Functional & Integrative Genomics

Article	Citations
RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes	142
Regulatory non-coding RNAs: a new frontier in regulation of plant biology	57
Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets	57
Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement	46
The NAC-type transcription factor GmNAC20 improves cold, salinity tolerance, and lateral root formation in transgenic rice plants	40
Prospective role and immunotherapeutic targets of sideroflexin protein family in lung adenocarcinoma: evidence from bioinformatics validation	38
Developing future heat-resilient vegetable crops	37
Potential of underutilized crops to introduce the nutritional diversity and achieve zero hunger	32
BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction	30
Host-mediated gene engineering and microbiome-based technology optimization for sustainable agriculture and environment	26
MiRNA-seq analysis of spleen and head kidney tissue from aquacultured largemouth bass (Micropterus salmoides) in response to Aeromonas hydrophila infection	25
An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges	24
A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment	20
Efficient genome editing in wheat using Cas9 and Cpf1 (AsCpf1 and LbCpf1) nucleases	20
Colorimetric and fluorometric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for diagnosis of SARS-CoV-2	19
Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing	19
Dynamics of Zea mays transcriptome in response to a polyphagous herbivore, Spodoptera litura	18
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana	18
Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance	17
LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants	17
Comparative proteomic and transcriptomic analysis reveals high pH–induced expression signatures of Chinese shrimp Fenneropenaeus chinensis	16
CircPVT1 facilitates the progression of oral squamous cell carcinoma by regulating miR-143-3p/SLC7A11 axis through MAPK signaling pathway	16
Regulatory mechanism and biological function of UHRF1–DNMT1-mediated DNA methylation	16
Identification and bioinformatics analysis of differentially expressed milk exosomal microRNAs in milk exosomes of heat-stressed Holstein cows	16
Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken	16

Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum	15
Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation	15
Genome-wide analysis of VPE family in four Gossypium species and transcriptional expression of VPEs in the upland cotton seedlings under abiotic stresses	15
Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle	15
Validation of molecular response of tuberization in response to elevated temperature by using a transient Virus Induced Gene Silencing (VIGS) in potato	14
Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars	14
Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root	13
A prospective prognostic signature for pancreatic adenocarcinoma based on ubiquitination-related mRNA-lncRNA with experimental validation in vitro and vivo	13
Emerging roles of non-coding RNAs in psoriasis pathogenesis	13
Transcriptome skimming of lentil (Lens culinaris Medikus) cultivars with contrast reaction to salt stress	13
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	13
Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea	12
Cuproptosis-related gene SLC31A1 expression correlates with the prognosis and tumor immune microenvironment in glioma	12
CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits	12
Prognostic and immune microenvironment analysis of cuproptosis-related LncRNAs in breast cancer	12
Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification	12
Exosomal miRNAs—a diagnostic biomarker acting as a guiding light in the diagnosis of prostate cancer	12
Single-cell transcriptome analysis revealing the intratumoral heterogeneity of ccRCC and validation of MT2A in pathogenesis	12
Advancing agro-ecological sustainability through emerging genetic approaches in crop improvement for plants	12
Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq	11
Comparative transcriptomics unravels new genes imparting scab resistance in apple (Malus x domestica Borkh.)	11
Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species	11
Application value of circulating LncRNA in diagnosis, treatment, and prognosis of breast cancer	11
A network-based approach to identify protein kinases critical for regulating srebf1 in lipid deposition causing obesity	11
The landscape of genome sequencing and assembling in plants	11
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	11
Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects	11
Effect of salinity on ccmfn gene RNA editing of mitochondria in wild barley and uncommon types of RNA editing	10
Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta	10
Elucidating the role of T-cell exhaustion-related genes in colorectal cancer: a single-cell bioinformatics perspective	10
microRNA-140-5p from human umbilical cord mesenchymal stem cells–released exosomes suppresses preeclampsia development	10
Evaluation of the differences between biofilm and planktonic Brucella abortus via metabolomics and proteomics	10
Identification and validation of a pyroptosis-related prognostic model for colorectal cancer	10
Genome-wide identification of Ran GTPase family genes from wheat (T. aestivum) and their expression profile during developmental stages and abiotic stress conditions	10
Pepsinogen C expression–related lncRNA/circRNA/mRNA profile and its co-mediated ceRNA network in gastric cancer	10
Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane	10
Integrated analysis of miRNA-mRNA regulatory network and functional verification of miR-338-3p in coronary heart disease	10
Glycolysis induces Th2 cell infiltration and significantly affects prognosis and immunotherapy response to lung adenocarcinoma	10
An overview of the transcriptional responses of two tolerant and susceptible sugarcane cultivars to borer (Diatraea saccharalis) infestation	10
Identifying key genes involved in yellow leaf variation in ‘Menghai Huangye’ based on biochemical and transcriptomic analysis	9
Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley	9
Genome-wide identification of the CER1 gene family in apple and response of MdCER1-1 to drought stress	9
The dysregulation of miRNAs in epilepsy and their regulatory role in inflammation and apoptosis	9
Formononetin ameliorates the LPS-induced inflammatory response and apoptosis of neuronal cells via NF-κB/NLRP3 signaling pathway	9
CRISPR/Cas9 genome editing in wheat: enhancing quality and productivity for global food security—a review	9
Knockdown of circMYOF inhibits cell growth, metastasis, and glycolysis through miR-145-5p/OTX1 regulatory axis in laryngeal squamous cell carcinoma	9
Fine mapping and candidate gene analysis of dwarf gene Rht14 in durum wheat (Triticum durum)	9
Identification of the three subtypes and the prognostic characteristics of stomach adenocarcinoma: analysis of the hypoxia-related long non-coding RNAs	9
Importance of clitellar tissue in the regeneration ability of earthworm Eudrilus eugeniae	9
Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak	9

Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1	9
The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms	9
The changing landscape of agriculture: role of precision breeding in developing smart crops	9
In silico development and experimental validation of a novel 7-gene signature based on PI3K pathway-related genes in bladder cancer	9
Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change	9
Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer	9
LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI	9
Astragaloside IV suppresses the migration and EMT progression of cervical cancer cells by inhibiting macrophage M2 polarization through TGFβ/Smad2/3 signaling	9
The potentialities of omics resources for millet improvement	9
Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines	9
Comparative transcriptome analyses identify genes involved into the biosynthesis of forsythin and forsythoside A in Forsythia suspensa	8
Mosquito gene targeted RNAi studies for vector control	8
MicroRNAs regulating Wnt signaling pathway in colorectal cancer: biological implications and clinical potentials	8
Circular RNAs acting as ceRNAs mediated by miRNAs may be involved in the synthesis of soybean fatty acids	8
Drought stress in maize: stress perception to molecular response and strategies for its improvement	8
Site-directed RNA editing by harnessing ADARs: advances and challenges	8
Screening of microRNA and mRNA related to secondary hair follicle morphogenesis and development and functional analysis in cashmere goats	8
LncRNA UCA1 epigenetically suppresses APAF1 expression to mediate the protective effect of sevoflurane against myocardial ischemia–reperfusion injury	8
Genome-wide exploration of oil biosynthesis genes in cultivated olive tree varieties (Olea europaea): insights into regulation of oil biosynthesis	8
Organ-specific or personalized treatment for COVID-19: rationale, evidence, and potential candidates	8
Comparative transcriptomic analysis and antioxidant defense mechanisms in clusterbean (Cyamopsis tetragonoloba (L.) Taub.) genotypes with contrasting drought tolerance	8
Association of DNA methylation and transcriptome reveals epigenetic etiology of heart failure	8
An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?	8
Immune-related biomarkers predict the prognosis and immune response of breast cancer based on bioinformatic analysis and machine learning	8
Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium	8
Sugar transporter ZmSWEET1b is responsible for assimilate allocation and salt stress response in maize	7
Evaluating the transmission feasibility of SARS-CoV-2 Omicron (B.1.1.529) variant to 143 mammalian hosts: insights from S protein RBD and host ACE2 interaction studies	7
Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire, Liangshan, and Qingyu pigs	7
MicroRNA: noncoding but still coding, another example of self-catalysis	7
RNA-sequencing identification and validation of genes differentially expressed in high-risk adenoma, advanced colorectal cancer, and normal controls	7
Weighted gene co-expression network analysis combined with machine learning validation to identify key hub biomarkers in colorectal cancer	7
RETRACTED ARTICLE: Breast cancer prognosis and immunological characteristics are predicted using the m6A/m5C/m1A/m7G-related long noncoding RNA signature	7
Exosomal microRNA-342-5p from human umbilical cord mesenchymal stem cells inhibits preeclampsia in rats	7
Identification and high-resolution mapping of a novel tiller number gene (tin6) by combining forward genetics screen and MutMap approach in bread wheat	7
Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression	7
Smart reprogramming of jujube germplasm against salinity tolerance through molecular tools	7
A novel mitochondria-related gene signature in esophageal carcinoma: prognostic, immune, and therapeutic features	7
Flavonoids: a review on biosynthesis and transportation mechanism in plants	7
Genome-wide identification of 14-3-3 gene family and characterization of their expression in developmental stages of Solanum tuberosum under multiple biotic and abiotic stress conditions	7
Molecular cloning and functional characterization of MhHEC2-like genes in Malus halliana reveals it enhances Fe (iron) deficiency tolerance	7
A scoping review on deep learning for next-generation RNA-Seq. data analysis	7
Molecular and genetic insights into secondary metabolic regulation underlying insect-pest resistance in legumes	7
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	7
Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea	7
ASmiR: a machine learning framework for prediction of abiotic stress–specific miRNAs in plants	7
Genome-wide comparative analysis of DNAJ genes and their co-expression patterns with HSP70s in aestivation of the sea cucumber Apostichopus japonicus	7
miR-330-3p alleviates the progression of atherosclerosis by downregulating AQP9	6
OCT4-mediated transcription confers oncogenic advantage for a subset of gastric tumors with poor clinical outcome	6
Unraveling the functional characterization of a jasmonate-induced flavonoid biosynthetic CYP45082G24 gene in Carthamus tinctorius	6
OsMBTB32, a MATH-BTB domain-containing protein that interacts with OsCUL1s to regulate salt tolerance in rice	6
Leaf rust responsive miRNA and their target genes in wheat	6
A rapid, efficient, and low-cost BiFC protocol and its application in studying in vivo interaction of seed-specific transcription factors, RISBZ and RPBF	6
The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum	6
Transcriptomic and metabolomic analyses of non-structural carbohydrates in red maple leaves	6
Construction and experimental validation of a B cell senescence–related gene signature to evaluate prognosis and immunotherapeutic sensitivity in bladder cancer	6
Craspase: A novel CRISPR/Cas dual gene editor	6
The causal role of intestinal microbiome in development of pre-eclampsia	6
Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma	6
Therapeutic and diagnostic applications of exosomal circRNAs in breast cancer	6
Japanese medaka Olpax6.1 mutant as a potential model for spondylo-ocular syndrome	6
Genome-wide analysis of zinc finger-homeodomain (ZF-HD) transcription factors in diploid and tetraploid cotton	6
LINC02381 suppresses cell proliferation and promotes apoptosis via attenuating IGF1R/PI3K/AKT signaling pathway in breast cancer	6
RETRACTED ARTICLE: ITGA3 acts as a purity-independent biomarker of both immunotherapy and chemotherapy resistance in pancreatic cancer: bioinformatics and experimental analysis	6
Screening Indels from the whole genome to identify the candidates and their association with economic traits in several goat breeds	6
Transcriptome analysis of oil palm pistil during pollination and fertilization to unravel the role of phytohormone biosynthesis and signaling genes	6
Role of circular RNAs in retinoblastoma	6
SORL1 stabilizes ABCB1 to promote cisplatin resistance in ovarian cancer	6
MicroRNAs from Holarrhena pubescens stems: Identification by small RNA Sequencing and their Potential Contribution to Human Gene Targets	6
Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs	6
Downregulated long intergenic non-coding RNA 00,174 represses malignant biological behaviors of lung cancer cells by regulating microRNA-584-3p/ribosomal protein S24 axis	6
RETRACTED ARTICLE: Circular RNA circDLG1 contributes to HCC progression by regulating the miR-141-3p/WTAP axis	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
LncRNA XIST sponges microRNA-448 to promote malignant behaviors of colorectal cancer cells via regulating GRHL2	6
Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies	6
ASLncR: a novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants	6
The roles of WRKY transcription factors in Malus spp. and Pyrus spp.	5
RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines	5
Qi-Long-Tian capsule alleviates pulmonary fibrosis development by modulating inflammatory response and gut microbiota	5
Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.)	5
New vision on the new era of genome study	5

LncRNA SLC25A21-AS1 increases the chemosensitivity and inhibits the progression of ovarian cancer by upregulating the expression of KCNK4	5
A zebrafish pparγ gene deletion reveals a protein kinase network associated with defective lipid metabolism	5
Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study	5
Global gene expression profiling in congenital diaphragmatic hernia (CDH) patients	5
RNA-seq analysis reveals an immunomodulatory peptide from highland barley activating RAW264.7 macrophages via TNF/NF-κB signaling pathway	5
Genome engineering of disease susceptibility genes for enhancing resistance in plants	5
RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species	5
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools	5
Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes	5
Health inequity in genomic personalized medicine in underrepresented populations: a look at the current evidence	5
Mechanism of histone deacetylase HDAC2 in FOXO3-mediated trophoblast pyroptosis in preeclampsia	5
Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture	5
Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice	5
circGRAMD1B contributes to migration, invasion and epithelial-mesenchymal transition of lung adenocarcinoma cells via modulating the expression of SOX4	5
Transcriptomic profiles of human livers undergoing rewarming machine perfusion before transplantation—first insights	5
Regulatory miRNAs, circRNAs and lncRNAs in cell cycle progression of breast cancer	5
Validation of reliable safe harbor locus for efficient porcine transgenesis	5
MiR-124-3p inhibits tumor progression in prostate cancer by targeting EZH2	5
Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees	5
Basics on network theory to analyze biological systems: a hands-on outlook	5
Proteomic analysis of coarse and fine skin tissues of Liaoning cashmere goat	5
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	5
HNRNPA2B1-mediated m6A modification of FOXM1 promotes drug resistance and inhibits ferroptosis in endometrial cancer via regulation of LCN2	5
Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma	5
Double-stranded RNA (dsRNA) technology to control forest insect pests and fungal pathogens: challenges and opportunities	5
Identification of glycolysis-associated long non-coding RNA regulatory subtypes and construction of prognostic signatures by transcriptomics for bladder cancer	5
CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks	5
A prognostic model based on tumor microenvironment-related lncRNAs predicts therapy response in pancreatic cancer	5