Author Archives: Alex

Genome-wide identification of enhancer elements

Posted on August 1, 2016 by Alex

June 2016 Authors: Sarah Tulin, Julius C. Barsi, Carlo Bocconcelli, and Joel Smith Info: The authors (from Woods Hole and Cal Tech) present a genome-wide regulatory element database for the sea urchin embryo. To do this, they developed a new … more »

Posted in Citation | Tagged , , , , | Comments Off on Genome-wide identification of enhancer elements

PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer

Posted on August 1, 2016 by Alex

June 2016 Authors: Jennifer M. Spangle, Koen M. Dreijerink, Anna C. Groner, Hailing Cheng, Carolynn E. Ohlson, Jaime Reyes, Charles Y. Lin, James Bradner, Jean J. Zhao, Thomas M. Roberts, and Myles Brown Info: In this breast cancer research study, … more »

Posted in Citation | Tagged , , | Comments Off on PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer

Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing

Posted on July 31, 2016 by Alex

June 2016 Authors: Shruthi Sridhar Vembar, Matthew Seetin, Christine Lambert, Maria Nattestad, Michael C. Schatz, Primo Baybayan, Artur Scherf, and Melissa Laird Smith Info: Scientists in France and the US used PacBio sequencing to characterize the AT-rich genome of this … more »

Posted in Citation | Tagged , , | Comments Off on Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing

A survey of the sorghum transcriptome using single-molecule long reads

Posted on July 31, 2016 by Alex

June 2016 Authors: Salah E. Abdel-Ghany, Michael Hamilton, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur & Anireddy S. N. Reddy Info: In this publication, scientists from Colorado State University and the National Center for Genome Resources … more »

Posted in Citation | Tagged , , , , | Comments Off on A survey of the sorghum transcriptome using single-molecule long reads

PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors

Posted on July 27, 2016 by Alex

Scientists at the University of Oregon have published a new method to detect PCR and sequencing errors that should help other researchers track rare SNPs with greater accuracy. PELE-seq, which gets our vote for best new protocol name, can be … more »

Posted in Blog | Tagged , , , , , | Comments Off on PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors

High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

Posted on July 27, 2016 by Alex

June 2016 Authors: Jessica L. Preston, Ariel E. Royall, Melissa A. Randel, Kristin L. Sikkink, Patrick C. Phillips, and Eric A. Johnson Info: Scientists at the University of Oregon developed a new protocol to reduce sequencing and PCR errors, resulting … more »

Posted in Citation | Comments Off on High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

Low-Coverage Sequencing No Challenge for Structural Variant Detection

Posted on July 21, 2016 by Alex

Is it really possible to detect somatic structural variants accurately from a single sequencing read? A new protocol from scientists at the Albert Einstein College of Medicine in New York and Voronezh State University in Russia was designed to do … more »

Posted in Blog | Tagged , | Comments Off on Low-Coverage Sequencing No Challenge for Structural Variant Detection

Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing

Posted on July 21, 2016 by Alex

June 2016 Authors: Wilber Quispe-Tintaya, Tatyana Gorbacheva, Moonsook Lee, Sergei Makhortov, Vasily N Popov, Jan Vijg & Alexander Y Maslov Info: Scientists report Structural Variant Search, a new method for detecting rare somatic structural variants even with low-coverage sequencing data. … more »

Posted in Citation | Tagged | Comments Off on Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing

Sage Sizing Platforms Recommended for 10x Genomics Libraries

Posted on July 18, 2016 by Alex

We’re pleased to report that 10x Genomics has released a new sample prep protocol for its Chromium platform that includes the BluePippin and PippinHT size selection platforms from Sage Science. 10x Genomics has gotten a lot of attention in recent … more »

Posted in Blog | Tagged , , | Comments Off on Sage Sizing Platforms Recommended for 10x Genomics Libraries

Double Pippin for Optimized RAD-seq

Posted on July 13, 2016 by Alex

Scientists in China and the UK recently published an open-access optimized protocol for RAD-seq in the Theoretical and Applied Genetics journal. The method is targeted at large studies of plants and enables users to specify sequence coverage parameters. From lead … more »

Posted in Blog | Tagged , , , , | Comments Off on Double Pippin for Optimized RAD-seq