Topic 134

regulatory transcription cis gene tf genes regulation expression tfs factors elements transcriptional factor genome binding motifs genomics sequence sites arabidopsis promoters promoter predict regulators plant conserved identified thaliana identify plants network networks identification coding transcriptome sequences seq motif regions functional tissues analysis enhancers specific enhancer co enriched genetic their evolution genomic chromatin dna across predicted known understanding regulate wide species stress rna comprehensive revealed rnas predicting variation lncrnas reporter data involved expressed approach biology acting validated important characterization phenotypic splice regulating variants transcripts accessibility myb majority chip massively diverse novel annotations putative pairs annotation start noncoding non functions datasets modules

139 items. Top items listed below.

Unraveling transcription factor functions through integrative inference of transcriptional networks in Arabidopsis thaliana yields novel regulators involved in reactive oxygen species stress signaling 134 31 16 9 4

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

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

Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated 134 31 9 5

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

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana 134 31 9 4

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

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

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

Inferring active cis-regulatory modules to predict functional regulatory elements 134 31 4

The regulatory landscape of early maize inflorescence development 134 31 9

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

A cis-regulatory atlas in maize at single-cell resolution 134 31 9

Evolution is in the details: Regulatory differences in modern human and Neandertal 134 31 9 4

Transcription factor binding dynamics shape noise across biological processes 134 31 9 3

Constructing Gene Regulatory Networks using Epigenetic Data 134 31 9 4

Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding 134 16 9 3

BARTweb: a web server for transcription factor association analysis 134 31 13 4

Prediction and characterization of transcription factors involved in drought stress response 134 9 4

Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanisms 134 112 4

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

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

Massively parallel identification of causal variants underlying gene expression differences in a yeast cross 134 31 19 9

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

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

Predicting Gene Expression from DNA Sequence using Residual Neural Network 134 105 26 9 4

Human library of cardiac promoters and enhancers 134 31 9

Dynamical gene regulatory networks are tuned by transcriptionalautoregulation with microRNA feedback. 134 31 9 3

Response of Regulatory Genetic Variation in Gene Expression to Environmental Change in Drosophila melanogaster 134 19 9 5

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

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

Independent evolution of transcript abundance and gene regulatory dynamics 134 31 9 5

Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit 134 16 3

The transcription regulatory code of a maize leaf 134 31 9

Dissecting the DNA binding landscape and gene regulatory network of p63 and p53 134 31 9 3

Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana 134 31 16 4

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

Allele-specific alternative splicing in human tissues 19 9 4

Linking the dynamics of chromatin occupancy and transcription with predictive models 7

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

Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model 134 31 16 9 4

Evolution of conserved noncoding sequences in Arabidopsis thaliana 134 40 9 5

Decoding transcriptional regulation via a human gene expression predictor 134 9 3

Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors 134 31 8 3

In Silico Identification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (Citrus sinensis L) 134 16 9 3

GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation 134 49 9

The activity of human enhancers is modulated by the splicing of their associated lncRNAs. 134 31 9

Transcription inhibitors with XRE DNA-binding and cupin signal-sensing domains drive metabolic diversification in Pseudomonas 134 79 9 5

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

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes 134 31 9 4

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

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence 31 4

Mapping the architecture of regulatory variation provides insights into the evolution of complex traits 134 31 9 3

The 5 regulatory region of the β actin gene in Clarias species is complex and variable in relation to ecological needs 134 31 9

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and widespread in trans effects on the protein regulatory network 134 31 9 3

Evolution of regulatory networks associated with traits under selection in cichlids 134 21 9 5

A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in embryonic stem cells 31 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

Regulatory signatures of drought response in stress resilient Sorghum bicolor 134 31 9 5

Parallel genetics of regulatory sequences in vivo 134 33 9

Bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory transcription components of RNA silencing machinery genes in wheat (Triticum aestivum L.) 134 16 9

Genome-wide predictions of genetic redundancy in Arabidopsis thaliana 134 16 9 5

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

An Arabidopsis gene expression predictor enables inference of transcriptional regulators 134 9

DiNeR: a Differential Graphical Model for analysis of co-regulation Network Rewiring 134 31 9 3

Prioritization of osteoporosis-associated GWAS SNPs using epigenomics and transcriptomics 134 19 9 3

Predicting transcriptional responses to cold stress across plant species 134 26 9 4

Comprehensive mapping of the human cytokine gene regulatory network 134 31 27 9 3

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

A novel design of transcriptional factor-mediated dynamic control of DNA recombination. 134 31 3

Identification of cellular context sensitive regulatory variation in mouse genomes 31 9 4

The Coevolution of Promoters and Transcription Factors in Animal and Plant Cells 134 31 16 9 5 3

Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat 134 9 5

Individual differences in honey bee (Apis mellifera) behavior enabled by plasticity in brain gene regulatory networks 134 31 9

Antisense ncRNAs during early vertebrate development are divided in groups with distinct features 134 49 9

miRFFLDB - An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. 134 74 31 9 4

Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression 31 9 3

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation 134 31 9

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

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Upregulation and cell specificity of C4 genes are derived from ancestral C3 gene regulatory networks 7 3

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

Gene expression profiling reveals subgenome dominance during Brassica napus seed development 134 120 9 3

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

Deep neural networks identify context-specific determinants of transcription factor binding affinity 105 26 4

Splicing conservation signals in plant long non-coding RNAs 134 40 9 5

Functional mapping of androgen receptor enhancer activity 31 9 3

TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells 31 9 3

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model 134 31 26 9 4

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

Rational Design of Minimal Synthetic Promoters for Plants 7

Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana 134 16 9 3

Decoding differential gene expression 134 112 26 4

Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors 31 9 3

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

Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 in Arabidopsis 16 9 3

An Expanded Role for WRINKLED1 Metabolic Control Based on Combined Phylogenetic and Biochemical Analyses 134 16 9 3

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

Plant Prionome maps reveal specific roles of prion-like proteins in stress and memory 134 31 16 9 3

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