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Biomedical subjects

Michael N Liebman

Publications and source records attributed to Michael N Liebman.

13 recordsLinked to original sources
PubMed2006

Assessing semantic similarity measures for the characterization of human regulatory pathways.

MOTIVATION: Pathway modeling requires the integration of multiple data including prior knowledge. In this study, we quantitatively assess the application of Gene Ontology (GO)-derived similarity measures for the characterization of direct and indirect interactions within human regulatory pathways. The characterization would help the integration of prior pathway knowledge for the modeling. RESULTS: Our analysis indicates information content-based measures outperform graph structure-based measures for stratifying protein interactions. Measures in terms of GO biological process and molecular function annotations can be used alone or together for the validation of protein interactions involved in the pathways. However, GO cellular component-derived measures may not have the ability to separate true positives from noise. Furthermore, we demonstrate that the functional similarity of proteins within known regulatory pathways decays rapidly as the path length between two proteins increases. Several logistic regression models are built to estimate the confidence of both direct and indirect interactions within a pathway, which may be used to score putative pathways inferred from a scaffold of molecular interactions.

Databases, Protein↗
PubMed2006

Co-occurrence analysis for discovery of novel breast cancer pathology patterns.

To discover novel patterns in pathology co-occurrence, we have developed algorithms to analyze and visualize pathology co-occurrence. With access to a database of pathology reports, collected under a single protocol and reviewed by a single pathologist, we can conduct an analysis greater in its scope than previous studies looking at breast pathology co-occurrence. Because this data set is unique, specialized methods for pathology co-occurrence analysis and visualization are developed. Primary analysis is through a co-occurrence score based on the Jaccard coefficient. Density maps are used to visualize global co-occurrence. When our co-occurrence analysis is applied to a population stratified by menopausal status, we can successfully identify statistically significant differences in pathology co-occurrence patterns between premenopausal and postmenopausal women. Genomic and proteomic experiments are planned to discover biological mechanisms that may underpin differences seen in pathology patterns between populations.

Algorithms↗
PubMed2004

Genomic instability in histologically normal breast tissues: implications for carcinogenesis.

Breast cancer is an important contributor to morbidity and mortality in society, but factors that affect the cause of the disease are poorly defined. Genomic instability drives tumorigenic processes in invasive carcinomas and premalignant breast lesions, and might promote the accumulation of genetic alterations in apparently normal tissues before histological abnormalities are detectable. Evidence suggests that genomic changes in breast parenchyma affect the behaviour of epithelial cells, and ultimately might affect tumour growth and progression. Inherent instability in genes that maintain genomic integrity, as well as exogenous chemicals and environmental pollutants, have been implicated in breast-cancer development. Although molecular mechanisms of tumorigenesis are unclear at present, carcinogenic agents could contribute to fields of genomic instability localised to specific areas of the breast. Understanding the functional importance of genomic instability in early carcinogenesis has important implications for improvement of diagnostic and treatment strategies.

Breast Neoplasms↗
PubMed2004

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

Breast Neoplasms↗
PubMed2003

Mycophenolate mofetil versus azathioprine therapy is associated with a significant protection against long-term renal allograft function deterioration.

BACKGROUND: To evaluate the association of long-term continuous mycophenolate mofetil (MMF) versus azathioprine (AZA) therapy and renal allograft function, as measured by the slope of reciprocal creatinine, we analyzed 49,666 primary renal allograft recipients reported to the United States Renal Data System between October 31, 1988 and June 30, 1998. METHODS: The primary study endpoint was defined as a greater than 20% decrease below a 6-month baseline of 1/serum creatinine (SCr) (slope of reciprocal creatinine) at or beyond 1 year after transplantation. A secondary endpoint was defined as reaching an SCr value greater than 1.6 mg/dL. Univariate Kaplan-Meier analysis and multivariate Cox proportional hazard models were used to investigate the risk of reaching the study endpoints. Multivariate analyses were corrected for potential confounding covariates. RESULTS: According to the Cox proportional hazard model, 12-month continued therapy of MMF versus AZA was associated with a protective effect against declining renal function, as measured by the slope of reciprocal creatinine (relative risk [RR]=0.84, confidence interval 0.78-0.91, P<0.001). For 24-month continued therapy of MMF versus AZA, MMF was associated with a further decreased risk for a decline in renal function (RR=0.66, confidence interval=0.57-0.77, P<0.001). Furthermore, MMF was associated with a protective effect against reaching the SCr threshold of 1.6 mg/dL (RR=0.80, P<0.001) beyond 12 months posttransplantation. CONCLUSIONS: Continuous use of MMF versus AZA was associated with a protective effect against declining renal function beyond 1 year after transplantation. Further study is needed to confirm that continued MMF therapy is protective against long-term deterioration in renal function.

Adult↗
PubMed2003

Intratumoral T cells, recurrence, and survival in epithelial ovarian cancer.

BACKGROUND: Although tumor-infiltrating T cells have been documented in ovarian carcinoma, a clear association with clinical outcome has not been established. METHODS: We performed immunohistochemical analysis of 186 frozen specimens from advanced-stage ovarian carcinomas to assess the distribution of tumor-infiltrating T cells and conducted outcome analyses. Molecular analyses were performed in some tumors by real-time polymerase chain reaction. RESULTS: CD3+ tumor-infiltrating T cells were detected within tumor-cell islets (intratumoral T cells) in 102 of the 186 tumors (54.8 percent); they were undetectable in 72 tumors (38.7 percent); the remaining 12 tumors (6.5 percent) could not be evaluated. There were significant differences in the distributions of progression-free survival and overall survival according to the presence or absence of intratumoral T cells (P<0.001 for both comparisons). The five-year overall survival rate was 38.0 percent among patients whose tumors contained T cells and 4.5 percent among patients whose tumors contained no T cells in islets. Significant differences in the distributions of progression-free survival and overall survival according to the presence or absence of intratumoral T cells (P<0.001 for both comparisons) were also seen among 74 patients with a complete clinical response after debulking and platinum-based chemotherapy: the five-year overall survival rate was 73.9 percent among patients whose tumors contained T cells and 11.9 percent among patients whose tumors contained no T cells in islets. The presence of intratumoral T cells independently correlated with delayed recurrence or delayed death in multivariate analysis and was associated with increased expression of interferon-gamma, interleukin-2, and lymphocyte-attracting chemokines within the tumor. The absence of intratumoral T cells was associated with increased levels of vascular endothelial growth factor. CONCLUSIONS: The presence of intratumoral T cells correlates with improved clinical outcome in advanced ovarian carcinoma.

Adult↗
PubMed2003

Long-term use of mycophenolate mofetil is associated with a reduction in the incidence and risk of late rejection.

To evaluate the association of long-term continuous (minimum 1 year) mycophenolate mofetil (MMF) vs. azathioprine (AZA) therapy with the incidence of late acute rejection, we analyzed 47 693 primary renal allograft recipients reported to the United States Renal Data System between 1988 and 1998. The primary study endpoint was acute rejection beyond 1 year after transplantation. Univariate Kaplan-Meier analysis and multivariate Cox proportional hazard models were used to investigate the risk of reaching the study endpoints. All multivariate analyses were corrected for potential confounding covariates. Mycophenolate mofetil was associated with a 65% decreased risk of developing late acute rejection as compared to AZA (RR = 0.35, CI 0.27-0.45, p < 0.001). The incidence of acute rejection episodes at 2 and 3 years post-transplantation was significantly lower in the MMF group (0.9% at 2 years, 1.1% at 3 years) than the AZA group (6.1% at 2 years, 9.3% at 3 years). In the primary vs. repeat late rejection analysis, MMF patients exhibited a decreased late acute rejection risk of 72% (RR = 0.28, p < 0.001) and 60%, respectively (RR = 0.40, p < 0.001). In African Americans, the late acute rejection risk was 70% lower in MMF patients than AZA patients (RR = 0.30, p < 0.001). Further study is indicated to determine the optimal duration of MMF therapy after renal allograft transplantation.

Black People↗
PubMed2002

Biomedical informatics: the future for drug development.

The problems that exist in drug development are well documented: the limited number of new chemical entities, increased cost of drug development, problems in clinical trials (Phase III), product launches that result in withdrawal, and pressure to reduce the cost of pharmaceuticals from the government. It appears that the promise of genomics has not yet reached its full potential to impact the process. This review identifies the need to develop and implement the area of biomedical informatics for increased success in drug development and healthcare in general.

Aging↗
PubMed2002

Opening Pandora's box: clinical data and the study of complex diseases.

Complex diseases have complex phenotypes, and proper diagnosis requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genetic information. Signaling information is one aspect of a grander "biomedical informatics" approach advocated for a better understanding of a patient's medically relevant disease phenotype.

Disease Progression↗
PubMedDate not supplied

Modeling and simulation of pathways in menopause.

The analytical representation and simulation of complex molecular pathways can contribute to understanding and evaluating physiological as well as pathological processes. We are interested in modeling the processes of menopause to stratify women in terms of the genotypic and environmental components and their implications for development of individualized risk of postmenopausal disorders, e.g., breast and ovarian cancer, cardiovascular disease, and osteoporosis. We have initiated this study using the UltraSAN package to analyze the pathway associated with estrogen production. This model incorporates detailed information about the hormone factors affecting estrogen production, and the simulations carried out are based on published experimental data corresponding to hormone levels during the course of the normal female reproductive cycle. The agreement between the experimental data and the simulation is typically less than 2 ng/ml or 2 pg/ml respectively for progesterone and estradiol output. This approach further permits inclusion of information about an SNP observed in the gene coding for the enzyme aromatase as a model to study the impact of reduced enzymatic activity on hormone levels.

Climacteric↗
PubMedDate not supplied

Microarray data simulator for improved selection of differentially expressed genes.

The development of microarray technology has allowed researchers to measure expression levels of thousands of genes simultaneously. Analysis of these data requires the best normalization and statistical approaches to account for the biological and technical variability inherent in the technique. To approach this problem we have developed a publicly available simulator of microarray hybridization experiments that can be used to help assess the accuracy of bioinformatic tools in discovering significant genes. After analyzing microarray hybridization experiments from over 50 samples, an estimate of various degrees of technical and biological variability was obtained. This information was used to develop a simulator of microarray hybridization data which modeled "normal tissue samples" and "diseased tissue samples" with known, defined, changes in gene expression (a "gold standard"). The data derived from the simulator were then used to evaluate the true positive and false negative rates of several normalization procedures and gene selection techniques. We found that the type of normalization approach used was an important aspect of data analysis. Global normalization was the least accurate approach. Evaluation of gene selection techniques showed that "Significance analysis of microarrays" (SAM) and "Patterns of Gene Expression" (PaGE) were more accurate than simple t-test analysis. We provide access to the microarray hybridization simulator as a public resource for biologists to further test new emerging genomic bioinfomatic tools.

Computer Simulation↗