Category Archives: Citation

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

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

Posted on October 30, 2017 by Alex

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 »

Posted in Citation | Tagged , | Comments Off on Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience

Posted on October 30, 2017 by Alex

October 2017 Authors: Manish Gandhi, Deborah Ferriola, Curt Lind, Jamie Duke, et al. Info: Scientists from the Mayo Clinic, Children’s Hospital of Philadelphia, and other institutions teamed up to develop a streamlined, NGS-based HLA typing protocol. This method uses the … more »

Posted in Citation | Tagged , , | Comments Off on Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience

Comprehensive Transcriptome Profiling of Balding and Non-Balding Scalps in Trichorhinophalangeal Syndrome Type I Patient

Posted on October 30, 2017 by Alex

October 2017 Authors: Yun-Ji Kim, Byulee Yoon, Kyudong Han, Byung Cheol Park Info: Scientists in Korea compared transcriptomes of RNA extracted from balding and non-balding scalp regions on the same patient to understand the genetics of hair loss. They found … more »

Posted in Citation | Tagged , , | Comments Off on Comprehensive Transcriptome Profiling of Balding and Non-Balding Scalps in Trichorhinophalangeal Syndrome Type I Patient

Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

Posted on October 25, 2017 by Alex

October 2017 Authors: Antonio Charlys da Costa, Julien Thézé, Shirley Cavalcante Vasconcelos Komninakis, Rodrigo Lopes Sanz-Duro, et al. Info: Scientists in Brazil and collaborators in the U.S. and Europe traced the transmission path of a recent chikungunya virus outbreak. They … more »

Posted in Citation | Tagged , | Comments Off on Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex

Posted on September 20, 2017 by Alex

September 2017 Authors: James Bennett and Paula Keeney Info: Scientists from Neurodegeneration Therapeutics used RNA-seq to compare microRNAs found in Alzheimer’s brain samples and controls. They identified 55 up-regulated genes and 191 down-regulated genes in the Alzheimer’s samples. PippinHT was … more »

Posted in Citation | Tagged , | Comments Off on Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex