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Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system. Deuterium, in the form of deuterated glucose or heavy water, can be used to measure rates of…
Biomedical research increasingly relies on integrating diverse data modalities, including gene expression profiles, medical images, and clinical metadata. While medical images and clinical metadata are routinely collected in clinical…
Generative models are typically evaluated by direct inspection of their generated samples, e.g., by visual inspection in the case of images. Further evaluation metrics like the Fr\'echet inception distance or maximum mean discrepancy are…
In neuroelectrophysiology one records electric potentials or magnetic fields generated by ensembles of synchronously active neurons in response to externally presented stimuli. These evoked responses are often produced by multiple…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Accurate predictions of reactive mixing are critical for many Earth and environmental science problems. To investigate mixing dynamics over time under different scenarios, a high-fidelity, finite-element-based numerical model is built to…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
The recognition performance of biometric systems strongly depends on the quality of the compared biometric samples. Motivated by the goal of establishing a common understanding of face image quality and enabling system interoperability, the…
The use of resistive technologies to MPGD detectors is taking advantage for many new applications, including high rate and energetic particle flux scenarios. The recent use of these technologies in large area detectors makes necessary to…
The problem addressed here is that of simultaneous treatment of several gene expression datasets, possibly collected under different experimental conditions and/or platforms. Using robust statistics, a large scale statistical analysis has…
In this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels'…
We consider integrative modeling of multiple gene networks and diverse genomic data, including protein-DNA binding, gene expression and DNA sequence data, to accurately identify the regulatory target genes of a transcription factor (TF).…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
The devices designed for the Internet-of-Things encompass a large variety of distinct processor architectures, forming a highly heterogeneous zoo. In order to tackle this, we employ a simulator to estimate the performance of the…
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical…
In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…