Now showing items 1-10 of 36
ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles
Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) has greatly improved the reliability with which transcription factor binding sites (TFBSs) can be identified from genome-wide profiling studies. ...
Asymmetric independence modeling identifies novel gene-environment interactions
(Springer Nature, 2019-02-21)
Most genetic or environmental factors work together in determining complex disease risk. Detecting gene-environment interactions may allow us to elucidate novel and targetable molecular mechanisms on how environmental ...
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific ...
Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling
Background Segmenting cell nuclei in microscopic images has become one of the most important routines in modern biological applications. With the vast amount of data, automatic localization, i.e. detection and segmentation, ...
Gene Selection for Multiclass Prediction by Weighted Fisher Criterion
Gene expression profiling has been widely used to study molecular signatures of many diseases and to develop molecular diagnostics for disease prediction. Gene selection, as an important step for improved diagnostics, ...
SIMAT: GC-SIM-MS data analysis tool
Background Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS ...
BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor
(Springer Nature, 2015-09-09)
Most published copy number datasets on solid tumors were obtained from specimens comprised of mixed cell populations, for which the varying tumor-stroma proportions are unknown or unreported. The inability to correct for ...
Convex Analysis of Mixtures for Separating Non-negative Well-grounded Sources
(Springer Nature, 2016-12-06)
Blind Source Separation (BSS) is a powerful tool for analyzing composite data patterns in many areas, such as computational biology. We introduce a novel BSS method, Convex Analysis of Mixtures (CAM), for separating ...
Motif-directed network component analysis for regulatory network inference
Background Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIP-on-chip data are available. However, ...