10 papers · ranked by Valyu relevance
Inbar Dahari, Orly E. Weiss, Amos Ayubi, Danny Baranes + 2 more
The morphology of dendritic trees critically shapes how neurons integrate and compute synaptic inputs. Dendritic morphogenesis results from the growth and spatial organization of branches, driven by intrinsic genetic programs, extrinsic environmental signals, activity-dependent processes, and spatial mechanisms such as…
Abhinav Sharma, Davi Josué Marcon, Johannes Loubser, Karla Valéria Batista Lima + 3 more
The MTBseq pipeline, published in 2018, was designed to address bioinformatics challenges in tuberculosis (TB) research using whole-genome sequencing (WGS) data. It was the first publicly available tool on GitHub to perform full analysis of WGS data for Mycobacterium tuberculosis complex (MTBC) encompassing quality…
Ge Zhang
bcftools is the standard toolkit for handling VCF and BCF variant files, but it processes records on a single core; its --threads option speeds up only compression of the output, not the work done on variant records. Processing large call sets is therefore slow, and users often divide the genome and reassemble the…
Jinyang Wang, Zhugang Wang, Di Liu, Isabelle Ledoux-Rak
Ultra-high sampling rates in coherent optical front-ends increasingly exceed the processing capabilities of real-time baseband processors, creating a bottleneck in coherent free-space optical communication systems. We propose a unified state-space framework to systematically parallelize digital signal processing (DSP)…
Nhan Ly-Trong, Samuel Martin, Nick Goldman, Nicola De Maio + 1 more
Phylogenetic analysis is essential to genomic epidemiology, for example in tracing the origin and evolution of SARS-CoV-2 variants during the COVID-19 pandemic. We previously introduced CMAPLE, a single-threaded implementation of the MAPLE algorithm designed for large-scale epidemiological genomic datasets. CMAPLE can…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
Shujun Peng, Xinhan Lin, Yu Zhang, Yuheng Xiao + 1 more
Parallel scan is a fundamental primitive widely used in a broad range of workloads, including parallel sorting, graph algorithms, and sampling in large language model inference. Although GPU-optimized parallel scan algorithms have been extensively studied, their reliance on vector units makes them inefficient on modern…
Ryo Emoto, Kiyoaki Ishii, Toshinari Takamura, Shigeyuki Matsui
Recent advances in biotechnology and personalized medicine have driven the development of efficient clinical trial methodologies for assessing treatment efficacy across multiple populations defined by treatment effect modifiers. Within-patient comparison of different treatments is a promising approach for improving…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
Ju-Chi Yu, Micaela Y. Chan, Liang Han, Erin Dickie + 1 more
A critical step in the analysis of large-scale functional brain networks in neuroimaging is parcellation, which defines the nodes of a brain network. Group or atlas-based parcellation schemes use a shared common space, ensuring that each individual has the same number of brain parcels, which facilitates standard…