Le, Nguyen Quoc Khanh Do, Duyen Thi Hung, Truong Nguyen Khanh Lam, Luu Ho Thanh Huynh, Tuan-Tu Nguyen, Ngan Thi Kim
Published in
International journal of molecular sciences
Essential genes contain key information of genomes that could be the key to a comprehensive understanding of life and evolution. Because of their importance, studies of essential genes have been considered a crucial problem in computational biology. Computational methods for identifying essential genes have become increasingly popular to reduce the...
Hsieh, Ming-Feng Lu, Chin Lung Tang, Chuan Yi
Published in
BMC Bioinformatics
BackgroundNext-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the ...
Anandakrishnan, Ramu Carpenetti, Tiffany L. Samuel, Peter Wasko, Breezy Johnson, Craig Smith, Christy Kim, Jessica Michalak, Pawel Kang, Lin Kinney, Nick
...
Published in
BMC Medical Education
BackgroundMedical treatment informed by Precision Medicine is becoming a standard practice for many diseases, and patients are curious about the consequences of genomic variants in their genome. However, most medical students’ understanding of Precision Medicine derives from classroom lectures. This format does little to foster an understanding for...
Manderstedt, Eric Lind-Halldén, Christina Lethagen, Stefan Halldén, Christer
Published in
TH Open: Companion Journal to Thrombosis and Haemostasis
Genome-wide association studies (GWASs) have identified genes that affect plasma von Willebrand factor (VWF) levels. ABO showed a strong effect, whereas smaller effects were seen for VWF , STXBP5 , STAB2 , SCARA5 , STX2 , TC2N , and CLEC4M . This study screened comprehensively for both common and rare variants in these eight genes by resequencing t...
Trevino, Cristina E. Holleman, Aaron M. Corbitt, Holly Maslen, Cheryl L. Rosser, Tracie C. Cutler, David J. Johnston, H. Richard Rambo-Martin, Benjamin L. Oberoi, Jai Dooley, Kenneth J.
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Published in
Scientific Reports
Atrioventricular septal defects (AVSD) are a severe congenital heart defect present in individuals with Down syndrome (DS) at a > 2000-fold increased prevalence compared to the general population. This study aimed to identify risk-associated genes and pathways and to examine a potential polygenic contribution to AVSD in DS. We analyzed a total coho...
Lee, Howon Wiegand, Daniel J. Griswold, Kettner Punthambaker, Sukanya Chun, Honggu Kohman, Richie E. Church, George M.
Published in
Nature Communications
Writing data in DNA is still a bottleneck due to the reliance on chemical synthesis methods. Here the authors report multiplexed enzymatic DNA synthesis using maskless photolithography.
Whalley, Justin P. Buchhalter, Ivo Rheinbay, Esther Raine, Keiran M. Stobbe, Miranda D. Kleinheinz, Kortine Werner, Johannes Beltran, Sergi Gut, Marta Hübschmann, Daniel
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Published in
Nature Communications
Working with cancer genomes from multiple projects can increase investigative power, but quality of sequences can vary. Here, the authors present a framework for comparing whole genome sequencing quality to help researchers guide downstream analyses and exclude poor quality samples.
Paruch, Lisa Paruch, Adam M. Eiken, Hans Geir Skogen, Monica Sørheim, Roald
Published in
Scientific Reports
Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial comm...
Walker, Sidney P. Barrett, Maurice Hogan, Glenn Flores Bueso, Yensi Claesson, Marcus J. Tangney, Mark
Published in
Scientific Reports
The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to ...
Samarakoon, Hiruna Punchihewa, Sanoj Senanayake, Anjana Hammond, Jillian M. Stevanovski, Igor Ferguson, James M. Ragel, Roshan Gamaarachchi, Hasindu Deveson, Ira W.
Published in
Communications Biology
Samarakoon et al. present Genopo, a portable toolkit for analysis of nanopore sequencing data on Android smartphone and tablet devices. Genopo enables field-based nanopore analysis using widely accessible technology.
