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Recent Posts
- Identifying the best PCR enzyme for library amplification in NGS
- Whole genome sequencing identifies associations for nonsyndromic sagittal craniosynostosis with the intergenic region of BMP2 and noncoding RNA gene LINC01428
- Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing
- In vitro size-selection of short circulating tumor DNA fragments from late-stage lung cancer patients enhance the detection of mutations and aneuploidies
- The haplotype-resolved T2T carnation (Dianthus caryophyllus) genome reveal the correlation between genome architecture and gene expression
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Author Archives: Alex
Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication
March 2017 Authors: Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, et al. Info: Scientists from China and the UK scanned the genomes of 352 varieties of cotton, both wild and domestic, to map variants associated with crop domestication throughout … more »
Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere
March 2017 Authors: Henk J. Schouten, Henri vande Geest, Sofia Papadimitriou, Marian Bemer, Jan G. Schaart, Marinus J. M. Smulders, Gabino Sanchez Perez, Elio Schijlen Info: Scientists from Wageningen University and Research sequenced and analyzed several Arabidopsis thaliana plants to … more »
Posted in Citation
Tagged BluePippin, PacBio
Comments Off on Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere
On DNA Day, Let’s Stop the Slicing and Dicing
Today is DNA Day, and we’re taking the opportunity to support the humane treatment of DNA. After all these years of harshly shearing these molecules and fragmenting them down to just a few hundred bases, can’t we agree that there … more »
At AACR, High-Profile Speakers and NGS Error Correction in the Spotlight
Last week’s annual meeting of the American Association for Cancer Research offered some great perspectives on innovation in oncology, both in the clinic and in academic labs. We were particularly impressed by former Vice President Joe Biden’s update on the … more »
Detecting DNA cytosine methylation using nanopore sequencing
February 2017 Authors: Jared Simpson, Rachael Workman, PC Zuzarte, Matei David, LJ Dursi & Winston Timp Info: In this paper, scientists report developing algorithms to distinguish methylated from unmethylated DNA using the Oxford Nanopore MinION sequencer. They evaluated its performance … more »
Posted in Citation
Tagged BluePippin, MinION, oxford nanopore
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Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone
February 2017 Authors: Adam D. Leaché, Jared A. Grummer, Rebecca B. Harris, and Ian K. Breckheimer Info: Scientists at the University of Washington analyzed samples collected over a 10-year period to better understand evolution of Sceloporus tristichus in a hybrid … more »
Posted in Citation
Tagged BluePippin
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Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution
February 2017 Authors: Gavin G. Rutledge, Ulrike Böhme, Mandy Sanders, Adam J. Reid, et al. Info: In this paper, scientists generated a new reference genome and a manually curated draft assembly for two Plasmodium species. This effort made it possible … more »
Posted in Citation
Tagged BluePippin, PacBio
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Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird
February 2017 Authors: Jennifer Walsh, Irby J. Lovette, Virginia Winder, Chris S. Elphick, Brian J. Olsen, Gregory Shriver, and Adrienne I. Kovach Info: Scientists at Cornell University and other institutions analyzed sparrow populations using reduced-representation sequencing to understand the genetic … more »
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Tagged BluePippin
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Small genomic insertions form enhancers that misregulate oncogenes
February 2017 Authors: Brian J. Abraham, Denes Hnisz, Abraham S. Weintraub, Nicholas Kwiatkowski, et al. Info: In this paper, scientists report using ChIP-seq to better understand the role of non-coding somatic insertions in tumorigenesis. They identified enhancer-associated small insertions, often … more »
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Tagged ChIP-Seq, HiSeq, Pippin Prep
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Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species
February 2017 Authors: Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick, Lúcia G. Lohmann Info: Scientists in Michigan and São Paulo, Brazil, performed ddRAD-seq on two separate populations of Amphirrhox longifolia to determine how many SNPs and organisms have … more »
Posted in Citation
Tagged ddRADseq, Pippin Prep
Comments Off on Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species