OOIR: Observatory of International Research

Papers

(The median citation count of Biochimica et Biophysica Acta-Gene Regulatory Mechanisms is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-11-01 to 2025-11-01.)

Article	Citations
Bioinformatic meta-analysis of transcriptomics of developing Drosophila muscles identifies temporal regulatory transcription factors including a Notch effector	58
From why to how; The gene expression knowledge commons	34
Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness	33
The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction	30
Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis	30
Illuminating ligand-induced dynamics in nuclear receptors through MD simulations	29
The nucleolus: Coordinating stress response and genomic stability	25
Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases	25
Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation	24
HBO1, a MYSTerious KAT and its links to cancer	22
Genome-wide survey identifies TNNI2 as a target of KLF7 that inhibits chicken adipogenesis via downregulating FABP4	20
Histone acetyltransferase 1 (HAT1) acetylates hypoxia-inducible factor 2 alpha (HIF2A) to execute hypoxia response	19
Dietary choline prevents high fat-induced disorder of hepatic cholesterol metabolism through SREBP-2/HNF-4α/CYP7A1 pathway in a freshwater teleost yellow catfish Pelteobagrus fulvidraco	18
Epigenetic modification facilitates proline synthase PYCR1 aberrant expression in gastric cancer	16
UBE4A catalyzes NRF1 ubiquitination and facilitates DDI2-mediated NRF1 cleavage	16
Effective role of Curcumin on expression regulation of EZH2 histone methyltransferase as a dynamic epigenetic factor in osteogenic differentiation of human mesenchymal stem cells	15
Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator	15
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons	15
Editorial Board	13
N/C-degron pathways and inhibitor development for PROTAC applications	13
Post-translational modifications of lysine-specific demethylase 1	13
The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins	13
Proteomic approaches to study ubiquitinomics	13
The gene regulation knowledge commons: the action area of GREEKC	13
The versatility of the proteasome in gene expression and silencing: Unraveling proteolytic and non-proteolytic functions	12

R-loop and its functions at the regulatory interfaces between transcription and (epi)genome	12
The crucial role of small heat shock proteins in prostate cancer: mechanisms and new therapeutic perspectives	12
DDX5 (p68) orchestrates β-catenin, RelA and SP1 mediated MGMT gene expression in human colon cancer cells: Implication in TMZ chemoresistance	12
Editorial Board	12
Post translational modifications at the verge of plant-geminivirus interaction	11
Specific DNA features of the RNA polymerase I core promoter element targeted by core factor	11
Inflammation-induced nitric oxide suppresses PPARα expression and function via downregulation of Sp1 transcriptional activity in adipocytes	11
Editorial Board	11
Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1)	10
Differences and similarities in recognition of co-factors by Taf14	10
EBV infection alters DNA methylation in primary human colon cells: A path to inflammation and carcinogenesis?	10
The yeast mRNA-binding protein Cth2 post-transcriptionally modulates ergosterol biosynthesis in response to iron deficiency	10
Regulatory systems of chicken alpha-globin gene domain suppress bidirectional transcription	10
The moonlighting of RAD23 in DNA repair and protein degradation	10
Sirtuin4 impacts mitochondrial homeostasis in pancreatic cancer cells by reducing the stability of AlkB homolog 1 via deacetylation of the HRD1-SEL1L complex	10
The N-degron pathway: From basic science to therapeutic applications	10
Quantitative proteomics revealed the transition of ergosterol biosynthesis and drug transporters processes during the development of fungal fluconazole resistance	10
Polycomb repressive complex 1 initiates and maintains tailless repression in Drosophila embryo	10
The mechanism of UP1 binding and unfolding of human telomeric DNA G-quadruplex	10
Unraveling the battle for lysine: A review of the competition among post-translational modifications	9
WT1 regulates HOXB9 gene expression in a bidirectional way	9
METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms	9
The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast	9
Machine learning based analysis of single-cell data reveals evidence of subject-specific single-cell gene expression profiles in acute myeloid leukaemia patients and healthy controls	9
Allelic variation within the major APOE CpG island affects its methylation in the brain of targeted replacement mice expressing human APOE	9
Ser392 phosphorylation modulated a switch between p53 and transcriptional condensates	9
UPS regulation of gene expression and genome integrity	8
The fine-tuned crosstalk between lysine acetylation and the circadian rhythm	8
KDM5A noncanonically binds antagonists MLL1/2 to mediate gene regulation and promotes epithelial to mesenchymal transition	8
Ubiquitination is a major modulator for the activation of inflammasomes and pyroptosis	8
Disruption of the gene regulatory programme in neurodevelopmental disorders	8
AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources	8
GLI1, a novel target of the ER stress regulator p97/VCP, promotes ATF6f-mediated activation of XBP1	8
Protein post-translational modifications: A key factor in colorectal cancer resistance mechanisms	8
Navigating the tumor landscape: VEGF, MicroRNAs, and the future of cancer treatment	8
Influence of cell volume on the gene transcription rate	8
Metabolic substrates, histone modifications, and heart failure	8
Human stem cell-specific epigenetic signatures control transgene expression	7
Insights into the target-directed miRNA degradation mechanism in Drosophila ovarian cell culture	7
The cellular pathways that maintain the quality control and transport of diverse potassium channels	7
Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture	7
Epigenetic oncogenesis, biomarkers and emerging chemotherapeutics for breast cancer	7
Isolation and characterisation of promoters from mouse genome to drive post-meiotic germ cell-specific robust gene expression for functional genomics studies	7
Regulation of c-Kit gene transcription selectively by bisacridine derivative through promoter dual i-motif structures	7
An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability	7
Editorial Board	7
MicroRNA-27a-3p targeting Vangl1 and Vangl2 inhibits cell proliferation in mouse granulosa cells	7
Transcriptional responses of three slc39a/zip members (zip4, zip5 and zip9) and their roles in Zn metabolism in grass carp (Ctenopharyngodon idella)	7
A novel endoplasmic reticulum adaptation is critical for the long-lived Caenorhabditis elegans rpn-10 proteasomal mutant	7
NtcA, LexA and heptamer repeats involved in the multifaceted regulation of DNA repair genes recF, recO and recR in the cyanobacterium Nostoc PCC7120	7

The functions of FOXP transcription factors and their regulation by post-translational modifications	7
Selenoprotein F (SELENOF)-mediated AKT1-FOXO3a-PYGL axis contributes to selenium supranutrition-induced glycogenolysis and lipogenesis	6
Reviewer Acknowledgement	6
UPS writes a new saga of SAGA	6
Iron restriction increases the expression of a cytotoxic cysteine proteinase TvCP2 by a novel mechanism of tvcp2 mRNA alternative polyadenylation in Trichomonas vaginalis	6
Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region	6
A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803	6
Identification of essential intron sequences that enhance gene expression independently of splicing in the yeast Saccharomyces cerevisiae	6
Damaged collagen detected by collagen hybridizing peptide as efficient diagnosis marker for early hepatic fibrosis	6
The essential link: How STAT3 connects tumor metabolism to immunity	6
Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein	6
Editorial Board	6
DNA-PKcs as an upstream mediator of OCT4-induced MYC activation in small cell lung cancer	6
Editorial Board	6
Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP	6
Editorial Board	6
Functional characterization of promoter regions in selenoprotein synthesis-relevant genes (sbp2, eefsec and sepsecs) and their selenium-dependent regulation in yellow catfish Pelteobagrus fulvidraco	6
DDX3X functionally and physically interacts with Estrogen Receptor-alpha	6
New roles for elongation factors in RNA polymerase II ubiquitylation and degradation	5
Gene Ontology representation for transcription factor functions	5
Editorial Board	5
Crosstalk between circular RNAs and the STAT3 signaling pathway in human cancer	5
Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro	5
H3K56 acetylation affects Candida albicans morphology and secreted soluble factors interacting with the host	5
Editorial Board	5
Growth rate is related to elongation of RNA polymerase II transcription in Saccharomyces cerevisiae	5
A putative PIWIL/piRNA–OTX2 network: An emerging model for epigenetic regulation of cancer stemness in retinoblastoma	5
Normalization of gene counts affects principal components-based exploratory analysis of RNA-sequencing data	5
Editorial Board	4
Incautious design of shRNAs for stable overexpression of miRNAs could result in generation of undesired isomiRs	4
Role of clusterin gene 3’-UTR polymorphisms and promoter hypomethylation in the pathogenesis of pseudoexfoliation syndrome and pseudoexfoliation glaucoma	4
Identification of RBMX as a splicing regulator in Parkinsonian mimetic induced alternative splicing of α-synuclein	4
Editorial Board	4
Transcriptional regulation of Znt family members znt4, znt5 and znt10 and their function in zinc transport in yellow catfish (Pelteobagrus fulvidraco)	4
Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2	4
LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer	4
Novel splice variants of LINC00963 suppress colorectal cancer cell proliferation via miR-10a/miR-143/miR-217/miR-512-mediated regulation of PI3K/AKT and Wnt/β-catenin signaling pathways	4
Editorial Board	4
TAT38 and TAT38 mimics potently inhibit adipogenesis by repressing C/EBPα, PPARγ, Pi-PPARγ, and SREBP1 expression	4
Post-translational regulation of proto-oncogene ZBTB7A expression by p53 status in cancer cells: HSP90-dependent stabilization vs. p53-KLHL20-ubiquitin proteasomal degradation	4
Epigenetic modifications of histones during osteoblast differentiation	4
Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells	4
Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription	4
Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity	4