Related papers: Triander: A new program for visual analysis of nuc…
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…
Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
A nonlinear Tracking-Differentiator is one-input-two-output system that can generate smooth approximation of measured signals and get the derivatives of the signals. The nonlinear tracking-Differentiator is explored to denoise and generate…
Due to the instrument's non-trivial resolution function, measurements on triple-axis spectrometers require extra care from the experimenter in order to obtain optimal results and to avoid unwanted spurious artefacts. We present a free and…
This paper proposes an open source visual analytics tool consisting of several views and perspectives on eye movement data collected during code reading tasks when writing computer programs. Hence the focus of this work is on code and…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
At present each neutron scattering facility has its own set of data treatment software, normally based on a proprietary data format. The travelling scientist is either forced to continually learn new software or to write conversion routines…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…
This paper introduces a novel toolbox named BIDEAL for the generation of biclusters, their analysis, visualization, and validation. The objective is to facilitate researchers to use forefront biclustering algorithms embedded on a single…
We present a software package, IDA, which can easily handle two-dimensional spectroscopy data. IDA has been written in IDL and offers a window-based interface. The available tools can visualize a recovered image from spectra at any desired…
Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the…
Novel multiplexing triple-axis neutron scattering spectrometers yield significant improvements of the common triple-axis instruments. While the planar scattering geometry keeps ensuring compatibility with complex sample environments, a…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Accurately modeling the relationship between perturbations, transcriptional responses, and phenotypic changes is essential for building an AI Virtual Cell (AIVC). However, existing methods typically constrained to modeling direct…
I have developed a code which allows images to be produced of a variety of interacting binaries for any system parameters. The resulting images are not only helpful in visualising the geometry of a given system but are also helpful in talks…
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning…