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Integrated analysis of transcriptome and proteome reveals the key genes and processes involved in ovarian development in Exopalaemon carinicauda

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Genome-wide identification and characterization of FORMIN gene family in potato (Solanum tuberosum L.) and their expression profiles in response to drought stress condition

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Genetic and Epigenetic Dysregulation of Transcriptional Enhancers in Cancer

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Whole‐genome sequencing analysis of Japanese autism spectrum disorder trios

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Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition

Tripathi, A. H., Singh, D., Bhati, J., Singh, D., Taunk, J., Alkahtani, J., Al-Hashimi, A., & Singh, M. P. (2025) · BMC Plant Biology · doi:10.1186/s12870-025-06086-9 · Cited by 6

Mechanisms for DNA Interplay in Eukaryotic Transcription Factors

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Deciphering enhancers of hearing loss genes for efficient and targeted gene therapy of hereditary deafness

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Genome‐Wide Identification of WRKY Transcription Factors in Lagerstroemia indica and Their Involvement in Color Formation

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Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis

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Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Navrátilová, P., Pavlu, S., Zhu, Z., Tulpová, Z., Kopecky, O., Novák, P., Stein, N., & Šimková, H. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101037 · Cited by 6

Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations

Yang, W., Zhao, P., Liu, Y., Cao, P., Ji, X., Gao, Y., Li, P., & Cheng, J. (2021) · BMC Genomics · doi:10.1186/s12864-021-08204-x · Cited by 6

Asymmetric predictive relationships across histone modifications

Li, H., & Guan, Y. (2022) · Nature Machine Intelligence · doi:10.1038/s42256-022-00455-x · Cited by 6

Fine mapping and candidate gene analysis of gummy stem blight resistance in cucumber stem

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eQTLs as causal instruments for the reconstruction of hormone linked gene networks

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A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives

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High Temperature Triggers Differential Expression of JUMONJI C (JmjC) Domain-Containing Histone Demethylase Genes in Leaf and Stolon Tissues of Potato (Solanum tuberosum L.) Genotypes

Mali, S., Dutta, M., Goel, K., Raturi, V., Kundu, P., Kumar, R. S., Gahlaut, V., Acharya, V., Gupta, V. K., Sood, S., et al. (2023) · Journal of Plant Growth Regulation · doi:10.1007/s00344-023-11094-w · Cited by 6

A genome‑wide approach to the systematic and comprehensive analysis of LIM gene family in sorghum (Sorghum bicolor L.)

Sarkar, M. A. R., Sarkar, S., Islam, M. S. U., Zohra, F. T., & Rahman, S. M. (2023) · Genomics & Informatics · doi:10.5808/gi.23007 · Cited by 6

Genome-Wide Identification and Characterization of LIM Gene Family in Grapevine (Vitis vinifera L.) and Their Expression Analysis at Early Bud Developmental Stages

Sarkar, M. A. R., Sarkar, S., Islam, M. S. U., Zohra, F. T., & Rahman, S. M. (2023) · Plant Molecular Biology Reporter · doi:10.1007/s11105-023-01416-3 · Cited by 6

Lineage‐specific genomics: Frequent birth and death in the human genome

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Computational deciphering of biotic stress associated genes in tomato ( Solanum lycopersicum )

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Genetic diversity near the DGAT1-2 gene for high oleic acid content and kernel trait variation in a maize breeding collection

Olmos, S. E., Trejo, J. M., Percibaldi, N. M., & Eyhérabide, G. H. (2018) · Molecular Breeding · doi:10.1007/s11032-018-0855-5 · Cited by 6

Novel mRNAs 3′ end-associated cis-regulatory elements with epigenomic signatures of mammalian enhancers in the Arabidopsis genome

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Non-linear Dynamics in Transcriptional Regulation: Biological Logic Gates

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Zebrafish Zic Genes Mediate Developmental Signaling

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Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheepPreprint

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Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow ( Salix spp.)

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Genome-wide identification, characterization, evolution, and expression pattern analyses of MADS-box gene family in rambutan

Dong, F., Wan, S., & Zhang, W. (2024) · Tropical Plants · doi:10.48130/tp-0024-0026 · Cited by 5

A network-enabled pipeline for gene discovery and validation in non-model plant species

Ko, D. K., & Brandizzí, F. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100963 · Cited by 5

Genome-Wide Identification of the YABBY Gene Family in Maize and Its Expression Analysis Under Low Phosphorus and High Nitrogen Stress

Li, F., Li, S., Yi, L., Zhao, P., Ma, C., Huang, X., Wang, J., Liu, C., Jiao, B., Mei, X., et al. (2025) · Plants · doi:10.3390/plants14172763 · Cited by 5

Bridging the variant-to-function gap in type 2 diabetes: advances and challenges

Maynard, A. G., Bhardwaj, R., Jones, T. R., & Claussnitzer, M. (2025) · Diabetologia · doi:10.1007/s00125-025-06600-6 · Cited by 7

Generative AI for synthetic biology: Designing biological parts, circuits, and genomes

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Seasonal Adaptation: Geographic Photoperiod–Temperature Patterns Explain Genetic Variation in the Common Vole Tsh Receptor

van Rosmalen, L., Schepers, R., Hao, W., Przybylska-Piech, A. S., Herman, J. S., Stojak, J., Wójcik, J. M., van de Zande, L., Searle, J. B., & Hut, R. A. (2023) · Genes · doi:10.3390/genes14020292 · Cited by 7

DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden

Konstantinidis, I., Sætrom, P., Brieuc, M. S. O., Jakobsen, K. S., Liedtke, H., Pohlmann, C., Tsoulia, T., & Fernandes, J. M. O. (2023) · Epigenetics · doi:10.1080/15592294.2023.2282323 · Cited by 5

Molecular Innovations Shaping Beak Morphology in Birds

Cheng, Y., Miller, M. J., & Lei, F. (2024) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-074906 · Cited by 8

ATAC‐seq in Emerging Model Organisms: Challenges and Strategies

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Functional Roles and Mechanistic Insights of YEATS Domain Proteins in Digestive System Tumors

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Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution

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Insights into nuclear dynamics using live‐cell imaging approaches

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The role of the FHA domain-containing protein family in pollen development of Brassica rapa L

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Comprehensive genome-wide analysis of polyamine and ethylene pathway genes in Cleistogenes songorica and CsSAMDC2 function in response to abiotic stress

Wu, F., Muvunyi, B. P., Qi, Y., Kanzana, G., Ma, T., Zhang, Z., Wang, Y., & Zhang, J. (2022) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2022.105029 · Cited by 5

Adaptive evolution and epigenetics

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Single-Cell Gene Expression Analysis Revealed Immune Cell Signatures of Delta COVID-19

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Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

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The Ancestral Modulation Hypothesis: Predicting Mechanistic Control of Sexually Heteromorphic Traits Using Evolutionary History

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Polygenic risk score (PRS) and its potential for breast cancer risk stratification

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Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

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Responsiveness to endurance training can be partly explained by the number of favorable single nucleotide polymorphisms an individual possesses

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Genome‐Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea (Vigna unguiculata (L.) Walp.)

Hasan, M. N., Mosharaf, M. P., Uddin, K. S., Das, K. R., Sultana, N., Noorunnahar, M., Naim, D., & Mollah, M. N. H. (2023) · BioMed Research International · doi:10.1155/2023/8832406 · Cited by 5

DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements

Chandrashekar, P. B., Chen, H., Lee, M., Ahmadinejad, N., & Liu, L. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.044 · Cited by 6

An InDel in the promoter of ribosomal protein S27-like gene regulates skeletal muscle growth in pigs

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Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis - and trans -regulation architectures

Nomura, Y., Okada, M., Tameshige, T., Takenaka, S., Shimizu, K. K., Nasuda, S., & Nagano, A. J. (2025) · Plant and Cell Physiology · doi:10.1093/pcp/pcaf011 · Cited by 5

Morphological Mutations: Lessons from the Cockscomb

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Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish

Fang, W., Wen, Y., & Wei, X. (2019) · Methods in molecular biology · doi:10.1007/978-1-0716-0175-4_10 · Cited by 6

Repression precedes independent evolutionary gains of a highly specific gene expression pattern

Pu, J. Y., Wang, Z., Cong, H., Chin, J. S. R., Justen, J., Finet, C., Yew, J. Y., & Chung, H. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109896 · Cited by 5

Divergence of X-linked trans regulatory proteins and the misexpression of gene targets in sterile Drosophila pseudoobscura hybrids

Go, A. C., & Civetta, A. (2022) · BMC Genomics · doi:10.1186/s12864-021-08267-w · Cited by 5

Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines

Zeng, P., Ge, X., & Li, Z. (2023) · Plants · doi:10.3390/plants12102029 · Cited by 6

Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

Chalivendra, S., Shi, S., Li, X., Kuang, Z., Giovinazzo, J., Zhang, L., Rossi, J., Wang, J., Saviola, A. J., Welty, R., et al. (2024) · RNA · doi:10.1261/rna.079917.123 · Cited by 5

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Horiuchi, Y., Harushima, Y., Fujisawa, H., Mochizuki, T., Fujita, M., Ohyanagi, H., & Kurata, N. (2015) · BMC Genomics · doi:10.1186/s12864-015-2319-1 · Cited by 5

Abiotic stress and self-destruction: ZmATG8 and ZmATG12 gene transcription and osmotic stress responses in maize

Tejeda, L. H. C., Viana, V. E., Maltzahn, L. E., Busanello, C., Barros, L. M., da Maia, L. C., de Oliveira, A. C., & Pegoraro, C. (2019) · Biotechnology Research and Innovation · doi:10.1016/j.biori.2019.12.001 · Cited by 5

Functional Conservation of Divergent p63-Bound cis-Regulatory Elements

Gallardo-Fuentes, L., Santos-Pereira, J. M., & Tena, J. J. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00339 · Cited by 5

Genome-Wide Analysis Reveals Transcription Factors Regulated by Spider-Mite Feeding in Cucumber (Cucumis sativus)

He, J., Bouwmeester, H. J., Dicke, M., & Kappers, I. F. (2020) · Plants · doi:10.3390/plants9081014 · Cited by 5

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

Shahid, M., Imran, Q. M., Hussain, A., Khan, M., Lee, S., Mun, B. G., & Yun, B. (2019) · Genes · doi:10.3390/genes10020173 · Cited by 5

Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes

Espíndola‐Hernández, P., Mueller, J. C., & Kempenaers, B. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac135 · Cited by 5

Anticipatory gene regulation driven by maternal effects in an insect–host system

Nespolo, R. F., Silva, A. X., Figueroa, C. C., & Bacigalupe, L. D. (2015) · Ecology and Evolution · doi:10.1002/ece3.1763 · Cited by 5

Noncoding DNA Evolution: Junk DNA Revisited

Ludwig, M. Z. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00168-2 · Cited by 5

Oxytocin, Vasopressin, and Diversity in Social Behavior

King, L. B., & Young, L. J. (2016) · Wiley eBooks · doi:10.1002/9781118760369.ch19 · Cited by 5

CRUP: A comprehensive framework to predict condition-specific regulatory unitsPreprint

Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schöpflin, R., Li, N., Kinkley, S., Hillmann, A., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/501601 · Cited by 5

Dense encoding of developmental regulatory information may constrain evolvabilityPreprint

Fuqua, T., Jordan, J., van Breugel, M. V., Halavatyi, A., Tischer, C., Polidoro, P., Abe, N., Tsai, A., Mann, R., Stern, D., et al. (2020) · bioRxiv · doi:10.1101/2020.04.17.046052 · Cited by 6

A genome-wide genetic screen uncovers novel determinants of human pigmentationPreprint

Bajpai, V. K., Swigut, T., Mohammed, J., Tycko, J., Naqvi, S., Villanueva, M. A., Kim, T. C., Arora, N., Pritchard, J. K., Bassik, M. C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.29.462413 · Cited by 5

The landscape of fitness effects of putatively functional noncoding mutations in humansPreprint

Di, C., Ramesh, S., Ernst, J., & Lohmueller, K. E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.14.654124 · Cited by 5

Comparative analysis of IRE1s in plants: insights into heat stress adaptation in Triticum aestivum

Singh, A., Samtani, H., Gangwar, H., Sharma, A., Jaiswal, V., Djalović, I. G., Prasad, P. V. V., & Gahlaut, V. (2024) · BMC Plant Biology · doi:10.1186/s12870-024-05785-z · Cited by 4

Inhibition of triglyceride metabolism‐associated enhancers alters lipid deposition during adipocyte differentiation

Zeng, S., Li, Z., Li, X., Du, Q., Zhang, Y., Zhong, Z., Wang, H., Zhang, S., Li, P., Li, H., et al. (2025) · The FASEB Journal · doi:10.1096/fj.202401137r · Cited by 6

Genomic and functional analysis of isochorismate synthase genes in sugarcane and their roles in disease resistance

Zeng, Z., Zhu, X., Chen, J., Zhang, S., Zhou, S., Li, K., & Shen, W. (2025) · The Crop Journal · doi:10.1016/j.cj.2025.05.013 · Cited by 4

Molecular mechanism of ATP‐binding cassette transporter‐mediated insecticide resistance

Lv, Y., Wang, P., Wei, Z., & Yang, X. (2025) · New plant protection. · doi:10.1002/npp2.70018 · Cited by 4

Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon

Yun, J., Burnett, A. C., Rogers, A., & Marais, D. L. D. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf218 · Cited by 4

Controlling gene expression using AI designed Cis-regulatory elements

Xia, Y., & Huo, Y. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.108802 · Cited by 4

Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture

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An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome

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Genomic identification of nitrogen assimilation-related genes and transcriptional characterization of their responses to nitrogen in allotetraploid rapeseed

Wang, Y., Hua, Y., Zhou, T., Huang, J., & Yue, C. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06599-0 · Cited by 4

Evolution and expression of the MADS-box flowering transition genes AGAMOUS-like 24/SHORT VEGETATIVE PHASE with emphasis in selected Neotropical orchids

Ramírez–Ramírez, J. A., Madrigal, Y., Álzate, J. F., & Pabón‐Mora, N. (2021) · Cells and Development · doi:10.1016/j.cdev.2021.203755 · Cited by 4

iDHS-FFLG: Identifying DNase I Hypersensitive Sites by Feature Fusion and Local–Global Feature Extraction Network

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Cis -regulatory landscapes in the evolution and development of the mammalian skull

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