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Genomics, Proteomics & Bioinformatics, Volume 22

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Volume 22, Number 1, 2024

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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:
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications.
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Gunhwan Ko, Jae Ho Lee, Young Mi Sim, Wangho Song, Byung-Ha Yoon, Iksu Byeon, Bang Hyuck Lee, Sangok Kim, Jinhyuk Choi, Insoo Jang, Hyerin Kim, Jin Ok Yang, Kiwon Jang, Sora Kim, Jong-Hwan Kim, Jongbum Jeon, Jaeeun Jung, Seungwoo Hwang, Ji-Hwan Park, Pan-Gyu Kim, Seon-Young Kim, Byungwook Lee:
KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data.
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Peipei Wang, Juntao Lin, Xiangyang Zheng, Xingzhi Xu:
RNase P: Beyond Precursor tRNA Processing.
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Acknowledgments to Reviewers 2023.
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Gang-Qing Hu, Li Liu, Dong Xu:
On the Responsible Use of Chatbots in Bioinformatics.
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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:
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice.
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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:
Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories.
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Junhai Qi, Chenjie Feng, Yulin Shi, Jianyi Yang, Fa Zhang, Guojun Li, Renmin Han:
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.
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Bingbing Hao, Kaifeng Chen, Linhui Zhai, Muyin Liu, Bin Liu, Minjia Tan:
Substrate and Functional Diversity of Protein Lysine Post-translational Modifications.
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Ke-Jia Shan, Changcheng Wu, Xiaolu Tang, Roujian Lu, Yaling Hu, Wenjie Tan, Jian Lu:
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses.
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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:
HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC.
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Liwen Xiao, Zhenqiang Zuo, Fangqing Zhao:
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies.
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Jiang Hu, Zhuo Wang, Fan Liang, Shanlin Liu, Kai Ye, De-Peng Wang:
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.
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Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye:
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach.
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Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou:
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.
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Manickam Ashokkumar, Wenwen Mei, Jackson J. Peterson, Yuriko Harigaya, David M. Murdoch, David M. Margolis, Caleb Kornfein, Alexander X. Oesterling, Zhicheng Guo, Cynthia Rudin, Yuchao Jiang, Edward P. Browne:
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation.
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Correction to: dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms.
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Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang:
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions.
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Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells.
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Zitian Huo, Yaqi Duan, Dongdong Zhan, Xizhen Xu, Nairen Zheng, Jing Cai, Ruifang Sun, Jianping Wang, Fang Cheng, Zhan Gao, Caixia Xu, Wanlin Liu, Yuting Dong, Sailong Ma, Qian Zhang, Yiyun Zheng, Liping Lou, Dong Kuang, Qian Chu, Jun Qin, Guoping Wang, Yi Wang:
Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer.
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Mohammad Saidur Rhaman, Muhammad Ali, Wenxiu Ye, Bosheng Li:
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics.
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Wenju Liu, Chuan Chen, Yawei Gao, Xinyu Cui, Yuhan Zhang, Liang Gu, Yuanlin He, Jing Li, Shaorong Gao, Rui Gao, Cizhong Jiang:
Transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development.
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Hangxing Jia, Shengjun Tan, Yong E. Zhang:
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs.
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Xi Wang, Qiwei Lian, Haoyu Dong, Shuo Xu, Yaru Su, Xiaohui Wu:
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data.
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Correction to: m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes.
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Tao Yu, Yingfeng Luo, Xinyu Tan, Dahe Zhao, Xiaochun Bi, Chenji Li, Yanning Zheng, Hua Xiang, Songnian Hu:
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.
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Chao Li, Bingchun Chen, Suo Langda, Peng Pu, Xiaojia Zhu, Shiwei Zhou, Peter Kalds, Ke Zhang, Meenu Bhati, Alexander Leonard, Shuhong Huang, Ran Li, Awang Cuoji, Xiran Wang, Haolin Zhu, Yujiang Wu, Renqin Cuomu, Ba Gui, Ming Li, Yutao Wang, Yan Li, Wenwen Fang, Ting Jia, Tianchun Pu, Xiangyu Pan, Yudong Cai, Chong He, Liming Wang, Yu Jiang, Jian-Lin Han, Yulin Chen, Ping Zhou, Hubert Pausch, Xiaolong Wang:
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep.
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Yiling Elaine Chen, Xinzhou Ge, Kyla Woyshner, Meilu McDermott, Antigoni Manousopoulou, Scott B. Ficarro, Jarrod A. Marto, Kexin Li, Leo David Wang, Jingyi Jessica Li:
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control.
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Ming Xiao, Rui Wei, Jun Yu, Chujie Gao, Fengyi Yang, Le Zhang:
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome.
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Wanlin Zhou, Haoran Shi, Zhiqiang Wang, Yuxin Huang, Lin Ni, Xudong Chen, Yan Liu, Haojie Li, Caixia Li, Yaxi Liu:
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq.
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Yanni Li, Eline H. van den Berg, Alexander Kurilshikov, Dasha V. Zhernakova, Ranko Gacesa, Shixian Hu, Esteban A. Lopera-Maya, Alexandra Zhernakova, Raúl Aguirre-Gamboa, Patrick Deelen, Lude Franke, Jan A. Kuivenhoven, Ilja M. Nolte, Serena Sanna, Harold Snieder, Morris A. Swertz, Peter M. Visscher, Judith M. Vonk, Cisca Wijmenga, Vincent E. de Meijer, Robin P. F. Dullaart, Hans Blokzijl, Eleonora A. M. Festen, Jingyuan Fu, Rinse K. Weersma:
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content.
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Huiling Liu, Wenxiu Ma:
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.
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Shan-Ju Yeh, Shreya Paithankar, Ruoqiao Chen, Jing Xing, Mengying Sun, Ke Liu, Jiayu Zhou, Bin Chen:
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning.
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Fei Leng, Song Mei, Xiaolin Zhou, Xuanshi Liu, Yefeng Yuan, Wenjian Xu, Chongyi Hao, Ruolan Guo, Chanjuan Hao, Wei Li, Peng Zhang:
DVsc: An Automated Framework for Efficiently Detecting Viral Infection from Single-cell Transcriptomics Data.
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Haojing Shao, Jue Ruan:
BSAlign: A Library for Nucleotide Sequence Alignment.
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Libo Jiang, Michael A Quail, Jack Fraser-Govil, Haipeng Wang, Xuequn Shi, Karen Oliver, Esther Mellado Gomez, Fengtang Yang, Zemin Ning:
The Bioinformatic Applications of Hi-C and Linked Reads.
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Yueqi Li, Jingyi Li, Wenxing Li, Shuaiyi Liang, Wudi Wei, Jiemei Chu, Jingzhen Lai, Yao Lin, Hubin Chen, Jinming Su, Xiaopeng Hu, Gang Wang, Jun Meng, Junjun Jiang, Li Ye, Sanqi An:
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level.
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Jin-Ting Zhou, Yungang Xu, Xiao-Huan Liu, Cheng Cheng, Jing-Na Fan, Xiaoming Li, Jun Yu, Shengbin Li:
Single-cell RNA-seq Reveals the Inhibitory Effect of Methamphetamine on Liver Immunity with the Involvement of Dopamine Receptor D1.

Volume 22, Number 3, 2024

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Hongzhe Guo, Liyuan Zhang, Xinran Cui, Liang Cheng, Tianyi Zhao, Yadong Wang:
SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers.
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Congfan Bu, Xinchang Zheng, Xuetong Zhao, Tianyi Xu, Xue Bai, Yaokai Jia, Meili Chen, Lili Hao, Jing-Fa Xiao, Zhang Zhang, Wenming Zhao, Bixia Tang, Yiming Bao:
GenBase: A Nucleotide Sequence Database.
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Xiuying Liu, Xianwen Ren:
Computational Strategies and Algorithms for Inferring Cellular Composition of Spatial Transcriptomics Data.
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Fei Qi, Junjie Chen, Yue Chen, Jianfeng Sun, Yiting Lin, Zipeng Chen, Philipp Kapranov:
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.
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Peng Jia, Xuanhao Yang, Xiaofei Yang, Tingjie Wang, Yu Xu, Kai Ye:
MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.
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Hong-Fu Li, Jing-Tian Wang, Qiong Zhao, Yuan-Ming Zhang:
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies.
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Yi Jiang, Minghan Qu, Minghui Jiang, Xuan Jiang, Shane Fernandez, Tenielle Porter, Simon M. Laws, Colin L. Masters, Huan Guo, Shanshan Cheng, Chaolong Wang:
MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data.
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Siyuan Cheng, Benpeng Miao, Tiandao Li, Guoyan Zhao, Bo Zhang:
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data.
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Xiaoping Liu, Zisong Wang, Hongjie Shi, Sheng Li, Xinghuan Wang:
CBioProfiler: A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization.
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Tianyi Ding, Shaliu Fu, Xiaoyu Zhang, Fan Yang, Jixing Zhang, Haowen Xu, Jiaqi Yang, Chaoqun Chen, Yibing Shi, Yiran Bai, Wannian Li, Xindi Chang, Shanjin Wang, Chao Zhang, Qi Liu, He Zhang:
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.
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Lan Mei, Yaopan Hou, Jiajun Zhou, Yetong Chang, Yuwei Liu, Di Wang, Yunpeng Zhang, Shangwei Ning, Xia Li:
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs.
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Ming-Xiao Zhao, Ruofan Ding, Qiang Chen, Junhua Meng, Fulai Li, Songsen Fu, Biling Huang, Yan Liu, Zhi-Liang Ji, Yufen Zhao:
Nphos: Database and Predictor of Protein N-phosphorylation.
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Jianmei Zhong, Junyao Yang, Yinghui Song, Zhihua Zhang, Chunming Wang, Renyang Tong, Chenglong Li, Nanhui Yu, Lianhong Zou, Sulai Liu, Jun Pu, Wei Lin:
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing.
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Zekai Liu, Zhen Yuan, Yunlei Guo, Ruilin Wang, Yusheng Guan, Zhanglian Wang, Yunan Chen, Tianlu Wang, Meining Jiang, Shuhui Bian:
SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine.

Volume 22, Number 4, 2024

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Mingyue Cheng, Hong Zhou, Haobo Zhang, Xinchao Zhang, Shuting Zhang, Hong Bai, Yugo Zha, Dan Luo, Dan Chen, Siyuan Chen, Kang Ning, Wei Liu:
Hidden Links Between Skin Microbiome and Skin Imaging Phenome.
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Cheng Zou, Jinwei Zhu, Jiangling Xiong, Yu Tian, Yousong Peng, Edwin Cheung, Dingxiao Zhang:
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types.
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Yao Lin, Jingyi Li, Shuaiyi Liang, Yaxin Chen, Yueqi Li, Yixian Cun, Lei Tian, Yuanli Zhou, Yitong Chen, Jiemei Chu, Hubin Chen, Qiang Luo, Ruili Zheng, Gang Wang, Hao Liang, Ping Cui, Sanqi An:
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types.
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Yuwei Zhang, Lihai Gong, Ruofan Ding, Wenyan Chen, Hao Rong, Yanguo Li, Fawziya Shameem, Korakkandan Arshad Ali, Lei Li, Qi Liao:
eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs.
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Tao Yue, Si-Yi Chen, Wen-Kang Shen, Zhan-Ye Zhang, Liming Cheng, An-Yuan Guo:
TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences.
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Weiwei Zhou, Minghai Su, Tiantongfei Jiang, Yunjin Xie, Jingyi Shi, Yingying Ma, Kang Xu, Gang Xu, Yongsheng Li, Juan Xu:
Cancer Stemness Online: A Resource for Investigating Cancer Stemness and Associations with Immune Response.
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Rou Zhang, Meng Hu, Yu Liu, Wanmeng Li, Zhiqiang Xu, Siyu He, Ying Lu, Yanqiu Gong, Xiuxuan Wang, Shan Hai, Shuangqing Li, Shiqian Qi, Yuan Li, Yang Shu, Dan Du, Huiyuan Zhang, Heng Xu, Zongguang Zhou, Peng Lei, Hai-Ning Chen, Lunzhi Dai:
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer.
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Yanguo Li, Chen Lin, Yidian Chu, Zhengyu Wei, Qi Ding, Shanshan Gu, Hongxia Deng, Qi Liao, Zhisen Shen:
Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing.
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Qian Cheng, Xiangfeng Wang:
Machine Learning for AI Breeding in Plants.
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Xueshuai Han, Zhaoqi Liu:
Aberrant Somatic Hypermutation at Super-enhancer Drives B Cell Lymphoma Transformation.
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Zhang Zhang:
Laws of Genome Nucleotide Composition.
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Yujie Wang, Chen Yang, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang, Chengqi Yi:
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility.

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