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<h4>Motivation</h4>Pedigrees reconstructed from biologically related ancient genomes have revealed many insights into (pre)history. To our knowledge, all reported ancient pedigrees have been primarily manually reconstructed, as existing pedigree reconstruction methods are ill-suited for the quality …
Read PDF<h4>Summary</h4>Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics research by effectively capturing biologically relevant relationships among molecular …
Read PDF<h4>Motivation</h4>Modern computational biology relies heavily on command-line tools that underpin analytical workflows, yet integrating these tools into R-based analyses poses substantial challenges for reproducibility, especially for researchers with limited computational expertise. While R excels at …
Read PDF<h4>Motivation</h4>Despite the widely recognized importance of replicability in biological research, computational methods to quantify irreplicability and identify irreplicable instances remain underdeveloped. This article presents an efficient and robust computational framework to address this gap.<h4>Results</h4>To tackle …
Read PDF<h4>Motivation</h4>Infectious diseases continue to be a leading cause of mortality and pose a significant global health threat. Thus, the development of tools for surveillance and early detection of emerging pathogens is needed.<h4>Results</h4>We introduce PathogenFinder2, a …
Read PDF<h4>Summary</h4>We present igv-reports, a command-line tool to create standalone HTML pages embedding interactive genomic visualizations of read alignments and associated annotations to support variant inspection workflows. The reports contain all data and code required for …
Read PDF<i>Lactobacillus plantarum</i> subsp. <i>plantarum</i> strain LB1-2, isolated from the hindgut of European honeybees in the Philippines, is active against <i>Paenibacillus larvae</i> and has broad activity against several Gram-positive and Gram-negative bacteria. The complete genome sequence …
Read PDFRhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna, Philippines. The 7.07-Mb complete genome comprises three replicons, one chromosome, and two plasmids, with a G+C content of 59.4% and 6,720 protein-coding …
Read PDFStreptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines, are active against Bacillus subtilis subsp. subtilis KCTC 3135<sup>T</sup>. The near-complete genome sequences reported here represent a possible source …
Read PDF<h4>Motivation</h4>Serial section electron microscopy (ssEM) is essential for studying biological cell structures at nanometer resolution. However, supporting film folding (SFF) degradation frequently occurs during sample preparation, causing structural distortions and information loss that severely impair …
Read PDFRalstonia solanacearum strain T523 is the major phytopathogen causing tomato bacterial wilt in the Philippines. Here, we report the complete chromosome and draft megaplasmid genomes with predicted gene inventories supporting rhizosphere processes, extensive plant virulence …
Read PDF<h4>Motivation</h4>Accurately identifying compound-protein interactions (CPIs) is critical for accelerating drug discovery. Recent deep learning methods have achieved impressive results, yet they primarily focus on local structures and neighborhood information, often overlooking high-order interaction patterns shared …
Read PDF<h4>Motivation</h4>How individuals with conditions, disabilities or abnormalities were treated gives us valuable insights into past societies. Chromosomal aneuploidies, the presence of an abnormal number of copies of the chromosomes, represent the most common large-scale chromosomal …
Read PDFWe report here the draft genome sequences of six bacteria isolated from the near-bottom waters and surface sediments of the Benham Bank, Philippine Rise, Philippines. These genome sequences represent candidate novel species and/or strains from …
Read PDFPlant science research has entered a transformative era driven by rapid technological developments in high-throughput sequencing, omics-based approaches, computational biology, and precision phenotyping [...].
Read PDFThis letter comments on the recently published AICellType platform for large language model (LLM)-based cell type annotation in single-cell and spatial transcriptomics. While appreciating the authors' systematic benchmarking and practical contribution, concerns are raised regarding …
Read PDFIn this paper, we report the draft genome sequence of <i>Streptomyces</i> sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability …
Read PDFDomestic cat hepadnavirus (DCH) is an infectious disease associated with chronic hepatitis in cats, which suggests a similarity with hepatitis B virus infections in humans. Since its first identification in Australia in 2018, DCH has …
Read PDF<h4>Motivation</h4>The routine exclusion of admixed individuals from traditional genome-wide association studies (GWAS) due to concerns about spurious associations has limited multi-ancestry genetic discovery. Tractor addresses this issue by incorporating local ancestry into association testing, enabling …
Read PDF<h4>Motivation</h4>Serine protease inhibitors (serpins) are a large family of proteins conserved in all animals. A prominent enigma about serpins is that, while members of this family share an archetypal folding scheme, individual proteins have diverse …
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