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Genomics, Proteomics & Bioinformatics, Volume 20
Volume 20, Number 1, February 2022
- Weihua Pan
, Jue Ruan
En Route to Completion: What Is An Ideal Reference Genome? 1-3
- Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye:
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. 4-13 - Ruicai Long
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits. 14-28 - Chunming Yang
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks. 29-41 - Jianjun Lu
A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert. 42-59 - Wentai Ma
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant. 60-69 - Chen Zhang
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells. 70-86 - Xinran Li
Defining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. 87-100 - Xin Liu
Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. 101-109 - Sue Yu
Npac Is A Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells. 110-128 - Jes-Niels Boeckel
SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy. 129-146 - Yikai Luo
Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development. 147-162 - Feiyang Ji
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response. 163-176 - Yaqiang Hong
Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. 177-191 - Xiao Du, Lili Li, Fan Liang, Sanyang Liu
Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies. 192-204
- Jiadong Lin
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. 205-218
Volume 20, Number 2, April 2022
- Rui Wang
Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using A Single-cell RNA-seq Approach. 223-245 - Jie Zhu, Liu Tian, Peishan Chen, Mo Han, Liju Song, Xin Tong, Xiaohuan Sun, Fangming Yang, Zhipeng Lin, Xing Liu, Chuan Liu, Xiaohan Wang, Yuxiang Lin, Kaiye Cai, Yong Hou, Xun Xu, Huanming Yang
Over 50, 000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. 246-259 - Zhenwei Liu
Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis. 260-273 - Anouck Becker
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial. 274-287 - Mingyue Li
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice. 288-303 - Zhuye Jie, Chen Chen
Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes. 304-321 - Xiaoai Zhang
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women. 322-333 - Hao Li
Panoramic Insights into Microevolution and Macroevolution of A Prevotella copri-containing Lineage in Primate Guts. 334-349 - Zhi-Yuan Wei
Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using A Captive Monkey Model. 350-365 - Yue Xie
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation. 366-381 - Yanze Li
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice. 382-393 - Yanxue Yu
First Glimpse of Gut Microbiota of Quarantine Insects in China. 394-404 - Jacqueline Rehner
Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies. 405-417 - Jing Fu
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae. 418-434
Volume 20, Number 3, June 2022
- Chunyan Fan
CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA-disease Associations and Its Application. 435-445 - Feng Xu
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms. 446-454 - Jianing Gao
FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery. 455-465
- Kyubin Lee
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. 466-482 - Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao:
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. 483-495 - Qiao Liu
DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. 496-507 - Fengxia Zhou
PHISDetector: A Tool to Detect Diverse In Silico Phage-host Interaction Signals for Virome Studies. 508-523 - Qichao Lian
inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities. 524-535
- Zhang Zhang
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences. 536-540 - Tongwu Zhang
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci. 541-548 - Zelin Liu
DEBKS: A Tool to Detect Differentially Expressed Circular RNAs. 549-556 - Ting Zhang
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA. 557-567 - Arsenij Ustjanzew
i2dash: Creation of Flexible, Interactive, and Web-based Dashboards for Visualization of Omics Data. 568-577 - Mikaela Koutrouli
NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization. 578-586 - Shuyu Zheng
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets. 587-596
Volume 20, Number 4, August 2022
- Yuejing Jiang
Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation. 597-613 - Zhengguang Guo
A Global Multiregional Proteomic Map of the Human Cerebral Cortex. 614-632 - Xiuxiu Jin, Jingyang Liu, Weiping Wang, Jiangfeng Li, Guangming Liu, Ruiqi Qiu, Mingzhu Yang, Meng Liu, Lin Yang, Xiaofeng Du, Bo Lei
Identification of Age-associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium. 633-647 - Qiushi Chen
Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. 648-656 - Songbiao Zhu
High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells. 657-669 - Lei Liu
New Metabolic Alterations and A Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma. 670-687 - Ning Zhang
Global Profiling of 2-hydroxyisobutyrylome in Common Wheat. 688-701 - Xuetong Li
Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches. 702-714 - Chen Xu
Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. 715-727 - Ning Liu
Comparative Secretome Analysis of Magnaporthe oryzae Identified Proteins Involved in Virulence and Cell Wall Integrity. 728-746 - Zhaoxu Gao
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis. 747-764 - Liu Yang
Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. 765-779
- Zhongyang Liu, Honglei Li, Zhaoyu Jin, Yang Li, Feifei Guo
Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs. 780-794 - Limin Shang
A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. 795-807
- Guang Song, Emily M. Lee, Jianbo Pan
Corrigendum to "An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication" [Genomics Proteomics Bioinformatics19 (1) (2021) 108-122]. 808-809
Volume 20, Number 5, October 2022
- Matthew Brendel
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review. 814-835 - Stefan Stanojevic
Computational Methods for Single-cell Multi-omics Integration and Alignment. 836-849 - Yawei Li
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis. 850-866 - Yuguo Zha
Microbial Dark Matter: from Discovery to Applications. 867-881
- Wubing Zhang
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation. 882-898 - Yongbing Zhao
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data. 899-911
- Alexandra J. Lee
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. 912-927 - Shao-Wu Zhang
DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data. 928-938 - Hui Wan
scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception. 939-958 - Juexiao Zhou
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS. 959-973 - Yiran Shan
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics. 974-988 - Sen Yang
DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning. 989-1001 - Hao-Dong Xu
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes. 1002-1012 - Yi-Heng Zhu
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. 1013-1027 - Zhiting Wei
DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery. 1028-1036
Volume 20, Number 6, December 2022
- Yixue Li
A Beloved Bioinformatician Buddy - In Memory of Professor Weimin Zhu. 1037-1039
- Mingpeng Zhang
Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree. 1040-1052 - Min Li
Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life. 1053-1065 - Yuli Li
Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle. 1066-1077 - Yang Zhang
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves. 1078-1091 - Qian Zhao
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution. 1092-1105 - Yinqing Yang
Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus corchorifolius). 1106-1118 - Zhongqiang Xia
Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants. 1119-1137 - Duo Chen
Multi-omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis galbana. 1138-1153 - Cuidan Li
Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China. 1154-1167 - Yingbo Shen, Rong Zhang
Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage. 1168-1179 - Khaista Rahman
Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening. 1180-1196
- Wan-Ping Lee
JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level. 1197-1206
- Mei-Jing Dong
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. 1207-1213
- Yali Hou
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes. 1214-1223 - Yuan Gao, Jinning Zhang
Single-cell Sequencing Reveals Clearance of Blastula Chromosomal Mosaicism in In Vitro Fertilization Babies. 1224-1231
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