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ORCIDGenomics, Proteomics & Bioinformatics, Volume 21
Volume 21, Number 1, February 2023
- Jianzhi Zhang
:
What Has Genomics Taught An Evolutionary Biologist? 1-12 - Ran Wang, Guangdun Peng, Patrick P. L. Tam, Naihe Jing:
Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies. 13-23 - Shuangsang Fang, Bichao Chen, Yong Zhang, Haixi Sun, Longqi Liu, Shiping Liu, Yuxiang Li, Xun Xu:
Computational Approaches and Challenges in Spatial Transcriptomics. 24-47 - Waleed Iqbal, Wanding Zhou:
Computational Methods for Single-cell DNA Methylome Analysis. 48-66 - Wenbin Ye, 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. 67-83 - Yali Liu, Harry Cheuk-Hay Lau, Wing Yin Cheng, Jun Yu:
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment. 84-96 - Jun Zhang, Wenli Liu, Halimureti Simayijiang, Ping Hu, Jiangwei Yan:
Application of Microbiome in Forensics. 97-107
- Chao 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. 108-126
- Gang 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:
The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates. 127-149 - Chengbo 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. 150-163 - Jianlei Gu, Jiawei Dai, Hui Lu, Hongyu Zhao:
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective. 164-176 - Oh 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. 177-189
- Zuguang Gu, Daniel Hübschmann:
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, 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. 216-227
- Renfei 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. 228-241
Volume 21, Number 2, April 2023
- Jian 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. 243-258 - Jingcheng Wu, Wenfan Chen, Yuxuan Zhou, Ying Chi, Xian-Sheng Hua, Jian Wu, Xun Gu, Shu-Qing Chen, Zhan Zhou:
TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database. 259-266 - Zexian 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. 267-277 - Shunheng Zhou, Yu'e Huang, Jiani Xing, Xu Zhou, Sina Chen, Jiahao Chen, Lihong Wang, Wei Jiang:
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis. 278-282 - Jianjian Wang, Shuang Li, Tianfeng Wang, Si Xu, Xu Wang, Xiaotong Kong, Xiaoyu Lu, Huixue Zhang, Lifang Li, Meng Feng, Shangwei Ning, Lihua Wang:
RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System. 283-291 - Tong 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. 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, Shanwen Sun, Yang Luo, Chaoyue Long, Jingwen Zhai, Yixiao Zhai, Guohua Wang:
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database. 311-323 - Zhongqiu 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. 324-336
- Zhihang Chen, Ziwei Luo, Di Zhang, Huiqin Li, Xuefei Liu, Kaiyu Zhu, Hongwan Zhang, Zongping Wang, Penghui Zhou, Jian Ren, An Zhao, Zhixiang Zuo:
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource. 337-348 - Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu:
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations. 349-358
- Yihe Pang, Bin Liu:
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning. 359-369 - Guangsheng 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. 370-384 - Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang:
RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants. 385-395 - Lei Du, Jin Zhang, Ying Zhao, Muheng Shang, Lei Guo, Junwei Han:
inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics. 396-413
- Shi-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. 414-426
Volume 21, Number 3, June 2023
- Weilong Kong, Yibin Wang, Shengcheng Zhang, Jiaxin Yu, Xingtan Zhang:
Recent Advances in Assembly of Complex Plant Genomes. 427-439
- Le 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. 440-454 - 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:
Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus. 455-469 - Ruobing 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. 470-482 - 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, 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. 483-500 - Jingqi Zhou, Ake Liu, Funan He, Yunbin Zhang, Libing Shen, Jun Yu, Xiang Zhang:
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. 501-514 - Sébastien 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. 515-534 - David Earl Hostallero, Lixuan Wei, Liewei Wang, Junmei Cairns, Amin Emad:
Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL. 535-550 - 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, Yinglan Zhao, Xiaobo Cen:
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons. 551-572 - Yan Zhang, Jingwen Zhang, Wei Zhang, Mohan Wang, Shuangqi Wang, Yao Xu, Lun Zhao, Xingwang Li, Guoliang Li:
Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes. 573-588 - Sheng 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. 589-600 - Guoli 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. 601-618 - Sijia Wu, Zhiwei Fan, Pora Kim, Liyu Huang, Xiaobo Zhou:
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. 619-631
- Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Chen Zhao, Nini Wang, Rasmus Heller, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang:
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. 632-648 - Zheng Wang, 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. 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, Jian-Hua Yang:
RNA Modifications and Epitranscriptomics. 675-677
- Bowen Song, Daiyun Huang, Yuxin Zhang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Kunqi Chen:
m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues. 678-694
- Yafen Wang, Xiang Zhou:
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, Jun Li:
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma. 707-728 - Zidong 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:
Transcriptome-wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis. 729-741 - Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Rivière:
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes. 742-755 - Ying Lv, Fei Han, Mengxia Liu, Ting Zhang, Guanshen Cui, Jiaojiao Wang, Ying Yang, Yun-Gui Yang, Wenqiang Yang:
Characteristics of N6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. 756-768 - Chen Zhu, Shuting Zhang, Chengzhe Zhou, Caiyun Tian, Biying Shi, Kai Xu, Linjie Huang, Yun Sun, Yuling Lin, Zhongxiong Lai, Yuqiong Guo:
RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. 769-787 - Feng 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. 788-804 - Xiao 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. 805-822 - Dan Song, Ke An, Wenlong Zhai, Luyao Feng, Yingjie Xu, Ran Sun, Yueqin Wang, Yun-Gui Yang, Quancheng Kan, Xin Tian:
NSUN2-mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma. 823-833 - Peng 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. 834-849 - Boyang Shi, Ke An, Yueqin Wang, Yuhan Fei, Caixia Guo, Qiangfeng Cliff Zhang, Yun-Gui Yang, Xin Tian, Quancheng Kan:
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, Jinyang Zhang, Fangqing Zhao:
Screening Linear and Circular RNA Transcripts from Stress Granules. 886-893
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