RNA sequencing for research and diagnostics in clinical oncology
Molecular diagnostics is becoming one of the major drivers of personalized oncology. With
hundreds of different approved anticancer drugs and regimens of their administration …
hundreds of different approved anticancer drugs and regimens of their administration …
Microarray meta-analysis and cross-platform normalization: integrative genomics for robust biomarker discovery
The diagnostic and prognostic potential of the vast quantity of publicly-available microarray
data has driven the development of methods for integrating the data from different …
data has driven the development of methods for integrating the data from different …
Quantitation of molecular pathway activation using RNA sequencing data
Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are
considered hotspots in biomedical sciences and thousands of IMPs have been discovered …
considered hotspots in biomedical sciences and thousands of IMPs have been discovered …
Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data
High throughput technologies opened a new era in biomedicine by enabling massive
analysis of gene expression at both RNA and protein levels. Unfortunately, expression data …
analysis of gene expression at both RNA and protein levels. Unfortunately, expression data …
Transcriptomic harmonization as the way for suppressing cross-platform bias and batch effect
(1) Background: Emergence of methods interrogating gene expression at high throughput
gave birth to quantitative transcriptomics, but also posed a question of inter-comparison of …
gave birth to quantitative transcriptomics, but also posed a question of inter-comparison of …
Differential network analysis from cross-platform gene expression data
Understanding how the structure of gene dependency network changes between two patient-
specific groups is an important task for genomic research. Although many computational …
specific groups is an important task for genomic research. Although many computational …
Shambhala: a platform-agnostic data harmonizer for gene expression data
Background Harmonization techniques make different gene expression profiles and their
sets compatible and ready for comparisons. Here we present a new bioinformatic tool …
sets compatible and ready for comparisons. Here we present a new bioinformatic tool …
Boosting in the presence of outliers: Adaptive classification with nonconvex loss functions
This article examines the role and the efficiency of nonconvex loss functions for binary
classification problems. In particular, we investigate how to design adaptive and effective …
classification problems. In particular, we investigate how to design adaptive and effective …
Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene …
Introduction: Co-normalization of RNA profiles obtained using different experimental
platforms and protocols opens avenue for comprehensive comparison of relevant features …
platforms and protocols opens avenue for comprehensive comparison of relevant features …
An integrative analysis system of gene expression using self-paced learning and SCAD-Net
Background Few proposed gene biomarkers have been satisfactory in clinical applications.
That is mainly due to the small studies sample size. Because of the batch effect, different …
That is mainly due to the small studies sample size. Because of the batch effect, different …