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Genomics, Proteomics & Bioinformatics, Volume 21
Volume 21, Number 1, February 2023
- Jianzhi Zhang
:
What Has Genomics Taught An Evolutionary Biologist? 1-12 - Ran Wang
Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies. 13-23 - Shuangsang Fang
Computational Approaches and Challenges in Spatial Transcriptomics. 24-47 - Waleed Iqbal
Computational Methods for Single-cell DNA Methylome Analysis. 48-66 - Wenbin Ye
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq. 67-83 - Yali Liu
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment. 84-96 - Jun Zhang
Application of Microbiome in Forensics. 97-107
- Chao Li
Computational Tools and Resources for CRISPR/Cas Genome Editing. 108-126
- Gang Chen
The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates. 127-149 - Chengbo Zhang
Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants. 150-163 - Jianlei Gu
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective. 164-176 - Oh Kwang Kwon
LDHA Desuccinylase Sirtuin 5 as A Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer. 177-189
- Zuguang Gu
simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results. 190-202
- Xiumei Xing, Cheng Ai, Tianjiao Wang, Yang Li, Huitao Liu, Pengfei Hu, Guiwu Wang, Huamiao Liu, Hongliang Wang, Ranran Zhang, Junjun Zheng, Xiaobo Wang, Lei Wang, Yuxiao Chang, Qian Qian, Jinghua Yu, Lixin Tang, Shigang Wu, Xiujuan Shao, Alun Li, Peng Cui, Wei Zhan, Sheng Zhao, Zhichao Wu, Xiqun Shao, Yimeng Dong, Min Rong, Yihong Tan, Xuezhe Cui, Shuzhuo Chang, Xingchao Song, Tongao Yang, Limin Sun, Yan Ju, Pei Zhao, Huanhuan Fan, Ying Liu, Xinhui Wang, Wanyun Yang, Min Yang, Tao Wei, Shanshan Song, Jiaping Xu, Zhigang Yue, Qiqi Liang, Chunyi Li, Jue Ruan, Fuhe Yang:
The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation. 203-215
- Wei-Zhen Zhou
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations. 216-227
- Renfei Ma
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. 228-241
Volume 21, Number 2, April 2023
- Jian Li
OOCDB: A Comprehensive, Systematic, and Real-time Organs-on-a-chip Database. 243-258 - Jingcheng Wu
TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database. 259-266 - Zexian Liu
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals. 267-277 - Shunheng Zhou
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis. 278-282 - Jianjian Wang
RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System. 283-291 - Tong Tang
CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs. 292-299 - 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:
VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns. 300-310 - Ke Ding
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database. 311-323 - Zhongqiu Li
WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors. 324-336
- Zhihang Chen
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource. 337-348 - Shaojun Wang
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations. 349-358
- Yihe Pang
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning. 359-369 - Guangsheng Pei
deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues. 370-384 - Hao Lu
RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants. 385-395 - Lei Du
inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics. 396-413
- Shi-Yuan Tong
mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants. 414-426
Volume 21, Number 3, June 2023
- Weilong Kong
Recent Advances in Assembly of Complex Plant Genomes. 427-439
- Le Wang
A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation. 440-454 - Yinquan Qu
Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus. 455-469 - Ruobing Han
Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution. 470-482 - Guobin Chang
The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation. 483-500 - Jingqi Zhou
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. 501-514 - Sébastien Leblanc
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. 515-534 - David Earl Hostallero
Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL. 535-550 - Liang Wang
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons. 551-572 - Yan Zhang
Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes. 573-588 - Sheng Hu Qian
Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals. 589-600 - Guoli Ji, Qi Tang
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies. 601-618 - Sijia Wu
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. 619-631
- Xiangyu Pan
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. 632-648 - Zheng Wang
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants. 649-661
- Fang-Yuan Shi, Yu Wang, Dong Huang, Yu Liang, Nan Liang, Xiao-Wei Chen, Ge Gao:
Computational Assessment of the Expression-modulating Potential for Non-coding Variants. 662-673
Volume 21, Number 4, August 2023
- Chengqi Yi
RNA Modifications and Epitranscriptomics. 675-677
- Bowen Song
m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues. 678-694
- Yafen Wang
N6-methyladenosine and Its Implications in Viruses. 695-706
- Yixian Cun, Sanqi An, Haiqing Zheng, Jing Lan, Wenfang Chen, Wanjun Luo, Chengguo Yao, Xincheng Li, Xiang Huang, Xiang Sun, Zehong Wu, Yameng Hu, Ziwen Li, Shuxia Zhang, Geyan Wu, Meisongzhu Yang, Miaoling Tang, Ruyuan Yu, Xinyi Liao, Guicheng Gao, Wei Zhao, Jinkai Wang
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma. 707-728 - Zidong Liu, Xiaoxu Chen, Pengfei Zhang, Fuyuan Li
Transcriptome-wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis. 729-741 - Lorane Le Franc
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes. 742-755 - Ying Lv
Characteristics of N6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. 756-768 - Chen Zhu
RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. 769-787 - Feng Yu
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice. 788-804 - Xiao Han
Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine Reprogramming During Early Human Development. 805-822 - Dan Song
NSUN2-mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma. 823-833 - Peng Yu
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues. 834-849 - Boyang Shi
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells. 850-865 - 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:
Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis). 866-885
- Shuai Chen
Screening Linear and Circular RNA Transcripts from Stress Granules. 886-893
Volume 21, Number 5, 2023
- Jun Yu
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology. 895-896 - Runsheng Chen
A Historic Retrospective on the Early Bioinformatics Research in China. 897-899 - Yiming Bao
From BIG Data Center to China National Center for Bioinformation. 900-903 - Zhang Zhang
Toward a New Paradigm of Genomics Research - Celebration of the 20th Anniversary of Beijing Institute of Genomics. 904-909 - Yaojun Wang
Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries. 910-912 - Bin Huang
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. 913-925 - Qiang Shi
Decoding Human Biology and Disease Using Single-Cell Omics Technologies. 926-949 - Lin-Fang Ju
Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development. 950-961 - Wenbin Li
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. 962-975 - Yuliang Pan
HPC-Atlas: Computationally Constructing a Comprehensive Atlas of Human Protein Complexes. 976-990 - Jennifer A. Karlow
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers. 991-1013 - Tingfu Du
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques. 1014-1029 - Yicong Shen
MicroRNA-Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice. 1030-1042 - Xiaopeng Xu
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning. 1043-1053 - Lina Ma
Database Commons: A Catalog of Worldwide Biological Databases. 1054-1058 - Enhui Jin
OBIA: An Open Biomedical Imaging Archive. 1059-1065 - Cuiping Li
RCoV19: A One-Stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-Warning. 1066-1079
Volume 21, Number 6, 2023
- Jingfa Xiao
T2T-YAO, T2T-SHUN, and More. 1081-1082 - Xue Zhang
T2T-YAO Reference Genome of Han Chinese - New Step in Advancing Precision Medicine in China. 1083-1084 - Yukun He
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese. 1085-1100 - Ann-Yae Na
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction. 1101-1116 - Yongshuai Han
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis. 1117-1132 - Yi Zhou
Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer. 1133-1148 - Jiazhen Zheng
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces. 1149-1162 - Deqi Yin
Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma Gondii. 1163-1181 - Wenjun Li
Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. 1182-1194 - Wing Yin Cheng
High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion. 1195-1205 - Zhi-Xue Yang
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing. 1206-1220 - Zi-Jun Quan
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing. 1221-1236 - Gongchen Zhang
Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer. 1237-1245 - Xin-Lu Meng
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction. 1246-1259 - Renbo Tan
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses. 1260-1265 - Farzaneh Esmaili
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. 1266-1285
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