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Genomics, Proteomics & Bioinformatics, Volume 19
Volume 19, Number 1, February 2021
- Zheng Zhao
, Ke-Nan Zhang
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients. 1-12
- Boyan Shen
Computational Screening of Phase-separating Proteins. 13-24 - José Alexandre Ferreira
Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. 25-43
- Xinxin Wang
The Role of DNA Methylation Reprogramming during Sex Determination and Transition in Zebrafish. 48-63 - Shuang-Ling Wu, Xiaoyi Zhang, Mengqi Chang, Changcai Huang, Jun Qian, Qing Li, Fang Yuan, Lihong Sun, Xinmiao Yu, Xinmiao Cui, Jiayi Jiang, Mengyao Cui, Ye Liu, Huan-Wen Wu, Zhi-Yong Liang, Xiaoyue Wang, Yamei Niu, Wei-Min Tong, Feng Jin:
Genome-wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer. 64-79 - Yuan Lv
Global Profiling of the Lysine Crotonylome in Different Pluripotent States. 80-93 - Xiaohua Xing
Quantitative Secretome Analysis Reveals Clinical Values of Carbonic Anhydrase II in Hepatocellular Carcinoma. 94-107 - Guang Song
An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication. 108-122 - Jie Wang
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models. 123-139
- Guangyu Wang
MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. 140-153 - Zhi Liu
PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community. 154-167
Volume 19, Number 2, April 2021
- Chunyu Huang
Single-cell RNA Sequencing Deciphers Immune Landscape of Human Recurrent Miscarriage. 169-171
- Sarthak Sinha
Profiling Chromatin Accessibility at Single-cell Resolution. 172-190 - Zhiliang Bai
Single-cell Analysis Technologies for Immuno-oncology Research: from Mechanistic Delineation to Biomarker Discovery. 191-207
- Feiyang Wang
Single-cell Immune Landscape of Human Recurrent Miscarriage. 208-222 - Grace E. Lidgerwood
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. 223-242 - József Á. Balog
Immunoprofiling of Drosophila Hemocytes by Single-cell Mass Cytometry. 243-252 - Xiliang Wang
Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2. 253-266 - Qianhui Huang
Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data. 267-281
- Zhenlan Liang
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. 282-291 - Kaikun Xie
redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer. 292-305 - Jiangyong Wei
DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation. 306-318 - Lin Li
c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network. 319-329 - Qianqian Song
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets. 330-341
Volume 19, Number 3, June 2021
- Luonan Chen
Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis. 343-345 - Liang Wu
scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence. 346-357 - Zijuan Xin
Mapping Human Pluripotent Stem Cell-derived Erythroid Differentiation by Single-cell Transcriptome Analysis. 358-376 - Haitao Luo
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity. 377-393 - Tao Hu
Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction. 394-407 - Gang Liu
Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells. 408-422 - Jianbo Li
Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs. 423-436 - Wei Ge
A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis. 437-451 - David G. Garmire
GranatumX: A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis. 452-460 - Jiayuan Zhong
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy. 461-474 - Wei Vivian Li
scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. 475-492 - Thanh Minh Nguyen
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data. 493-503 - David Conchouso
Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. 504-518
Volume 19, Number 4, August 2021
- Ya Cui
From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-seq Data. 519-521
- Xi Cheng
SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models. 522-533
- Xujun Wang
RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators. 534-548 - Zihu Guo
NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. 549-564 - Shengquan Chen
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers. 565-577
- Tingting Chen
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types. 578-583 - Meili Chen
Genome Warehouse: A Public Repository Housing Genome-scale Data. 584-589 - Yu Wang, Fang-Yuan Shi, Yu Liang, Ge Gao:
REVA as A Well-curated Database for Human Expression-modulating Variants. 590-601 - Yanyan Li
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. 602-610 - Jiangming Huang
OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation. 611-618
- Lilin Yin
rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study. 619-628 - Jiabo Wang
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction. 629-640 - Shaopeng Liu
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. 641-651 - Xintao Qiu
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis. 652-661 - Guanghong Zuo
CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes. 662-667
Volume 19, Number 5, October 2021
- Zhaowei Xu
COVID-ONE-hi: The One-stop Database for COVID-19-specific Humoral Immunity and Clinical Parameters. 669-678
- Tao Zuo
Gut Microbiome Alterations in COVID-19. 679-688 - Xiulan Chen
Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. 689-706
- Ruona Shi
Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses. 707-726 - Shuhui Song, Cuiping Li
Genomic Epidemiology of SARS-CoV-2 in Pakistan. 727-740 - Tingting Li
Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples. 741-753 - Yaping Sun
Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species/JUN Pathway. 754-771 - Pengju Zhao
Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation. 772-786 - Yun-Mei Wang
Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait. 787-799 - Xiaozeng Yang
Elucidation of the MicroRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity. 800-814
- Xuan He
Characterizing RNA Pseudouridylation by Convolutional Neural Networks. 815-833 - Yuqing Yang
kLDM: Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors. 834-847 - Kjersti Rise
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks. 848-859
- Yin Shen
CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes. 860-871
Volume 19, Number 6, December 2021
- Yangyang Li
ASER: Animal Sex Reversal Database. 873-881 - Gongwang Yu
Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures. 882-900 - Edward Simpson
Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines. 901-912 - Bo Hu
The mRNA-miRNA-lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma. 913-925 - Tina Fuchs
Trilineage Sequencing Reveals Complex TCRβ Transcriptomes in Neutrophils and Monocytes Alongside T Cells. 926-936 - Yi Wang
Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants. 937-948 - Na L. Gao
Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes. 949-957 - Yinzhen Xu
Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. 958-972 - Jean-Sébastien Milanese
eTumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients. 973-985 - Hammad Naveed
Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors. 986-997 - Fatima Zohra Smaili
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs. 998-1011 - Bo Wang
Computational Assessment of Protein-protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes. 1012-1022 - Zhi Huang, Zhi Han, Tongxin Wang, Wei Shao, Shunian Xiang, Paul Salama
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining. 1023-1031 - Zixiao Lu
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images. 1032-1042 - Frieder Hadlich
rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays. 1043-1049
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