Article
Microbiology
A. E. Roder, K. E. E. Johnson, M. Knoll, M. Khalfan, B. Wang, S. Schultz-Cherry, S. Banakis, A. Kreitman, C. Mederos, J. -H. Youn, R. Mercado, W. Wang, M. Chung, D. Ruchnewitz, M. I. Samanovic, M. J. Mulligan, M. Laessig, M. Luksza, S. Das, D. Gresham, E. Ghedin
Summary: High error rates in viral RNA-dependent RNA polymerases result in diverse populations of viruses within infected hosts. However, detecting minority variants in viral sequence data is challenging due to errors introduced during sample preparation and analysis. This study evaluated seven variant-calling tools using synthetic RNA controls and simulated data. The choice of variant caller and the use of replicate sequencing were found to have the greatest impact on single-nucleotide variant (SNV) discovery. The study provides guidance on identifying minority variants in SARS-CoV-2 clinical specimens and establishes heuristics for future studies on viral diversity and evolution.
Article
Virology
Patrick Davis, Donald Seto, Padmanabhan Mahadevan
Summary: CoreGenes5.0 is an updated and user-friendly web-based software tool for the identification of core genes and data mining in viral and bacterial genomes. It has been useful in resolving issues in bacteriophage taxonomic analysis and provides easy analysis of custom or proprietary datasets.
Article
Biochemistry & Molecular Biology
Robert Literman, Rachel Schwartz
Summary: Despite whole-genome sequencing data, evolutionary relationships remain controversial due to challenges in accurately modeling complex phylogenetic signals. Noncoding sequence sites provide more data and proportionally more concordant sites compared to coding sequences, which are also predominant drivers of tree incongruence.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Information Systems
Nephi A. Walton, Radha Nagarajan, Chen Wang, Murat Sincan, Robert R. Freimuth, David B. Everman, Derek C. Walton, Scott P. Mcgrath, Dominick J. Lemas, Panayiotis Benos, Alexander Alekseyenko, Qianqian Song, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
Summary: Substantial informatics research and development are needed to fully realize the clinical potential of AI in genomics. Developing larger datasets is crucial for emulating the success of AI in other domains. It is important to ensure that AI methods do not worsen existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical for effectively scaling such technologies across institutions. The current focus should be on using these technologies in collaboration with clinicians, highlighting their value in clinical decision-making.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Daniel Tello, Laura Natalia Gonzalez-Garcia, Jorge Gomez, Juan Camilo Zuluaga-Monares, Rogelio Garcia, Ricardo Angel, Daniel Mahecha, Erick Duarte, Maria del Rosario Leon, Fernando Reyes, Camilo Escobar-Velasquez, Mario Linares-Vasquez, Nicolas Cardozo, Jorge Duitama
Summary: The article introduces the latest functionalities implemented in NGSEP 4 for identifying orthogroups and conducting whole genome alignments. NGSEP 4 also includes a new graphical user interface based on JavaFX technology. These new developments are expected to be very useful for studies in evolutionary biology and population genomics.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Mariana Lenharo
Summary: The most popular platform for sharing SARS-CoV-2 sequence data has faced criticism for governance issues, and scientists need to determine the next steps.
Article
Biology
Raphael Meheust, Cindy J. Castelle, Alexander L. Jaffe, Jillian F. Banfield
Summary: Archaea play important roles in the environment, and recent genomic analyses have provided new insights into their distribution and functionalities. This study identified representative genomes of Archaea and analyzed the co-occurring proteins that distinguish major lineages. The results highlighted the presence of new eukaryotic signature proteins in Asgard and the dominance of hypothetical proteins in lineage-specific families.
Article
Virology
Vincent Wilde, Bruno Canard, Francois Ferron
Summary: The appearance of genetic variants affects vaccination efficiency and treatment options, necessitating the mapping and correlation of observed mutations in the proteome and genome. We have developed an user-friendly web service software called Viral Instant Mutation Viewer (VIMVer), which enables direct identification of mutations in the genome and corresponding viral proteome. Since its emergence in 2019, the SARS-CoV-2 virus responsible for the COVID-19 pandemic has produced a vast amount of data, making it one of the most extensively studied viruses in the Nidovirales order. Our tool allows for rapid identification, mapping, and display of new mutations at the nucleotide and amino acid level compared to a reference sequence (Wuhan-1) for any SARS-CoV-2 nucleotide sequence. Additionally, the web service provides information on the lineage or relative position of the variant of interest through a link to the Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow is available online and the source code is released under a public license, allowing for easy adaptation for further development on other viruses.
Article
Biochemistry & Molecular Biology
Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
Summary: The Pop-Gen Pipeline Platform (PPP) is an open-source software platform designed for population genomic analyses in a consistent and standardized Python environment. The platform encompasses entire workflows for input preparation, file format conversion, various population genomic analyses, and output generation, with reproducibility and extensibility in mind. Users can download and use PPP at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Oncology
Christopher P. Wardell, Emilie Darrigues, Annick De Loose, Madison P. Lee, Murat Gokden, Issam Makhoul, Alan J. Tackett, Analiz Rodriguez
Summary: Brain metastases are the most common brain tumors in adults, with most mutations occurring before metastasis and a specific copy number event identified. Melanoma BMs show distinct characteristics compared to other subtypes, and poor survival is associated with race and treatment options.
Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Silong Jiang, Qiaoxiu Yin, Dongxue Li, Xian Wu, Yong Wang, Delu Wang, Zhuo Chen
Summary: Lasiodiplodia theobromae is a phytopathogenic fungus that causes leaf spot on tea plants in Guizhou Province, China, impacting tea productivity and quality. This study presents high-quality transcriptome and small RNA sequences of L. theobromae under in vitro conditions and during tea leaf infection, offering insights for future research on pathogen-specific genes, host-pathogen interactions, and disease resistance.
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Editorial Material
Multidisciplinary Sciences
Sergei L. Kosakovsky Pond, Darren Martin
Summary: Molnupiravir, an antiviral drug for COVID-19, can cause multiple mutations in the SARS-CoV-2 genome, potentially accelerating the evolution and transmission of viral variants.
Article
Immunology
Yao Wang, Hao Zhuang, Xiao-han Jiang, Rui-han Zou, Hai-yang Wang, Zhi-ning Fan
Summary: Using WGCNA and random forest algorithm, this study identified nine gene signatures associated with the exacerbation of Ulcerative colitis (UC). A novel genotyping scheme was constructed to predict the severity of UC and screen UC patients suitable for CS-IV treatment. Furthermore, a small molecule drug (Exisulind) with potential therapeutic effects for UC was identified, providing new ideas and materials for personalized clinical treatment plans for UC patients.
FRONTIERS IN IMMUNOLOGY
(2023)
