12 papers · ranked by Valyu relevance
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Reza Bozorgpour
This study aims to establish predictive criteria for identifying cerebral aneurysms that are likely to respond favorably—either stabilizing or shrinking—following flow diverter stent (FDS) treatment. We analyzed the pre-treatment hemodynamics and geometry of four patient-specific aneurysms to determine features linked…
Kelly Maggs, Markus K. Youssef, Cyril Pulver, Jovan Isma + 6 more
Standard single-cell RNA-seq analysis frameworks aggregate over-lapping biological processes and impose a single parametrization, conflating distinct programs. Here, we introduce a topological framework that detects and disentangles multiple cyclic processes directly from single-cell transcriptomic data. We validate…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Junichiro Makino, Toshikazu Ebisuzaki, Ryutaro Himeno, Yoshihide Hayashizaki
Rapidly increasing amount of short read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Jose L Figueroa, Richard Allen White
We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC)…
Haojing Shao, Jue Ruan
Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics research. Although classic dynamic-programming algorithms (e.g., Smith-Waterman and Needleman–Wunsch) guarantee to produce the optimal result, their time complexity hinders the application of large-scale sequence alignment.…
Yuma Osako, Aineias Arango, Toshitake Asabuki
Animals flexibly combine learned behaviors into novel actions without practicing their combinations, yet the computational mechanisms that enable independently acquired computations to be expressed in parallel remain unclear. Here we show that feedback geometry during learning determines whether recurrent dynamics can…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…
Ghanshyam Chandra, Md. Vasimuddin, Sanchit Misra, Chirag Jain
Recent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spanning entire chromosomes. The increase in the assembly contiguity and the reduced number of assembly contigs also implies…
Helena Wright-Wieckowski, Jason Friedman, Joseph M. Galea, Katja Kornysheva
Results in human and non-human primates have shown that elements of a movement sequence are pre-ordered in parallel competitively before execution, a process known as competitive queueing (CQ). However, it is unclear whether the preplanning of individual movements persists in continuous skilled actions that involve…