AnnoMe: user-defined classification of HR-MS/MS spectra for natural product discovery [0.03%]
annoMe：用户定义的HR-MS/MS谱图分类法在天然产物发现中的应用
Christoph Bueschl,Tomas Rypar,Lenka Molcanova et al.
Christoph Bueschl et al.
Summary: Annotation of HR-MS/MS spectra is a complex task that can be tackled either by expert interpretation or machine learning models that rely on large spectral/structural databases for training. Frequently, users wan...
SCOT+: a comprehensive software suite for single-cell alignment using optimal transport [0.03%]
SCOT+：使用最优传输的单细胞数据对齐综合软件套件
Colin Baker,Tuan Pham,Pinar Demetci et al.
Colin Baker et al.
Summary: New advances in single-cell multi-omics experiments have allowed biologists to examine how various biological factors regulate processes in concert on the cellular level. However, measuring multiple cellular feat...
Ekin Deniz Aksu,Martin Vingron
Ekin Deniz Aksu
Identification of in vivo transcription factor (TF) binding sites is crucial to understand gene regulation, but the lack of scalability in their experimental identification directs researchers towards computational models. These models are ...
Abraham Guerra
Abraham Guerra
The pangenome, representing the complete genetic repertoire of a species, has become a central concept in modern prokaryotic genomics, moving the field beyond the limitations of a single reference genome. This review provides a comprehensiv...
MPore: database-driven identification of active methyltransferases in prokaryotic genomes from nanopore sequencing [0.03%]
基于纳米孔测序的模式识别方法_MPore：数据库驱动的原核生物基因组中活性甲基转移酶鉴定数据库
Azlan Nisar,Lars Vogelgsang,Sebastian Fuchs et al.
Azlan Nisar et al.
Motivation: In prokaryotic genomes, methylation is an important epigenetic modification that regulates the uptake of foreign DNA; it can also contribute to replication or virulence. We present MPore, a novel method for th...
CDCR-Rank: a computational model for predicting drug combination dose response using ranking-based optimization [0.03%]
基于排序优化的预测药物组合剂量响应的计算模型CDCR-Rank
Mohammadamin Moragheb,Karim Abbasi,Parvin Razzaghi et al.
Mohammadamin Moragheb et al.
Motivation: Predicting synergistic drug combinations for cancer therapies is vital but challenged by interaction complexity and vast combinatorial possibilities. To address this, we propose a novel ranking-based approach ...
PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins [0.03%]
PZLAST-MAG：大规模宏基因组蛋白质全长序列相似性搜索服务器
Koichi Higashi,Hitoshi Ishikawa,Ken Kurokawa et al.
Koichi Higashi et al.
Motivation: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary anal...
Synonymous but not silent: functional codon bias reveals decoupled mitonuclear evolution in parasitic worms [0.03%]
同义但不沉默：功能密码子偏爱揭示寄生蠕虫线粒体与细胞核脱耦的协同进化
Kanhu Charan Das,Ruchishree Konhar,Devendra Kumar Biswal
Kanhu Charan Das
Motivation: The Codon usage bias, the preference for certain "silent" codons over others, is determined by a competition between two main forces: mutational pressure (random changes in DNA) and translational selection (th...
VectorSage: enhancing PubMed article retrieval with advanced semantic search [0.03%]
VectorSage：利用先进的语义搜索增强PubMed文献检索功能
Yasas Wijesekara,Rahul Brahma,Mehdi Lotfi et al.
Yasas Wijesekara et al.
Motivation: The exponential growth of academic literature has presented unprecedented opportunities. However, it also underscores the need for advanced search methodologies to support efficient knowledge discovery. While ...
T Quinn Smith,Amatur Rahman,Zachary A Szpiech
T Quinn Smith
Motivation: We introduce Empirical Genotype Generalizer for Samples (EGGS) which accepts empirical genotypes with missing data and replicates the distribution of missing genotypes along the empirical segment in other repl...