Zexin Xue,Michael Bailey,Abhinav Gupta et al.
Zexin Xue et al.
Molecular structure prediction is essential for understanding therapeutic functions and accelerating pharmaceutical research. While state-of-the-art deep learning models like AlphaFold demonstrate strong performance on general protein backb...
USTAR-CR: Efficient and Compact Compression of k-Mer Sets Through Colored de Bruijn Graphs [0.03%]
基于着色de Bruin图的k-mer集合高效压缩方法(USTAR-CR)
Enrico Rossignolo,Matteo Comin
Enrico Rossignolo
A core task in computational genomics is transforming input sequences into their constituent k-mers. Efficiently storing these k-mer collections is crucial for scaling bioinformatics workflows. A common strategy involves representing the k-...
Learning Protein Structure Representation with Orientation-Aware Networks [0.03%]
基于方向感知网络的蛋白质结构表征学习
Jiahan Li,Shitong Luo,Congyue Deng et al.
Jiahan Li et al.
The intricate three-dimensional structures of proteins dictate their diverse biological functions. Accurately representing these structures, particularly the fine-grained orientational relationships between amino acids, is crucial for under...
Elucidating Transitions of k-mer-Based Objects Across k-mer Sizes [0.03%]
基于k- mer的物体在不同k- mer大小下的转换分析
Adam Park,David Koslicki
Adam Park
The widespread adoption of k-mers in computational biology has enabled efficient methods for utilizing genomic sequences in a variety of biological tasks. However, understanding the influence of k-mer sizes within these methods remains a pe...
A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications [0.03%]
含节段重复的基因物种概率协调算法
Yao-Ban Chan,Celine Scornavacca,Michael Charleston
Yao-Ban Chan
Reconciliations are a mathematical tool to compare the phylogenetic trees of genes to the species that contain them, accounting for events such as gene duplication and loss. Traditional reconciliation methods have predominantly relied on pa...
Multi-Perspective Natural Vector: A Novel Method for Viral Sequence Feature Extraction [0.03%]
多视角自然向量：一种新颖的病毒序列特征提取方法
Xiang Shi,Jiayi Kang,Nan Sun et al.
Xiang Shi et al.
The rapid expansion of biological data in recent decades has highlighted the need for efficient methods in sequence analysis. Traditional pairwise alignment approaches are both time-consuming and memory-intensive. Alignment-free (AF) method...
Conformal Prediction with Knowledge Graphs for Reliable Antimicrobial Resistance Detection with MALDI-TOF Mass Spectra [0.03%]
基于康福尔预测的知识图在基质辅助激光解吸/电离飞行时间质谱抗微生物药物抗药性检测中的应用研究
Nina Corvelo Benz,Lucas Miranda,Dexiong Chen et al.
Nina Corvelo Benz et al.
Bacterial antimicrobial resistance is one of the most pressing global health challenges. Infections with resistant pathogens increase patient morbidity and mortality due to limited treatment options. Rapid and reliable identification of res...
Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification [0.03%]
基于最大匹配的全基因组种子链提升读段分类性能
Nathaniel K Brown,Vikram S Shivakumar,Ben Langmead
Nathaniel K Brown
Given a set of exact matches, chaining consists of finding those which are colinear with respect to the reference. However, this requires superlinear time in the number of matches and is not suitable for approaches such as read classificati...
Zi-Wei Bai,Ricky X F Chen,Michael Fuchs
Zi-Wei Bai
An enumerative study of RNA secondary structures according to various characteristics is a topic of key importance in computational biology. RNA secondary structure pairs have also been studied in various contexts. Recently, the homology gr...
StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data [0.03%]
星系CDP：基于CRISPR的谱系追踪数据的快速且准确重构细胞谱系树的动态规划算法
Junyan Dai,Erin K Molloy
Junyan Dai
CRISPR-based lineage tracing, coupled with single-cell RNA sequencing, has emerged as a promising approach for studying development and disease progression at the cellular level. Thus, cell lineage tree (CLT) reconstruction has attracted si...