Topic 9

genes gene expression genomics rna genome identified seq sequencing transcriptional regulatory transcriptome analysis transcription wide associated cancer identify genetic specific expressed enriched types single genomic variants chromatin transcriptomic loci profiles regulation association genetics cell differentially disease tissues tissue coding epigenetic signatures methylation revealed risk pathways reveals dna tumor profiling elements performed human atlas landscape comprehensive analyses differential novel enrichment heterogeneity molecular gwas data functional factors transcripts phenotypes including involved samples candidate regions type development identification across patients identifies cells cis transcriptomes tumors developmental enhancers subtypes rnas targets signature enhancer were studies mrna associations distinct differentiation cancers promoters regulators somatic biology

2647 items. Top items listed below.

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage 134 9

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts 120 9 3

Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis 31 9 3

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice 9 3

Identification and functional analysis of long non-coding RNAs in autism spectrum disorders 9

Whole-organism mapping of the genetics of gene expression at cellular resolution 19 9 4

Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response 9 3

Impact of cell-type and context-dependent regulatory variants on human immune traits 19 9

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data 31 7 4

Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures 120 43 9

Co-expression signatures of combinatorial gene regulation 134 31 9 3

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex 9

Single nuclei chromatin profiles of ventral midbrain reveal cell identity transcription factors and cell type-specific gene regulatory variation 9 3

Integrative multi-omics analyses identify cell-type disease genes and regulatory networks across schizophrenia and Alzheimer's disease 9

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

Sex differences in the human brain transcriptome of cases with schizophrenia 120 9

Allele-specific alternative splicing in human tissues 19 9 4

Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana 134 9 5

A novel single-cell based method for breast cancer prognosis 43 26 4

Multi-tissue transcriptome-wide association studies 19 4

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana 43 31 9 3

Global Dynamic Molecular Profiles of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing 120 9 3

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome 134 9 4

Persistent cell proliferation signals correlates with increased glycolysis in tumor hypoxia microenvironment across cancer types 186 9

Gene regulatory network of human GM-CSF secreting T helper cells 31 9 3

Functional impact and regulation of global alternative splicing patterns in heart development and disease 120 9 3

Human library of cardiac promoters and enhancers 134 31 9

The landscape of metabolic pathway dependencies in cancer cell lines 186 9 3

Pan-Cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. 31 9 3

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis 43 9 4

Towards understanding the regulation of histone H1 somatic subtypes with OMICs. 31 9 3

Common postzygotic mutational signature in multiple healthy adult tissues related to embryonic hypoxia 9 3

Enrichment of genomic variation in pathways linked to autism 9 4

Epigenetic regulation of differentially expressed genes between various glioma types 31 9

Systematic characterization of somatic mutation-mediated microRNA regulatory network perturbations 74 9

Genome-wide maps of enhancer regulation connect risk variants to disease genes 19 9 3

The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes 31 20 9 5

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy 152 14 9 3

A mouse tissue atlas of small non-coding RNA 120 9

Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19 73 9 1

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs 134 49 31 9 3

Evolutionarily Conserved Transcription Factors Drive the Oxidative Stress Response in Drosophila 134 31 9 3

Functional mapping of androgen receptor enhancer activity 31 9 3

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

TATA and paused promoters active in differentiated tissues have distinct expression characteristics 31 9

Deciphering cellular transcriptional alterations in Alzheimer's disease brains 32 9 4

Ovarian Cancer Risk Variants are Enriched in Histotype-Specific Enhancers that Disrupt Transcription Factor Binding Sites 31 9

Tissue-specific expression of young small-scale duplications in human central nervous systemregions 120 9 5

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

A limited set of transcriptional programs define major cell types 148 120 9

The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression 31 9 3

Aging leads to stochastic loss of silencing at transposons in mammary luminal epithelial cells 81 31 9 3

Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis 9 5

Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression 31 9

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders 9

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks 134 7

Genome-wide analysis of cis-regulatory changes in the metabolic adaptation of cavefish 31 9 3

Sex and estrogen receptor β have modest effects on gene expression in the mouse brain posterior cortex 56 9 2

Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes 97 9 4

An Integrative Analysis of the Age-Associated Genomic, Transcriptomic and Epigenetic Landscape across Cancers 87 9

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation 31 9 3

Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers 134 9 3

Leveraging functional annotation to identify genes associated with complex diseases 19 9 4

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions 139 112 9

A systematic dissection of human primary osteoblasts in vivo at single-cell resolution 120 43 9 3

Schizophrenia Risk Alleles Often Affect The Expression of Many Genes and Each Gene May Have a Different Effect On The Risk; A Mediation Analysis. 19 9 5

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns 134 9 5

Transcriptional and Cellular Diversity of the Human Heart 120 9

Comprehensive evaluation of human brain gene expression deconvolution methods 175 43 9 4

Epigenome-based Splicing Prediction using a Recurrent Neural Network 31 9 4

Gene expression variability in human and chimpanzee populations share common determinants 19 9 5

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution 43 9 4

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits 7 3

Identification of the associated expression patterns as potential predictive markers for cancer prognosis 112 9

Co-expression networks from gene expression variability between genetically identical seedlings can reveal novel regulatory relationships 134 9 5 4

Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression 134 31 9 4

Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data 9 4

Loss of the Pioneer Factor FOXA1 Results in Genome-wide Epigenetic Reprogramming and activation of Interferon-Response Genes including CD274/PD-L1 31 9 3

Mobile Element Insertions and Associated Structural Variants in Longitudinal Breast Cancer Samples 97 9

Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation 120 9 3

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression 43 9 4

Dynamic Analysis of Alternative Polyadenylation from Single-Cell RNA-Seq(scDaPars) Reveals Cell Subpopulations Invisible to Gene Expression Analysis 43 9 4 3

Imputing missing RNA-seq data from DNA methylation by using transfer learning based-deep neural network 105 26 4

Modeling regulatory network topology improves genome-wide analyses of complex human traits 19 9 4

Gene expression in the cardiovascular system of the domestic sheep (Ovis aries); a new tool to advance our understanding of cardiovascular disease. 120 9

Transcription factor-target relationships complicated by knockout analysis 134 9 3

The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells 97 9 4

Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression 9

Evolution of regulatory signatures in primate cortical neurons at cell type resolution 9

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells 9

Transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis 9

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning 89 7 3

Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data 175 43 9 4

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis 19 9 4

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data 97 25 9 4

Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma 87 9

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing 43 9 4

miRNA activity inferred from single cell mRNA expression 43 4

Detection of differential RNA modifications from direct RNA sequencing of human cell lines 147 13 4