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At least 433 records · Page 24Linked to original sources
PubMed2022

Systems Analysis Reveals Contraceptive-Induced Alteration of Cervicovaginal Gene Expression in a Randomized Trial.

Hormonal contraceptives (HCs) are vital in managing the reproductive health of women. However, HC usage has been linked to perturbations in cervicovaginal immunity and increased risk of sexually transmitted infections. Here, we evaluated the impact of three HCs on the cervicovaginal environment using high-throughput transcriptomics. From 2015 to 2017, 130 adolescent females aged 15-19 years were enrolled into a substudy of UChoose, a single-site, open-label randomized, crossover trial (NCT02404038) and randomized to injectable norethisterone-enanthate (Net-En), combined oral contraceptives (COC), or etonorgesterol/ethinyl-estradiol-combined contraceptive vaginal ring (CCVR). Cervicovaginal samples were collected after 16 weeks of randomized HC use and analyzed by RNA-Seq, 16S rRNA gene sequencing, and Luminex analysis. Participants in the CCVR arm had a significant elevation of transcriptional networks driven by IL-6, IL-1, and NFKB, and lower expression of genes supporting epithelial barrier integrity. An integrated multivariate analysis demonstrated that networks of microbial dysbiosis and inflammation best discriminated the CCVR arm from the other contraceptive groups, while genes involved in epithelial cell differentiation were predictive of the Net-En and COC arms. Collectively, these data from a randomized trial represent the most comprehensive "omics" analyses of the cervicovaginal response to HCs and provide important mechanistic guidelines for the provision of HCs in sub-Saharan Africa.

HIV↗
PubMed2026

Multilevel genomic, transcriptomic, and epidemiologic evidence linking diabetic retinopathy to Alzheimer disease.

BACKGROUND: Diabetic retinopathy (DR) and Alzheimer disease (AD) share metabolic and vascular dysfunctions, but the extent to which they reflect overlapping genetic susceptibility and neurovascular-metabolic regulatory pathways remains unclear. We combined multi-omics analyses with population-based data to examine the genetic convergence, cellular pathways, and longitudinal association between DR and AD. METHODS: We performed a two-sample Mendelian randomisation (MR) to estimate the association between genetically predicted DR liability and AD risk. We used Bayesian colocalisation analysis to identify shared genomic loci, and summary-data-based MR (SMR) to detect expression-mediated genes jointly associated with DR and AD. We analysed single-cell RNA sequencing data to characterise shared cellular features and related biological pathways. We also conducted an MR-based mediation analysis to explore whether lipid-related, metabolic, or inflammatory traits mediated the observed DR-AD association, and a longitudinal analysis of the UK Biobank cohort to assess the association between DR and incident AD. RESULTS: With the MR analysis, we found that genetically predicted liability to DR was associated with a modest increase in AD risk. Colocalisation analysis supported a shared genetic signal. We identified three genes with shared expression-mediated associations across DR and AD through SMR. Functional enrichment analyses revealed partially overlapping neurovascular and metabolic pathways. Using MR-based mediation analysis, we found no significant intermediary traits linking DR and AD. Findings from the UK Biobank cohort were directionally consistent with the genetic analyses. CONCLUSIONS: Genetic liability to DR is associated with an increased risk of AD and is accompanied by shared expression-mediated effects and convergent neurovascular-metabolic pathways. These findings support the possibility that DR may serve as a clinically accessible indicator of increased neurodegenerative vulnerability.

Humans↗
PubMed2026

Comparative metabolomic and transcriptomic profiling of flavonoid diversity and antioxidant capacity in three Isatis species.

Flavonoids are key bioactive compounds in plants with significant health benefits. This study employs an integrated multi-omics approach to investigate flavonoid diversity and antioxidant capacity across three Isatis species: I. oblongata, I. tinctoria, and I. indigotica. Metabolomic profiling identified 200 flavonoids, with glycosides being the most abundant class. I. tinctoria exhibited the highest total flavonoid content and antioxidant activity, strongly correlated with the accumulation of 53 core differential flavonoid metabolites, most of which were glycosylated derivatives. Transcriptomic analysis revealed coordinated upregulation of phenylpropanoid pathway genes and specific UDP-glycosyltransferases (UGTs) in I. tinctoria, providing a genetic basis for its enhanced glycoside production. The study establishes a clear genotype-metabolite-phenotype linkage, highlighting glycosylation as a key mechanism underlying flavonoid-driven antioxidant superiority in Isatis. Although the current evidence is primarily correlative, the consistent and strong associations across independent transcriptomic, metabolomic, and antioxidant datasets provide a robust foundation for this conclusion. These findings offer new insights into the metabolic evolution and regulatory networks of flavonoids, with implications for breeding and metabolic engineering of high-value medicinal plants.

Flavonoids↗
PubMed2026

Multi-Omics Landscape of Paraspinal Muscles in Spinal Muscular Atrophy With Scoliosis.

Most spinal muscular atrophy (SMA) patients develop severe scoliosis by late adolescence. Given that the paraspinal muscles-particularly the multifidus-are indispensable for maintaining spinal stability, their site-specific multi-omics characteristics in SMA remain insufficiently defined. Herein, integrated multi-omics sequencing was performed on bilateral multifidus samples from SMA patients and surgical controls. We identified 5219 differentially expressed genes, 1063 differentially expressed proteins and 370 differential metabolites between the control and SMA, showing significant enrichment in glucose and amino acid metabolism pathways, specifically key steps of glycolysis/gluconeogenesis. Key enzymes in the glycolytic process such as PFKM, ENO3 and PKM1 were markedly downregulated. Notably, a comparative analysis of the bilateral paraspinal muscles in SMA revealed asymmetrical metabolic signatures in carbohydrate and amino acid processing between the concave and convex sides. Key regulatory enzymes exhibited significant differential expression: PYGL, a central driver of starch and sucrose metabolism; creatine kinase, involved in arginine and proline metabolism; and PGAM2, a key mediator of glycine, serine, and threonine metabolism. These metabolic signatures indicate a complex metabolic reprogramming in the multifidus, where asymmetric disparities point to the influence of mechanical loading, while systemic dysregulation aligns with the effects of SMN depletion.

Humans↗
PubMed2003

[From genomics, proteomics to cytomics, or from cytometry to cytomics].

Cytomics, an ad hoc term, represents a new field which connects cyto- with -omics. The cyto- arises from analytical cytology or cytometry, which has developed for more than three decades and includes a serial of quantitative technology which can separate the heterogenetic cell populations into different cytomes by molecular probes. The -omics comes from proteomics which is determined by genomics. Therefore, cytomics is to separate the cytomes by cytometry technology and identify their proteomes controlled by genome or special genes. Cytomics project consists of two parts of technology, one is separation of cytomes and another is post-sorting analysis. Development of cytomics related technology would help us to understand molecular basis of different cytomes and the transition between them, to gradually grasp the details of genomics, and to know of how to apply them for clinical work. Thus, a new horizon will appear.

Cell Biology↗
PubMed2024

Recent advances in environmental antibiotic resistance genes detection and research focus: From genes to ecosystems.

Antibiotic resistance genes (ARGs) persistence and potential harm have become more widely recognized in the environment due to its fast-paced research. However, the bibliometric review on the detection, research hotspot, and development trend of environmental ARGs has not been widely conducted. It is essential to provide a comprehensive overview of the last 30 years of research on environmental ARGs to clarify the changes in the research landscape and ascertain future prospects. This study presents a visualized analysis of data from the Web of Science to enhance our understanding of ARGs. The findings indicate that solid-phase extraction provides a reliable method for extracting ARG. Technological advancements in commercial kits and microfluidics have facilitated the efficacy of ARGs extraction with significantly reducing processing times. PCR and its derivatives, DNA sequencing, and multi-omics technology are the prevalent methodologies for ARGs detection, enabling the expansion of ARG research from individual strains to more intricate microbial communities in the environment. Furthermore, due to the development of combination, hybridization and mass spectrometer technologies, considerable advancements have been achieved in terms of sensitivity and accuracy as well as lowering the cost of ARGs detection. Currently, high-frequency terms such as "Antibiotic Resistance, Antibiotics, and Metagenomics" are the center of attention for study in this area. Prominent topics include the investigation of anthropogenic impacts on environmental resistance, as well as the dynamics of migration, dissemination, and adaptation of environmental ARGs, etc. The research on environmental ARGs has made significant advancements in the fields of "Microbiology" and "Biotechnology Applied Microbiology". Over the past decade, there has been a notable increase in the fields of "Environmental Sciences Ecology" and "Engineering" with a similar growth trend observed in "Water Resources". These three domains are expected to continue driving extensive study within the realm of environmental ARGs.

Drug Resistance, Microbial↗
PubMed2026

A High-Resolution Stereo-Seq Spatial Transcriptomic Resource for Adult Holstein Cattle Liver.

The bovine liver is a highly compartmentalized organ that plays essential roles in continuous gluconeogenesis and nitrogen recycling; however, its spatial molecular architecture has remained largely uncharacterized due to the limitations of traditional bulk and single-cell approaches. To address this gap, Spatial Enhanced Resolution Omics-sequencing (Stereo-seq) was utilized to generate a subcellular-resolution (500 nm) transcriptomic map of an adult Holstein cattle liver, and a refined reference-guided workflow was implemented to overcome standard annotation limitations in livestock. Raw sequencing data were processed using the Stereo-seq Analysis Workflow and analyzed with Stereopy, Seurat, SingleR, and reference-guided workflows. Spatial aggregation was evaluated at Bin20, Bin50, Bin100, Bin150, and Bin200. Increasing bin size increased molecular identifier counts and detected-gene complexity while progressively reducing spatial granularity. Bin50, corresponding to 50 × 50 DNA nanoballs and an approximate nominal footprint of 25 × 25 µm, was therefore selected as a practical intermediate aggregation level for the primary analyses. Quality-control assessment, Leiden clustering, UMAP visualization, reference-based cell-type annotation, cluster-marker analysis, and spatial mapping of canonical hepatic genes demonstrated preservation of biologically interpretable liver transcriptional organization. Raw sequencing data processed spatial matrices, annotated objects, and analysis code are publicly available to support reanalysis and computational benchmarking. In summary, we present a Stereo-seq spatial transcriptomic resource generated from liver tissue of an adult Holstein cow. This initial resource provides a valuable foundation for future studies of bovine liver biology, comparative genomics, and the spatial basis of livestock health and production traits.

Animals↗
PubMed2026

Integrated analysis reveals the impact of obesity on triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is a highly aggressive and heterogeneous breast cancer subtype with limited therapeutic options. While the prevalence of overweight/obese (OW/OB) women continues to rise, the impact of obesity on molecular features of TNBC remains incompletely understood. We investigated clinicopathological and molecular data (including genomic, transcriptomic, proteomic and metabolomic profiling) using our original multi-omics database of TNBC (N = 465) for associations with patient body mass index (BMI). Multi-omics profiling revealed that OW/OB patients exhibited worse survival as well as elevated inflammation of tumor microenvironment, higher expression of immune checkpoints, and dysregulated lipid metabolism. Our in vivo experiments demonstrated that tumors in obese mice displayed faster growth rates, a higher proportion of PD-1+CD8+ T cells and enhanced responsiveness to anti-PD-1 treatment. In addition, we analyzed data from four independent clinical trials and discovered that OW/OB patients demonstrated higher pathological complete response rates and longer progression-free survival following anti-PD-1-based immunotherapy. In conclusion, our study systematically revealed that obesity is associated with coordinated immune-metabolic remodeling in TNBC, characterized by checkpoint enrichment and lipid dysregulation, which may help explain the enhanced anti-PD-1 responsiveness and should be taken into account in the field of precision medicine.

Immunity↗
PubMed2004

Aging-related research in the "-omics" age.

The application of high-throughput technologies to aging-related research has the potential to dramatically enhance our understanding of how longevity is determined at a molecular level. Genome-scale studies are being carried out in every major model system used for aging-related research, and new technologies are being developed to rapidly identify mutations or small-molecules that increase life span. A meta-analysis of data derived from genome-wide studies of aging in simple eukaryotes will allow the identification of conserved determinants of longevity that can be tested in mammals.

Aging↗
PubMed2026

Is impulsivity simply a failure of self-control? Evidence based on multi-omics analyses of genomics, metabolomics and brain imaging.

High impulsivity-a hallmark of various adverse life outcomes such as substance abuse, impulsive buying, violence, and crime-has typically been considered as a failure of self-control. However, is impulsivity simply a failure of self-control? To address this issue, we employed multi-omics combined with brain imaging approach in a large-scale sample (Nbrain imaging=1524, Ngenomics=835, Nmetabolomics=946) to elucidate the relationship between impulsivity and self-control. Mendelian randomization showed a bidirectional association between impulsivity and self-control, suggesting that they influenced each other. Partial least squares analysis highlighted that self-control primarily implicates the frontal lobe regions (e.g., superior frontal gyrus), whereas impulsivity involves the amygdala, insula, and basal ganglia. The cerebellum, superior frontal gyrus, and middle frontal gyrus were identified as shared areas in impulsivity and self-control. Furthermore, gene-based association analysis identified heterochromatin protein 1 binding protein 3 as specifically related to impulsivity, while pathway enrichment analysis demonstrated that arginine and proline metabolism was a common metabolic pathway associated with both impulsivity and self-control. Overall findings demonstrate that impulsivity and self-control involve both shared and distinct brain regions, genetic and metabolic foundations. The brain imaging results suggest that impulsivity is related not only to self-control-related processes but also to the motivation to pursue rewards. Together, this large-scale integrative study firstly provides a side-by-side map of genomic, metabolic, and limbic-network signatures of impulsivity distinct from self-control, offering a foundation for mechanism-driven biomarker and intervention research in maladaptive impulsivity.

Impulsive Behavior↗
PubMed2025

Immediate and durable effects of maternal tobacco consumption on placental DNA methylation: a replication and discovery study.

An increasing number of epigenome-wide association studies report tobacco smoking-associated DNA methylation levels. However, comprehensive replication studies remain scarce, particularly in placenta, despite their crucial interest in such a large-scale context. Using DNA methylation data from the EPIC array of 341 new placentas (85 smokers, 219 non-smokers, and 37 former smokers) from the EDEN cohort, we used a candidate approach to replicate maternal smoking-associated CpGs and regions previously identified using the 450K array, and an exploratory approach to discover new associations within EPIC-specific CpGs. Smoking-associated changes in DNA methylation in CpGs and regions were classified as either transient or persistent (indicating epigenetic memory), depending on the stability of their association with smoking status. Among candidate loci, 38% of probes and 9% of regions were replicated, providing robust evidence of effects of prenatal smoke exposure on methylation patterns of these loci. LEKR1 was the top hit in both the initial and replication studies. Most of the replicated loci were transient CpGs (i.e. current smokers), while persistent CpGs (i.e. former smokers) remained scarce and somewhat inconsistent with previous findings. The additional exploratory analysis identified 733 novel probes and 75 novel regions, including 18% and 30% of transient loci, respectively. Results suggested that most of the effects were related to in utero exposure only, supporting pregnant women's efforts to quit smoking. This replication study also evidences the importance of reproducible work in omic investigations to provide a more in-depth and robust understanding of the effects of environmental exposures on health biomarkers..

DNA methylation↗
PubMed2026

Identification of cryosensitive niches and a targetable FOS/AP‑1 program in the human ovarian cortex by single‑cell and spatial transcriptomics.

BACKGROUND: The ovary is a vital and dynamic reproductive organ. Ovarian tissue cryopreservation (OTC) plays a vital role in preserving female fertility. However, the cellular subtypes most susceptible to cryoinjury and the molecular mechanisms underlying cryopreservation-associated damage remain poorly understood. This study aimed to identify cell populations vulnerable to freezing-thawing and to elucidate the key transcriptomic alterations and signaling pathways associated with ovarian cryoinjury at the single-cell and spatial levels. METHODS: Ovarian cortical tissues from patients undergoing three gender reassignment surgery (GRS) were divided into fresh and vitrification-rapid warming groups. Following collagenase IV digestion, 10x Genomics single-cell RNA-seq was used for dissociated ovarian cell suspensions (27,185 fresh and 25,480 frozen-thawed cells). Eight major cell clusters were identified. Additionally, 110 oocytes (66 fresh, 44 vitrification-rapid warming) were isolated and analyzed using the Smart-seq2 platform. Spatial transcriptomics was performed via BGI Stereo-seq. Molecular validation was performed via β-galactosidase staining, immunofluorescence, and qRT-PCR. RESULTS: Cryopreservation significantly altered the activity of pathways related to focal adhesion, oxidative stress, and apoptosis, particularly in stromal and perivascular cells. The number of FOS-positive perivascular cells was notably increased after vitrification-rapid warming, whereas the number of PTGDS-positive stromal cells decreased. Oocyte analysis revealed that cryopreservation primarily disrupted pathways involved in the cell cycle and meiosis, although the damage was not irreversible, supporting the relative safety of long-term cryostorage. Spatial transcriptomics and functional validation further confirmed the rapid and robust activation of the FOS/AP-1 pathway after vitrification-rapid warming, particularly in perivascular and granulosa cells. Treatment with T-5224 (a FOS/AP-1 inhibitor) significantly rescued the morphology and function of cultured frozen-thawed ovaries. CONCLUSIONS: Stromal and perivascular cells are the main cell types that are sensitive to ovarian cryopreservation. The FOS/AP-1 pathway is markedly activated after, suggesting the exacerbation of metabolic impairment. In oocytes within the ovarian cortex, the cell cycle and meiosis-related physiological processes were the primary processes affected.

Female↗
PubMed2003

Medical malpractice predictors and risk factors for ophthalmologists performing LASIK and PRK surgery.

PURPOSE: To identify physician predictors in laser-assisted in-situ keratomileusis (LASIK) and photorefractive keratectomy (PRK) surgery that correlate with a higher risk for malpractice liability claims and lawsuits. METHODOLOGY: A retrospective, longitudinal, cohort study comparing physician characteristics of 100 consecutive Ophthalmic Mutual Insurance Company (OMIC) LASIK and PRK claims and suits to demographic and practice pattern data for all active refractive surgeons insured by OMIC between 1996 and 2002. Background information and data were obtained from OMIC underwriting applications, a physician practice pattern survey, and claims file records. Using an outcome of whether or not a physician had a prior history of a claim or suit, logistic regression analyses were used separately for each predictor as well as controlling for refractive surgery volume. RESULTS: Logistic regression analysis demonstrated that the most important predictor of filing a claim was surgical volume, with those performing more surgery having a greater risk of incurring a claim (odds ratio [OR], 31.4 for >1,000/year versus 0 to 20/year; 95% confidence interval [CI], 7.9 - 125; P = .0001). Having one or more prior claims was the only other predictor examined that remained statistically significant after controlling for patient volume (OR, 6.4; 95% CI 2.5 - 16.4; P = .0001). Physician gender, advertising, preoperative time spent with patient, and comanagement appeared to be strong predictors in multivariate analyses when surgical volume was greater than 100 cases per year. CONCLUSION: The chances of incurring a malpractice claim or suit for PRK or LASIK correlates significantly with higher surgical volume and a history of a prior claim or suit. Additional risk factors that increase in importance with higher surgical volume include gender, advertising, preoperative time spent with patient, and comanagement with optometrists. These findings may be used in the future to help improve the quality of care for patients undergoing refractive surgery and provide data for underwriting criteria and risk management protocols to proactively manage and reduce the risk of claims and lawsuits against refractive surgeons.

Adult↗
PubMed2025

Multi-Omics and Integrative Analytics in Natural Products Discovery.

Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and isolating these compounds can be slow and often yield diminishing returns. Fortunately, advanced multi-omics and computational approaches present powerful solutions to these challenges. This review highlights innovative methodologies that integrate metabolomics, genomics, transcriptomics, and proteomics with bioinformatics and analytical chemistry to accelerate NP discovery. For instance, untargeted metabolomics platforms like high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Global Natural Products Social (GNPS) molecular networking allow for comprehensive profiling of new compounds, while targeted isotope-labeling strategies enhance this process. Additionally, genome and metagenome mining tools such as antibiotics and secondary metabolite analysis shell (antiSMASH), Deep Biosynthetic Gene Cluster (DeepBGC), and Pipeline for Reconstructing Integrated Syntheses of Metabolites (PRISM) quickly identify biosynthetic gene clusters (BGCs) in both cultured and uncultured organisms, often using heterologous expression to validate products. Transcriptomic analyses, including RNA sequencing (RNA-seq), co-expression networks, and fluxomics, help clarify how pathways are regulated, while quantitative proteomics techniques like tandem mass tags/isobaric tags for relative and absolute quantitation (TMT/iTRAQ) and label-free methods, along with chemoproteomics approaches such as cellular thermal shift assay and thermal proteome profiling (TPP), uncover molecular targets and their mechanisms of action. This review also places significant emphasis on the role of artificial intelligence (AI) and machine learning (ML) in integrating multi-omics data, spanning activities from constructing gene-metabolite correlation networks to leveraging knowledge graphs and graph neural networks for data fusion and functional prediction. Finally, this review concludes by discussing the synergistic benefits of multi-omics for natural-product discovery, addressing current technical challenges, and exploring future directions toward high-throughput, intelligent data integration for next-generation NP research.

Biological Products↗
PubMed2026

Human Systems Immunology in the Omics Era: Challenges, Methods, and Emerging Directions.

The human immune system is a highly complex, dynamic, and heterogeneous network shaped by genetic, environmental, and temporal influences. Advances in high-throughput omics technologies have transformed our ability to study this complexity directly and comprehensively in human cohorts. These developments have positioned systems immunology as a powerful framework for investigating coordinated immune responses, identifying regulatory mechanisms, and linking molecular patterns to clinical phenotypes. However, the analytical challenges inherent to large-scale, multimodal datasets-including batch effects, small sample sizes, high dimensionality, and substantial interindividual heterogeneity-require rigorous study design, robust statistical modeling, and thoughtful data analysis strategies. In this review, we summarize key technological foundations enabling modern human systems immunology, outline common analytical pitfalls and effective mitigation approaches, discuss data integration concepts, and highlight emerging opportunities in the field. Together, these technological and analytical advances are redefining how immune function is measured and interpreted in real-world human biology and hold significant promise for enhancing mechanistic insight, biomarker discovery, and precision medicine across immunological diseases and interventions.

Humans↗
PubMed2026

Drug repurposing using transcriptomics: principles and unmet needs in cardiovascular disease.

Although cardiovascular disease is the leading cause of death globally, therapeutic development in this field is slow. Given the high cost of developing new drugs and running clinical trials for cardiovascular disease, repurposing of drugs with approved safety profiles is an attractive strategy for therapeutic development that can significantly reduce the time and cost investment before phase II clinical trials. In the era of "Omics," various new methods and several large databases have been developed to enable the use of transcriptomics data for drug repurposing. This review summarizes the principles and workflow of signature mapping, which forms the foundation of statistical models used for transcriptome-based drug repurposing. We highlight the features of different analysis pipelines and databases that have been developed for signature mapping. These analysis pipelines prioritize genes that are statistically important, an approach that fundamentally differs from the pharmacological approach of identifying disease-driving and therapeutically targetable pathways. Outcomes of signature mapping pipelines are sensitive to the quality of input data, and results are not always reproducible. Moreover, all widely used RNA-seq databases are derived from cancer research and lack high-quality molecular data for cardiovascular disease. These unmet needs call for interdisciplinary collaboration and large networks of cardiovascular research-oriented biobanks to create the databases needed for transcriptomic-based signature mapping for drug repurposing efforts.

Drug Repositioning↗
PubMed2004

The -omics era and its impact.

OBJECTIVE: To review the advances in clinically useful molecular biologic techniques and to identify their applications, as presented at the 12th Annual William Beaumont Hospital DNA Symposium. DATA SOURCES: The 7 manuscripts submitted were reviewed and their major findings were compared with literature on the same or related topics. STUDY SELECTION: Manuscripts address the use of molecular techniques in the detection of severe acute respiratory syndrome (SARS) and bacterial ribosome mutations, which may lead to ribosome-targeted drug resistance; pharmacogenomics as a clinical laboratory service and example of warfarin dosing using CYP2C9 mutation analysis; definition of the potential of cytosine arabinoside incorporation into DNA to disrupt transcription using an in vitro model of oligonucleotides; use of laser capture microdissection to isolate solid tumor cells free of nontumor cells; and molecular methods used to classify lymphomas. DATA SYNTHESIS: Two current issues related to the use of molecular tests in the clinical laboratories are (1) decentralization of molecular-based testing to a variety of nonmolecular laboratories and (2) need for wider acceptance of molecular-based testing through its incorporation in clinical practice guidelines. Molecular methods have had a major impact on infectious disease through the rapid identification of new infectious agents, SARS, and the characterization of drug resistance. Pharmacogenomics identifies the genetic basis for heritable and interindividual variation in response to drugs. The incorporation of the nucleoside analog, cytosine arabinoside, into DNA leads to local perturbation of DNA structure and reduces the ability of transcription factors to bind to their specific DNA binding elements as measured by electrophoretic mobility shift assays. Laser capture microdissection of tumor cells can provide an adequate number of cells for whole genome amplification. Gene expression microassay profiles of various lymphomas have modified classification systems and predict prognosis and response to therapy. CONCLUSIONS: The current -omics era will continue to emphasize the use of microarrays and database software for genomic, transcriptomic, and proteomic screening to search for a useful clinical assay. The number of molecular pathologic techniques will expand as additional disease-associated mutations are defined.

Animals↗
PubMed2005

Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists.

We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with "omics" platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.

Arabidopsis↗