12 papers · ranked by Valyu relevance
Michael C. Robitaille, Jeff M. Byers, Joseph A. Christodoulides, Marc P. Raphael
Cell segmentation is crucial to the field of cell biology, as the accurate extraction of cell morphology, migration, and ultimately behavior from time-lapse live cell imagery are of paramount importance to elucidate and understand basic cellular processes. Here, we introduce a novel segmentation approach centered…
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Fragment-based drug design (FBDD) has become a key approach in structure-based drug discovery, allowing researchers to systematically develop molecular fragments into potent ligands. Although recent generative AI models, such as diffusion-based approaches, show great potential for designing new molecules, applying them…
Xiaoxin Ye, Joshua W K Ho
Flow cytometry is a popular technology for quantitative single-cell profiling of cell surface markers. It enables expression measurement of tens of cell surface protein markers in millions of single cells. It is a powerful tool for discovering cell sub-populations and quantifying cell population heterogeneity.…
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…
Mingfu Shao, Carl Kingsford
Motivated by transcript assembly and multiple genome assembly problems, in this paper, we study the following minimum path flow decomposition problem: given a directed acyclic graph G = (V,E) with source s and sink t and a flow f, compute a set of s-t paths P and assign weight w(p) for p ∈ P such that , and |P| is…
Menachem Sklarz, Michal Gordon, Vered Chalifa-Caspi
Bioinformatics workflows (WFs) in general, and those involving High Throughput Sequencing data in particular, typically involve executing a sequence of programs on raw sequence files from as many as thousands of samples. Management of these WFs is laborious and error-prone. We have developed NeatSeq-Flow, a python…
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Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…
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Photoredox catalysis plays an important role in the synthesis of pharmaceutically relevant compounds, such as C(sp3)-rich tertiary amines. The difficulty of identifying underlying mechanistic models for such novel transformations, coupled with the large reaction space of this reaction class, mean that developing a…
Jiyizhe Zhang, Naoto Sugisawa, Kobi Felton, Shinichiro Fuse + 1 more
Amide bond formation is one of the most prevalent reactions in pharmaceutical industry, among which the Schotten-Baumann reaction has attracted attention as a potential green amide formation approach. However, the use of water in the reaction system often causes undesired hydrolysis and can generate a multiphase…
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Digital twins are virtual companions for the design, scale-up, and control of chemical processes. Equipping digital twins with mechanistic models of their mirrored unit operation expands their range of applicability compared to pure data-driven models. As constructing mechanistic models requires time, effort, and…
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Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture…