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ORCIDGenomics, Proteomics & Bioinformatics, Volume 23
Volume 23, Number 1, 2025
- Jinhua He
, Haitao Luo, Wei Wang, Dechao Bu, Zhengkai Zou, Haolin Wang, Hongzhen Tang, Zeping Han, Wenfeng Luo, Jian Shen, Fangmei Xie, Yi Zhao, Zhiming Xiang:
CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer. - Guohao Han, Peng Yang, Yongjin Zhang, Qiaowei Li, Xinhao Fan, Ruipu Chen, Chao Yan, Mu Zeng, Yalan Yang, Zhonglin Tang:
PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies. - Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei, Xu Qiao, Rui Gao, Zhiping Liu, Xiaowo Wang:
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data. - Hitesh Kore, Satomi Okano, Keshava K. Datta, Jackson Thorp, Parthiban Periasamy, Mayur Divate, Upekha Liyanage, Gunter Hartel, Shivashankar H. Nagaraj, Harsha Gowda:
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome. - Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics.
- Siqi Li, Shuwei Li, Siqi Liu, Yan Ren:
Mass Spectrometry-based Solutions for Single-cell Proteomics. - Zhenyang Zhang, Zitao Chen, Jinyan Teng, Shuli Liu, Qing Lin, Jun Wu, Yahui Gao, Zhonghao Bai, Lingzhao Fang, Zhe Zhang, Qishan Wang, George Liu, Bingjie Li, Yuchun Pan:
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis. - Bingru Zhao, Hanpeng Luo, Xuefeng Fu, Guoming Zhang, Emily L. Clark, Feng Wang, Brian P. Dalrymple, V. Hutton Oddy, Philip E. Vercoe, Cuiling Wu, George E. Liu, Cong-jun Li, Ruidong Xiang, Kechuan Tian, Yanli Zhang, Lingzhao Fang:
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep. - Zheng Jia, Yaqing Liu, Shoufang Qu, Wenbin Li, Lin Gao, Lin Dong, Yun Xing, Yadi Cheng, Huan Fang, Yuting Yi, Yuxing Chu, Chao Zhang, Yanming Xie, Chunli Wang, Zhe Li, Zhihong Zhang, Zhipeng Xu, Yang Wang, Wenxin Zhang, Xiaoping Gu, Shuang Yang, Jinghua Li, Liangshen Wei, Yuanting Zheng, Guohui Ding, Leming Shi, Xin Yi, Jianming Ying, Jie Huang:
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment. - Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye:
Long and Accurate: How HiFi Sequencing is Transforming Genomics. - Taoyu Chen, Guoguo Tang, Tianhao Li, Zhining Yanghong, Chao Hou, Zezhou Du, Kaiqiang You, Liwei Ma, Tingting Li:
PhaSeDis: A Manually Curated Database of Phase Separation-disease Associations and Corresponding Small Molecules. - Tao Zhang, Yiyun Liu, Xutong Guo, Xinran Zhang, Xinchang Zheng, Mochen Zhang, Yiming Bao:
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences. - Wenbin Huang, Zhenwei Qian, Jieni Zhang, Yi Ding, Bin Wang, Jiuxiang Lin, Xiannian Zhang, Huaxiang Zhao, Feng Chen:
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate. - Yingke Ma, Xuetong Zhao, Yaokai Jia, Zhenxian Han, Caixia Yu, Zhuojing Fan, Zhang Zhang, Jingfa Xiao, Wenming Zhao, Yiming Bao, Meili Chen:
The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion. - Junwei Liu, Xiaoping Cen, Chenxin Yi, Feng-ao Wang, Junxiang Ding, Jinyu Cheng, Qinhua Wu, Baowen Gai, Yiwen Zhou, Ruikun He, Feng Gao, Yixue Li:
Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis. - Mengjie Wang, Laihua Li, Qing Cheng, Hao Zhang, Zhaode Liu, Yiqiang Cui, Jiahao Sha, Yan Yuan:
HumanTestisDB: A Comprehensive Atlas of Testicular Transcriptomes and Cellular Interactions. - Zhijin Liu, Xiongfei Zhang, Peipei Wang, Minheng Hong, Xiaochan Yan, Xiaoqiu Qi, Qian Zhao, Zhenghao Chen, Huajian Nie, Hui Li, Ziwen Li, Liye Zhang, Jiwei Qi, Chaolei He, Nguyen Van Truong, Minh D. Le, Tilo Nadler, Hiroo Imai, Christian Roos, Ming Li:
Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments. - Zhu-Li Li, Yan Xie, Yafen Wang, Jing Wang, Xiang Zhou, Xiao-Lian Zhang:
NSUN2-mediated HCV RNA m5C Methylation Facilitates Viral RNA Stability and Replication.
Volume 23, Number 2, 2025
- Fuhong He, Zhaojun Zhang, Xiangdong Fang, Qian-Fei Wang:
Biomedical Big Data and Artificial Intelligence in Blood. - Jiaqi Liu, Yalun Li, Wanxiangfu Tang, Tianyi Qian, Lijun Dai, Ziqi Jia, Heng Cao, Chenghao Liu, Yuchen Liu, Yansong Huang, Jiang Wu, Dongxu Ma, Guangdong Qiao, Hua Bao, Shuang Chang, Dongqin Zhu, Shanshan Yang, Xuxiaochen Wu, Xue Wu, Hengyi Xu, Hongyan Chen, Yang Shao, Xiang Wang, Zhihua Liu, Jianzhong Su:
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response. - Huaichao Luo, Changchun Wu, Sisi Yu, Hanxiao Ren, Xing Yin, Ruiling Zu, Lubei Rao, Peiying Zhang, Xingmei Zhang, Ruohao Wu, Ping Leng, Kaijiong Zhang, Qi Peng, Bangrong Cao, Rui Qin, Hulin Wei, Jianlin Qiao, Shanling Xu, Qun Yi, Yang Zhang, Jian Huang, Dongsheng Wang:
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights. - Xin-ping Cai, Qianru Zhang, Bolin Liu, Lulu Sun, Yuxuan Li:
HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies. - Ying Yi, Yongfei Hu, Juanjuan Kang, Qifa Liu, Yan Huang, Dong Wang:
Biological Data Resources and Machine Learning Frameworks for Hematology Research. - Shulan Tian, W. Garrett Jenkinson, Alejandro Ferrer, Huihuang Yan, Joel A Morales-Rosado, Kevin L. Wang, Terra L. Lasho, Benjamin B. Yan, Saurabh Baheti, Janet E. Olson, Linda B. Baughn, Wei Ding, Susan L. Slager, Mrinal S. Patnaik, Konstantinos N. Lazaridis, Eric W. Klee:
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP. - Yuting Dai, Wenjiang Ouyang, Wen Jin, Fan Zhang, Wenyan Cheng, Jianfeng Li, Shuo He, Junqi Zou, Shijia Cao, Chenxin Zhou, Junchen Luo, Gang Lv, Jinyan Huang, Hai Fang, Xiao-Jian Sun, Kankan Wang, Saijuan Chen:
Resolving Leukemia Heterogeneity and Lineage Aberrations with HematoMap. - Zhixin Kang, Tongtong Zhu, Dong Zou, Mengyao Liu, Yifan Zhang, Lu Wang, Zhang Zhang, Feng Liu:
HemAtlas: A Multi-omics Hematopoiesis Database. - Zhenyi Wang, Yuxin Miao, Hongjun Li, Wenyan Cheng, Minglei Shi, Gang Lv, Yating Zhu, Junyi Zhang, Tingting Tan, Jin Gu, Michael Q. Zhang, Jianfeng Li, Hai Fang, Zhu Chen, Saijuan Chen:
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells. - Shuai Liu, Yanyan Li, Tingrui Song, Jingjing Zhang, Peng Zhang, Huaxia Luo, Sijia Zhang, Yiwei Niu, Tao Xu, Shunmin He:
Pathogen Adaptation of HLA Alleles and Its Correlation with Autoimmune Diseases in the Han Chinese. - Xuezhu Wang, Liping Zuo, Yanying Yu, Xinyi Xiong, Jian Xu, Bing Qiao, Jia Chen, Hao Cai, Qi Yan, Hongxiao Han, Xin-xin Cao, Jun Deng, Chunyan Sun, Jian Li:
Clonal Hematopoietic Mutations in Plasma Cell Disorders: Clinical Subgroups and Shared Pathogenesis.
Volume 23, Number 3, 2025
- Jenea Imani Adams, Eric Kutschera, Qiang Hu, Chun-Jie Liu, Qian Liu, Kathryn Kadash-Edmondson, Song Liu, Yi Xing:
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud. - Weidong Liu, Yuhua Wang, Shuxin Yao, Guoqiang Han, Jin Hu, Rong Yin, Fuling Zhou, Ying Cheng, Haojian Zhang:
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development. - Jin A, Ju Xiang, Xiangmao Meng, Yue Sheng, Hongling Peng, Min Li:
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes. - Wenyan Wu, Jingyi Zhang, Huiying Sun, Xiaoyu Wu, Han Wang, Bowen Cui, Shuang Zhao, Kefei Wu, Yanjun Pan, Rongrong Fan, Ying Zhong, Xiang Wang, Ying Wang, Xiaoxiao Chen, Jianan Rao, Ronghua Wang, Kai Luo, Xinrong Liu, Liang Zheng, Shuhong Shen, Meng Yin, Yangyang Xie, Yu Liu:
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-cell Acute Lymphoblastic Leukemia. - Xingmin Wang, Qianqian Zhang, Xianming Chen, Yushan Huang, Wei Zhang, Liuhua Liao, Xinhua Zhang, Binbin Huang, Yueyan Huang, Yuhua Ye, Mengyang Song, Jinquan Lao, Juanjuan Chen, Xiaoqin Feng, Xingjiang Long, Zhixiang Liu, Weijian Zhu, Lian Yu, Chengwu Fan, Deguo Tang, Tianyu Zhong, Mingyan Fang, Caiyun Li, Chao Niu, Li Huang, Bin Lin, Xiaoyun Hua, Xin Jin, Zilin Li, Xiangmin Xu:
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia. - Azahara Fuentes-Trillo, Alicia Serrano-Alcalá, Blanca Ferrer-Lores, Laura Ventura-López, Enrique Seda, Ana-Bárbara García-García, Blanca Navarro, María José Terol, Felipe Javier Chaves:
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing. - Yihao Wang, Pan Shen, Zhenhui Wu, Bodan Tu, Cheng Zhang, Yongqiang Zhou, Yisi Liu, Guibin Wang, Zhijie Bai, Xianglin Tang, Chengcai Lai, Haitao Lu, Wei Zhou, Yue Gao:
Plasma Proteomic Profiling Reveals ITGA2B as A Key Regulator of Heart Health in High-altitude Settlers. - Guangmin Zheng, Song Wu, Zhaojun Zhang, Zijuan Xin, Lijuan Zhang, Siqi Zhao, Jing Wu, Yanxia Liu, Meng Li, Xiuyan Ruan, Nan Qiao, Yiming Bao, Hongzhu Qu, Xiangdong Fang:
EryDB: A Transcriptomic Profile Database for Erythropoiesis and Erythroid-related Diseases. - Ya Zhang, Mengfang Xia, Zhenyi Yi, Pinpin Sui, Xudong He, Liping Wang, Qiyi Chen, Hong-Hu Zhu, Gang Huang, Qian-Fei Wang:
Integrated Computational and Functional Screening Identifies G9a Inhibitors for SETD2-mutant Leukemia. - Weijun Zhou, Wenting Xiang, Jinyi Yu, Zhihan Ruan, Yichen Pan, Kankan Wang, Jian Liu:
NeoTCR: An Immunoinformatic Database of Experimentally-supported Functional Neoantigen-specific TCR Sequences. - Chen Wang, Hong Zhao, Hongkui Zhang, Sijie Sun, Yongbiao Xue:
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility. - Yunzhe Wang, James Wengler, Yuzhu Fang, Joseph Zhou, Hang Ruan, Zhao Zhang, Leng Han:
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources. - Xin Dong, Zhen Zhou, Yanan Wang, Ayesha Nisar, Shaoyan Pu, Longbao Lv, Yijiang Li, Xuemei Lu, Yonghan He:
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues. - Mengmeng Wei, Jingcheng Wu, Shengzuo Bai, Yuxuan Zhou, Yichang Chen, Xue Zhang, Wenyi Zhao, Ying Chi, Gang Pan, Feng Zhu, Shuqing Chen, Zhan Zhou:
TRAIT: A Comprehensive Database for T-cell Receptor-antigen Interactions. - Yuansong Zeng, Yuedong Yang:
Foundation Model: A New Era for Plant Single-cell Genomics. - Miaomiao Chen, Yujie Gou, Ming Lei, Leming Xiao, Miaoying Zhao, Xinhe Huang, Dan Liu, Zihao Feng, Di Peng, Yu Xue:
EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species. - Guangshuo Cao, Haoyu Chao, Wenqi Zheng, Yangming Lan, Kaiyan Lu, Yueyi Wang, Ming Chen, He Zhang, Dijun Chen:
scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. - Xuejing Zhang, Dongyuan Ma, Feng Liu:
CRISPR Technology and Its Emerging Applications. - Ran Li, Yu Zang, Zhentang Liu, Jingyi Yang, Nana Wang, Jiajun Liu, Enlin Wu, Riga Wu, Hongyu Sun:
clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples. - Wanfei Liu, Peng Cui:
Haplotype-based Pangenomics: A Blueprint for Climate Adaptation in Plants.
Volume 23, Number 4, 2025
- Sisi Zhang, Xu Chen, Enhui Jin, Anke Wang, Tingting Chen, Xiaolong Zhang, Junwei Zhu, Lili Dong, Yanling Sun, Caixia Yu, Yubo Zhou, Zhuojing Fan, Huanxin Chen, Shuang Zhai, Yubin Sun, Qiancheng Chen, Jing-Fa Xiao, Shuhui Song, Zhang Zhang, Yiming Bao, Yanqing Wang, Wenming Zhao:
The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data. - Di Zhu, Yuzhan Wang, Hao Qu, Chungang Feng, Hui Zhang, Zheya Sheng, Yunliang Jiang, Qinghua Nie, Suqiao Chu, Dingming Shu, Ziqin Jiang, Dexiang Zhang, Lingzhao Fang, Hui Li, Zhenqiang Xu, Yiqiang Zhao, Yuzhe Wang, Xiaoxiang Hu:
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes. - Rujia Dai, Ming Zhang, Tianyao Chu, Richard Kopp, Chunling Zhang, Kefu Liu, Yue Wang, Xusheng Wang, Chao Chen, Chunyu Liu:
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data. - Natália Aniceto, Nuno Martinho, Ismael Rufino, Rita C. Guedes:
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank. - Tun Xu, Stephen J. Bush, Yizhuo Che, Huanhuan Zhao, Tingjie Wang, Peng Jia, Songbo Wang, Peisen Sun, Pengyu Zhang, Shenghan Gao, Yu Xu, Chengyao Wang, Ningxin Dang, Yong E. Zhang, Xiaofei Yang, Kai Ye:
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream. - Xuhua Yan, Jinmiao Chen, Ruiqing Zheng, Min Li:
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration. - Xiuju Chen, Yanyu Sui, Jiayi Gu, Liang Wang, Ningxia Sun:
Implication of the Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes. - Kang Xu, Yujie Liu, Chongwen Lv, Ya Luo, Jingyi Shi, Haozhe Zou, Weiwei Zhou, Dezhong Lv, Changbo Yang, Yongsheng Li, Juan Xu:
LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues. - Chengchao Wu, Tianshu Zhou, Wenfu Ke, Wei Xiong, Zhihui Zhang, Siheng Zhang, Jinyue Wang, Lulu Deng, Keji Yan, Man Wang, Shenglong He, Qi Gong, Chao Ma, Xiaping Chen, Yan Li, He Long, Chong Guo, Gang Cao, Zhijun Zhang:
Deciphering Haplotype-level Chromosome Conformation Alteration in Down Syndrome by Haplotype-resolved Multi-omics Analysis. - Bitao Zhong, Rui Fan, Yue Ma, Xiangwen Ji, Qinghua Cui, Chunmei Cui:
MedImg: An Integrated Database for Public Medical Images. - Jiayue Meng, Mengyao Han, Yuwei Huang, Liang Li, Yuanhu Ju, Daqing Lv, Xiaoyi Chen, Liyun Yuan, Guoqing Zhang:
PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation. - Tianyuan Zhang, Mian Jiang, Hanzhou Li, YunYun Gao, Salsabeel Yousuf, Kaimin Yu, Xinxin Yi, Jun Wang, Lulu Yang, Yong-Xin Liu:
Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio. - Xueli Xu, Yanran Liang, Miaoxiu Tang, Jiongliang Wang, Xi Wang, Yixue Li, Jie Wang:
ScReNI: Single-cell Regulatory Network Inference Through Integrating scRNA-seq and scATAC-seq Data.
Volume 23, Number 5, 2025
- Mengying Wang, Liyang Sun, Xin Xu, Ruoqi Dai, Qilong Tan, Yun Zhu, Andi Xu, Weifang Zheng, Yuanxing Tu, Dan Zhou, Wenyuan Li, Xifeng Wu:
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese. - Tao Deng, Mengqian Huang, Kaichen Xu, Yan Lu, Yucheng Xu, Siyu Chen, Nina Xie, Qiuyue Tao, Hao Wu, Xiaobo Sun:
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data. - Guangya Duan, Sisi Zhang, Bixia Tang, Jing-Fa Xiao, Zhang Zhang, Peng Cui, Jun Yu, Wenming Zhao:
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics. - Xueyun Huo, Xianhui Sun, Xiangyang Xing, Jing Lu, Jingjing Zhang, Yanyan Jiang, Xiao Zhu, Changlong Li, Jianyi Lv, Meng Guo, Lixue Cao, Xin Liu, Zhenwen Cheng, Dengke Pan, Shunmin He, Chen Zhang, Xiaoyan Du:
Genome-wide Genetic Mutations Accumulated in Pigs Genome-edited for Xenotransplantation and Their Filial Generation. - Qunhao Niu, Jiayuan Wu, Tianyi Wu, Tianliu Zhang, Tianzhen Wang, Xu Zheng, Zhida Zhao, Ling Xu, Zezhao Wang, Bo Zhu, Lupei Zhang, Huijiang Gao, George E. Liu, Junya Li, Lingyang Xu:
Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle. - Fang Yang, Xuping Tian, Yanling Jin, Anping Du, Yanqiang Ding, Zhihua Liao, Kaize He, Yonggui Zhao, Ling Guo, Yao Xiao, Yaliang Xu, Shuang Chen, Yuqing Che, Li Tan, Songhu Wang, Jiatang Li, Zhuolin Yi, Lanchai Chen, Leyi Zhao, Fangyuan Zhang, Guoyou Li, Jinmeng Li, Qinli Xiong, Yongmei Zhang, Qing Zhang, Xuan Hieu Cao, Hai Zhao:
Duckweed Evolution: from Land back to Water. - Bitao Zhong, Shaoqi Wang, Xiaoxi Jing, Aniruddh P. Patel, Yajie Zhao, Minxian Wang:
Harnessing Large Cohorts and AI to Bridge Genomic Discovery and Clinical Practice. - Jie Song, Wenwen Chen, Jin Huang, Huan Song:
Toward Responsible and Sustainable Data Sharing in Large-scale Cohort-based Genomic Research.
Volume 23, Number 6, 2025
- Zerui Wang, Xin Cheng, Yibin Xu, Zhiyi Wang, Liyan Ma, Caiming Li, Shize Jiang, Yuchen Li, Shuilong Guo, Wenbin Du:
Unveiling Neonatal Pneumonia Microbiome by High-throughput Sequencing and Droplet Culturomics. - Chenfei Wang, Jiaojiao Zhou, Hong Zhang, Zihan Zhuang, Gali Bai, Ming Tang, Song Liu, Tao Liu:
Computational Analyses and Challenges of Single-cell ATAC-seq.
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