To Share or Not to Share: Understanding and Modeling Individual Disclosure Preferences in Recommender Systems for the Workplace

Newly-formed teams often encounter the challenge of members coming together to collaborate on a project without prior knowledge of each other’s working and communication styles. This lack of familiarity can lead to conflicts and misunderstandings, hindering effective teamwork. Derived from research in social recommender systems, team...

Smart sturen op optimaal werkplekgebruik

Gemiddeld staat 40-50 procent van de werkplekken op kantoor leeg. Dit zorgt voor rust en flexibiliteit, maar is qua kosten en duurzaamheid niet efficiënt. Een gemiddelde werkplekbezetting van 75 procent wordt als optimaal gezien. Op basis van literatuur en interviews met dertien experts bespreekt dit artikel welke factoren van invloed zijn op de...

A Landscape of Pharmacogenomic Interactions in Cancer

Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancerdriven alterations identified in 11,289 tumors from 29 tissues (integrating somatic mutations, copy...

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Mining large datasets using machine learning approaches often leads to models that are hard to interpret and not amenable to the generation of hypotheses that can be experimentally tested. We present ‘Logic Optimization for Binary Input to Continuous Output’ (LOBICO), a computational approach that infers small and easily interpretable logic...

Inferring the influence of cultivation parameters on transcriptional regulation

Exactly how an organism adapts its transcriptional program in response to intra- and extracellular signals remains elusive. Development of computational approaches that use the large amounts of diverse intracellular data to unravel the cell's transcriptional program is one of today's main challenges in bioinformatics research. This thesis...

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

OA Fund TU delft Background: Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on...

Combinatorial influence of environmental parameters on transcription factor activity

Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in...

Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae.

Transcriptional responses to four weak organic acids (benzoate, sorbate, acetate and propionate) were investigated in anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. To enable quantitative comparison of the responses to the acids, their concentrations were chosen such that they caused a 50% decrease of the biomass...

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

When transcriptome meets metabolome: Fast cellular responses of yeast to sudden relief of glucose limitation

Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as...