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Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter

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Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit

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Spotlight on the Granules (Grainyhead-Like Proteins) – From an Evolutionary Conserved Controller of Epithelial Trait to Pioneering the Chromatin Landscape

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Rapid Identification of Pollen- and Anther-Specific Genes in Response to High-Temperature Stress Based on Transcriptome Profiling Analysis in Cotton

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Designing realistic regulatory DNA with autoregressive language modelsPreprint

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De novo gene integration into regulatory networks via interaction with conserved genes in peach

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An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice

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Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes

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Cis-regulatory dynamics in plant domestication

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A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution

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Intra-Specific Regulatory Variation in Drosophila pseudoobscura

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Dissection of expression‐quantitative trait locus and allele specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations

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Genome-scale characterization of the vacuole nitrate transporter Chloride Channel (CLC) genes and their transcriptional responses to diverse nutrient stresses in allotetraploid rapeseed

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A cis-Acting Mutation in the PxABCG1 Promoter Is Associated with Cry1Ac Resistance in Plutella xylostella (L.)

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MAP4K4 controlled transcription factor POUM1 regulates PxABCG1 expression influencing Cry1Ac resistance in Plutella xylostella (L.)

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Genome-wide analysis of the LBD family in rice: Gene functions, structure and evolution

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Enhancer Runaway and the Evolution of Diploid Gene Expression

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Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway

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Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator

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Emx2 underlies the development and evolution of marsupial gliding membranes

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Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

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Comprehensive Expression Profiling of Rice Tetraspanin Genes Reveals Diverse Roles During Development and Abiotic Stress

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Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat

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Transcription factor binding sites are frequently under accelerated evolution in primates

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Exploiting budding yeast natural variation for industrial processes

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Structure of the Transcriptional Regulatory Network Correlates with Regulatory Divergence in Drosophila

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Asymmetric Evolution of Protein Domains in the Leucine-Rich Repeat Receptor-Like Kinase Family of Plant Signaling Proteins

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Comprehensive Analyses of Nitric Oxide-Induced Plant Stem Cell-Related Genes in Arabidopsis thaliana

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Parallel and population-specific gene regulatory evolution in cold-adapted fly populations

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In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

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Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change

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Genome-Wide Identification of the Thaumatin-like Protein Family Genes in Gossypium barbadense and Analysis of Their Responses to Verticillium dahliae Infection

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Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development

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Composite Molecular Assemblies: Nanoscale Structural Control and Spectroelectrochemical Diversity

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Can We Predict Gene Expression by Understanding Proximal Promoter Architecture?

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Nonadditive and Asymmetric Allelic Expression of Growth Hormone in Hybrid Tilapia

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Few Fixed Variants between Trophic Specialist Pupfish Species Reveal CandidateCis-Regulatory Alleles Underlying Rapid Craniofacial Divergence

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Comparative Analyses between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana Using Random Forest and Support Vector Machine

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Myeloid cell leukemia-1 dependence in acute myeloid leukemia: a novel approach to patient therapy

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Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene

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Identification and expression analysis of phosphate transporter genes and metabolites in response to phosphate stress in Capsicum annuum

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Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis

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Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii

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Ascorbate oxidases in bread wheat: gene regulatory network, transcripts profiling, and interaction analyses provide insight into their role in plant development and stress response

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Breaking bad: The mutagenic effect of DNA repair

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Phenotypic novelty by CRISPR in plants

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Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated

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Genome-Wide Analysis of the PHT Gene Family and Its Response to Mycorrhizal Symbiosis in Tomatoes under Phosphate Starvation Conditions

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Epistatic Interactions in the ArabinoseCis-Regulatory Element

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Identification of cis-elements and evaluation of upstream regulatory region of a rice anther-specific gene, OSIPP3, conferring pollen-specific expression in Oryza sativa (L.) ssp. indica

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Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder

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Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters

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Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation

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Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa

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MeCP2 and transcriptional control of eukaryotic gene expression

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CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes

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NF-YB family transcription factors in Arabidopsis: Structure, phylogeny, and expression analysis in biotic and abiotic stresses

Bhattacharjee, B., & Hallan, V. K. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1067427 · Cited by 24

Divergent combinations of cis-regulatory elements control the evolution of phenotypic plasticity

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Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress

Zhang, D., Yu, Z., Zeng, B., & Liu, X. (2024) · BMC Plant Biology · doi:10.1186/s12870-023-04698-7 · Cited by 24

Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids

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Mapping active promoters by Ch IP ‐seq profiling of H3K4me3 in cichlid fish – a first step to uncover cis‐regulatory elements in ecological model teleosts

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Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate

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Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in Synthetic Brassica napus and Derivatives (AC, AAC, CCA, CCAA)

Tan, C., Pan, Q., Cui, C., Xiang, Y., Ge, X.-H., & Li, Z. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01432 · Cited by 23

Epigenetic modifications by polyphenolic compounds alter gene expression in the hippocampus

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MIPS: Functional dynamics in evolutionary pathways of plant kingdom

Hazra, A., Dasgupta, N., Sengupta, C., & Das, S. (2019) · Genomics · doi:10.1016/j.ygeno.2019.01.004 · Cited by 24

Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene Casein Kinase I in upland cotton

Li, Y., Fu, Y., Li, Y., Zhang, R., Yang, J., Ma, H., Min, L., & Zhang, X. (2025) · Science China Life Sciences · doi:10.1007/s11427-024-2755-9 · Cited by 23

Inside the supergene of the bird with four sexes

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Genome-wide mining of wheat B-BOX zinc finger (BBX) gene family provides new insights into light stress responses

Chen, S., Jiang, W. J., Yin, J., Wang, S., Fang, Z., Ma, D. M., & Gao, D. (2021) · Australian Journal of Agricultural Research · doi:10.1071/cp20342 · Cited by 23

Comprehensive analysis of formin gene family highlights candidate genes related to pollen cytoskeleton and male fertility in wheat (Triticum aestivum L.)

Duan, W., Liu, Z., Bai, J., Yuan, S., Li, Y., Lu, F., Zhang, T., Sun, J., Zhang, F., Zhao, C., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07878-7 · Cited by 23

In vivo CRISPR‐Cas9‐mediated DNA chop identifies a cochlear outer hair cell‐specific enhancer

Sun, Y., Zhang, Y., Zhang, D., Wang, G., Song, L., & Liu, Z. (2022) · The FASEB Journal · doi:10.1096/fj.202100421rr · Cited by 19

Tissue Specificity of Gene Expression Evolves Across Mammal Species

Jiang, W., & Chen, L. (2022) · Journal of Computational Biology · doi:10.1089/cmb.2021.0592 · Cited by 23

Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from human non-coding genomes

Bykova, M., Hou, Y., Eng, C., & Cheng, F. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac208 · Cited by 24

Identification of AREB/ABF Gene Family Involved in the Response of ABA under Salt and Drought Stresses in Jute (Corchorus olitorius L.)

Fiallos-Salguero, M. S., Li, J., Li, Y., Xu, J., Fang, P., Wang, Y., Zhang, L., & Tao, A. (2023) · Plants · doi:10.3390/plants12051161 · Cited by 23

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

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Systematic pan-cancer analysis of somatic allele frequency

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Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method

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Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes

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Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes

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Cr-Prom: A Convolutional Neural Network-Based Model for the Prediction of Rice Promoters

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Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergencePreprint

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The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR

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Map-Based Functional Analysis of the GhNLP Genes Reveals Their Roles in Enhancing Tolerance to N-Deficiency in Cotton

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