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Identification of highly repetitive barley enhancers with long-range regulation potential via STARR-seq Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-02-21 Wanlin Zhou, Haoran Shi, Zhiqiang Wang, Yuxin Huang, Lin Ni, Xudong Chen, Yan Liu, Haojie Li, Caixia Li, Yaxi Liu
Abstract Enhancers are DNA sequences that can strengthen transcription initiation. However, the global identification of plant enhancers is complicated due to uncertainty in the distance and orientation of enhancers, especially in species with large genomes. In this study, we performed self-transcribing active regulatory region sequencing (STARR-seq) for the first time to identify enhancers across
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HCCDB v2.0: Decompose expression variations by single-cell RNA-seq and spatial transcriptomics in HCC Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-02-04 Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yupeng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yongchang Zheng, Jin Gu
Abstract Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). Integrated 15 transcriptomic datasets of HCC clinical samples, the first version of HCCDB (HCC database) was released in 2018. Through the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets, it provides a systematic view of
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NeoTCR: an immunoinformatic database of experimentally-supported functional neoantigen-specific TCR sequences Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-02-04 Weijun Zhou, Wenting Xiang, Jinyi Yu, Zhihan Ruan, Yichen Pan, Kankan Wang, Jian Liu
Abstract Neoantigen-based immunotherapy has demonstrated long-lasting antitumor activity. The recognition of neoantigens by T cell receptors (TCRs) is considered a trigger for antitumor responses. Due to the overwhelming number of TCR repertoires in the human genome, pinpointing neoantigen-specific TCRs is a formidable challenge. Recent studies have identified a number of functional neoantigen-specific
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CpG island definition and methylation mapping of the T2T-YAO genome Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-02-02 Ming Xiao, Rui Wei, Jun Yu, Chujie Gao, Fengyi Yang, Le Zhang
Abstract Precisely defining and mapping all cytosine positions and their clusters, known as CpG islands (CGIs), as well as their methylation status are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in
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Pindel-TD: a tandem duplication detector based on a pattern growth approach Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-23 Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye
Abstract Tandem duplication (TD) is a major type of structural variation (SV) that plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals. Herein, we developed a TD detection module for the Pindel tool, referred
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FP-Zernike: an open-source structural database construction toolkit for fast structure retrieval Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-21 Junhai Qi, Chenjie Feng, Yulin Shi, Jianyi Yang, Fa Zhang, Guojun Li, Renmin Han
Abstract The release of AlphaFold2 has sparked a rapid expansion in protein model databases. Efficient protein structure retrieval is crucial for the analysis of structure models, while measuring the similarity between structures is the key challenge in structural retrieval. Although existing structure alignment algorithms can address this challenge, they are often time-consuming. Currently, the state-of-the-art
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A Two-color Single-molecule Sequencing Platform and Its Clinical Applications Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-12 Fang Chen, Bin Liu, Meirong Chen, Zefei Jiang, Zhiliang Zhou, Ping Wu, Meng Zhang, Huan Jin, Linsen Li, Liuyan Lu, Huan Shang, Lei Liu, Weiyue Chen, Jianfeng Xu, Ruitao Sun, Guangming Wang, Jiao Zheng, Jifang Qi, Bo Yang, Lidong Zeng, Yan Li, Hui Lv, Nannan Zhao, Wen Wang, Jinsen Cai, Yongfeng Liu, Weiwei Luo, Juan Zhang, Yanhua Zhang, Jicai Fan, Haitao Dan, Xuesen He, Wei Huang, Lei Sun, Qin Yan
Abstract DNA sequencers have become increasingly important research and diagnostic tools over the past 20 years. We have developed a single-molecule desktop sequencer, GenoCare 1600 (GenoCare), which utilizes amplification-free library preparation and two-color sequencing-by-synthesis chemistry, making it more user-friendly compared to previous single-molecule sequencing platforms for clinical use
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SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-11 Zekai Liu, Zhen Yuan, Yunlei Guo, Ruilin Wang, Yusheng Guan, Zhanglian Wang, Yunan Chen, Tianlu Wang, Meining Jiang, Shuhui Bian
Abstract Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here we introduce the single-cell multi-omics atlas of reproduction
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Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-11 Manickam Ashokkumar, Wenwen Mei, Jackson J Peterson, Yuriko Harigaya, David M Murdoch, David M Margolis, Caleb Kornfein, Alex Oesterling, Zhicheng Guo, Cynthia D Rudin, Yuchao Jiang, Edward P Browne
Abstract Despite the success of antiretroviral therapy, human immunodeficiency virus (HIV) cannot be cured because of a reservoir of latently infected cells that evades therapy. To understand the mechanisms of HIV latency, we employed an integrated single-cell RNA sequencing (RNA-seq) and single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq) approach to simultaneously profile
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MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-11 Peng Jia, Xuanhao Yang, Xiaofei Yang, Tingjie Wang, Yu Xu, Kai Ye
Abstract Microsatellite instability (MSI) is an indispensable biomarker in cancer immunotherapy. Currently, MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection. However, the MSI detection method on expression data, especially single-cell expression data, is still lacking, limiting the scope of
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Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Liwen Xiao, Zhenqiang Zuo, Fangqing Zhao
Abstract The microbiome plays a critical role in the process of conception and the outcomes of pregnancy. Disruptions in microbiome homeostasis in women of reproductive age can lead to various pregnancy complications, which significantly impact maternal and fetal health. Recent studies have associated the microbiome in the female reproductive tract (FRT) with assisted reproductive technology (ART)
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Transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Wenju Liu, Xinyu Cui, Yuhan Zhang, Liang Gu, Yuanlin He, Jing Li, Shaorong Gao, Rui Gao, Cizhong Jiang
Abstract The development and maturation of follicles is a sophisticated and multistage process. The dynamic gene expression of oocytes and the surrounding somatic cells and the dialogs between these cells are critical to this process. We accurately classified the follicle development into nine stages and profiled the gene expression of mouse oocytes, the companion granulosa cells, and cumulus cells
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DVsc: An Automated Framework for Efficiently Detecting Viral Infection from Single-Cell Transcriptomics Data Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Fei Leng, Song Mei, Xiaolin Zhou, Xuanshi Liu, Yefeng Yuan, Wenjian Xu, Chongyi Hao, Ruolan Guo, Chanjuan Hao, Wei Li, Peng Zhang
Abstract Single-cell RNA sequencing (scRNA-seq) has emerged as a valuable tool for studying cellular heterogeneity in various fields, particularly in virological research. By studying the viral and cellular transcriptomes, the dynamics of viral infection can be investigated at a single-cell resolution. However, limited studies have been conducted to investigate whether RNA transcripts from clinical
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Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Ke-jia Shan, Changcheng Wu, Xiaolu Tang, Roujian Lu, Yaling Hu, Wenjie Tan, Jian Lu
Abstract The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered
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Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Binzhong Wang, Bin Wu, Xueqing Liu, Yacheng Hu, Yao Ming, Mingzhou Bai, Juanjuan Liu, Kan Xiao, Qingkai Zeng, Jing Yang, Hongqi Wang, Baifu Guo, Chun Tan, Zixuan Hu, Xun Zhao, Yanhong Li, Zhen Yue, Junpu Mei, Wei Jiang, Yuanjin Yang, Zhiyuan Li, Yong Gao, Lei Chen, Jianbo Jian, Hejun Du
Abstract The order Acipenseriformes, which includes sturgeons and paddlefishes, represents “living fossils” with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species
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GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Jianting An, Jing Wang, Siming Kong, Shi Song, Wei Chen, Peng Yuan, Qilong He, Yidong Chen, Ye Li, Yi Yang, Wei Wang, Rong Li, Liying Yan, Zhiqiang Yan, Jie Qiao
Abstract Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been
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TransCell: In silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Shan-Ju Yeh, Shreya Paithankar, Ruoqiao Chen, Jing Xing, Mengying Sun, Ke Liu, Jiayu Zhou, Bin Chen
Abstract Gene expression profiling of new or modified cell lines becomes routine today; however, obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines, including those derived from underrepresented groups, is not trivial when resources are minimal. Using gene expression to predict other measurements has been actively explored; however, systematic investigation
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Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-10 Tao Yu, Yingfeng Luo, Xinyu Tan, Dahe Zhao, Xiaochun Bi, Chenji Li, Yanning Zheng, Hua Xiang, Songnian Hu
Abstract Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. By analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic
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On the Responsible Use of Chatbots in Bioinformatics Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-05 Gangqing Hu, Li Liu, Dong Xu
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Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-04 Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang
Abstract Since its establishment in 2013, BioLiP has become one of the widely used resources for protein–ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein–ligand interactions are represented in the form of single-chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known
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NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2024-01-04 Jiang Hu, Zhuo Wang, Fan Liang, Shan-Lin Liu, Kai Ye, De-Peng Wang
Abstract The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes
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A Historic Retrospective on the Early Bioinformatics Research in China Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-11-03 Runsheng Chen
Abstract not available
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Toward A New Paradigm of Genomics Research: —Celebration of the 20th Anniversary of Beijing Institute of Genomics Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-29 Zhang Zhang, Songnian Hu, Jun Yu
Twenty years after the completion and forty years after the proposal of the Human Genome Project (HGP), genomics, together with its twin field – bioinformatics, has entered a new paradigm, where its bioscience-related, discipline-centric applications have been creating many new research frontiers. Beijing Institute of Genomics (BIG) and now also known as China National Center for Bioinformation (CNCB)
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RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-26 Cuiping Li, Lina Ma, Dong Zou, Rongqin Zhang, Xue Bai, Lun Li, Gangao Wu, Tianhao Huang, Wei Zhao, Enhui Jin, Yiming Bao, Shuhui Song
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, , and of the severe acute respiratory syndrome coronavirus 2 (). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This
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Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-ever-omics to Holovivology Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-24 Jun Yu
Abstract not available
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A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-19 Farzaneh Esmaili, Mahdi Pourmirzaei, Shahin Ramazi, Seyedehsamaneh Shojaeilangari, Elham Yavari
(PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The
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RNA Modifications and Epitranscriptomics Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-19 Chengqi Yi, Jianhua Yang
Abstract not available
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From BIG Data Center to China National Center for Bioinformation Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-12 Yiming Bao, Yongbiao Xue
Abstract not available
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OBIA: An Open Biomedical Imaging Archive Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-10-06 Enhui Jin, Dongli Zhao, Gangao Wu, Junwei Zhu, Zhonghuang Wang, Zhiyao Wei, Sisi Zhang, Anke Wang, Bixia Tang, Xu Chen, Yanling Sun, Zhe Zhang, Wenming Zhao, Yuanguang Meng
With the development of artificial intelligence (AI) technologies, data play an important role in scientific research and clinical application, but the available resources are limited. Here we present (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, and accepts the
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T2T-YAO Reference Genome of Han Chinese — New Step in Advancing Precision Medicine in China Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-09-22 Xue Zhang
Abstract not available
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T2T-YAO, T2T-SHUN, and more Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-09-22 Jingfa Xiao, Jun Yu
Abstract not available
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Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-09-22 Jennifer A. Karlow, Erica C. Pehrsson, Xiaoyun Xing, Mark Watson, Siddhartha Devarakonda, Ramaswamy Govindan, Ting Wang
Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment outcome. To determine the potential contribution of alterations to tumor phenotype in (NSCLC) in both smoker and never-smoker patients, we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary
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Decoding Human Biology and Disease Using Single-cell Omics Technologies Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-09-20 Qiang Shi, Xueyan Chen, Zemin Zhang
Over the past decade, advances in (SCO) technologies have enabled the investigation of at an unprecedented resolution and scale, opening a new avenue for understanding human biology and . In this review, we summarize the developments of sequencing-based SCO technologies and , and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a
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HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-09-18 Yuliang Pan, Ruiyi Li, Wengen Li, Liuzhenghao Lv, Jihong Guan, Shuigeng Zhou
A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of . Unfortunately, we still lack such a comprehensive atlas of experimentally validated protein complexes, which prevents us from gaining a complete understanding of the
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The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-08-29 Guobin Chang, Xiaoya Yuan, Qixin Guo, Hao Bai, Xiaofang Cao, Meng Liu, Zhixiu Wang, Bichun Li, Shasha Wang, Yong Jiang, Zhiquan Wang, Yang Zhang, Qi Xu, Qianqian Song, Rui Pan, Lingling Qiu, Tiantian Gu, Xinsheng Wu, Yulin Bi, Zhengfeng Cao, Guohong Chen
The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune
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Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-08-30 Yongshuai Han, Shihui Wang, Yaomei Wang, Yumin Huang, Chengjie Gao, Xinhua Guo, Lixiang Chen, Huizhi Zhao, Xiuli An
The fetal liver (FL) is the key erythropoietic organ during fetal development, but knowledge on human FL erythropoiesis is very limited. In this study, we sorted primary erythroblasts from FL cells and performed RNA sequencing (RNA-seq) analyses. We found that temporal gene expression patterns reflected changes in function during primary human FL . Notably, the expression of genes enriched in proteolysis
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T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-08-16 Yukun He, Yanan Chu, Shuming Guo, Jiang Hu, Ran Li, Yali Zheng, Xinqian Ma, Zhenglin Du, Lili Zhao, Wenyi Yu, Jianbo Xue, Wenjie Bian, Feifei Yang, Xi Chen, Pingan Zhang, Rihan Wu, Yifan Ma, Changjun Shao, Jing Chen, Jian Wang, Jiwei Li, Jing Wu, Xiaoyi Hu, Qiuyue Long, Mingzheng Jiang, Hongli Ye, Shixu Song, Guangyao Li, Yue Wei, Yu Xu, Yanliang Ma, Yanwen Chen, Keqiang Wang, Jing Bao, Wen Xi, Fang
Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version — T2T-CHM13 — reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete human genome
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Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-07-13 Tingfu Du, Chunchun Gao, Shuaiyao Lu, Qianlan Liu, Yun Yang, Wenhai Yu, Wenjie Li, Yong Qiao Sun, Cong Tang, Junbin Wang, Jiahong Gao, Yong Zhang, Fangyu Luo, Ying Yang, Yun-Gui Yang, Xiaozhong Peng
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inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-07-11 Lei Du, Jin Zhang, Ying Zhao, Muheng Shang, Lei Guo, Junwei Han
Identifying genetic risk factors for Alzheimer’s disease (AD) is an important research topic. To date, different endophenotypes, such as imaging-derived endophenotypes and proteomic expression-derived endophenotypes, have shown the great value in uncovering risk genes compared to case–control studies. Biologically, a co-varying pattern of different omics-derived endophenotypes could result from the
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AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-06-24 Xiaopeng Xu, Tiantian Xu, Juexiao Zhou, Xingyu Liao, Ruochi Zhang, Yu Wang, Lu Zhang, Xin Gao
Antibody leads must fulfill multiple desirable properties to be clinical candidates. Primarily due to the low throughput in the experimental procedure, the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development, because addressing one issue usually causes another. We developed a (RL) method, named AB-Gen, for antibody library design using a
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Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-06-22 Yaojun Wang, Shiwei Sun
Abstract not available
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Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-05-19 Liang Wang, Xiaojie Wang, Chunqi Liu, Wei Xu, Weihong Kuang, Qian Bu, Hongchun Li, Ying Zhao, Linhong Jiang, Yaxing Chen, Feng Qin, Shu Li, Qinfan Wei, Xiaocong Liu, Bin Liu, Yuanyuan Chen, Yanping Dai, Hongbo Wang, Jingwei Tian, Gang Cao, Xiaobo Cen
The expression of linear DNA sequence is precisely regulated by the three-dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neurons is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology
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The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-29 Xin-Lu Meng, Peng-Bo Yuan, Xue-Ju Wang, Jing Hang, Xiao-Ming Shi, Yang-Yu Zhao, Yuan Wei
In perinatal medicine, intrauterine growth restriction (IUGR) is one of the greatest challenges. The etiology of IUGR is multifactorial, but most cases are thought to arise from placental insufficiency. However, identifying the placental cause of IUGR can be difficult due to numerous confounding factors. Selective IUGR (sIUGR) would be a good model to investigate how impaired placentation affects fetal
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Recent Advances in Assembly of Plant Complex Genomes Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-25 Weilong Kong, Yibin Wang, Shengcheng Zhang, Jiaxin Yu, Xingtan Zhang
Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly
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Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-22 Chengbo Zhang, Zhenghan Lian, Bo Xu, Qingzhong Shen, Mingwei Bao, Zunxi Huang, Hongchen Jiang, Wenjun Li
The gut microbiome is closely related to host nutrition and health. However, the relationships between gut microorganisms and host lifestyle are not well characterized. In the absence of confounding geographic variation, we defined clear patterns of variation in the gut microbiomes of Asian elephants (AEs) in the Wild Elephant Valley, Xishuangbanna, China, along a lifestyle gradient (completely captive
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Novel Time-dependent Multi-omics Integration in Sepsis-associated Liver Dysfunction Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-20 Ann-Yae Na, Hyojin Lee, Eun Ki Min, Sanjita Paudel, So Young Choi, HyunChae Sim, Kwang-Hyeon Liu, Ki-Tae Kim, Jong-Sup Bae, Sangkyu Lee
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NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-17 Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu
As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0 integrates multi-source information to improve the performance. However, it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins. Recently, protein language models have been proposed to learn informative
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Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-04-17 Lin-Fang Ju, Heng-Ji Xu, Yun-Gui Yang, Ying Yang
During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of , ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation
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Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-03-30 Bin Huang, Lupeng Kong, Chao Wang, Fusong Ju, Qi Zhang, Jianwei Zhu, Tiansu Gong, Haicang Zhang, Chungong Yu, Wei-Mou Zheng, Dongbo Bu
is an interdisciplinary research topic that has attracted researchers from multiple fields, including biochemistry, medicine, physics, mathematics, and computer science. These researchers adopt various research paradigms to attack the same structure prediction problem: biochemists and physicists attempt to reveal the principles governing ; mathematicians, especially statisticians, usually start from
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Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis) Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-16 Yongsheng Wang, Huihui Wang, Huiyuan Wang, Ruifan Zhou, Ji Wu, Zekun Zhang, Yandong Jin, Tao Li, Markus V. Kohnen, Xuqing Liu, Wentao Wei, Kai Chen, Yubang Gao, Jiazhi Ding, Hangxiao Zhang, Bo Liu, Chentao Lin, Lianfeng Gu
Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features
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VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-16 Ye Chen, Yuyan Wang, Ping Zhou, Hao Huang, Rui Li, Zhen Zeng, Zifeng Cui, Rui Tian, Zhuang Jin, Jiashuo Liu, Zhaoyue Huang, Lifang Li, Zheying Huang, Xun Tian, Meiying Yu, Zheng Hu
Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein–Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental
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RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-14 Chen Zhu, Shuting Zhang, Chengzhe Zhou, Caiyun Tian, Biying Shi, Kai Xu, Linjie Huang, Yun Sun, Yuling Lin, Zhongxiong Lai, Yuqiong Guo
The epitranscriptomic mark N6-methyladenosine (m6A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m6A-mediated regulatory mechanism on flavor-related
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Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-14 Wenbin Li, Lin Gao, Xin Yi, Shuangfeng Shi, Jie Huang, Leming Shi, Xiaoyan Zhou, Lingying Wu, Jianming Ying
Defects in genes involved in the cause (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a for assessing the therapeutic response of tumor cells to and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits
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Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-11 Yinquan Qu, Xulan Shang, Ziyan Zeng, Yanhao Yu, Guoliang Bian, Wenling Wang, Li Liu, Li Tian, Shengcheng Zhang, Qian Wang, Dejin Xie, Xuequn Chen, Zhenyang Liao, Yibin Wang, Jian Qin, Wanxia Yang, Caowen Sun, Xiangxiang Fu, Xingtan Zhang, Shengzuo Fang
Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B (CA-B). Here, we present three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative
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Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-11 David Earl Hostallero, Lixuan Wei, Liewei Wang, Junmei Cairns, Amin Emad
Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized medicine. Here, we developed a deep learning framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization
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Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-02-11 Feng Yu, Huanhuan Qi, Li Gao, Sen Luo, Rebecca Njeri Damaris, Yinggen Ke, Wenhua Wu, Pingfang Yang
Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N6-methyladenosine (m6A)
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What Has Genomics Taught An Evolutionary Biologist? Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-01-28 Jianzhi Zhang
Genomics, an interdisciplinary field of biology on the structure, function, and evolution of genomes, has revolutionized many subdisciplines of life sciences, including my field of evolutionary biology, by supplying huge data, bringing high-throughput technologies, and offering a new approach to biology. In this review, I describe what I have learned from genomics and highlight the fundamental knowledge
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The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-01-25 Sijia Wu, Zhiwei Fan, Pora Kim, Liyu Huang, Xiaobo Zhou
Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events
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Mapping Multiple Factors-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-01-23 Yan Zhang, Jingwen Zhang, Wei Zhang, Mohan Wang, Shuangqi Wang, Yao Xu, Lun Zhao, Xingwang Li, Guoliang Li
Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, dysregulation of long-range chromatin interactions in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction
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Corrigendum to “An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication” [Genomics Proteomics Bioinformatics19 (1) (2021) 108–122] Genom. Proteom. Bioinform. (IF 9.5) Pub Date : 2023-01-19 Guang Song, Emily M. Lee, Jianbo Pan, Miao Xu, Hee-Sool Rho, Yichen Cheng, Nadia Whitt, Shu Yang, Jennifer Kouznetsova, Carleen Klumpp-Thomas, Samuel G. Michael, Cedric Moore, Ki-Jun Yoon, Kimberly M. Christian, Anton Simeonov, Wenwei Huang, Menghang Xia, Ruili Huang, Madhu Lal-Nag, Hengli Tang, Heng Zhu
Abstract not available