Article
Biochemistry & Molecular Biology
Christos Tzaferis, Evangelos Karatzas, Fotis A. Baltoumas, Georgios A. Pavlopoulos, George Kollias, Dimitris Konstantopoulos
Summary: Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell resolution remain challenges in the biomedical field. SCALA is a bioinformatics tool for analyzing and visualizing single-cell RNA sequencing and Assay for Transposase-Accessible Chromatin using sequencing data-sets. It offers independent or integrative analysis options and various analysis modules to aid biomedical researchers in exploring, analyzing, and visualizing their data without coding experience.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Review
Biochemical Research Methods
Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky
Summary: Advancements in next-generation sequencing have enabled detailed assessment of viral population complexity within hosts, extracting crucial epidemiological and biomedical information. However, the complex analysis of NGS data is required to handle the rapidly mutating viral populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Ping Zhang, Min Wang, Tao Zhou, Daozhen Chen
Summary: SeqWiz is a state-of-the-art toolkit for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. It introduces two derived data formats, SQPD and SET, which outperform traditional FASTA or PEFF formats in terms of time and resource consumption. SeqWiz also provides compatible functions for handling traditional text formats and can promote the implementation of complementary proteomics for precision proteomics.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Interdisciplinary Applications
Simon Foll, Martin Maritsch, Federica Spinola, Varun Mishra, Filipe Barata, Tobias Kowatsch, Elgar Fleisch, Felix Wortmann
Summary: Researchers use wearable sensing data and machine learning models to predict health and behavioral outcomes, but data from commercial wearables often contain noise and artifacts. FLIRT is an open-source Python package that focuses on processing physiological data from commercial wearables, utilizing state-of-the-art algorithms for robust preprocessing and generating standardized feature vectors to improve reproducibility and performance in classification tasks.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2021)
Article
Biochemical Research Methods
Rasmus Amund Henriksen, Lei Zhao, Thorfinn Sand Korneliussen
Summary: This article presents a multithreaded simulator for next-generation sequencing data, which can simulate reads faster than currently available methods and programs. It can simulate reads with platform-specific characteristics based on nucleotide quality score profiles and includes a post-mortem damage model for simulating ancient DNA. The program is implemented in a multithreading framework and is significantly faster than currently available tools, while also offering additional features and output formats.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Review
Public, Environmental & Occupational Health
Yulian Li, Wentao Bian, Shiping Wu, Jie Zhang, Dan Li
Summary: This meta-analysis evaluated the performance of mNGS in diagnosing tuberculosis and found that it has high sensitivity and can rapidly diagnose Mycobacterium tuberculosis. Various factors, such as sample types, study types, and sample sizes, may contribute to heterogeneity. In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Article
Medical Laboratory Technology
Xiaohua Fang, Chaofeng Zhu, Xiaofan Zhu, Yin Feng, Zhihui Jiao, Huikun Duan, Xiangdong Kong, Ning Liu
Summary: This study evaluated gene variations in Chinese MPS patients using targeted NGS technology and identified 11 novel variants associated with disease. MPS II was found to be the most common type in China. The study expands the variation spectrum of MPS, which is important for disease management and genetic counseling.
CLINICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Leszek P. Pryszcz, Eva Maria Novoa
Summary: ModPhred is a versatile toolkit for DNA and RNA modification analysis from nanopore sequencing reads. It integrates modification information within file formats and allows for simple and efficient visualization and analysis.
Editorial Material
Oncology
Jun Li, Hu Chen, Yumeng Wang, Mei-Ju May Chen, Han Liang
Summary: DrBioRight, a natural language-oriented and artificial intelligence-driven analytics platform, allows the research community to analyze omics data in an intuitive, efficient, transparent, and collaborative manner. The emerging next-generation analytics will maximize the utility of omics data and lead to a new paradigm for biomedical research.
Article
Genetics & Heredity
Manal Alaamery, Jahad Alghamdi, Salam Massadeh, Mona Alsawaji, Nora Aljawini, Nour Albesher, Bader Alghamdi, Mansour Almutairi, Fayez Hejaili, Majid Alfadhel, Batoul Baz, Bader Almuzzaini, Adel F. Almutairi, Mubarak Abdullah, Francisco J. Quintana, Abdullah Sayyari
Summary: This study aimed to investigate the genetic causes of end-stage renal disease (ESRD) in Saudi kidney disease patients, using a targeted next-generation sequencing gene panel. The results identified several genetic variants associated with ESRD and CKD in this population, including novel variants not previously reported in other populations. Further studies are needed to validate these findings in larger sample sizes and different ethnic groups.
FRONTIERS IN GENETICS
(2022)