Author Archives: Alex

Scientists Compare PacBio, Oxford Nanopore Transcriptome Results

Posted on September 14, 2017 by Alex

We enjoy a good technology evaluation as much as the next scientist, particularly when it comes to sequencing. So we were quite interested in a recent F1000Research publication about long-read sequencing platforms from researchers at the University of Iowa, the … more »

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Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

Posted on September 8, 2017 by Alex

September 2017 Authors: Ben Niu and Roberto Kolter Info: Scientists from Harvard Medical School released the full genome sequences of seven bacterial species they chose for a model community to understand microbial effects on the growth of maize root. They … more »

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Podcast: Nanopore Expert Mark Akeson on Challenges and Opportunities in Sequencing

Posted on September 5, 2017 by Alex

Mark Akeson knows a thing or two about perseverance. After spending years as a soil biologist in Guatemala where he endured a series of parasite infections, he went on to become a pioneer in nanopore sequencing technology, which he has … more »

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A SINE insertion in ATP1B2 in Belgian Shepherd dogs affected by spongy degeneration with cerebellar ataxia (SDCA2)

Posted on August 18, 2017 by Alex

August 2017 Authors: Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, et al. Info: Scientists in Europe and the US studied the genetic basis for a neurodegenerative disorder in dogs. Through whole genome sequencing data, they found a SINE insertion … more »

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Nabsys Returns: CEO Barrett Bready on the Importance of Structural Variation

Posted on July 27, 2017 by Alex

A new podcast from Mendelspod features an interesting interview with Barrett Bready, CEO of electronic mapping firm Nabsys, who emphasizes the growing need to incorporate structural variation data into genome studies. In the discussion, Bready describes his company’s platform, which … more »

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Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

Posted on July 25, 2017 by Alex

August 2017 Authors: Albrecht V, Zweiniger C, Surendranath V, Lang K, et al. Info: Scientists in Germany describe a high-throughput approach for characterizing novel HLA alleles. The method involves sequencing the full gene with PacBio and MiSeq. For PacBio sequencing, … more »

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Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity

Posted on July 25, 2017 by Alex

July 2017 Authors: Kelley Yan, Olivier Gevaert, Grace Zheng, Benedict Anchang, et al. Info: In this project from scientists at Stanford University School of Medicine and other institutions, comparative RNA-seq was used to analyze putative mouse intestinal stem cells. The … more »

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Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice

Posted on July 25, 2017 by Alex

July 2017 Authors: Justin Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John Hoidal, and Namakkal Rajasekaran Info: Scientists from the University of Alabama at Birmingham and other institutions studied a gene previously associated with oxidative stress, analyzing differential expression in … more »

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ddRAD-seq Study Explores Behavioral Roles in Speciation

Posted on July 25, 2017 by Alex

A new preprint from the Hoekstra lab at Harvard makes great use of the double digest RAD-seq protocol to better understand reproductive barriers and speciation in closely related species of mice. Since it was the Hoekstra lab that gave us … more »

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Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

Posted on July 24, 2017 by Alex

July 2017 Authors: Qingshan Xu, Junyan Zhu, Shiqi Zhao, Yan Hou, et al. Info: Scientists from Anhui Agricultural University in China performed long-read transcriptome sequencing of the tea plant Camellia sinensis to better understand its production of flavonoids, theanine, and … more »

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