Results 1 to 10 of about 1,873,067 (319)

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

npj Science of Food, 2021
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal ...
Kristen L. Beck, Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, B. Carol Huang, Nguyet Kong, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Ban Kawas, Matthew Davis, Robert J. Prill, Harsha Krishnareddy, Ed Seabolt, Carl H. Marlowe, Sophie Pierre, André Quintanar, Laxmi Parida, Geraud Dubois, James Kaufman, Bart C. Weimer   +21 more
doaj   +1 more source

Epitachophoresis is a novel versatile total nucleic acid extraction method

Scientific Reports, 2021
Epitachophoresis is a novel next generation extraction system capable of isolating DNA and RNA simultaneously from clinically relevant samples. Here we build on the versatility of Epitachophoresis by extracting diverse nucleic acids ranging in lengths ...
Vladimira Datinska, Pantea Gheibi, Keynttisha Jefferson, Jaeyoung Yang, Sri Paladugu, Carolina Dallett, Ivona Voracova, Frantisek Foret, Yann Astier   +8 more
doaj   +1 more source

Truvari: refined structural variant comparison preserves allelic diversity

Genome Biology, 2022
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same.
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

Unraveling the salt tolerance of Phi29 DNA polymerase using compartmentalized self-replication and microfluidics platform

Frontiers in Microbiology, 2023
In Phi29-α–hemolysin (α-HL) nanopore sequencing systems, a strong electrochemical signal is dependent on a high concentration of salt. However, high salt concentrations adversely affect polymerase activity.
Yaping Sun, Danny Hsu Ko, Jie Gao, Kang Fu, Yaping Gao, Qiwen Zhang, Salem Baldi, Tao Hong, Igor Ivanov, Yun He, Hui Tian   +10 more
doaj   +1 more source

Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates

BMC Evolutionary Biology, 2020
Background Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families.
R. Alan Harris, Muthuswamy Raveendran, Kim C. Worley, Jeffrey Rogers   +3 more
doaj   +1 more source

PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation

Genome Biology, 2021
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive ...
Medhat Mahmoud, Harshavardhan Doddapaneni, Winston Timp, Fritz J. Sedlazeck   +3 more
doaj   +1 more source

Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation

Genome Biology, 2023
Background Systematic characterization of how  genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits.
Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li, Rui Chen   +10 more
doaj   +1 more source

Genomic variant benchmark: if you cannot measure it, you cannot improve it

Genome Biology, 2023
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges.
Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J. Sedlazeck, Medhat Mahmoud   +4 more
doaj   +1 more source

Deep convolutional neural networks for accurate somatic mutation detection

Nature Communications, 2019
Somatic mutations are crucial to the understanding of cancer genesis, progression, and treatment, but are still challenging to detect. Here the authors present NeuSomatic, a convolutional neural network approach for accurate somatic mutation detection ...
Sayed Mohammad Ebrahim Sahraeian, Ruolin Liu, Bayo Lau, Karl Podesta, Marghoob Mohiyuddin, Hugo Y. K. Lam   +5 more
doaj   +1 more source

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads

BMC Genomics, 2017
Background Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing.
Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski, Richard A. Gibbs   +10 more
doaj   +1 more source