Functional & Integrative Genomics

Article	Citations
Deciphering the RNA-binding protein interaction with the mRNAs encoded from human chromosome 15q11.2 BP1-BP2 microdeletion region	219
Identification of diagnostic molecules and potential therapeutic agents for atopic dermatitis by single-cell RNA sequencing combined with a systematic computing framework that integrates network pharm	89
SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome	85
Retraction Note: RAD54L promotes progression of hepatocellular carcinoma via the homologous recombination repair pathway	46
Retraction Note: Molecular subtypes based on PANoptosis-related genes and tumor microenvironment infiltration characteristics in lower-grade glioma	45
Retraction Note: Comparison of preoperative ultrasound and MRI in the diagnosis of microvascular invasion in hepatocellular carcinoma	44
RETRACTED ARTICLE: Molecular mechanism study and tumor heterogeneity of Chinese angelica and Fructus aurantii in the treatment of colorectal cancer through computational and molecular dynamics	43
MATN2 overexpression suppresses tumor growth in ovarian cancer via PTEN/PI3K/AKT pathway	42
circGRAMD1B contributes to migration, invasion and epithelial-mesenchymal transition of lung adenocarcinoma cells via modulating the expression of SOX4	41
Hyper-methylation of ABCG1 as an epigenetics biomarker in non-small cell lung cancer	36
Construction of a pancreatic cancer prediction model for oxidative stress-related lncRNA	29
Pan-cancer secreted proteome and skeletal muscle regulation: insight from a proteogenomic data-driven knowledge base	25
Liensinine ameliorates ischemia–reperfusion-induced brain injury by inhibiting autophagy via PI3K/AKT signaling	22
Identification and characterization of TMV-induced volatile signals in Nicotiana benthamiana: evidence for JA/ET defense pathway priming in congeneric neighbors via airborne (E)-2-octenal	21
Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma	20
Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing	20
The impact of the Hedgehog signal pathway on the tumor immune microenvironment of gastric adenocarcinoma by integrated analysis of scRNA-seq and RNA-seq datasets	19
The complete plastid genome and characteristics analysis of Achillea millefolium	19
Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution	19
CMTM 6 promotes the development of thyroid cancer by inhibiting NIS activity through activating the MAPK signaling pathway	18
Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hotspots, functional patterns, and molecule repurposing for monkeypox virus	18
MPZL1 suppresses the cancer stem-like properties of lung cancer through β-catenin/TCF4 signaling	17
Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study	17
Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max)	17
Transcriptomic analysis the mechanisms of anti-osteoporosis of desert-living Cistanche herb in ovariectomized rats of postmenopausal osteoporosis	17

Long noncoding RNA LINC00482 silencing sensitizes non-small cell lung cancer cells to cisplatin by downregulating CLASRP via E2F1	17
Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes	17
Characterization of 4-coumarate CoA ligase (4CL) gene family and functional study of Sm4CL2/3/7/9 in Salvia miltiorrhiza	16
Retroperitoneal liposarcoma and craniosynostosis: possible genomic relationship, case report, and literature review	16
TFAP2A-regulated CRNDE enhances colon cancer progression and chemoresistance via RIPK3 interaction	16
Major regulators of the multi-step metastatic process are potential therapeutic targets for breast cancer management	15
Epigenetic modification mediated by PHF20/METTL14/HOXA13 signaling axis modulates osteogenic differentiation of mesenchymal stem cells	15
Erythrocyte miRNA-92a-3p interactions with PfEMP1 as determinants of clinical malaria	15
Xuanhong Dingchuan Tang suppresses bronchial asthma inflammation via the microRNA-107-3p/PTGS2/MAPK axis	14
TBP activates DCBLD1 transcription to promote cell cycle progression in cervical cancer	14
Correction to: Decoding the role of durum wheat ascorbate peroxidase TdAPX7B-2 in abiotic stress response	14
Circular RNA circ_0022707 impedes the progression of preeclampsia via the miR-3135b/GHR/PI3K/Akt axis	14
GPC2 promotes prostate cancer progression via MDK-mediated activation of PI3K/AKT signaling pathway	14
The role of lipoprotein‑associated phospholipase A2 in inflammatory response and macrophage infiltration in sepsis and the regulatory mechanisms	13
CutIn: a ready-to-use construct for rapid generation of urgently needed transgenic cell lines in emerging infection research	13
ANPS: machine learning based server for identification of anti-nutritional proteins in plants	13
Nuclear integration of MYB36 and APX-1 genes impart heat tolerance in wheat	13
CRISPR-Cas9-mediated deletion enhancer of MECOM play a tumor suppressor role in ovarian cancer	13
Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice	13
Exosome theranostics: Comparative analysis of P body and exosome proteins and their mutations for clinical applications	13
Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma	13
Exploring circular RNAs as biomarkers for Parkinson’s disease and their expression changes after aerobic exercise rehabilitation	13
Biotechnological studies towards improvement of finger millet using multi-omics approaches	12
Organ-specific or personalized treatment for COVID-19: rationale, evidence, and potential candidates	12
Pepsinogen C expression–related lncRNA/circRNA/mRNA profile and its co-mediated ceRNA network in gastric cancer	12
Identification of glycolysis-associated long non-coding RNA regulatory subtypes and construction of prognostic signatures by transcriptomics for bladder cancer	12
Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey	12
RNA sequencing in Artemisia annua L explored the genetic and metabolic responses to hardly soluble aluminum phosphate treatment	12
Programmed cell death and melatonin: A comprehensive review	12
Validation of reliable safe harbor locus for efficient porcine transgenesis	12
Genome-wide exploration of oil biosynthesis genes in cultivated olive tree varieties (Olea europaea): insights into regulation of oil biosynthesis	12
Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica)	12
HNRNPA2B1-mediated m6A modification of FOXM1 promotes drug resistance and inhibits ferroptosis in endometrial cancer via regulation of LCN2	12
Comparative transcriptomics unravels new genes imparting scab resistance in apple (Malus x domestica Borkh.)	12
A zebrafish pparγ gene deletion reveals a protein kinase network associated with defective lipid metabolism	12
TRIP 13-dependent pathways promote the development of gastric cancer	11
Novel and known miRNAs in zebu (Tharparkar) and crossbred (Karan-Fries) cattle under heat stress	11
Dissection of valine-glutamine genes and their responses to drought stress in Arachis hypogaea cv. Tifrunner	11
Identification of TIMPs signatures in Randall plaque from single-cell RNA sequencing (scRNA-Seq) analysis	11
Retraction Note: Circular RNA circDLG1 contributes to HCC progression by regulating the miR-141-3p/WTAP axis	11
Circ-IP6K2 suppresses tumor progression by modulating the miR-1292-5p/CAMK2N1 signal in clear cell renal cell carcinoma	11
Deciphering the role of cartilage protein 1 in human dermal fibroblasts: a transcriptomic approach	11
A variant rs6214 within IGF-1 confers risk for ulcerative colitis in Chinese Han populations	11
Endophytic bacterial diversity by 16S rRNA gene sequencing of Pak choi roots under fluazinam, Trichoderma harzianum, and Sophora flavescens inoculation	11
C2CD4A/B variants in the predisposition of lung cancer in the Chinese Han population	11
Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars	11
SIGMAR1 targets AMPK/ULK1 pathway to inhibit SH-SY5Y cell apoptosis by regulating endoplasmic reticulum stress and autophagy	11
Comprehensive pan-cancer analysis reveals that C5orf34 regulates the proliferation and mortality of lung cancer	11
A network-based approach to identify protein kinases critical for regulating srebf1 in lipid deposition causing obesity	10
Small RNA sequencing and identification of Andrographis paniculata miRNAs with potential cross‑kingdom human gene targets	10

Circular RNAs acting as ceRNAs mediated by miRNAs may be involved in the synthesis of soybean fatty acids	10
Transcriptome analysis and differential expression in Arabidopsis thaliana in response to rohitukine (a chromone alkaloid) treatment	10
GsPKS24, a calcineurin B-like protein-interacting protein kinase gene from Glycine soja, positively regulates tolerance to pH stress and ABA signal transduction	10
Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis	10
pSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites	10
PTP1B inhibitor alleviates deleterious septic lung injury through Src signaling	10
RETRACTED ARTICLE: Ensemble learning-based gene signature and risk model for predicting prognosis of triple-negative breast cancer	10
Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)	10
Dynamics of Zea mays transcriptome in response to a polyphagous herbivore, Spodoptera litura	10
Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database	10
Genome-wide association study reveals effect of nsSNPs on candidate genes in rice during iron deficiency	10
Correction to: The whole genomic analysis of the Orf virus strains ORFV‑SC and ORFV‑SC1 from the Sichuan province and their weak pathological response in rabbits	9
mmu-microRNA-92a-3p attenuates pulmonary fibrosis by modulating Cpeb4-mediated Smad2/3 signaling pathway	9
Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance	9
Transcriptome analysis of oil palm pistil during pollination and fertilization to unravel the role of phytohormone biosynthesis and signaling genes	9
Drought stress in maize: stress perception to molecular response and strategies for its improvement	9
Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium	9
Double-stranded RNA (dsRNA) technology to control forest insect pests and fungal pathogens: challenges and opportunities	9
Construction and validation of a novel signature based on epithelial-mesenchymal transition–related genes to predict prognosis and immunotherapy response in hepatocellular carcinoma by comprehensive a	9
Interplay of calcium signaling and ERF-VII stability in plant hypoxia tolerance	9
Breast cancer genomic analyses reveal genes, mutations, and signaling networks	9
Emerging roles of non-coding RNAs in psoriasis pathogenesis	9
Upregulated microRNA-210-3p improves sevoflurane-induced protective effect on ventricular remodeling in rats with myocardial infarction by inhibiting ADCY9	9
Genome editing: An insight into disease resistance, production efficiency, and biomedical applications in livestock	9
Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure	9
LncRNA-encoded peptides: the case of the lncRNA gene located downstream of EIN2	9
CmirC update 2024: a multi-omics database for clustered miRNAs	9
NEDD4 facilitates the progression of endometrial carcinoma by enhancing PAMR1 protein degradation through ubiquitination	9
Correction to: Fantastic genes: where and how to find them? Exploiting rice genetic resources for the improvement of yield, tolerance, and resistance to a wide array of stresses in rice	9
RNA-seq analysis reveals an immunomodulatory peptide from highland barley activating RAW264.7 macrophages via TNF/NF-κB signaling pathway	9
DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility	9
A novel mitochondria-related gene signature in esophageal carcinoma: prognostic, immune, and therapeutic features	9
Construction and experimental validation of a B cell senescence–related gene signature to evaluate prognosis and immunotherapeutic sensitivity in bladder cancer	8
Fusarium wilt pandemic: current understanding and molecular perspectives	8
LncRNA SLC25A21-AS1 increases the chemosensitivity and inhibits the progression of ovarian cancer by upregulating the expression of KCNK4	8
Circular RNAs: a small piece in the heart failure puzzle	8
Identification and validation of TME-related signatures to predict prognosis and response to anti-tumor therapies in skin cutaneous melanoma	8
DKC1 aggravates gastric cancer cell migration and invasion through up-regulating the expression of TNFAIP6	8
Identification of the STY13 gene family across the entire genome and an analysis of the essential function of GhSTY13-12 in cotton’s response to abiotic stress	8
LINC00942 inhibits ferroptosis and induces the immunosuppression of regulatory T cells by recruiting IGF2BP3/SLC7A11 in hepatocellular carcinoma	8
Linking genomic and proteomic signatures to brain amyloid burden: insights from GR@ACE/DEGESCO	8
The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms	8
CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits	8
Exploring the diagnostic value, prognostic value, and biological functions of NPC gene family members in hepatocellular carcinoma based on a multi-omics analysis	8
LncRNA XIST/miR-455-3p/HOXC4 axis promotes breast cancer development by activating TGF-β/SMAD signaling pathway	8
Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression	8
Regulatory non-coding RNAs: a new frontier in regulation of plant biology	8
Epidemiology, pathogenesis, immune evasion mechanism and vaccine development of porcine Deltacoronavirus	7
Regulatory dynamics of Nanog in chondrocyte dedifferentiation: role of KLF4/p53 and p38/AKT signaling	7
Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease	7
Aberrant DNA methylation as a key modulator of cell death pathways: insights into cancer progression and other diseases	7
IL-1R8 expression in DLBCL regulates NK cell recruitment and influences patient prognosis	7
Deltex E3 ubiquitin ligase 4 promotes thyroid cancer progression through stearoyl-CoA desaturase 1	7
Mulberry fruit repairs alcoholic liver injury by modulating lipid metabolism and the expression of miR-155 and PPARα in rats	7
Harnessing the potential of mutation breeding, CRISPR genome editing, and beyond for sustainable agriculture	7
Iodine-125 seed inhibits proliferation and promotes apoptosis of cholangiocarcinoma cells by inducing the ROS/p53 axis	7
DDB2 and MDM2 genes are promising markers for radiation diagnosis and estimation of radiation dose independent of trauma and burns	7
Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture	7
Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae	7
DAB2IP stabilizes p27Kip1 via suppressing PI3K/AKT signaling in clear cell renal cell carcinoma	7
CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine	7
AZD7648 (DNA-PKcs inhibitor): a two-edged sword for editing genomes	7
Immune-related biomarkers predict the prognosis and immune response of breast cancer based on bioinformatic analysis and machine learning	7
Depletion of PIEZO1 expression is accompanied by upregulating p53 signaling in mice with perioperative neurocognitive disorder	7
Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits	7
CRISPR/Cas9 genome editing in wheat: enhancing quality and productivity for global food security—a review	7
Machine learning-based mRNA signature in early acute myocardial infarction patients: the perspective toward immunological, predictive, and personalized	7
Genome-wide characterization of long terminal repeat retrotransposons provides insights into trait evolution of four cucurbit species	7
The potentialities of omics resources for millet improvement	7
Elucidating circRNA-miRNA-mRNA competing endogenous regulatory RNA network during leaf rust pathogenesis in wheat (Triticum aestivum L.)	6
Draft genome sequence of Staphylococcus aureus sequence type 5 SA01 isolated from bloodstream infection and comparative analysis with reference strains	6
Correction to: De novo transcriptome sequencing of drought tolerance–associated genes in little millet (Panicum sumatrense L.)	6
Advancing agro-ecological sustainability through emerging genetic approaches in crop improvement for plants	6
Strigolactone signaling gene from soybean GmMAX2a enhances the drought and salt-alkaline resistance in Arabidopsis via regulating transcriptional profiles of stress-related genes	6
Smart reprogramming of jujube germplasm against salinity tolerance through molecular tools	6
CRISPR/Cas9-mediated knockin of IRES-tdTomato at Ins2 locus reveals no RFP-positive cells in mouse islets	6
Unraveling the potential of senescence-related genes in guiding clinical therapy of lung adenocarcinoma patients	6
Correction to: Understanding population structure and detection of QTLs for curding related traits in Indian cauliflower by genotyping by sequencing analysis	6
Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]	6
Cloning and functional analysis of the DXR gene and promoter region in Osmanthus fragrans var. semperflorens	6

The whole genomic analysis of the Orf virus strains ORFV-SC and ORFV-SC1 from the Sichuan province and their weak pathological response in rabbits	6
Data mining of transcriptional biomarkers at different cotton fiber developmental stages	6
NSUN7 promotes cervical cancer progression through activation of ErbB signaling pathway	6
Identification and bioinformatics analysis of differentially expressed milk exosomal microRNAs in milk exosomes of heat-stressed Holstein cows	6
Long non-coding RNA SNHG1/microRNA-195-5p/Yes-associated protein axis affects the proliferation and metastasis of gastric cancer via the Hippo signaling pathway	6
Targeting nucleotide metabolic pathways in colorectal cancer by integrating scRNA-seq, spatial transcriptome, and bulk RNA-seq data	6
Transcription factor Dp-1 knockdown downregulates thymidine kinase 1 expression to protect against proliferation and epithelial-mesenchymal transition in cervical cancer	6
Exploring the glycolytic cross-talk genes between inflammatory bowel disease and colorectal cancer	6
Correction to: MicroRNAs regulating Wnt signaling pathway in colorectal cancer: biological implications and clinical potentials	6
Identification of exosomes-related lncRNAs in clear cell renal cell carcinoma based on Bayesian spike-and-slab lasso approach	6
Identification of genes governing resistance to PCN (Globodera rostochiensis) through transcriptome analysis in Solanum tuberosum	6
Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus	6
Altered vitamin B12 metabolism in the central nervous system is associated with the modification of ribosomal gene expression: new insights from comparative RNA dataset analysis	6
SENP3 mediates the activation of the Wnt/β-catenin signaling pathway to accelerate the growth and metastasis of oesophagal squamous cell carcinoma in mice	6
Epigenetic gene silencing in plants: Insights from triplet repeat expansion in Arabidopsis	5
Breaking the yield-quality tradeoff: OsNLP3 in rice	5
An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?	5
Comparative transcriptomics of drought stress response of taproot meristem region of contrasting purple carrot breeding lines supported by physio-biochemical parameters	5
Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes	5
Effects of glyphosate exposure on the miRNA expression profile and construction of the miRNA-mRNA regulatory network in mouse bone marrow cells	5
RETRACTED ARTICLE: Identification of biomarkers of hepatocellular carcinoma gene prognosis based on the immune-related lncRNA signature of transcriptome data	5
Mechanism of histone deacetylase HDAC2 in FOXO3-mediated trophoblast pyroptosis in preeclampsia	5
Correction to: Flavonoids: a review on biosynthesis and transportation mechanism in plants	5
Comprehensive multiomics and in silico approach uncovers prognostic, immunological, and therapeutic roles of ANLN in lung adenocarcinoma	5
Transcriptome- and metabolome-based candidate mechanism of BCR-ABL-independent resistance to olverembatinib in Philadelphia chromosome–positive acute lymphoblastic leukemia	5
MicroRNA: noncoding but still coding, another example of self-catalysis	5
Infection by a multidrug-resistant Corynebacterium diphtheriae strain: prediction of virulence factors, CRISPR-Cas system analysis, and structural implications of mutations conferring rifampin resista	5
Spinach-based RNA mimicking GFP in plant cells	5
Optimised stacked machine learning algorithms for genomics and genetics disorder detection in the healthcare industry	5
Toward the development of Ac/Ds transposon-mediated gene tagging system for functional genomics in oat (Avena sativa L.)	5
GAS5/METTL14/ESR1 genetic variants are related to the susceptibility of coronary heart disease	5
MiR-22-3p suppresses NSCLC cell migration and EMT via targeting RAC1 expression	5
RETRACTED ARTICLE: Integration of clinical and spatial data to explore lipid metabolism-related genes for predicting prognosis and immune microenvironment in gliomas	5
Correction to: Huang Qin decoction increases SLC6A4 expression and blocks the NFκB-mediated NLRP3/Caspase1/GSDMD pathway to disrupt colitisassociated carcinogenesis	5
Retraction Note: ITGA3 acts as a purity-independent biomarker of both immunotherapy and chemotherapy resistance in pancreatic cancer: bioinformatics and experimental analysis	5
Genotyping by sequencing; a strategy for identification and mapping of induced mutation in newly developed wheat mutant lines	5
Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders	5
Transcription factor YY1 adversely governs ovarian granulosa cell growth in PCOS by transcription activation-mediated CDKN1C upregulation	5
Comparative transcriptome analysis reveals candidate genes related to the sex differentiation of Schisandra chinensis	5
Cancer pharmacoinformatics: Databases and analytical tools	5
Understanding the evolution of miRNA biogenesis machinery in plants with special focus on rice	5
Regulation of m6A (N6-Methyladenosine) methylation modifiers in solid cancers	5
Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis	5
New vision on the new era of genome study	5
Hypoxia-induced circRTN4IP1 promotes progression and glycolysis of hepatocellular carcinoma cells	5
Retraction Note: Vacuolar protein sorting 35 (VPS35) acts as a tumor promoter via facilitating cell cycle progression in pancreatic ductal adenocarcinoma	5
Correction to: Single‑cell analysis identified PDIA3 as regulator of malignant characteristics and macrophage function in human cancers	5
From genetic correlations of Alzheimer’s disease to classification with artificial neural network models	5
Integrated analysis of the miRNA and mRNA expression profiles in Leiocassis longirostris at gonadal maturation	5
Ubiquitination-specific protease 7 enhances stemness of hepatocellular carcinoma by stabilizing basic transcription factor 3	5
Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification	5