Logic gene network design: a software tool based on modularity and standardization

Data mining the TopoChip

Two Splice Factor Mutant Leukemia Subgroups Uncovered at the Boundaries of MDS and AML using Combined Gene Expression and DNA-Methylation Profiling

Acute Myeloid Leukemia is a highly diverse disease containing many cytogenetic and molecular abnormalities. We analyzed the DNA methylation<br/>(DMP) and gene expression profiles (GEP) of 344 AML patients using an unsupervised and supervised approach. We hypothesized to better<br/>characterize the disease phenotype by combing these features as...

Relating sequence properties to protein secretion

Aspergillus niger is widely used for industrial enzyme production. Knowledge on high-level protein secretion could be useful to improve production rates. We used sequencebased classification methods to identify important properties<br/>for successful high-level secretion, which will be used to redesign proteins for improved secretion.

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion

We introduce a multi-scale kernel diffusion framework and apply it to a large collection of murine retroviral insertional mutagenesis data. The diffusion strength plays the role of scale parameter. As a result, in addition to detecting genes with frequent mutations in their genomic vicinity (red nodes in the interaction graph) we can also find...

Proposal for an enzyme redesign method to improve production rates in Aspergillus niger

Understanding mushroom development

Co-expression Network Analysis of the Developing Human Brain Implicates Synaptogenesis and Mitochondrial Function as Central Mechanisms in Autism

We analyzed the spatial-temporal co-expression relationships of 455 genes previously implicated in Autism spectrum disorder (ASD) using the BrainSpan transcriptome atlas. Understanding how the heterogenous set of ASD-related genes contribute to normal brain development helps identifying cellular/molecular processes which are commonly disrupted...

Predicting functional effect of human missense mutations

Our aim is to prioritize human missense mutations by their probability of being disease causing. Such a computational method could be used to obtain a reduced set of mutations with a relatively large fraction of disease related mutations, thereby aiding in the search for this type of mutation within a large mutation set.<br/><br/>Whereas a range...

Genome-wide coexpression of steroid receptors in the mouse brain: identifying signaling pathways and functionally coordinated regions

Steroid hormones coordinate the activity of many brain regions by binding to nuclear receptors that act as transcription factors. This study uses genome-wide correlation of gene expression in the mouse brain to discover (i) brain regions that respond in a similar manner to particular steroids, (ii) signaling pathways that are used in a steroid...

Karyollele specific expression in Agaricus Bisporus

Interpreting a migraine GWAS using gene expression in healthy human brain

Migraine is a common brain disorder, with a heritability of 50%. Genome-wide association studies have identified several loci, but interpretation remains challenging. We integrated migraine GWAS data with spatial gene expression data of adult brains from the Allen Human Brain Atlas, to identify specific brain regions and molecular pathways...