Research Topics
Species | Susmita DattaSummaryAffiliation: University of Louisville Country: USA Publications
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Detail Information
Publications
Fetal alcohol syndrome (FAS) in C57BL/6 mice detected through proteomics screening of the amniotic fluidSusmita Datta
Department of Bioinformatics and Biostatistics, School of Public Health and Information Science, University of Louisville, Louisville, Kentucky 40292, USA
Birth Defects Res A Clin Mol Teratol 82:177-86. 2008..The present study used this murine model to screen amniotic fluid for biomarkers that could potentially discriminate between FAS-positive and FAS-negative pregnancies...- Evaluation of clustering algorithms for gene expression dataSusmita Datta
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
BMC Bioinformatics 7:S17. 2006..A closely related problem is that of selecting a clustering algorithm that is "optimal" in some sense from a rather impressive list of clustering algorithms that currently exist... - Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classesSusmita Datta
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
BMC Bioinformatics 7:397. 2006..Such a reference set may come from prior biological knowledge specific to a microarray study or may be formed using the growing databases of gene ontologies (GO) for the annotated genes of the relevant species... - Computational biology touches all basesSusmita Datta
Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40292, USA
Genome Biol 10:303. 2009..A report of the 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, USA, 4-7 December 2008... 
Biologically supervised hierarchical clustering algorithms for gene expression dataGrzegorz M Boratyn
Kidney Disease Program and Clinical Proteomics Center, University of Louisville, KY, USA
Conf Proc IEEE Eng Med Biol Soc 1:5515-8. 2006..R-codes of the clustering algorithm are available from the authors upon request...- RankAggreg, an R package for weighted rank aggregationVasyl Pihur
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
BMC Bioinformatics 10:62. 2009..One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise... 
Reconstruction of genetic association networks from microarray data: a partial least squares approachVasyl Pihur
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40292, USA
Bioinformatics 24:561-8. 2008..Here, we introduce a novel computational method based on the partial least squares (PLS) regression technique for reconstruction of genetic networks from microarray data...- Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approachVasyl Pihur
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
Bioinformatics 23:1607-15. 2007..An automated and objective way of reconciling the rankings is needed... - An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional dataSusmita Datta
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
BMC Bioinformatics 11:427. 2010.... - A statistical framework for differential network analysis from microarray dataRyan Gill
Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
BMC Bioinformatics 11:95. 2010.... - Differential expression of microRNA expression in tamoxifen-sensitive MCF-7 versus tamoxifen-resistant LY2 human breast cancer cellsTissa T Manavalan
Department of Biochemistry and Molecular Biology, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
Cancer Lett 313:26-43. 2011..Agreement in the direction of anticipated regulation was detected for 12 putative targets. These miRNAs with opposite expression between the two cell lines may be involved in endocrine resistance... - Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studiesSutirtha Chakraborty
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
Bioinformatics 28:799-806. 2012.... - Feature selection and machine learning with mass spectrometry dataSusmita Datta
Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, USA
Methods Mol Biol 593:205-29. 2010..In this chapter, we provide a review of major contributions toward feature selection and classification of proteomic mass spectra involving MALDI-TOF and SELDI-TOF technology... - Modeling microRNA-mRNA interactions using PLS regression in human colon cancerXiaohong Li
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
BMC Med Genomics 4:44. 2011.... - Statistical inference methods for sparse biological time series dataJuliet Ndukum
Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
BMC Syst Biol 5:57. 2011..For the statistical analysis we first fit several nonlinear mixed effect regression models to the longitudinal profiles and then used an ANOVA likelihood ratio method in order to test for significant differences between the profiles... - Finding common genes in multiple cancer types through meta-analysis of microarray experiments: a rank aggregation approachV Pihur
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40292, USA
Genomics 92:400-3. 2008.... - Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSOSusmita Datta
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky 40202, USA
Biometrics 63:259-71. 2007..This reanalysis using the mean imputed PLS and LASSO identifies a number of genes that were known to be related to cancer or tumor activities from previous studies... - Gene expression profiling of epithelial ovarian tumours correlated with malignant potentialSusanne Warrenfeltz
Genetics Department, University of Georgia, Athens Georgia 30602, USA
Mol Cancer 3:27. 2004..Improved knowledge of gene expression changes and functional pathways associated with these clinical phenotypes may lead to new treatment targets, markers for early detection and a better understanding of disease progression... - Empirical Bayes screening of many p-values with applications to microarray studiesSusmita Datta
Department of Mathematics and Statistics, Department of Biology, Georgia State University, Atlanta, 30303, USA
Bioinformatics 21:1987-94. 2005..AVAILABILITY: R code for EBS is available from the authors upon request. SUPPLEMENTARY INFORMATION: http://www.stat.uga.edu/~datta/EBS/supp.htm.. - An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experimentsSusmita Datta
Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA
Bioinformatics 20:235-42. 2004..Dudoit et al. have advocated use of permutation-based step-down P-value adjustments to correct the observed significance levels for the individual (i.e. for each gene) two sample t-tests... - Comparisons and validation of statistical clustering techniques for microarray gene expression dataSusmita Datta
Department of Mathematics and Statistics and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
Bioinformatics 19:459-66. 2003..At the moment there do not seem to be any clear-cut guidelines regarding the choice of a clustering algorithm to be used for grouping genes based on their expression profiles... - Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptidesGerrit J Schut
Department of Biochemistry and Molecular Biology and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, USA
J Bacteriol 185:3935-47. 2003..The degree of coordinate regulation revealed by the microarray data was unanticipated and shows that P. furiosus can readily adapt to a change in its primary carbon source... - Rare chromosomal deletions and duplications increase risk of schizophreniaJennifer L Stone
Nature 455:237-41. 2008..Our results provide strong support for a model of schizophrenia pathogenesis that includes the effects of multiple rare structural variants, both genome-wide and at specific loci... - Failure to confirm allelic association between markers at the CAPON gene locus and schizophrenia in a British sampleVinay Puri
Molecular Psychiatry Laboratory, Department of Mental Health Sciences, Royal Free and University College London Medical School, Windeyer Institute of Medical Sciences, London, W1T 4JF, UK
Biol Psychiatry 59:195-7. 2006..A second Chinese study found a base pair polymorphism at the CAPON gene also associated with schizophrenia... - Genetic mapping of variation in spatial learning in the mouseDaniela Steinberger
Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
J Neurosci 23:2426-33. 2003..QTL that influence differences in fearful behavior (on chromosomes 1, 3, 7, 15, and 19) operate while mice are trained in the water maze apparatus...