Building Multiscale Markov State Models by Systematic Mapping of Temporal Communities [0.03%]
基于时空社区映射的多尺度马尔可夫状态模型构建方法
Nir Nitskansky,Kessem Clein,Barak Raveh
Nir Nitskansky
Motivation: Biomolecules undergo dynamic transitions among metastable states to carry out their biological functions. Markov State Models (MSMs) effectively capture these metastable states and transitions at a defined tem...
scRegulate: Single-Cell Regulatory-Embedded Variational Inference of Transcription Factor Activity from Gene Expression [0.03%]
基于基因表达的单细胞转录因子活性的监管嵌入变分推断（scRegulate）
Mehrdad Zandigohar,Jalees Rehman,Yang Dai
Mehrdad Zandigohar
Motivation: Accurately inferring transcription factor (TF) activity from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in computational biology. While existing methods rely on statistical mod...
DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing [0.03%]
基于Transformer和时间卷积网络的纳米孔测序精确条形码解复用方法 DemuxTrans
Liyuan Shu,Deyu Zhuang,Jiao Tang et al.
Liyuan Shu et al.
Motivation: Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches strug...
Morpheus: A fragment-based algorithm to predict fold-switching behaviour in proteins across proteomes [0.03%]
莫菲斯：一种基于片段的算法预测蛋白质组中蛋白质折叠转换行为
Vijay Subramanian,Rajeswari Appadurai,Harikrishnan Venkatesh et al.
Vijay Subramanian et al.
Motivation: Functionally important "fold-switching" proteins, which do not obey the classical folding dogma, are now thought to be widespread. Algorithms that can accurately annotate fold-switching proteins from sequence ...
Assessing differential cell composition in single-cell studies using voomCLR [0.03%]
利用 voomCLR 评估 单细胞研究中的不同细胞组成比例
Alemu Takele Assefa,Bie Verbist,Koen Van den Berge
Alemu Takele Assefa
Motivation: In single-cell studies, a common question is whether there is a change in cell composition between conditions. While ideally, one needs absolute cell counts (number of cells per volumetric unit in a sample) to...
SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection [0.03%]
SISTEM：基于基因型驱动选择的肿瘤进化、转移和DNA测序数据模拟
Samson Weiner,Mukul S Bansal
Samson Weiner
Summary: SISTEM is a software package and mathematical framework for simulating tumor evolution and cell migrations at single-cell resolution. Unlike existing frameworks which simulate cancer cell populations under the ne...
Benchmarking Methods for Measuring Biosynthetic Gene Cluster Similarity and Determination of Gene Cluster Families [0.03%]
生物合成基因簇相似性测定及基因簇家族确定的方法评估
Abiodun S Oyedele,Allison S Walker
Abiodun S Oyedele
Motivation: Natural products are often produced by a set of biosynthetic enzymes which are encoded by genes clustered together in the producer's genome, referred to as a biosynthetic gene cluster (BGC). The ability to com...
Jan van Eck,Dea Gogishvili,Wilson Silva et al.
Jan van Eck et al.
Motivation: Protein language models (PLMs) have revolutionised computational biology through their ability to generate powerful sequence representations for diverse prediction tasks. However, their black-box nature limits...
FracFixR: A compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data [0.03%]
基于RNA测序数据的分数绝对比例估计的组合统计框架FracFixR
Alice Cleynen,Agin Ravindran,Nikolay Shirokikh
Alice Cleynen
Summary: RNA fractionation followed by high-throughput sequencing (RNA-seq) is widely used to study RNA localization, translation, structure, stability and subcellular compartmentalization. Interpreting fractionated RNA-s...
PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder [0.03%]
基于质谱的蛋白质组学数据的条件自编码器蛋白丰度离群值检测(PROTRIDER)
Daniela Klaproth-Andrade,Ines F Scheller,Georgios Tsitsiridis et al.
Daniela Klaproth-Andrade et al.
Motivation: Detection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for rare disease diagnostics and tumor characterization. While numerous methods...