10 papers · ranked by Valyu relevance
Haodong Liu, Pinglu Zhang, Yanming Wei, Qinzhong Tian + 3 more
Partial order alignment (POA) has emerged as a fundamental component in long-read error correction, assembly and pangenomics. However, conventional POA algorithms are limited by high time and memory requirements, making them inefficient for large-scale datasets. Here, we present minipoa, a fast and memory-efficient POA…
Dan Flomin, David Pellow, Ron Shamir
The rapid, continuous growth of deep sequencing experiments requires development and improvement of many bioinformatics applications for analysis of large sequencing datasets, including k-mer counting and assembly. Several applications reduce RAM usage by binning sequences. Binning is done by employing minimizer…
Joseph J. Vallino, Olivia M. Ahern, Julie A. Huber
Protists and viruses dynamically alter the flow of mass and energy through microbial food webs via predation. Simple microbial food web models show that the addition of microbial predators can increase the primary production of a microbial community but only for some configurations of food web structure. Under the…
Minindu Weerakoon, Christopher T Saunders, Haynes Heaton
Most multiple sequence alignment and string-graph alignment algorithms focus on global alignment, but many applications exist for semi-global and local string-graph alignment. Long reads require enormous amounts of memory and runtime to fill out large dynamic programming tables. Effective algorithms for finding the…
Virginia Delli, Charles-Antoine Seux, Julien Dehame, Sooraj Nair + 2 more
Gonadotropin-releasing hormone (GnRH) neurons are the final common target of a complex network of cells cooperating for the central control of reproduction. The balance between excitatory and inhibitory transsynaptic and non-synaptic inputs is crucial for the maintenance of the GnRH rhythms: the pulse and the surge.…
Serena R. Sweet, Jessica E. Biddinger, Jessie B. Zimmermann, Gina L. Yu + 1 more
Drinking and feeding are tightly coordinated homeostatic events and the paraventricular nucleus of the hypothalamus (PVH) represents a possible node of neural integration for signals related to energy and fluid homeostasis. We used TRAP2;Ai14 and Fos labeling to visualize neurons in the PVH and median preoptic nucleus…
Lucas R. van Dijk, Abigail L. Manson, Ashlee M. Earl, Kiran V Garimella + 1 more
Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches…
Albert Jiménez-Blanco, Lorién López-Villellas, Juan Carlos Moure, Miquel Moreto + 1 more
Sequence-to-graph alignment is a central problem in bioinformatics, with applications in multiple sequence alignment (MSA) and pangenome analysis, among others. However, current algorithms for optimal affine-gap alignment impose high memory and computational requirements, limiting their scalability to aligning long…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Hratch Baghdassarian, Pablo Di Giusto, Juan Tibocha-Bonilla, Erick Armingol + 4 more
Genome-scale metabolic models (M-models) provide mechanistic insight into intracellular metabolism by simulating fluxes subject to nutrient and energy resource constraints. However, they cannot account for a major component of resource allocation, since they do not explicitly account for the cost of producing and…