Article
Biochemical Research Methods
Matthias Zytnicki, Christine Gaspin
Summary: This study introduces a new tool, srnaMapper, for the comprehensive mapping of short RNAs, considering their unique features. The tool is efficient in terms of computation time and error handling.
BMC BIOINFORMATICS
(2022)
Article
Microbiology
Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis, Tuval Ben Yehezkel
Summary: LoopSeq is a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads, enabling direct identification of microbial genes and species in complex samples. Compared to standard Illumina amplicon sequencing, LoopSeq offers an order-of-magnitude improvement in length and accuracy, allowing accurate identification of species and strains from complex to low-biomass microbiome samples.
Article
Biotechnology & Applied Microbiology
Fatih Karaoglanoglu, Cedric Chauve, Faraz Hach
Summary: Genion is a sensitive and fast gene fusion detection method that accurately identifies gene fusions in both simulated and real datasets, with better clustering accuracy than other methods. In the breast cancer cell line MCF-7, Genion correctly identifies all experimentally validated gene fusions.
Article
Biochemistry & Molecular Biology
Zilong Li, Jonas Meisner, Anders Albrechtsen
Summary: Principal component analysis (PCA) is widely used for dimensionality reduction and uncovering latent structure in statistics, machine learning, and genomics. To address the challenges of ever-growing data, this paper proposes a novel algorithm called PCAone, which achieves fast and memory-efficient PCA and outperforms existing methods in comprehensive evaluations using multiple large-scale real-world datasets.
Article
Biochemistry & Molecular Biology
Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Summary: DNA sequencing data are improving in terms of longer reads and lower error rates. In this paper, a novel strategy called mapquik is introduced, which creates accurate longer reads by anchoring alignments through matches of consecutively sampled minimizers. Mapquik significantly accelerates the seeding and chaining steps in read mapping, achieving high sensitivity and ultrafast mapping. The results show that mapquik outperforms the state-of-the-art tool minimap2 in terms of speed and accuracy.
Article
Biochemical Research Methods
E. Sacristan-Horcajada, S. Gonzalez-de la Fuente, R. Peiro-Pastor, F. Carrasco-Ramiro, R. Amils, J. M. Requena, J. Berenguer, B. Aguado
Summary: Researchers have developed a NGS long-reads indels correction pipeline called ARAMIS, which combines multiple correction software in one step using accurate short reads to address insertions and deletions errors in long-read sequencing. The study found systematic sequencing errors in PacBio sequences affecting homopolymeric regions, and that the type of indel errors introduced during PacBio sequencing are related to the GC content of the organism.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jamshed Khan, Rob Patro
Summary: The study introduces a novel algorithm, Cuttlefish, for constructing the (colored) compacted de Bruijn graph from a collection of genome references. Cuttlefish models de Bruijn graph vertices as finite-state automata and tracks transitioning states with low memory usage. Experimental results show that Cuttlefish scales better and performs faster compared to existing approaches when dealing with a larger number and scale of input references.
Article
Biochemical Research Methods
Wen Yang, Lusheng Wang
Summary: For DNA sequence analysis, the challenge lies in the short length of sequencing reads, which can be addressed by utilizing long reads. By designing new mapping and local alignment algorithms, this study showed improved alignments for Nanopore and SMRT data sets. The new method successfully aligned a higher percentage of letters from reads to reference genomes, compared to the best known method, while also achieving faster performance.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Computer Science, Theory & Methods
Kun Li, Liang Yuan, Yunquan Zhang, Gongwei Chen
Summary: In this article, a novel data structure is proposed to capture the most important information among data samples, supporting a hierarchical clustering strategy. A parallel library that combines clustering and regression techniques is utilized to accelerate computation and improve accuracy.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Article
Computer Science, Interdisciplinary Applications
Yong Wang, Qian Zhang, Gai-Ge Wang, Zhongyi Hu
Summary: This study proposes an improved many-objective evolutionary algorithm called 1by1EA-CHV, which achieves better performance in solving large-scale optimization problems by using circle chaotic mapping and a solution ranking mechanism based on the hypervolume indicator.
JOURNAL OF COMPUTATIONAL DESIGN AND ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Warodom Wirojsirasak, Patcharin Songsri, Nakorn Jongrungklang, Sithichoke Tangphatsornruang, Peeraya Klomsa-ard, Kittipat Ukoskit
Summary: In this study, a large-scale candidate gene association analysis was conducted to identify genetic variants underlying drought tolerance in sugarcane. The results revealed several marker-trait associations (MTAs) in candidate genes related to physiological adaptation, phytohormone metabolism, and drought-inducible genes. These findings provide valuable genetic and genomic resources for improving drought tolerance in sugarcane.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Sau-Dan Lee, Man Wu, Kwok-Wai Lo, Kevin Y. Yip
Summary: In this study, a pipeline called ASPIRE is proposed for accurately reconstructing viral genomes from short reads data of human samples. ASPIRE improves the quality of the reconstructed genomes through additional components such as iterative refinement and sequence corrections, especially for samples with significant differences from the reference genome.
Article
Genetics & Heredity
Ze-Gang Wei, Xing-Guo Fan, Hao Zhang, Xiao-Dan Zhang, Fei Liu, Yu Qian, Shao-Wu Zhang
Summary: In this paper, a novel mapper called kngMap is introduced for aligning long noisy SMS reads to a reference sequence using a k-mer neighborhood graph. Experimental results show that kngMap has higher sensitivity and can produce consecutive alignments for the whole read.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Jingjie Jin, Zixi Chen, Jinchao Liu, Hongli Du, Gong Zhang
Summary: Accurate and robust somatic mutation detection is crucial for cancer treatment and research. This study compared five commonly-used somatic mutation calling pipelines and evaluated their precision, recall, and speed. The results showed high accuracy and recall rate for all pipelines in cases with high mutation rates. However, there were significant differences among the pipelines for low frequency mutations, with FANSe performing the best. The flaws in filter were identified as the major cause of low sensitivity in the other pipelines. In terms of speed, FANSe pipeline was much faster than the others, with a speed advantage of 8.8 to 19 times. These benchmarking results provide valuable insights for choosing appropriate somatic mutation calling pipelines in cancer applications.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Rounak Dey, Wei Zhou, Tuomo Kiiskinen, Aki Havulinna, Amanda Elliott, Juha Karjalainen, Mitja Kurki, Ashley Qin, Seunggeun Lee, Aarno Palotie, Benjamin Neale, Mark Daly, Xihong Lin
Summary: With the analysis of large biobanks, this study proposes an efficient and accurate method for genome-wide survival association analysis. The method accounts for population structure and relatedness and utilizes advanced optimization strategies to reduce computational cost. Simulation studies and real data analysis demonstrate the performance of the method.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Jing Zhao, Bo Qin, Rainer Nikolay, Christian M. T. Spahn, Gong Zhang
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Biotechnology & Applied Microbiology
Xihao Liao, Jing Zhao, Shuli Liang, Jingjie Jin, Cheng Li, Ruiming Xiao, Lu Li, Meijin Guo, Gong Zhang, Ying Lin
BIOTECHNOLOGY FOR BIOFUELS
(2019)
Editorial Material
Parasitology
Sebastian Kirchner, Andrew P. Waters
TRENDS IN PARASITOLOGY
(2019)
Article
Multidisciplinary Sciences
Lei Gao, Yong Hu, Yahui Tian, Zhenzhen Fan, Kun Wang, Hongdan Li, Qian Zhou, Guandi Zeng, Xin Hu, Lei Yu, Shiyu Zhou, Xinyuan Tong, Hsinyi Huang, Haiquan Chen, Qingsong Liu, Wanting Liu, Gong Zhang, Musheng Zeng, Guangbiao Zhou, Qingyu He, Hongbin Ji, Liang Chen
NATURE COMMUNICATIONS
(2019)
Article
Genetics & Heredity
Jing Zhao, Hong Zhang, Bo Qin, Rainer Nikolay, Qing-Yu He, Christian M. T. Spahn, Gong Zhang
FRONTIERS IN GENETICS
(2019)
Article
Microbiology
Tianyuan Shi, Qiuxia Wei, Zhen Wang, Gong Zhang, Xuesong Sun, Qing-Yu He
Article
Genetics & Heredity
Zhibiao Mai, Wanting Liu, Wen Ding, Gong Zhang
Article
Biochemistry & Molecular Biology
Shaohua Lu, Jing Zhang, Xinlei Lian, Li Sun, Kun Meng, Yang Chen, Zhenghua Sun, Xingfeng Yin, Yaxing Li, Jing Zhao, Tong Wang, Gong Zhang, Qing-Yu He
NUCLEIC ACIDS RESEARCH
(2019)
Article
Respiratory System
Giovana B. Bampi, Robert Rauscher, Sebastian Kirchner, Kathryn E. Oliver, Marcel J. C. Bijvelds, Leonardo A. Santos, Johannes Wagner, Raymond A. Frizzell, Hugo R. de Jonge, Eric J. Sorscher, Zoya Ignatova
JOURNAL OF CYSTIC FIBROSIS
(2020)
Article
Biochemical Research Methods
Xin Cao, Zhong Guo, Hualong Wang, Yuelei Dong, Songhui Lu, Qing-Yu He, Xuesong Sun, Gong Zhang
Summary: Harmful algal blooms are a global threat to marine ecosystems and human health. This study used translatome sequencing to investigate the molecular mechanisms of the Prorocentrum donghaiense algae. Through analyzing the translatome and proteome, the study found that up-regulation of energy and material production pathways in phosphor-rich conditions led to exponential growth of the algae in HABs. The researchers also demonstrated that mild translation delay using low concentrations of cycloheximide can control algal blooms without harming other aquatic organisms or humans.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Zhi-Biao Mai, Zhong-Hua Zhou, Qing-Yu He, Gong Zhang
Summary: This article introduces a contig-scaffolding strategy for high robustness and accuracy in protein sequence assembly. The strategy minimizes bias in the hydrolysis process by integrating multiple unspecific hydrolysis methods and uses a multistep assembly algorithm with error correction. Experimental results demonstrate the effectiveness of this strategy in assembling protein sequences with high coverage and accuracy, even for membrane proteins.
ANALYTICAL CHEMISTRY
(2022)
Article
Cell Biology
Xiaohui Liu, Lu Li, Chengjie Geng, Shiyuan Wen, Cuiqiong Zhang, Chunmiao Deng, Xuejuan Gao, Gong Zhang, Qing-Yu He, Langxia Liu
Summary: The RNA helicase DDX17 has been found to promote proliferation, migration, and invasion of lung adenocarcinoma cells. It interacts with the mRNA of MYL9 and MAGEA6, upregulating their levels. Moreover, DDX17 regulates cell function by controlling actin cytoskeleton rearrangement and cell adhesion. In LUAD cells, autophagy may be inhibited by DDX17 through the MAGEA6/AMPK alpha 1 axis.
CELL DEATH DISCOVERY
(2022)
Article
Public, Environmental & Occupational Health
Jing Wang, Patrick Kwan, Gong Zhang, Mingwang Shen, Loretta Piccenna, Terence J. O'Brien, Lei Zhang
Summary: China is faced with a growing aging population and understanding the health status of older adults is crucial for resource allocation and healthcare provision. This study aimed to comprehensively assess the disability level and identify risk factors associated with disability among older adults in China. A multidimensional ability assessment survey was used to evaluate daily living activities, mental status, sensory and communication abilities, and social participation. Demographic risk factors were analyzed using logistic regression and the correlations between the four dimensions of ability were assessed.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Biochemistry & Molecular Biology
Xiaolong Lu, Yang Chen, Gong Zhang
Summary: We analyzed SARS-CoV-2 sequence data from the end of 2019 to January 2023 and found that most genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. The Ka/Ks of the S-gene increases from the original strain to different variants, but decreases within one variant over time. Additionally, only S-gene mutations show a trend of accumulating more positive charges, indicating a functional evolution that facilitates infection.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Endocrinology & Metabolism
Yao Sun, Mingxiang Cai, Jiayong Zhong, Li Yang, Jia Xiao, Fujun Jin, Hui Xue, Xiangning Liu, Huisheng Liu, Yongbiao Zhang, Dong Jiang, An Hong, Xunming Ji, Zuolin Wang, Gong Zhang, Xiaogang Wang