GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

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The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

The collimation system of the Future Circular Collider, operating with leptons (FCC-ee), must protect not only the experiments against backgrounds, but also the machine itself from beam losses. With a 17.8 MJ stored energy of the electron and positron beam ...

Neurodegenerative and neuroinflammatory disorders often involve complex pathophysiological mechanisms that are â to this date â only partially understood. A more comprehensive understanding of those microstructural processes and their characterization ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

In algorithms for solving optimization problems constrained to a smooth manifold, retractions are a well-established tool to ensure that the iterates stay on the manifold. More recently, it has been demonstrated that retractions are a useful concept for ot ...

Motivated by the transfer of proofs between proof systems, and in particular from first order automated theorem provers (ATPs) to interactive theorem provers (ITPs), we specify an extension of the TPTP derivation text format to describe proofs in first-ord ...

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

The opportunities provided by adopting digitally-generated visual tools in urban participatory planning are compelling. These visual tools can promote interactions between authorities and citizens and among citizens. However, the urban participatory practi ...

Revision behavior in adaptive writing support systems is an important and relatively new area of research that can improve the design and effectiveness of these tools, and promote students' self-regulated learning (SRL). Understanding how these tools are u ...

Training science and engineering students to become responsible citizens and professionals requires novel and creative pedagogical approaches, such as design thinking. This concept relies on processes and tools to develop creativity and problem-solving ski ...

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Pre-adoption phases of innovation are understudied in the innovation literature. This article addresses preadoption phases of innovation by running a prospective analysis. We assess the readiness of municipalities for the adoption of a digital tool that br ...

GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

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Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Collimation simulations for the FCC-ee

Development and clinical validation of computational imaging biomarkers for neurodegenerative diseases

The dynamic genetic determinants of increased transcriptional divergence in spermatids

From low-rank retractions to dynamical low-rank approximation and back

SC-TPTP: An Extension of the TPTP Derivation Format for Sequent-Based Calculus

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Chromatin modules and their implication in genomic organization and gene regulation

Media Coverage of 3D Visual Tools Used in Urban Participatory Planning

Understanding Revision Behavior in Adaptive Writing Support Systems for Education

Digital Intervention for Collaborative and Human-Centered Activities in Design-Based Learning Scenarios

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Statistical learning quantifies transposable element-mediated cis-regulation

Assessing the readiness of municipalities for digital process innovation