Functional & Integrative Genomics

Article	Citations
RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes	77
Regulatory non-coding RNAs: a new frontier in regulation of plant biology	50
Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets	39
Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement	39
Prospective role and immunotherapeutic targets of sideroflexin protein family in lung adenocarcinoma: evidence from bioinformatics validation	31
The NAC-type transcription factor GmNAC20 improves cold, salinity tolerance, and lateral root formation in transgenic rice plants	31
Developing future heat-resilient vegetable crops	26
Potential of underutilized crops to introduce the nutritional diversity and achieve zero hunger	24
MiRNA-seq analysis of spleen and head kidney tissue from aquacultured largemouth bass (Micropterus salmoides) in response to Aeromonas hydrophila infection	21
BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction	20
Host-mediated gene engineering and microbiome-based technology optimization for sustainable agriculture and environment	20
Efficient genome editing in wheat using Cas9 and Cpf1 (AsCpf1 and LbCpf1) nucleases	19
Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing	18
LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants	17
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana	15
An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges	15
Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea	15
Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance	14
Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken	14
Colorimetric and fluorometric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for diagnosis of SARS-CoV-2	14
Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum	13
Dynamics of Zea mays transcriptome in response to a polyphagous herbivore, Spodoptera litura	13
Genome-wide characterization of the cellulose synthase gene superfamily in Pyrus bretschneideri and reveal its potential role in stone cell formation	13
Genome-wide analysis of VPE family in four Gossypium species and transcriptional expression of VPEs in the upland cotton seedlings under abiotic stresses	13
Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars	13

Comparative proteomic and transcriptomic analysis reveals high pH–induced expression signatures of Chinese shrimp Fenneropenaeus chinensis	12
Transcriptome skimming of lentil (Lens culinaris Medikus) cultivars with contrast reaction to salt stress	12
Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects	11
Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea	11
Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle	11
CircPVT1 facilitates the progression of oral squamous cell carcinoma by regulating miR-143-3p/SLC7A11 axis through MAPK signaling pathway	11
Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines	11
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	10
Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane	10
Regulatory mechanism and biological function of UHRF1–DNMT1-mediated DNA methylation	10
The landscape of genome sequencing and assembling in plants	10
Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification	10
Prognostic and immune microenvironment analysis of cuproptosis-related LncRNAs in breast cancer	10
Validation of molecular response of tuberization in response to elevated temperature by using a transient Virus Induced Gene Silencing (VIGS) in potato	10
A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment	10
Comparative transcriptomics unravels new genes imparting scab resistance in apple (Malus x domestica Borkh.)	10
Evaluation of the differences between biofilm and planktonic Brucella abortus via metabolomics and proteomics	10
Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root	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
Identifying key genes involved in yellow leaf variation in ‘Menghai Huangye’ based on biochemical and transcriptomic analysis	9
LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI	9
microRNA-140-5p from human umbilical cord mesenchymal stem cells–released exosomes suppresses preeclampsia development	9
Advancing agro-ecological sustainability through emerging genetic approaches in crop improvement for plants	9
Emerging roles of non-coding RNAs in psoriasis pathogenesis	9
Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines	9
Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley	9
Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak	9
Identification and bioinformatics analysis of differentially expressed milk exosomal microRNAs in milk exosomes of heat-stressed Holstein cows	9
Pepsinogen C expression–related lncRNA/circRNA/mRNA profile and its co-mediated ceRNA network in gastric cancer	9
CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits	9
A prospective prognostic signature for pancreatic adenocarcinoma based on ubiquitination-related mRNA-lncRNA with experimental validation in vitro and vivo	9
Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation	9
Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq	9
An overview of the transcriptional responses of two tolerant and susceptible sugarcane cultivars to borer (Diatraea saccharalis) infestation	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
A network-based approach to identify protein kinases critical for regulating srebf1 in lipid deposition causing obesity	9
LncRNA UCA1 epigenetically suppresses APAF1 expression to mediate the protective effect of sevoflurane against myocardial ischemia–reperfusion injury	8
Immune-related biomarkers predict the prognosis and immune response of breast cancer based on bioinformatic analysis and machine learning	8
Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer	8
Elucidating the role of T-cell exhaustion-related genes in colorectal cancer: a single-cell bioinformatics perspective	8
Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait	8
Importance of clitellar tissue in the regeneration ability of earthworm Eudrilus eugeniae	8
MicroRNAs regulating Wnt signaling pathway in colorectal cancer: biological implications and clinical potentials	8
Screening of microRNA and mRNA related to secondary hair follicle morphogenesis and development and functional analysis in cashmere goats	8
Exosomal miRNAs—a diagnostic biomarker acting as a guiding light in the diagnosis of prostate cancer	7
The changing landscape of agriculture: role of precision breeding in developing smart crops	7
Effect of salinity on ccmfn gene RNA editing of mitochondria in wild barley and uncommon types of RNA editing	7
Fine mapping and candidate gene analysis of dwarf gene Rht14 in durum wheat (Triticum durum)	7
Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species	7
RNA-sequencing identification and validation of genes differentially expressed in high-risk adenoma, advanced colorectal cancer, and normal controls	7

Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium	7
In silico development and experimental validation of a novel 7-gene signature based on PI3K pathway-related genes in bladder cancer	7
Breast cancer prognosis and immunological characteristics are predicted using the m6A/m5C/m1A/m7G-related long noncoding RNA signature	7
Identification of the three subtypes and the prognostic characteristics of stomach adenocarcinoma: analysis of the hypoxia-related long non-coding RNAs	7
Comparative transcriptome analyses identify genes involved into the biosynthesis of forsythin and forsythoside A in Forsythia suspensa	7
An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?	7
Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1	7
Transcriptome analysis of different rice cultivars provides novel insights into the rice response to bacterial leaf streak infection	7
CRISPR/Cas9 genome editing shows the important role of AZC_2928 gene in nitrogen-fixing bacteria of plants	7
Integrated analysis of miRNA-mRNA regulatory network and functional verification of miR-338-3p in coronary heart disease	7
Association of DNA methylation and transcriptome reveals epigenetic etiology of heart failure	7
Application value of circulating LncRNA in diagnosis, treatment, and prognosis of breast cancer	7
Organ-specific or personalized treatment for COVID-19: rationale, evidence, and potential candidates	7
Identification and high-resolution mapping of a novel tiller number gene (tin6) by combining forward genetics screen and MutMap approach in bread wheat	6
Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression	6
Smart reprogramming of jujube germplasm against salinity tolerance through molecular tools	6
Circular RNAs acting as ceRNAs mediated by miRNAs may be involved in the synthesis of soybean fatty acids	6
Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea	6
Weighted gene co-expression network analysis combined with machine learning validation to identify key hub biomarkers in colorectal cancer	6
Site-directed RNA editing by harnessing ADARs: advances and challenges	6
Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta	6
LINC02381 suppresses cell proliferation and promotes apoptosis via attenuating IGF1R/PI3K/AKT signaling pathway in breast cancer	6
Cuproptosis-related gene SLC31A1 expression correlates with the prognosis and tumor immune microenvironment in glioma	6
Chaperone client proteins evolve slower than non-client proteins	6
The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms	6
Role of circular RNAs in retinoblastoma	6
Comparative transcriptomic analysis and antioxidant defense mechanisms in clusterbean (Cyamopsis tetragonoloba (L.) Taub.) genotypes with contrasting drought tolerance	6
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	6
Exosomal microRNA-342-5p from human umbilical cord mesenchymal stem cells inhibits preeclampsia in rats	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
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
Transcriptomic and metabolomic analyses of non-structural carbohydrates in red maple leaves	6
Genome-wide exploration of oil biosynthesis genes in cultivated olive tree varieties (Olea europaea): insights into regulation of oil biosynthesis	6
Knockdown of circMYOF inhibits cell growth, metastasis, and glycolysis through miR-145-5p/OTX1 regulatory axis in laryngeal squamous cell carcinoma	6
OCT4-mediated transcription confers oncogenic advantage for a subset of gastric tumors with poor clinical outcome	6
Genome-wide comparative analysis of DNAJ genes and their co-expression patterns with HSP70s in aestivation of the sea cucumber Apostichopus japonicus	6
A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.)	5
Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma	5
Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs	5
Molecular cloning and functional characterization of MhHEC2-like genes in Malus halliana reveals it enhances Fe (iron) deficiency tolerance	5
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	5
Occurrence of differing metabolic dysregulations, a glucose driven and another fatty acid centric in gastric cancer subtypes	5
LncRNA XIST sponges microRNA-448 to promote malignant behaviors of colorectal cancer cells via regulating GRHL2	5
Identification of glycolysis-associated long non-coding RNA regulatory subtypes and construction of prognostic signatures by transcriptomics for bladder cancer	5
ASmiR: a machine learning framework for prediction of abiotic stress–specific miRNAs in plants	5
SORL1 stabilizes ABCB1 to promote cisplatin resistance in ovarian cancer	5
Identification and validation of a pyroptosis-related prognostic model for colorectal cancer	5
Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes	5
Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat	5
Leaf rust responsive miRNA and their target genes in wheat	5
CRISPR/Cas9 genome editing in wheat: enhancing quality and productivity for global food security—a review	5
Construction and experimental validation of a B cell senescence–related gene signature to evaluate prognosis and immunotherapeutic sensitivity in bladder cancer	5
Global gene expression profiling in congenital diaphragmatic hernia (CDH) patients	5
A prognostic model based on tumor microenvironment-related lncRNAs predicts therapy response in pancreatic cancer	5
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	5
RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines	5
Basics on network theory to analyze biological systems: a hands-on outlook	5
The dysregulation of miRNAs in epilepsy and their regulatory role in inflammation and apoptosis	5
Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies	5
A novel mitochondria-related gene signature in esophageal carcinoma: prognostic, immune, and therapeutic features	5
Identification of seven hypoxia-related genes signature and risk score models for predicting prognosis for ovarian cancer	4
Genome-wide identification of the CER1 gene family in apple and response of MdCER1-1 to drought stress	4
The roles of WRKY transcription factors in Malus spp. and Pyrus spp.	4
Genome-wide analysis of zinc finger-homeodomain (ZF-HD) transcription factors in diploid and tetraploid cotton	4
Glycolysis induces Th2 cell infiltration and significantly affects prognosis and immunotherapy response to lung adenocarcinoma	4
Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire, Liangshan, and Qingyu pigs	4
ITGA3 acts as a purity-independent biomarker of both immunotherapy and chemotherapy resistance in pancreatic cancer: bioinformatics and experimental analysis	4
Screening Indels from the whole genome to identify the candidates and their association with economic traits in several goat breeds	4
Transcriptome analysis of oil palm pistil during pollination and fertilization to unravel the role of phytohormone biosynthesis and signaling genes	4
Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus)	4
circGRAMD1B contributes to migration, invasion and epithelial-mesenchymal transition of lung adenocarcinoma cells via modulating the expression of SOX4	4
RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species	4
Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality	4
MicroRNAs from Holarrhena pubescens stems: Identification by small RNA Sequencing and their Potential Contribution to Human Gene Targets	4
Qi-Long-Tian capsule alleviates pulmonary fibrosis development by modulating inflammatory response and gut microbiota	4
Synergistic soil-less medium for enhanced yield of crops: a step towards incorporating genomic tools for attaining net zero hunger	4
Comparative analysis of mitochondrial genomes provides insights into the mechanisms underlying an S-type cytoplasmic male sterility (CMS) system in wheat (Triticum aestivum L.)	4
Prognostic subtypes of thyroid cancer was constructed based on single cell and bulk-RNA sequencing data and verified its authenticity	4
New vision on the new era of genome study	4
The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum	4

Flavonoids: a review on biosynthesis and transportation mechanism in plants	4
Comparative de novo transcriptome analysis of barley varieties with different malting qualities	4
Comparative transcriptome analysis reveals that deletion of CheY influences gene expressions of ABC transports and metabolism in Haemophilus parasuis	4
Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study	4
Oncogenic GBX2 promotes the malignant behaviors of bladder cancer cells by binding to the ITGA5 promoter and activating its transcription	4
Unraveling the functional characterization of a jasmonate-induced flavonoid biosynthetic CYP45082G24 gene in Carthamus tinctorius	4
Insights on decoding wheat and barley genomes	4
Circular RNA circDLG1 contributes to HCC progression by regulating the miR-141-3p/WTAP axis	4
Systematic pan-cancer analysis identifies transmembrane protein 158 as a potential therapeutic, prognostic and immunological biomarker	4
Single-cell transcriptome analysis revealing the intratumoral heterogeneity of ccRCC and validation of MT2A in pathogenesis	4
Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.)	4
Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture	4
Ensemble learning-based gene signature and risk model for predicting prognosis of triple-negative breast cancer	4
Craspase: A novel CRISPR/Cas dual gene editor	4
Major regulators of the multi-step metastatic process are potential therapeutic targets for breast cancer management	4
Mosquito gene targeted RNAi studies for vector control	4
Liensinine ameliorates ischemia–reperfusion-induced brain injury by inhibiting autophagy via PI3K/AKT signaling	4