15 papers · ranked by Valyu relevance
Trina De, Vardan Andriasyan, Artur Yakimovich
Virological plaque assays are the primary method for quantifying infectious particles in a suspension, achieved by incubating a serial dilution of the virus with a monolayer of indicator cells. Existing software tools for quantification of plaque assay images lack modularity, show measurements disagreement or are…
Fabian Woller, Lis Arend, Christian Fuchsberger, Markus List + 1 more
Statistical analyses in biomedical research areas often deal with datasets consisting of several thousand samples and variables. Population-based cohort studies, such as the Cooperative Health Research in South Tyrol (CHRIS) study or the Study of Health in Pomerania (SHIP) , typically include several thousand study…
Clémentine Battistel, Jean-Christophe Mouren, Benjamin Morga, Camille Pelletier + 8 more
Sequencing technologies continue to evolve, providing novel opportunities for disease surveillance and control. These advancements are crucial for diagnosing diseases and identifying genetically distinct variants with diverse host reservoir species and geographical distributions. Recent progress in sequencing-based…
Robert A. Petit III, Chayse M. Rowley, Taylor R. Fearing, Stefaan Verwimp + 5 more
Sequence-based typing is critical for microbial genomics, yet existing tools are often developed in isolation, leading to duplicated effort, inconsistent formats, and limited community participation. To address this, we developed camlhmp ([https://github.com/rpetit3/camlhmp]()), a framework for creating, executing, and…
Ravi Pal, Akos Rudas, Tiffany Williams, Jeffrey N. Chiang + 2 more
This study presents an automatic feature extraction tool that first detects temporal location of landmarks within each cardiac cycle of ABP and PPG waveforms, including the systolic phase onset, systolic phase peak, dicrotic notch, and diastolic phase peak. Then, based on these landmarks, extracts 852 features per…
Saroja Somasundaram, Nelson J. Johansen, Trygve E. Bakken, Jeremy A. Miller
High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package…
Zimeng Wu, Octavian Voiculescu, Alessandro Mongera, Roberto Mayor + 2 more
Advances in microscopy and bioimage analysis are enabling unprecedented quantitative observation of dynamic biological systems. Smart microscopy closes the loop by feeding back image-derived information to control image acquisition on the fly, paving the way for increasingly autonomous and sophisticated experiments.…
Vipin Kataria, Nitin Kumar
Business analysts and non-technical users need insights from enterprise data lakes but lack SQL expertise to query them directly. While large language models (LLMs) can translate natural language to SQL, existing text-to-SQL approaches face critical limitations: severe SQL injection vulnerabilities, inability to…
Tatsat Banerjee, Bedri Abubaker-Sharif, Peter N. Devreotes, Pablo A. Iglesias
3## DISCUSSION We have developed Membrane Kymograph Generator, a free, open-source, user-friendly, cross-platform software that addresses a significant gap in quantitative live-cell imaging analysis by fully automating the generation and downstream analysis of kymographs along dynamic cell boundaries. This software…
Mariano Ruz Jurado, David Rodriguez Morales, Lukas Zanders, Elijah Genetzakis + 3 more
Advances in omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have provided an unbiased framework to study cellular heterogeneity, shifts in cell type composition, and the dynamics of cells in different organs and tissues (). The workflow for generating scRNA-seq data can be summarised into four…
Luna Xingyu Li, Carissa Bleker, Sylvain Soliman, Laurence Calzone + 13 more
Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce…
Julie R. Pivin-Bachler, Egon L. van den Broek
Title: Summary Machine learning struggles with imbalanced data. Although several mitigation approaches exist, their application depends on the extent of imbalance. To determine the latter, a protocol was developed. Across 428 synthetic and 70 real datasets, 8 imbalance measures were benchmarked and evaluated using…
Dave Bunten, Jenna Tomkinson, Erik Serrano, Michael J. Lippincott + 4 more
Title: Summary High-content imaging (HCI) involves the automated acquisition and quantitative analysis of cell phenotypes from microscopy images. These studies often rely on screening, which can involve thousands of chemical or genetic perturbations that produce terabytes of microscopy data. To extract meaningful…
Lukas Heumos, Yuge Ji, Lilly May, Tessa D. Green + 25 more
Advances in single-cell technology have enabled the measurement of cell-resolved molecular states across a variety of cell lines and tissues under a plethora of genetic, chemical, environmental or disease perturbations. Current methods focus on differential comparison or are specific to a particular task in a…
Arjumand Fatima, Onaiza Maqbool
Developer discussions particularly on programming related questions answering (Q&A) sites, contain useful information, which, if mined and analysed carefully can be transformed into insightful recommendations for developers about which software to use or prefer over others, matching with one’s requirements for…