OOIR: Observatory of International Research

Papers

(The median citation count of Biochimica et Biophysica Acta-Gene Regulatory Mechanisms is 3. 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 2021-06-01 to 2025-06-01.)

Article	Citations
From why to how; The gene expression knowledge commons	40
Bioinformatic meta-analysis of transcriptomics of developing Drosophila muscles identifies temporal regulatory transcription factors including a Notch effector	30
Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness	26
The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction	26
Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis	23
The nucleolus: Coordinating stress response and genomic stability	22
Illuminating ligand-induced dynamics in nuclear receptors through MD simulations	21
Editorial Board	21
Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases	20
UBE4A catalyzes NRF1 ubiquitination and facilitates DDI2-mediated NRF1 cleavage	18
HBO1, a MYSTerious KAT and its links to cancer	15
Genome-wide survey identifies TNNI2 as a target of KLF7 that inhibits chicken adipogenesis via downregulating FABP4	15
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	13
Epigenetic modification facilitates proline synthase PYCR1 aberrant expression in gastric cancer	13
Histone acetyltransferase 1 (HAT1) acetylates hypoxia-inducible factor 2 alpha (HIF2A) to execute hypoxia response	13
The gene regulation knowledge commons: the action area of GREEKC	12
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons	12
Editorial Board	12
Proteomic approaches to study ubiquitinomics	11
Post-translational modifications of lysine-specific demethylase 1	11
Editorial Board	10
R-loop and its functions at the regulatory interfaces between transcription and (epi)genome	10
N/C-degron pathways and inhibitor development for PROTAC applications	10
DDX5 (p68) orchestrates β-catenin, RelA and SP1 mediated MGMT gene expression in human colon cancer cells: Implication in TMZ chemoresistance	10
Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator	10

The versatility of the proteasome in gene expression and silencing: Unraveling proteolytic and non-proteolytic functions	10
Effective role of Curcumin on expression regulation of EZH2 histone methyltransferase as a dynamic epigenetic factor in osteogenic differentiation of human mesenchymal stem cells	10
The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins	10
Post translational modifications at the verge of plant-geminivirus interaction	10
The crucial role of small heat shock proteins in prostate cancer: mechanisms and new therapeutic perspectives	9
Regulatory systems of chicken alpha-globin gene domain suppress bidirectional transcription	9
Inflammation-induced nitric oxide suppresses PPARα expression and function via downregulation of Sp1 transcriptional activity in adipocytes	9
Quantitative proteomics revealed the transition of ergosterol biosynthesis and drug transporters processes during the development of fungal fluconazole resistance	9
Editorial Board	9
The N-degron pathway: From basic science to therapeutic applications	9
The mechanism of UP1 binding and unfolding of human telomeric DNA G-quadruplex	8
Specific DNA features of the RNA polymerase I core promoter element targeted by core factor	8
Sirtuin4 impacts mitochondrial homeostasis in pancreatic cancer cells by reducing the stability of AlkB homolog 1 via deacetylation of the HRD1-SEL1L complex	8
EBV infection alters DNA methylation in primary human colon cells: A path to inflammation and carcinogenesis?	8
Differences and similarities in recognition of co-factors by Taf14	8
The moonlighting of RAD23 in DNA repair and protein degradation	8
Ser392 phosphorylation modulated a switch between p53 and transcriptional condensates	8
WT1 regulates HOXB9 gene expression in a bidirectional way	8
Polycomb repressive complex 1 initiates and maintains tailless repression in Drosophila embryo	8
METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms	8
Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1)	8
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	8
The yeast mRNA-binding protein Cth2 post-transcriptionally modulates ergosterol biosynthesis in response to iron deficiency	8
Disruption of the gene regulatory programme in neurodevelopmental disorders	7
The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast	7
MicroRNA-27a-3p targeting Vangl1 and Vangl2 inhibits cell proliferation in mouse granulosa cells	7
UPS regulation of gene expression and genome integrity	7
Unraveling the battle for lysine: A review of the competition among post-translational modifications	7
Allelic variation within the major APOE CpG island affects its methylation in the brain of targeted replacement mice expressing human APOE	7
Influence of cell volume on the gene transcription rate	7
Human stem cell-specific epigenetic signatures control transgene expression	7
The fine-tuned crosstalk between lysine acetylation and the circadian rhythm	7
AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources	7
KDM5A noncanonically binds antagonists MLL1/2 to mediate gene regulation and promotes epithelial to mesenchymal transition	7
Protein post-translational modifications: A key factor in colorectal cancer resistance mechanisms	6
Navigating the tumor landscape: VEGF, MicroRNAs, and the future of cancer treatment	6
A novel endoplasmic reticulum adaptation is critical for the long-lived Caenorhabditis elegans rpn-10 proteasomal mutant	6
Insights into the target-directed miRNA degradation mechanism in Drosophila ovarian cell culture	6
Ubiquitination is a major modulator for the activation of inflammasomes and pyroptosis	6
Metabolic substrates, histone modifications, and heart failure	6
Epigenetic oncogenesis, biomarkers and emerging chemotherapeutics for breast cancer	6
The functions of FOXP transcription factors and their regulation by post-translational modifications	6
GLI1, a novel target of the ER stress regulator p97/VCP, promotes ATF6f-mediated activation of XBP1	6
Isolation and characterisation of promoters from mouse genome to drive post-meiotic germ cell-specific robust gene expression for functional genomics studies	6
Regulation of c-Kit gene transcription selectively by bisacridine derivative through promoter dual i-motif structures	6
Transcriptional responses of three slc39a/zip members (zip4, zip5 and zip9) and their roles in Zn metabolism in grass carp (Ctenopharyngodon idella)	6
DDX3X functionally and physically interacts with Estrogen Receptor-alpha	5
Editorial Board	5
Editorial Board	5
Editorial Board	5

The cellular pathways that maintain the quality control and transport of diverse potassium channels	5
A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803	5
Editorial Board	5
UPS writes a new saga of SAGA	5
Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP	5
Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein	5
NtcA, LexA and heptamer repeats involved in the multifaceted regulation of DNA repair genes recF, recO and recR in the cyanobacterium Nostoc PCC7120	5
DNA-PKcs as an upstream mediator of OCT4-induced MYC activation in small cell lung cancer	5
Damaged collagen detected by collagen hybridizing peptide as efficient diagnosis marker for early hepatic fibrosis	5
Selenoprotein F (SELENOF)-mediated AKT1-FOXO3a-PYGL axis contributes to selenium supranutrition-induced glycogenolysis and lipogenesis	5
Reviewer Acknowledgement	5
Identification of essential intron sequences that enhance gene expression independently of splicing in the yeast Saccharomyces cerevisiae	5
Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture	5
An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability	5
Iron restriction increases the expression of a cytotoxic cysteine proteinase TvCP2 by a novel mechanism of tvcp2 mRNA alternative polyadenylation in Trichomonas vaginalis	5
Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region	5
New roles for elongation factors in RNA polymerase II ubiquitylation and degradation	4
Editorial Board	4
Gene Ontology representation for transcription factor functions	4
ERα-dependent estrogen-TNFα signaling crosstalk increases cisplatin tolerance and migration of lung adenocarcinoma cells	4
Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells	4
Editorial Board	4
Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36	4
The essential link: How STAT3 connects tumor metabolism to immunity	4
Editorial Board	4
Normalization of gene counts affects principal components-based exploratory analysis of RNA-sequencing data	4
Identification of RBMX as a splicing regulator in Parkinsonian mimetic induced alternative splicing of α-synuclein	4
Editorial Board	4
Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro	4
Crosstalk between circular RNAs and the STAT3 signaling pathway in human cancer	4
Epigenetic modifications of histones during osteoblast differentiation	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
H3K56 acetylation affects Candida albicans morphology and secreted soluble factors interacting with the host	4
Role of clusterin gene 3’-UTR polymorphisms and promoter hypomethylation in the pathogenesis of pseudoexfoliation syndrome and pseudoexfoliation glaucoma	4
Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity	3
Post-translational regulation of proto-oncogene ZBTB7A expression by p53 status in cancer cells: HSP90-dependent stabilization vs. p53-KLHL20-ubiquitin proteasomal degradation	3
Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription	3
Editorial Board	3
Structural basis of the interaction between TFIIS and Leo1 from Arabidopsis thaliana	3
Modulation of Krüppel-like factors (KLFs) interaction with their binding partners in cancers through acetylation and phosphorylation	3
TAT38 and TAT38 mimics potently inhibit adipogenesis by repressing C/EBPα, PPARγ, Pi-PPARγ, and SREBP1 expression	3
Incautious design of shRNAs for stable overexpression of miRNAs could result in generation of undesired isomiRs	3
Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2	3
A GO catalogue of human DNA-binding transcription factors	3
Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels	3
Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure	3
Transcriptional regulation of Znt family members znt4, znt5 and znt10 and their function in zinc transport in yellow catfish (Pelteobagrus fulvidraco)	3
Editorial Board	3
LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer	3
Editorial Board	3
Editorial Board	3
The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes	3