Simulating Protein Dynamics in Cell Signaling Pathways: A Mathematical Model Approach Incorporating Negative Interaction Mechanisms [0.03%]
Minsoo Kim,Eunjung Kim
Minsoo Kim
This study presents an improved mathematical model that incorporates negative interaction mechanisms to predict the dynamics of cell signaling pathways. By employing stochastic differential equations and the Euler-Maruyama method, we simula...
Random Projection Methods Outperform Principal Component Analysis for Dimensionality Reduction in Single Cell RNA-Seq [0.03%]
Mohamed Abdelnaby,Marmar R Moussa
Mohamed Abdelnaby
Principal component analysis (PCA) is one of the most frequently used dimensionality reduction methods for high-dimensional datasets, especially single-cell RNA sequencing (scRNA-seq). Despite its popularity, PCA faces challenges, particula...
Evaluating Protein Language Model Embeddings for Viral Clade Assignment [0.03%]
评估蛋白质语言模型嵌入在病毒谱系分配中的应用
Brendonas Stakauskas,Virginijus MarcinkeviČius
Brendonas Stakauskas
Protein language models (PLMs) provide powerful sequence representations, yet their effectiveness for unsupervised viral clade assignment remains uncertain. In this study, we evaluated embeddings from ProtT5, ProtBert, CARP, and several ESM...
DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images [0.03%]
基于混沌增强万花筒图像的深度学习辅助蛋白质序列分析(DANCE)方法
Taslim Murad,Prakash Chourasia,Sarwan Ali et al.
Taslim Murad et al.
Cancer is a complex disease characterized by uncontrolled cell growth and requires an accurate classification for effective treatment. T cell receptors (TCRs), crucial proteins in the immune system, play a pivotal role in antigen recognitio...
From Small Parsimony to Horizontal Gene Transfer: Inferring Horizontal Transfer and Gene Loss for Single-Origin Characters [0.03%]
从简约法到基因水平转移：单一起源特征的水平基因转移和基因丢失推理
Alitzel López Sánchez,Guillaume E Scholz,Peter F Stadler et al.
Alitzel López Sánchez et al.
The simple underlying pattern of presence-absence of a character within a species tree provides useful steps to trace complex evolutionary histories. Character-based models such as perfect transfer networks and its galled variant aim to lev...
Leonardo Gemin,Cinzia Pizzi,Matteo Comin
Leonardo Gemin
Many state-of-the-art tools for sequence analysis are based on alignment-free techniques to manage high-throughput processing. Several routine tasks such as querying, indexing, and similarity search are based on k-mer statistics. In order t...
Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing [0.03%]
Illumina MiSeq平台扩增子测序中PHRED分数的特征评估
Seth Sims,Yury Khudyakov,Alexander Zelikovsky
Seth Sims
PHRED scores are confidence values associated with each basecall generated by sequencers. The score is defined as a monotonic function of the probability that the basecall is incorrect. The calibration of PHRED scores has previously been ex...
Yue Zhang,David Sankoff
Yue Zhang
Comparative analysis of sequence similarity distributions reveals evolutionary mechanisms shaping gene families. In Salmonidae, whole-genome duplication (WGD) and rapid speciation pose a challenge for modeling retained homologs and sequence...
CherryRed: A Software Implementation of Cherry Distance with a New Optimization and Heuristic [0.03%]
樱桃红：一种带优化和启发式的樱桃距离的新软件实现方法
Kaari Landry,Olivier Tremblay-Savard
Kaari Landry
Representing complex evolutionary relationships, such as hybridization and horizontal gene transfer, increasingly requires phylogenetic networks (over phylogenetic trees). Methods of construction of such networks rely on a measure of differ...
FDS-CAP: Modeling Fragmented Disease Subgraphs with Component-Level Attention for Comorbidity Prediction [0.03%]
FDS-CAP：使用组件级注意力建模碎片化疾病子图以进行共病预测
Ashwag Altayyar,Li Liao
Ashwag Altayyar
Understanding comorbidity between human diseases is essential for uncovering shared pathophysiological mechanisms and improving diagnostic and therapeutic strategies. Although prior studies have investigated genetic and network-based diseas...