Results 41 to 50 of about 33,182 (260)

Single‐molecule DNA flow‐stretch assays for high‐throughput DNA–protein interaction studies

FEBS Open Bio, EarlyView.
We describe an optimised single‐molecule DNA flow‐stretch assay that visualises DNA–protein interactions in real time. Linear DNA fragments are tethered to a surface and stretched by buffer flow for fluorescence imaging. Using λ and φX174 DNA, this protocol enhances reproducibility and accessibility, providing a versatile approach for studying diverse ...
Ayush Kumar Ganguli, Mohammad Nour Alsamsam, Ugnė Bagdonaitė, Van Truc Vu, Chun‐Jen Huang, Polina Kuzhir, Mindaugas Zaremba, Aurimas Kopūstas, Marijonas Tutkus   +8 more
wiley   +1 more source

ISAP-MATLAB Package for Sensitivity Analysis of High-Dimensional Stochastic Chemical Networks

Journal of Statistical Software, 2018
Stochastic simulation and modeling play an important role to elucidate the fundamental mechanisms in complex biochemical networks. The parametric sensitivity analysis of reaction networks becomes a powerful mathematical and computational tool, yielding ...
Weilong Hu, Yannis Pantazis, Markos A. Katsoulakis   +2 more
doaj   +1 more source

Low-degree learning and the metric entropy of polynomials

Discrete Analysis, 2023
Low-degree learning and the metric entropy of polynomials, Discrete Analysis 2023:17, 23 pp. This paper is a follow-up to a paper by the first two authors on the general problem of designing algorithms that can efficiently learn functions defined on ...
Alexandros Eskenazis, Paata Ivanisvili, Lauritz Streck   +2 more
doaj   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

On Invertibility of Large Binary Matrices

Mathematics
Many data processing applications involve binary matrices for storing digital information. At present, there are limited results in the literature about algorithms for inverting large binary matrices.
Ibrahim Mammadov, Pavel Loskot, Thomas Honold   +2 more
doaj   +1 more source

Algorithms for effective querying of compound graph-based pathway databases

BMC Bioinformatics, 2009
Background Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood ...
Demir Emek, Cetintas Ahmet, Dogrusoz Ugur, Babur Ozgun   +3 more
doaj   +1 more source

Quasi-Polynomial Time Approximation Schemes for Packing and Covering Problems in Planar Graphs [PDF]

, 2018
We consider two optimization problems in planar graphs. In {Maximum Weight Independent Set of Objects} we are given a graph G and a family D of {objects}, each being a connected subgraph of G with a prescribed weight, and the task is to find a maximum ...
Herman, Grzegorz, Pilipczuk, Michal, Wiese, Andreas, van Leeuwen, Erik Jan, Bast, Hannah, Van Leeuwen, Erik, Azar, Yossi, Pilipczuk, Michał, Sub Algorithms and Complexity, Leeuwen, Erik Jan van, Algorithms and Complexity   +10 more
core   +1 more source

Parameterized Complexity of Streaming Diameter and Connectivity Problems

, 2022
We initiate the investigation of the parameterized complexity of Diameter and Connectivity in the streaming paradigm. On the positive end, we show that knowing a vertex cover of size k allows for algorithms in the Adjacency List (AL) streaming model ...
Nederlof, Jesper, Oostveen, Jelle J., Sub Algorithms and Complexity, Leeuwen, Erik Jan van, Dell, Holger, Algorithms and Complexity   +5 more
core   +1 more source

RoundMi: A quantitative method to analyze mitochondrial morphology in mitotic cells

FEBS Open Bio, EarlyView.
RoundMi is a workflow for rapid analysis of mitochondrial morphology in mitotic cells. By combining adaptive preprocessing with automated segmentation and quantification, it enables accurate measurements from single focal plane images, reducing acquisition time and computational demands while remaining compatible with high‐throughput fixed and live ...
Elmira Parvindokht Bararpour, Christine Volmert, Valentina Piano   +2 more
wiley   +1 more source

Uncovering G Protein‐Coupled Receptors: Novel Targets and Biomarkers for Predicting Glioma Prognosis

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Background Low‐grade gliomas (LGG) exhibit significant heterogeneity and recurrence risk. G protein‐coupled receptors (GPCR) contribute to glioma malignant progression, but their prognostic value remains unclear. This work attempts to formulate a GPCR‐based outcome‐predicting model for LGG. Methods Based on TCGA LGG data, the enrichment scores
Jun Yang, Dongxu Zhang, Dongyuan Liu, Da Lin, Hao Wang   +4 more
wiley   +1 more source