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Chromosome-level Reference Genome Provides Insights into Divergence and Stress Adaptation of the African Oil Palm
Available online 24 November 2022Author links open overlay panelAbstractThe palm family (Arecaceae), consisting of ∼ 2600 ...
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells
Available online 24 November 2022Author links open overlay panelAbstractEpidermal growth factor receptor-tyrosine kinase i...
Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution
Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and...
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database
Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulat...
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning
Disordered flexible linkers (DFLs) are the functional disordered regions in proteins, which are the sub-regions of intrins...
CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs
Cancer therapy resistance and recurrence (CTRR) are the dominant causes of death in cancer patients. Recent studies have i...
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins
The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated ...
Computational Approaches and Challenges in Spatial Transcriptomics
The development of spatial transcriptomics technologies has transformed genetic research from a single-cell data level to ...
Genomes of Two Flying Squid Species Provide Novel Sights into Adaptations of Cephalopods to Pelagic Life
The genome and annotation of these two purpleback flying squid species and raw sequence data and acquired RNA-seq data wer...
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses
Genome-wide transcriptome profiling identifies genes that are prone to differential expression across contexts, as well as...
Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii
The MS proteomics data was deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset...
TSNAdb v2.0: the Updated Version of Tumor-specific Neoantigen Database
In recent years, neoantigens have been recognized as ideal targets for tumor immunotherapy. With the development of neoant...
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities
The protein interaction AP-MS data for both IP_762813 and PHB1 in HEK293 cells were deposited to the ProteomeXchange Conso...
NSUN2-mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma
The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive [40] in the National Genom...
DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery
Transcriptional phenotypic drug discovery has achieved great success, and various compound perturbation-based data resourc...
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq
Alternative polyadenylation (APA) plays important roles in modulating mRNA stability, translation, and subcellular localiz...
High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion
The datasets generated in the current study are available in the Genome Sequence Archive (GSA) [29] at the National Genomi...
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis
Ferroptosis is a form of regulated cell death driven by the accumulation of lipid hydroperoxides. Regulation of ferroptosi...
Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces
The genomic and transcriptomic data have been deposited in the genome sequence archive (GSA) [49] at the National Genomics...
Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes
Available online 8 September 2022AbstractExploring the natural diversity of functional genes/proteins from environmental D...
m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues
Available online 9 September 2022AbstractAs the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladen...
Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants
The genome assemblies, gene annotation, and Illumina re-sequencing short reads have been deposited in the Genome Sequence ...
Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals
In the evolutionary model of dosage compensation, per-allele expression level of the X chromosome was proposed to have two...
Application of Microbiome in Forensics
Recent advances in next-generation sequencing technology and improvements in bioinformatics have expanded the scope of mic...
Genomic Variation in the Tea Leafhopper Reveals the Basis of Adaptive Evolution
The genome sequences and re-sequencing reads have been deposited in BioProject (https://www.ncbi.nlm.nih.gov/bioproject) a...
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource
Immunotherapy is a promising cancer treatment method; however, only a few patients benefit from it. The development of new...
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice
Abdominal aortic aneurysm (AAA) is a permanent dilatation of the abdominal aorta and is highly lethal. The main purpose of...
Multi-omics analyses provide insight into the biosynthesis pathways of fucoxanthin in Isochrysis galbana
Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucox...
CHDbase: A comprehensive knowledgebase for congenital heart disease-related genes and clinical manifestations
Congenital heart disease (CHD) is one of the most common causes of major birth defects, with a prevalence of 1%. Although ...
Dynamic landscapes of tRNA transcriptomes and translatomes in diverse mouse tissues
The raw sequencing data of DM-tRNA-seq and RiboTag-seq in this study have been deposited in the Genome Sequence Archive [5...