Category Archives: Citation

Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients

Posted on February 12, 2018 by Alex

January 2018 Authors: K. Nudel, X. Zhao, S. Basu, X. Dong, et al. Info: Scientists from Harvard Medical School and other institutions used whole genome sequencing and MALDI/TOF to analyze seven C. striatum infections, all resistant to multiple drugs. They … more »

Posted in Citation | Tagged , | Comments Off on Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients

Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

Posted on February 12, 2018 by Alex

January 2018 Authors: Dong An, Hieu X. Cao, Changsheng Li, Klaus Humbeck and Wenqin Wang Info: In this paper, researchers offer best practices for using the Iso-Seq method with PacBio sequencing to analyze plant transcriptomes. They recommend BluePippin for size … more »

Posted in Citation | Tagged , | Comments Off on Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly

Posted on February 12, 2018 by Alex

January 2018 Authors: Mun Hua Tan, Christopher Austin, Michael Hammer, Yin Peng Lee, Laurence Croft, Han Ming Gan Info: This paper presents the first hybrid genome assembly of Amphiprion ocellaris, the clown anemonefish. The team combined data from Illumina and … more »

Posted in Citation | Tagged , | Comments Off on Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly

Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers

Posted on February 12, 2018 by Alex

January 2018 Authors: Fabrice Touzain, Laetitia Le Devendec, Claire de Boisséson, Sandrine Baron, et al. Info: In this study of avian E. coli collected from slaughterhouses or diseased broilers, scientists analyzed resistance to extended-spectrum cephalosporins. Sequencing was performed with Illumina … more »

Posted in Citation | Tagged , | Comments Off on Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

Posted on January 4, 2018 by Alex

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 , | Comments Off on Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

Posted on December 10, 2017 by Alex

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 »

Posted in Citation | Tagged , | Comments Off on Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Posted on November 18, 2017 by Alex

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 , | Comments Off on Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

Posted on November 8, 2017 by Alex

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 , | 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

Posted on October 31, 2017 by Alex

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 , | Comments Off on De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

Posted on October 31, 2017 by Alex

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 »

Posted in Citation | Tagged | Comments Off on A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value