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Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)
Raw sequencing data from mRNA sequencing, circRNA sequencing, degradome sequencing, and small RNA sequencing are available...
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency
DNA damage responseHomologous recombination repair deficiencyPoly (ADP-ribose) polymerase inhibitorBiomarkerHarmonization©...
RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering
The raw sequencing data have been deposited in the Genome Sequence Archive [75] at National Genomics Data Center, Beijing ...
VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns
Available online 16 February 2023Author links open overlay panel, , , , , , , , , , , , , , , AbstractIntegration of oncog...
Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL
KeywordsDrug responseDeep learningExplainable AICancerGene knockdown experimentData availabilityAn implementation of TINDL...
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice
KeywordsDirect RNA resequencingPolyadenylated transcriptomeN6-methyladenosineN5-methylcytosineRiceData availabilityThe raw...
Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus
The whole genome sequencing raw data including Illumina short reads, PacBio long reads, Hi-C interaction reads, and transc...
What Has Genomics Taught An Evolutionary Biologist?
Available online 28 January 2023Author links open overlay panelAbstractGenomics, an interdisciplinary field of biology on ...
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers
All the analysis results involved in this study were available at https://ccsm.uth.edu/CAeditome/.The results here are in ...
Mapping Multiple Factors-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes
Sequence data generated in this study have been deposited in the Genome Sequence Archive [65] at National Genomics Data Ce...
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies
Available online 18 January 2023Author links open overlay panelAbstractAlternative polyadenylation (APA) contributes to tr...
Artificial Intelligence in Omics
Available online 12 January 2023Author links open overlay panel© 2023 The Authors. Published by Elsevier B.V. and Science ...
Organs-on-a-chip Database (OOCDB): A Comprehensive, Systematic, and Real-time Organs-on-a-chip Database
OOCDB is available at http://www.organchip.cn/.This study is mainly supported by the National Natural Science Foundation o...
scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception
Available online 3 January 2023Author links open overlay panelAbstractCurrent cell-type annotation tools of single-cell RN...
DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning
Available online 3 January 2023Author links open overlay panelAbstractThe high-content image-based assay is commonly lever...
The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates
Available online 29 December 2022Author links open overlay panelAbstractJasminum sambac (jasmine flower), a world-renowned...
A Beloved Bioinformatician Buddy —In Memory of Professor Weimin Zhu
Available online 29 December 2022Author links open overlay panel© 2022 The Authors. Published by Elsevier B.V. and Science...
Computational Methods for Single-cell Multi-omics Integration and Alignment
Available online 26 December 2022Author links open overlay panelAbstractRecently developed technologies to generate single...
Database Commons: A Catalog of Worldwide Biological Databases
Available online 23 December 2022Author links open overlay panelAbstractBiological databases serve as a global fundamental...
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics
Available online 19 December 2022Author links open overlay panelAbstractSequencing-based spatial transcriptomics (ST) is a...
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared to SpCas9 in Genome Editing
Available online 20 December 2022Author links open overlay panelAbstractA series of the clustered regularly interspaced sh...
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review
Available online 14 December 2022Author links open overlay panelAbstractSingle-cell RNA sequencing (scRNA-seq) has become ...
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS
Available online 15 December 2022Author links open overlay panelAbstractThe accurate annotation of transcription start sit...
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes
Available online 13 December 2022Author links open overlay panelAbstractIdentification of B-cell epitopes (BCEs) plays an ...
N6-Methyladenosine Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes
All data relative to this study are publicly available at the National Center for Biotechnology Information Gene Expressio...
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals
The data in iHypoxia database is available at http://ihypoxia.omicsbio.info and https://doi.org/10.6084/m9.figshare.188813...
Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage
Available online 5 December 2022Author links open overlay panelAbstractEmergence of the colistin resistance gene, mcr-1, h...
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation
The datasets supporting the conclusions of this article are accessible at http://mapd.cistrome.org.© 2022 The Authors. Pub...
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network
Available online 7 December 2022Author links open overlay panelAbstractThe genetic information coded in DNA leads to trait...
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation
The raw sequencing data reported in this study have been deposited in the Genome Sequence Archive [78] at the National Gen...
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