Journal: Genomics, Proteomics & Bioinformatics

Volume 21, Issue 4

675 -- 677Chengqi Yi, Jian-Hua Yang. RNA Modifications and Epitranscriptomics
678 -- 694Bowen Song, Daiyun Huang, Yuxin Zhang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Kunqi Chen. 6A-affecting Mutations in 23 Human Tissues
695 -- 706Yafen Wang, Xiang Zhou. 6-methyladenosine and Its Implications in Viruses
707 -- 728Yixian 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, Jun Li. 6A by SRSF7 Promotes the Progression of Glioblastoma
729 -- 741Zidong Liu, Xiaoxu Chen, Pengfei Zhang, Fuyuan Li, Lingkai Zhang, Xueliang Li, Tao Huang, Yi Zheng, Taiyong Yu, Tao Zhang, Wenxian Zeng, Hongzhao Lu, Yinghua Lv. 6A mRNA Methylation During Porcine Spermatogenesis
742 -- 755Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Rivière. 6A-RNA Epitranscriptomes
756 -- 768Ying Lv, Fei Han, Mengxia Liu, Ting Zhang, Guanshen Cui, Jiaojiao Wang, Ying Yang, Yun-Gui Yang, Wenqiang Yang. Chlamydomonas reinhardtii
769 -- 787Chen Zhu, Shuting Zhang, Chengzhe Zhou, Caiyun Tian, Biying Shi, Kai Xu, Linjie Huang, Yun Sun, Yuling Lin, Zhongxiong Lai, Yuqiong Guo. 6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering
788 -- 804Feng Yu, Huanhuan Qi, Li Gao, Sen Luo, Rebecca Njeri Damaris, Yinggen Ke, Wenhua Wu, Pingfang Yang. Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice
805 -- 822Xiao Han, Jia Guo, Mengke Wang, Nan Zhang, Jie Ren, Ying Yang, Xu Chi, Yusheng Chen, Huan Yao, Yongliang Zhao, Yun-Gui Yang, Yingpu Sun, Jiawei Xu. Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine Reprogramming During Early Human Development
823 -- 833Dan Song, Ke An, Wenlong Zhai, Luyao Feng, Yingjie Xu, Ran Sun, Yueqin Wang, Yun-Gui Yang, Quancheng Kan, Xin Tian. 5C Modification Regulates the Progression of Hepatocellular Carcinoma
834 -- 849Peng Yu, Siting Zhou, Yan Gao, Yu Liang, Wenbing Guo, Dan Ohtan Wang, Shuaiwen Ding, Shuibin Lin, Jinkai Wang, Yixian Cun. Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues
850 -- 865Boyang Shi, Ke An, Yueqin Wang, Yuhan Fei, Caixia Guo, Qiangfeng Cliff Zhang, Yun-Gui Yang, Xin Tian, Quancheng Kan. YRDC Translation in NSCLC Cells
866 -- 885Yongsheng 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. Phyllostachys edulis)
886 -- 893Shuai Chen, Jinyang Zhang, Fangqing Zhao. Screening Linear and Circular RNA Transcripts from Stress Granules

Volume 21, Issue 3

427 -- 439Weilong Kong, Yibin Wang 0004, Shengcheng Zhang, Jiaxin Yu, Xingtan Zhang. Recent Advances in Assembly of Complex Plant Genomes
440 -- 454Le Wang, May Lee, Zi Yi Wan, Bin Bai, Baoqing Ye, Yuzer Alfiko, Rahmadsyah Rahmadsyah, Sigit Purwantomo, Zhuojun Song, Antonius Suwanto, Gen Hua Yue. A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation
455 -- 469Yinquan 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 0004, Jian Qin, Wanxia Yang, Caowen Sun, Xiangxiang Fu, Xingtan Zhang, Shengzuo Fang. Cyclocarya paliurus
470 -- 482Ruobing Han, Lei Han, Xunwu Zhao, Qianghui Wang, Yanling Xia, Heping Li. Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution
483 -- 500Guobin 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, Yu Zhang, Yang Chen, Hong Li, Jianfeng Liu, Wangcheng Dai, Guohong Chen. The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation
501 -- 514Jingqi Zhou, Ake Liu, Funan He, Yunbin Zhang, Libing Shen, Jun Yu 0004, Xiang Zhang. Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation
515 -- 534Sébastien Leblanc, Marie A. Brunet, Jean-Francois Jacques, Amina M. Lekehal, Andréa Duclos, Alexia Tremblay, Alexis Bruggeman-Gascon, Sondos Samandi, Mylène Brunelle, Alan A. Cohen, Michelle S. Scott, Xavier Roucou. Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities
535 -- 550David Earl Hostallero, Lixuan Wei, Liewei Wang, Junmei Cairns, Amin Emad. Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL
551 -- 572Liang 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, Yinglan Zhao, Xiaobo Cen. Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons
573 -- 588Yan Zhang, Jingwen Zhang, Wei Zhang, Mohan Wang, Shuangqi Wang, Yao Xu, Lun Zhao, Xingwang Li, Guoliang Li 0002. Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes
589 -- 600Sheng Hu Qian, Yu-Li Xiong, Lu Chen, Yingjie Geng, Xiao-Man Tang, Zhen-Xia Chen. Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals
601 -- 618Guoli Ji, Qi Tang, Sheng Zhu, Junyi Zhu, Pengchao Ye, Shuting Xia, Xiaohui Wu. stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies
619 -- 631Sijia Wu, Zhiwei Fan, Pora Kim, Liyu Huang, Xiaobo Zhou 0005. The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers
632 -- 648Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Chen Zhao, Nini Wang, Rasmus Heller, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang 0001. CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network
649 -- 661Zheng Wang 0069, Guihu Zhao, Bin Li, Zhenghuan Fang, Qian Chen, Xiaomeng Wang, Tengfei Luo, Yijing Wang, Qiao Zhou, Kuokuo Li, Lu Xia, Yi Zhang, Xun Zhou, Hongxu Pan, Yuwen Zhao, Yige Wang, Lin Wang, Jifeng Guo, Beisha Tang, Kun Xia, Jinchen Li. Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants
662 -- 673Fang-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

Volume 21, Issue 2

243 -- 258Jian Li, Weicheng Liang, Zaozao Chen, Xingyu Li, Pan Gu, Anna Liu, Pin Chen, Qiwei Li, Xueyin Mei, Jing Yang, Jun Liu, Lincao Jiang, Zhongze Gu. OOCDB: A Comprehensive, Systematic, and Real-time Organs-on-a-chip Database
259 -- 266Jingcheng Wu, Wenfan Chen, Yuxuan Zhou, Ying Chi, Xian-Sheng Hua 0001, Jian Wu 0001, Xun Gu, Shu-Qing Chen, Zhan Zhou. TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database
267 -- 277Zexian Liu, Panqin Wang, Qingfeng Zhang, Shihua Li, Yuxin Zhang, Yutong Guo, Chongchong Jia, Tian Shao, Lin Li, Han Cheng, Zhenlong Wang. iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals
278 -- 282Shunheng Zhou, Yu'e Huang, Jiani Xing, Xu Zhou, Sina Chen, Jiahao Chen, Lihong Wang, Wei Jiang 0023. ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis
283 -- 291Jianjian Wang, Shuang Li, Tianfeng Wang, Si Xu, Xu Wang, Xiaotong Kong, Xiaoyu Lu, Huixue Zhang, Lifang Li, Meng Feng, Shangwei Ning, Lihua Wang 0002. RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System
292 -- 299Tong Tang, Xingyun Liu, Rongrong Wu, Li Shen, Shumin Ren, Bairong Shen. CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs
300 -- 310Ye 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
311 -- 323Ke Ding, Shanwen Sun, Yang Luo, Chaoyue Long, Jingwen Zhai, Yixiao Zhai, Guohua Wang. PlantCADB: A Comprehensive Plant Chromatin Accessibility Database
324 -- 336Zhongqiu Li, Yiheng Hu, Xuelian Ma, Lingling Da, Jiajie She, Yue Liu, Xin Yi, Yaxin Cao, Wenying Xu, Yuannian Jiao, Zhen Su. WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors
337 -- 348ZhiHang Chen, Ziwei Luo, Di Zhang, Huiqin Li, Xuefei Liu, Kaiyu Zhu, Hongwan Zhang, Zongping Wang, Penghui Zhou, Jian Ren 0002, An Zhao, Zhixiang Zuo. TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource
349 -- 358Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu. NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations
359 -- 369Yihe Pang, Bin Liu 0014. TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning
370 -- 384Guangsheng Pei, Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao. deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues
385 -- 395Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang. RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants
396 -- 413Lei Du, Jin Zhang, Ying Zhao, Muheng Shang, Lei Guo 0002, Junwei Han. inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics
414 -- 426Shi-Yuan Tong, Ke-fan, Zai-Wei Zhou, Lin-Yun Liu, Shu-Qing Zhang, Yinghui Fu, Guang-Zhong Wang, Ying Zhu, Yong-Chun Yu. mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants

Volume 21, Issue 1

1 -- 12Jianzhi Zhang. What Has Genomics Taught An Evolutionary Biologist?
13 -- 23Ran Wang, Guangdun Peng, Patrick P. L. Tam, Naihe Jing. Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies
24 -- 47Shuangsang Fang, Bichao Chen, Yong Zhang 0036, Haixi Sun, Longqi Liu, Shiping Liu, Yuxiang Li, Xun Xu. Computational Approaches and Challenges in Spatial Transcriptomics
48 -- 66Waleed Iqbal, Wanding Zhou. Computational Methods for Single-cell DNA Methylome Analysis
67 -- 83Wenbin Ye 0002, Qiwei Lian, Congting Ye, Xiaohui Wu. A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq
84 -- 96Yali Liu, Harry Cheuk-Hay Lau, Wing Yin Cheng, Jun Yu 0009. Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment
97 -- 107Jun Zhang, Wenli Liu, Halimureti Simayijiang, Ping Hu, Jiangwei Yan. Application of Microbiome in Forensics
108 -- 126Chao Li, Wen Chu, Rafaqat Ali Gill, Shifei Sang, Yuqin Shi, Xuezhi Hu, Yuting Yang, Qamar U. Zaman, Baohong Zhang. Computational Tools and Resources for CRISPR/Cas Genome Editing
127 -- 149Gang Chen, Salma Mostafa, Zhaogeng Lu, Ran Du, Jiawen Cui, Yun Wang, Qinggang Liao, Jinkai Lu, Xinyu Mao, Bang Chang, Quan Gan, Li Wang, Zhichao Jia, Xiulian Yang, Yingfang Zhu, Jianbin Yan, Biao Jin. Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates
150 -- 163Chengbo Zhang, Zhenghan Lian, Bo Xu, Qingzhong Shen, Mingwei Bao, Zunxi Huang, Hongchen Jiang, Wenjun Li. Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants
164 -- 176Jianlei Gu, Jiawei Dai, Hui Lu 0004, Hongyu Zhao. Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective
177 -- 189Oh Kwang Kwon, In Hyuk Bang, So-Young Choi, Ju Mi Jeon, Ann-Yae Na, Yan Gao, Sam Seok Cho, Sung Hwan Ki, Youngshik Choe, Jun Nyung Lee, Yun-Sok Ha, Eun Ju Bae, Tae-Gyun Kwon, Byung-Hyun Park, Sangkyu Lee. LDHA Desuccinylase Sirtuin 5 as A Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer
190 -- 202Zuguang Gu, Daniel Hübschmann. simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results
203 -- 215Xiumei 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 0004, 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
216 -- 227Wei-Zhen Zhou, Wenke Li, Huayan Shen, Ruby W. Wang, Wen Chen, Yujing Zhang, Qingyi Zeng, Hao Wang, Meng Yuan, Ziyi Zeng, Jinhui Cui, Chuan-Yun Li, Fred Y. Ye, Zhou Zhou. CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations
228 -- 241Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, Tzong-Yi Lee. KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites