–373 (20 January 2011). Abstract Recent studies of transcription have revealed a level of complexity not previously appreciated even a few years ago, both in the intricate use of post-initiation control and the mass production […]