Article
Biochemical Research Methods
Zhenmiao Zhang, Chao Yang, Werner Pieter Veldsman, Xiaodong Fang, Lu Zhang
Summary: This paper comprehensively evaluates 19 commonly used assembly tools on metagenomic sequencing datasets from simulation, mock communities, and human gut microbiomes. It finds that long-read assemblers generate high contig contiguity but fail to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtain the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing are promising methods to improve both total assembly length and the number of near-complete MAGs. The paper also discusses the running time and memory consumption of these assembly tools and provides practical guidance for selecting them.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Tianjiao Zhang, Jie Zhou, Wentao Gao, Yuran Jia, Yanan Wei, Guohua Wang
Summary: High-quality genome chromosome-scale sequences are crucial for genomics downstream analysis, especially in the construction of haplotype-resolved and complete genomes. The emergence of long-read sequencing technology has greatly improved complex genome assembly. Among various computational methods, uncollapsed assembly is the most accurate and complete way to represent genomes. Genome assembly is closely related to haplotype reconstruction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yong Zhang, Hong-Wei Lu, Jue Ruan
Summary: With the rapid development of sequencing technologies, the number and quality of published genome assemblies have significantly increased. To address the need for higher genome evaluation standards, a Genome Assembly Evaluating Pipeline (GAEP) has been developed, providing a comprehensive assessment for genome quality in terms of continuity, completeness, and correctness.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Genetics & Heredity
Carlus Deneke, Holger Brendebach, Laura Uelze, Maria Borowiak, Burkhard Malorny, Simon H. Tausch
Summary: AQUAMIS is a Snakemake workflow designed for extensive quality control and assembly of raw Illumina sequencing data, allowing laboratories to automate their initial analysis of microbial whole-genome sequencing data. The workflow performs all steps of primary sequence analysis and visualizes the results in an interactive HTML report with species-specific QC thresholds, as well as providing a standard-compliant JSON file for easy downstream analyses. Its ability to reliably predict contaminations in high throughput routine sequencing environments has been demonstrated through analysis of thousands of microbial isolates and in-silico contaminated datasets. Intergenus and intragenus contaminations can be most accurately detected using a combination of different QC metrics available within AQUAMIS.
Review
Biochemical Research Methods
Junwei Luo, Yawei Wei, Mengna Lyu, Zhengjiang Wu, Xiaoyan Liu, Huimin Luo, Chaokun Yan
Summary: This article discusses the significance of scaffolding methods in genome assembly and the challenges they face, as well as the impact of various types of reads on assembly quality. It emphasizes the importance of researchers gaining a deep understanding of the latest scaffolding methods to address these challenges.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Sivasubramanian Rajarammohan, Lovenpreet Kaur, Anjali Verma, Dalwinder Singh, Shrikant Mantri, Joy K. Roy, Tilak Raj Sharma, Ashwani Pareek, Pramod Kaitheri Kandoth
Summary: In this study, the genome of the grass pea (Lathyrus sativus) cultivar Pusa-24, which is tolerant to multiple abiotic stresses, was successfully sequenced and assembled. The assembled genome was 3.80 Gb in length, with a scaffold N50 of 421.39 Mb. This genome assembly will greatly facilitate genetic and genomic studies in this important legume crop.
Article
Biochemistry & Molecular Biology
Pengfei Zhang, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, Zexiao Yang
Summary: This study compared different assembly strategies for Haemophilus parasuis, a bacterium causing Glasser's disease in swine, and found that assembly with PacBio or ONT reads followed by polishing with Illumina reads resulted in high-quality genome reconstruction. Additionally, correction with Homopolish after ONT-only assembly was equally effective. Aligning transcripts to assembled genomes revealed that ONT assembly errors were mainly insertions and deletions in homopolymer regions, affecting protein prediction. Polishing can fill indels and correct mistakes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Xianrong Xie, Huilong Du, Huiwu Tang, Jianian Tang, Xiyu Tan, Weizhi Liu, Tie Li, Zhansheng Lin, Chengzhi Liang, Yao-Guang Liu
Summary: This study successfully generated a high-quality genome assembly of Oryza rufipogon, revealing insights into the genomic structure of the wild rice, its homology with cultivated rice, and the polyphyletic origins of O. sativa subspecies.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mengmeng Liu, Cheng Li, Tang Jiang, Ruipu Wang, Yong Wang, Wen'e Zhang, Xuejun Pan
Summary: A high-quality chromosome-scale genome assembly was successfully built for Canna indica using PacBio sequencing and Hi-C genome scaffolding. The genome was predicted to contain 31,130 genes, with 30,816 genes functionally annotated. Transcriptome analysis revealed the genes involved in petal coloration and co-expression network analysis identified key genes regulating deep red and yellow petal coloration. This study provides insights into the molecular basis of flower coloration in Canna indica and has implications for the conservation and breeding of ornamental plants.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Xueping Li, Shiyang Xu, Jungao Zhang, Minquan Li
Summary: Fusarium equiseti, a plant pathogen with potential probiotic effects, has unclear molecular mechanisms. Our genomic sequence analysis provides a valuable resource for future studies on gene expression, regulation, function, evolution, disease prevention, and control related to this pathogen.
Article
Biology
Arne Ludwig, Martin Pippel, Gene Myers, Michael Hiller
Summary: In this study, we present DENTIST, a sensitive, highly accurate, and automated pipeline method for closing gaps in short-read assemblies with long error-prone reads. Through tests on real genomic data, we demonstrate that DENTIST achieves higher accuracy and similar sensitivity compared to previous methods.
Review
Biochemistry & Molecular Biology
Yue Meng, Yu Lei, Jianlong Gao, Yuxuan Liu, Enze Ma, Yunhong Ding, Yixin Bian, Hongquan Zu, Yucui Dong, Xiao Zhu
Summary: Sequence assembly algorithms have evolved rapidly with the growth of genome sequencing technology, but misassemblies in contigs may affect downstream data analysis. Therefore, developing efficient and accurate assembly algorithms and misassembly identification methods is crucial.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
V. Sichel, G. Sarah, N. Girollet, V. Laucou, C. Roux, M. Roques, P. Mournet, L. Le Cunff, P. F. Bert, P. This, T. Lacombe
Summary: Chimerism is the presence of multiple genotypes in a single individual, which has been used to understand plant development and is valuable in breeding new cultivars. The viticulture industry has benefited economically from chimeras, especially when they induce significant changes in wine characteristics. Chimeras that affect crucial agronomic traits, but have not been identified yet, are also important. The most stable type of chimera, periclinal chimera, can be propagated through cuttings. In this study, we used new generation sequencing, bioinformatics tools, and parental sequences to detect periclinal chimeras in 'Merlot' grapevine cultivar.
Article
Evolutionary Biology
Ying Zhang, Yuridia Reynoso, David Reznick, Xu Wang
Summary: This study presents a high-quality reference genome of the blackstripe livebearer Poeciliopsis prolifica, which possesses a structure similar to the mammalian placenta. Phylogenomic analyses reveal the evolutionary relationship between P. prolifica and the guppy (Poecilia reticulata). The research provides essential resources and tools for investigating the genetic basis of placentation.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Biao Han, Longxin Wang, Yang Xian, Xiao-Man Xie, Wen-Qing Li, Ye Zhao, Ren-Gang Zhang, Xiaochun Qin, De-Zhu Li, Kai-Hua Jia
Summary: In this study, a high-quality genome of Quercus variabilis was generated using PacBio HiFi and Hi-C sequencing. The genome size was 787 Mb, with 12 pseudo-chromosomes. Q. variabilis was found to be closely related to Q. suber and no species-specific whole genome duplications were identified. These genomic resources will be valuable for breeding strategies and comparative genomics in oak species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Toxicology
Dongying Li, Bridgett Knox, Binsheng Gong, Si Chen, Lei Guo, Zhichao Liu, Weida Tong, Baitang Ning
Summary: The study focused on investigating miRNA biomarkers for KCZ-induced liver injury by integrating in vivo, in vitro, and bioinformatics analyses. Significant dysregulation of miR-34a-5p, miR-331-3p, and miR-15b-3p was associated with cytoplasmic vacuolization in rat livers with KCZ-induced injury. These miRNAs, along with miR-676, showed evolutionary conservation and could potentially serve as translational biomarkers for early detection of liver injury.
TOXICOLOGICAL SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Li Zeng, Dongying Li, Weida Tong, Tieliu Shi, Baitang Ning
Summary: The study proposes a method to monitor and predict the impact of viral mutations on drug safety and efficacy, emphasizing the importance of the three main viral proteins and suggesting the establishment of an interactive database.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Chemistry, Medicinal
Dongying Li, Binsheng Gong, Joshua Xu, Baitang Ning, Weida Tong
Summary: This study investigated the impact of sequencing depth and library preparation on toxicological interpretation in RNA-seq using three samples. Results showed that a minimum of 20 million reads was sufficient to reveal key toxicity pathways, and identification of differentially expressed genes was positively associated with sequencing depth. Overall, RNA-seq had higher statistical power and overlap ratio in toxicological insights compared to TempO-seq and microarray.
CHEMICAL RESEARCH IN TOXICOLOGY
(2021)
Review
Pharmacology & Pharmacy
Kiara Fairman, Miao Li, Baitang Ning, Annie Lumen
Summary: PBPK modeling is a powerful tool with potential applications in the development of RNAi therapeutics, a class of drugs with unique pharmacokinetic properties. While there is active research in this area, there are still challenges to fully evaluating the utility of PBPK models for RNAi therapeutics. The current computational modeling approaches can support efficient development and approval of RNAi therapeutics, but further exploration and standardization are needed to optimize their use.
BIOCHEMICAL PHARMACOLOGY
(2021)
Editorial Material
Pharmacology & Pharmacy
Baitang Ning, Ai-Ming Yu
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Engineering, Environmental
Zhongyu Wang, Jingwen Chen, Huixiao Hong
Summary: This study developed 30 QSAR models based on PPAR gamma binding affinity data, using molecular fingerprints, two-dimensional descriptors, and five machine learning algorithms. Local discontinuity scores were positively correlated with prediction errors of the models, and innovative ADs outperformed traditional ones. The curated data sets and models can be used to evaluate adverse effects of chemicals.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Virology
Bohu Pan, Zuowei Ji, Sugunadevi Sakkiah, Wenjing Guo, Jie Liu, Tucker A. Patterson, Huixiao Hong
Summary: The transmission of SARS-CoV-2 is primarily through person-to-person contact, and phylogenetic analysis revealed a co-expansion tendency of the virus among neighboring countries. Pairwise sequence similarity analysis showed that SARS-CoV-2 is transmitted locally and evolves during transmission, with no significant differences in genomes grouped by host age or sex.
Article
Biochemistry & Molecular Biology
Sugunadevi Sakkiah, Chandrabose Selvaraj, Wenjing Guo, Jie Liu, Weigong Ge, Tucker A. Patterson, Huixiao Hong
Summary: ERalpha is a ligand-dependent transcriptional factor, and this study used molecular docking, molecular dynamics simulations, and quantum mechanical calculations to elucidate the dynamic binding patterns of agonists and antagonists in ER alpha. The results showed that OHT binds ER alpha more tightly in the antagonist conformer, while E2 prefers the agonist conformer, which may have implications for drug development and risk assessment related to ER-mediated responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Srilatha Sakamuru, Jinghua Zhao, Menghang Xia, Huixiao Hong, Anton Simeonov, Iosif Vaisman, Ruili Huang
Summary: Novel computational models were developed to predict the activity of opioid receptors based on chemical structures, successfully identifying new active compounds. Experimental validation showed that the best performing model, using the random forest classifier, achieved hit rates ranging from 2.3% to 15.8%, enriching hit rates by >= 2-fold compared to the original assay.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Multidisciplinary
Wenjing Guo, Jie Liu, Fan Dong, Ru Chen, Jayanti Das, Weigong Ge, Xiaoming Xu, Huixiao Hong
Summary: The study developed models for predicting the gas adsorption capacities of MOFs using two deep learning algorithms (MLP and LSTM) and evaluated their performance. The results showed that these deep learning models are more accurate than traditional machine learning algorithms, especially for predicting gas adsorption capacities at low pressures.
Article
Chemistry, Medicinal
Ting Li, Ruth Roberts, Zhichao Liu, Weida Tong
Summary: Animal studies are crucial for drug evaluation to ensure safety. We have proposed a novel framework called TransOrGAN that uses a generative adversarial network to map gene expression profiles across different organ systems, sexes, and ages in rodents. Our proof-of-concept study demonstrates that TransOrGAN can accurately infer transcriptomic profiles between organs, sexes, and ages, providing an opportunity to reduce animal usage and assess overall toxicity.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Myeongsang Lee, Marian Major, Huixiao Hong
Summary: Since November 2021, the Omicron variant of SARS-CoV-2 has been the dominant cause of COVID-19 and has shown increased transmission and infection rates. The Omicron spike protein has unique properties and can evade neutralizing antibodies due to mutations in the receptor binding domain. This review analyzes the structural changes of the Omicron spike protein in the presence and absence of ACE2 and antibodies, which can contribute to the development of effective vaccines against the Omicron variant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Nicole Bussola, Joshua Xu, Leihong Wu, Lorenzo Gorini, Yifan Zhang, Cesare Furlanello, Weida Tong
Summary: The pathology of animal studies is important for toxicity evaluations and regulatory assessments. However, manual examination of slides by pathologists is time-consuming and has variability issues. To address this, researchers developed PathologAI, a weakly supervised approach for classifying rat images without explicit lesion annotation. PathologAI can provide an inexpensive and rapid screening tool for preclinical applications and toxicological studies.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Article
Chemistry, Medicinal
Magnus Gray, Joshua Xu, Weida Tong, Leihong Wu
Summary: In order to improve the efficiency of document organization and review in regulatory agencies, researchers used an artificial intelligence-based natural language processing method (BERT) to automatically classify free-text information into standardized sections, supporting a holistic review of drug safety and efficacy.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Review
Pharmacology & Pharmacy
Magnus Gray, Ravi Samala, Qi Liu, Denny Skiles, Joshua Xu, Weida Tong, Leihong Wu
Summary: This literature review examines the current state of research on AI bias, including its sources, as well as methods for measuring, benchmarking, and mitigating it. The paper specifically focuses on biases and methods of mitigation relevant to the healthcare field, and offers a perspective on bias measurement and mitigation in regulatory science decision making.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
