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
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Hui Jiang, Jing Tian, Jiaxin Yang, Xiang Dong, Zhixiang Zhong, Geoffrey Mwachala, Caifei Zhang, Guangwan Hu, Qingfeng Wang
Summary: This study presents the complete chloroplast genomes of six Polystachya species, providing insights into the structural characteristics of the chloroplast genome of Polystachya. It also identifies highly variable sequences that could be used as DNA markers for studying genetic variability and evolution in Polystachya. Furthermore, the phylogenetic analysis supports the inclusion of Polystachya in the tribe Vandeae.
Article
Biochemistry & Molecular Biology
Wenyue Huang, Xiaona Hu, Yanlin Ren, Minggui Song, Chuang Ma, Zhenyan Miao
Summary: The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants. However, the lack of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data has hindered systematic and efficient analysis on specific genes. In order to address this issue, an advanced plant multi-omics platform, IPOP, has been established, which collects and analyzes various types of data and provides tools to facilitate evolutionary and functional analysis. This platform offers valuable insights and data for cross-species comparison and evolutionary research in the plant sciences community.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Zhengyang Niu, Zheli Lin, Yi Tong, Xin Chen, Yunfei Deng
Summary: This study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.
Article
Computer Science, Software Engineering
Sehi L'Yi, Qianwen Wang, Fritz Lekschas, Nils Gehlenborg
Summary: This article introduces an interactive and scalable grammar called Gosling for genomics data visualization, along with its accompanying JavaScript toolkit Gosling.js. The grammar balances expressiveness for comprehensive multi-scale genomics visualizations with accessibility for domain scientists, addressing the issue of limited customization in existing tools.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Engineering, Environmental
Renjun Yang, Shuyu Liu, Nuoya Yin, Yang Zhang, Francesco Faiola
Summary: Chemical pollution is a prominent environmental problem. This study analyzed and visualized Tox21 qHTS data to reveal and summarize the toxic effects of environmental pollutants. A total of 158 environmental concern chemicals (COECs) were detected and classified into 13 COEC groups based on structure and activity similarities.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Genetics & Heredity
Xi Hu, Jialin Song, Jacqueline Chyr, Jinping Wan, Xiaoyan Wang, Jianqiang Du, Junbo Duan, Huqin Zhang, Xiaobo Zhou, Xiaoming Wu
Summary: This study introduces a web-based platform called APAview, which is used to explore APA features in hematological malignancies and perform APA statistical analysis. The platform simplifies the process of APA data pre-processing, analysis, and visualization, making it convenient for APA feature screening and mining.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
Summary: The recent advance of single-cell copy number variation (CNV) analysis is important in addressing intratumor heterogeneity and restoring tumor-evolving trajectories. However, existing tools lack real-time interaction and are hard to reproduce. We present an online platform for real-time interactive visualization of single-cell genomics data to accelerate the understanding of cancer clonal evolution.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Leonardo Mancabelli, Walter Mancino, Gabriele Andrea Lugli, Christian Milani, Alice Viappiani, Rosaria Anzalone, Giulia Longhi, Douwe van Sinderen, Marco Ventura, Francesca Turroni
Summary: The vaginal microbiota is predominantly composed of Lactobacillus genus, with Lactobacillus crispatus strains associated with a healthy vaginal environment. A study of 94 healthy vaginal samples revealed that L. crispatus was the most representative species and negatively correlated with pathogenic bacteria. The genetic adaptation of L. crispatus strains to their ecological niche was shown through comparative genomics analysis, and in vitro experiments demonstrated the species' ability to modulate the vaginal microbial consortia.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lahcen I. Campbell, Joachim Nwezeobi, Sharon L. van Brunschot, Tadeo Kaweesi, Susan E. Seal, Rekha A. R. Swamy, Annet Namuddu, Gareth L. Maslen, Habibu Mugerwa, Irina M. Armean, Leanne Haggerty, Fergal J. Martin, Osnat Malka, Diego Santos-Garcia, Ksenia Juravel, Shai Morin, Michael E. Stephens, Paul Visendi Muhindira, Paul J. Kersey, M. N. Maruthi, Christopher A. Omongo, Jesus Navas-Castillo, Elvira Fiallo-Olive, Ibrahim Umar Mohammed, Hua-Ling Wang, Joseph Onyeka, Titus Alicai, John Colvin
Summary: This study provides insights into the genetics underlying the biology of Bemisia tabaci sensu lato, including the identification of three biological species within African cassava populations and the analysis of gene families related to detoxification, sugar metabolism, and vector competency. The findings contribute to the development of innovative whitefly and virus-control strategies.
Article
Plant Sciences
Yue Jing, Mutsumi Watanabe, Fayezeh Aarabi, Alisdair R. Fernie, Monica Borghi, Takayuki Tohge
Summary: This study comprehensively analyzed the responses of four Brassicaceae species to UV-B radiation, revealing a reprogramming of the central metabolic pathway and the production of specific classes of flavonoids with increased protection against UV-B radiation. The activation of the phenylpropanoid-acetate pathway and the increase in phenylacylated-flavonoid glucosides were also observed across species. Interestingly, the expression of acyltransferase genes of the SCPLs protein class was constitutive but downregulated in response to UV-B radiation, possibly independent of the HY5 signaling pathway.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Shuya Liu, Qing Xu, Kuiyan Liu, Yongfang Zhao, Nansheng Chen
Summary: In this study, complete chloroplast genomes of five Skeletonema species were constructed, showing high synteny and conservation with similar gene numbers. The presence of duplicate petF genes in both the chloroplast and nuclear genomes was observed. Selection analysis indicated purifying selection on protein-coding genes, while divergent regions were identified as potential markers for phylogenetic inference and genetic polymorphism detection. Furthermore, divergence times estimated using protein-coding genes suggest the establishment of these species around 33 million years ago, consistent with previous estimates using mitochondrial DNA. Overall, this study provides insights into the molecular evolution of Skeletonema chloroplast genomes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mark Kunitomi, Mary Roth, Vandana Mukherjee, James H. Kaufman
Summary: The rapid growth in biological sequence data is changing our understanding of genotypic diversity, challenging traditional bioinformatic tools. To address these challenges, a relational database called Functional Genomics Platform is created to store pre-computed important relationships between biological entities. This platform allows efficient querying and provides rich data and connections for microbial studies.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Computer Science, Software Engineering
Sehi Lyi, Nils Gehlenborg
Summary: A series of recent studies have focused on designing responsive multi-view visualizations, but there are still unresolved questions. This paper presents a framework for designing responsive multi-view visualizations for genomics data. Existing genomics visualization tools rarely support responsiveness. The paper identifies usability issues and discusses approaches to address them, as well as extending the Gosling visualization grammar to support responsive constructs. The study suggests considering different input modalities in future research.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Biochemistry & Molecular Biology
Zhang Zhang, Wenming Zhao, Jingfa Xiao, Yiming Bao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Yang Gao, Chao Zhang, Liyun Yuan, Shuhua Xu, Zhilin Ning, Yan Lu, Jingyao Zeng, Na Yuan, Junwei Zhu, Mengyu Pan, Hao Zhang, Qi Wang, Shuo Shi, Meiye Jiang, Mingming Lu, Qiheng Qian, Qianwen Gao, Yunfei Shang, Jinyue Wang, Zhenglin Du, Dongmei Tian, Pei Wang, Bixia Tang, Cuiping Li, Xufei Teng, Xiaonan Liu, Dong Zou, Shuhui Song, Zhuang Xiong, Mengwei Li, Fei Yang, Yingke Ma, Jian Sang, Zhaohua Li, Rujiao Li, Zhonghuang Wang, Qianghui Zhu, Xin Li, Sisi Zhang, Hailong Kang, Lili Dong, Cui Ying, Guangya Duan, Menghua Li, Xiaoyang Zhi, Yunchao Ling, Ruifang Cao, Zhao Jiang, Haokui Zhou, Daqing Lv, Wan Liu, Hans-Peter Klenk, Yadong Zhang, Zhewen Zhang, Tingting Chen, Xu Chen, Yanqing Wang, Song Wu, Zheng Gong, Meili Chen, Shuangsang Fang, Lili Zhang, Jincheng Guo, Yiwei Niu, Yang Wu, Hui Li, Lianhe Zhao, Xiyuan Li, Xueyi Teng, Xianhui Sun, Liang Sun, Yi Zhao, Jiajia Wang, Peng Zhang, Yanyan Li, Yu Zheng, Xiaomin Chen, Hua Xue, Yiheng Teng, Quan Kang, Yajing Hao, Jiabao Cao, Lin Liu, Zhao Li, Qianpeng Li, Qiang Du, Amir A. Abbasi, Huma Shireen, Nashaiman Pervaiz, Fatima Batool, Rabail Z. Raza, Lina Ma, Guangyi Niu, Yuansheng Zhang, Tongtong Zhu, Lili Hao, Guoliang Wang, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Zhonghai Li, Yang Zhang, Houling Wang, Yi Zhang, Xinli Xia, Hongwei Guo, Junwen Zhu, Qing Zhou, Hongen Kang, Li Lan, Xin Zhang, Yongbiao Xue, Yubin Sun, Shuang Zhai, Lei Yu, Mingyuan Sun, Huanxin Chen, Hui Hu, An-Yuan Guo, Shaofeng Lin, Yu Xue, Chenwei Wang, Wanshan Ning, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Wanying Wu, Peifeng Ji, Fangqing Zhao, Hao Luo, Feng Gao, Yaping Guo, Hao Yuan, Yong E. Zhang, Qiong Zhang, Jiaqi Zhou, Zhou Huang, Qinghua Cui, Ya-Ru Miao, Chen Ruan, Chunhui Yuan, Ming Chen, Jin-Pu Jin, Feng Tian, Ge Gao, Ying Shi, Lan Yao, Xiangshang Li, Chuan-Yun Li, Qing Tang, Di Peng
NUCLEIC ACIDS RESEARCH
(2020)
Article
Agronomy
Zhipeng Zhou, Guoliang Li, Siyu Tan, Dongdong Li, Thea Mi Weiss, Xiangfeng Wang, Shaojiang Chen, Tobias Wuerschum, Wenxin Liu
Article
Biochemistry & Molecular Biology
Huan Zhang, Qian Zhang, Hong Zhai, Shaopei Gao, Li Yang, Zhen Wang, Yuetong Xu, Jinxi Huo, Zhitong Ren, Ning Zhao, Xiangfeng Wang, Jigang Li, Qingchang Liu, Shaozhen He
Article
Plant Sciences
Hong Li, Shuqin Jiang, Chen Li, Lei Liu, Zechuan Lin, Hang He, Xing-Wang Deng, Ziding Zhang, Xiangfeng Wang
Article
Genetics & Heredity
Jun Yan, Dong Zou, Chen Li, Zhang Zhang, Shuhui Song, Xiangfeng Wang
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
Article
Plant Sciences
Xiaoyan Liang, Songyu Liu, Tao Wang, Fenrong Li, Jinkui Cheng, Jinsheng Lai, Feng Qin, Zhen Li, Xiangfeng Wang, Caifu Jiang
Summary: Research has shown that natural maize varieties display a large diversity of salt tolerance, yet the genetic variants underlying such diversity remain poorly discovered and applied. An LC-MS-based untargeted metabolomics approach identified 37 metabolite biomarkers related to SIOS tolerance, and 10 candidate genes significantly associated with SIOS tolerance and METO abundances. A citrate synthase, a glucosyltransferase, and a cytochrome P450 were validated to underlie genotype-METO-SIOS tolerance associations and improve the SIOS tolerance of elite maize inbred lines through additive effects.
Article
Genetics & Heredity
Chunming Yang, Jun Yan, Shuqin Jiang, Xia Li, Haowei Min, Xiangfeng Wang, Dongyun Hao
Summary: In this study, the genomes of 250 soybean landraces and cultivars were sequenced to investigate their population structure, genetic diversity and architecture, and selective sweep regions. Five novel agronomically important genes were identified, and the effects of functional mutations were examined. Phenotype-gene network analysis revealed the crucial role of hub nodes in complex phenotypic associations.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Qian Cheng, Shuqing Jiang, Feng Xu, Qian Wang, Yingjie Xiao, Ruyang Zhang, Jiuran Zhao, Jianbing Yan, Chuang Ma, Xiangfeng Wang
Summary: This study utilizes genomic selection and genome optimization to assist in the selection of superior maize lines based on genotype contributions to a simulated genome. By predicting the optimal genotype combinations and selecting lines with complementary sets of advantageous alleles, the breeding process can be optimized for maize inbred line development.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Yanyan Wang, Yibo Cao, Xiaoyan Liang, Junhong Zhuang, Xiangfeng Wang, Feng Qin, Caifu Jiang
Summary: The study reveals that ZmSTL1 plays a crucial role in conferring salt tolerance in maize by affecting lignin deposition and Na+ transport. The findings suggest that modifying the Casparian strip barrier could be a potential approach for developing salt-tolerant crops.
NATURE COMMUNICATIONS
(2022)
Review
Plant Sciences
Jun Yan, Xiangfeng Wang
Summary: Advances in high-throughput omics technologies have led to the era of big data in plant biology research. Machine learning plays a crucial role in plant systems biology due to its excellent performance and wide application in analyzing big data. However, supervised machine learning algorithms require a large number of labeled samples as training data to achieve optimal performance. In cases where obtaining sufficient labeled training data is impossible or expensive, unsupervised learning and semi-supervised learning paradigms are indispensable.
Review
Plant Sciences
Jun Yan, Xiangfeng Wang
Summary: Machine learning (ML) shows great potential in translating biological knowledge and omics data into precision-designed plant breeding, bridging the gap between basic research and breeding practice. ML algorithms can be used to analyze multi-omics data, infer gene-regulation networks, and prioritize target genes for knowledge-driven molecular design breeding.
TRENDS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Ran Fu, Xiangfeng Wang
Summary: This research mathematically modeled the phenotypic plasticity in inbred and hybrid maize lines using phenotypic and genotypic data. They found that the phenotypic plasticity is associated with hybrid performance and yield combining ability.
PLANT COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Jun Yan, Yuetong Xu, Qian Cheng, Shuqin Jiang, Qian Wang, Yingjie Xiao, Chuang Ma, Jianbing Yan, Xiangfeng Wang
Summary: LightGBM is an ensemble model of decision trees used for classification and regression prediction, showing superior performance in genomic selection-assisted breeding. Through benchmark tests, it demonstrates advantages in prediction precision, model stability, and computing efficiency.
Article
Biochemistry & Molecular Biology
Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jingfa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Xue Yongbiao, Tao Zhang, Wang Kang, Jing Qu, Weiqi Zhang, Guang-Hui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Honggen Wang, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Fei Yang, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, HaiChun Jing, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir A. Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, XiaoTong Luo
Summary: The Chinese National Genomics Data Center, under the China National Center for Bioinformation, is continuously expanding, updating, and enriching a suite of database resources to support global research activities. A new resource called 2019nCoVR provides a global landscape of SARS-CoV-2 genomic sequences, while other resources such as BIG Search have been significantly updated to improve access to a large number of biological resources.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Shi-Jian Zhang, Lei Liu, Ruolin Yang, Xiangfeng Wang
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
