11 papers · ranked by Valyu relevance
Ron Sheinin, Shai Dulberg, Ayelet Kaminitz, Roded Sharan + 1 more
Cell-cell crosstalk involves simultaneous interactions of multiple receptors and ligands, followed by downstream signaling cascades working through receptors converging at dominant transcription factors which then integrate and propagate multiple signals into a cellular response. Single cell RNAseq of multiple cell…
Tiansu Gong, Fusong Ju, Dongbo Bu
Pseudoknots are key structure motifs of RNA and pseudoknotted RNAs play important roles in a variety of biological processes. Here, we present KnotFold, an accurate approach to the prediction of RNA secondary structure including pseudoknots. The key elements of Knot-Fold include a learned potential function and a…
Francisco Sena, Eliel Ingervo, Shahbaz Khan, Andrey Prjibelski + 2 more
A decomposition of a network flow is a set of weighted paths whose superposition equals the flow. The problem of characterising and computing safe walks for flow decompositions has so far seen only a partial solution by restricting the flow decomposition to consist of paths, and the graph to be directed and acyclic…
Ke Chen, Abhishek Talesara, Sanchal Thakkar, Mingfu Shao
The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed…
Fernando H. C. Dias, Alexandru I. Tomescu
Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous, since is obtained from noisy read coverages.…
Sebastiano Montante, Daniel Yokosawa, Leon Li, Alexander Butyaev + 17 more
Manual flow cytometry gating requires up to one hour per sample with 32% inter-expert variability, creating critical bottlenecks in immunological research reproducibility. To address this, we developed flowMagic, a machine learning algorithm for automated gating that is trained on both expert-curated data (template…
Anna Kriuchechnikova, Tatiana Levdik, Alexey Brazhe
Many living systems self-organize into tree-like hierarchical branching patterns. How the function of these systems is shaped by their morphology, and whether it reflects optimization of any resource or cost draws a sustained interest. Applications in computational biology and biomimetics require tools to generate…
Armina Mortazavi, Jianfei Jiang, Philip Laric, Dominic A. Helmerich + 4 more
Mechanical forces at the cell–substrate interface govern processes from migration to differentiation, yet mapping these forces at high spatial resolution remains challenging. Traction force microscopy (TFM) addresses this by quantifying substrate deformations using fiducial markers, which are conventionally fluorescent…
Bin Fu, Caroline L. Jones, Daniel Heraghty, Shengbo Yang + 7 more
Imaging flow cytometry using Fourier light-field microscopy enables high-throughput three-dimensional cellular imaging, capable of capturing thousands of events per second. However, volumetric reconstruction speed remains orders of magnitude slower than the acquisition speed. The current state of art uses…
Pierre Bohec, Florian Dupuy, Victoria Tishkova, Valentine Seveau de Noray + 2 more
Experiments with gradients of soluble bioactive species have significantly advanced with microfluidic developments that enable cell observation and stringent control of environmental conditions. While some methodologies rely on flow to establish gradients, other opt for flow-free conditions, which is particularly…
Alexander Borst, Winfried Denk
Volume electron microscopy together with computer-based image analysis are yielding neural circuit diagrams of ever larger regions of the brain [1-10]. These datasets are usually represented in a cell-to-cell connectivity matrix and contain important information about prevalent circuit motifs allowing to directly test…