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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
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads
December 2017 Authors: Yi-Jyun Luo, Miyuki Kanda, Ryo Koyanagi, Kanako Hisata, et al. Info: Scientists from the Okinawa Institute of Science and Technology Graduate University and Okayama University in Japan generated draft genomes and transcriptomes of ribbon worms and horseshoe … more »
Posted in Citation
Tagged BluePippin, SageELF
Comments Off on Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads
A Look Back at 2017
As we start to make lists of New Year’s resolutions (with bets on how long they’ll last), it’s the perfect time for a moment to absorb the themes and highlights of 2017. In our corner of the world, that means … more »
Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
December 2017 Authors: Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, et al. Info: Scientists at Erasmus Medical Center determined that analysis of genome-wide methylation is challenging when fragment sizes are too small and that better epigenetic results are … more »
Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses
We always keep our eyes peeled for interesting new research from scientists using Sage Science automated DNA size selection instruments, and several recent preprints caught our attention. Here’s a look: Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome … more »
Posted in Blog
Tagged BluePippin, ddRADseq, ONT, PacBio
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Mapping and phasing of structural variation in patient genomes using nanopore sequencing
November 2017 Authors: Mircea Cretu Stancu, Markus van Roosmalen, Ivo Renkens, Marleen Nieboer, et al. Info: Scientists used the Oxford MinION nanopore sequencer with a novel pipeline, NanoSV, to detect structural variants from the genomes of two patients. They found … more »
Posted in Citation
Tagged oxford nanopore, PippinHT
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Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
November 2017 Authors: Bing Cheng, Agnelo Furtado, Robert Henry Info: In this study, researchers generated the transcriptome of the tetraploid Arabica coffee bean, focusing on caffeine and sucrose genes for in-depth analysis. They used the PacBio Iso-Seq method with BluePippin … more »
Posted in Citation
Tagged BluePippin, PacBio
Comments Off on Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
October 2017 Authors: Maximilian Schmidt, Alxander Vogel, Alisandra Denton, Benjamin Istace, et al. Info: Scientists used Oxford Nanopore technology to sequence Solanum pennellii, a wild species of tomato. They generated a median read length of nearly 12 Kb and produced … more »
Posted in Citation
Tagged BluePippin, ONT
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Podcast: Genome Assembly Guru Deanna Church on Linked Reads and Single-Cell Genomics
If you’ve ever relied on the human reference genome, don’t miss this podcast with assembly pioneer Deanna Church. Mendelspod’s Theral Timpson interviews the genome informatics expert who made her name as an integral part of the reference project at the … more »
Posted in Blog
Tagged 10x Genomics, podcast
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A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
October 2017 Authors: Changsong Zou, Aojun Chen, Lihong Xiao, Heike Muller, et al. Info: Scientists deployed several sequencing platforms to characterize the genome of Chenopodium quinoa, an important and highly nutritious cereal crop. They analyzed the assembly to better understand … more »
Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify
October 2017 Authors: Malgorzata Komor, Thang Pham, Annemieke Hiemstra, Sander Piersma, et al. Info: In this paper, scientists from the Netherlands Cancer Institute, VU University Medical Center, and other institutions describe results from a new pipeline to detect differentially expressed … more »