matrix factorization

Metagenomic binning through low density hashing

Opal improves metagenomic binning by using low-density hashing to achieve faster and more accurate identification of sequencing read origins compared to existing methods.

An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

The paper introduces cwDTW, a wavelet-based DTW algorithm for nanopore sequencing signal alignment, achieving high accuracy and speed compared to existing methods.

BROCKMAN: Deciphering variance in epigenomic regulators by k-mer factorization

BROCKMAN identifies transcription factor activity variation in single-cell ATAC-seq data by analyzing k-mer frequencies associated with epigenomic marks.

ARKS: chromosome-scale scaffolding of human genomedrafts with linked read kmers

ARKS improves human genome assemblies using linked read kmers, achieving five-fold better contiguity than baseline methods.

Multi-Omics factor analysis - a framework for unsupervised integration of multi-omic data sets

MOFA, a sparse Bayesian factor model with mixed likelihoods, separates shared from modality-specific multi-omic variation, recovering IGHV, trisomy 12 and oxidative-stress axes in 200 leukaemia samples.

SuperDCA for genome-wide epistasis analysis

SuperDCA enables genome-wide epistasis analysis in bacteria by efficiently modeling interactions among polymorphisms, revealing novel biological insights in Streptococcus pneumoniae.

Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep

The paper develops a substitution matrix-based method to model tooth enamel pellicle peptide interactions with hydroxyapatite, achieving high discrimination accuracy.

Fast Inference of Individual Admixture Coefficients Using Geographic Data

The paper introduces new algorithms that use geographic data to estimate ancestry proportions and frequencies, showing faster runtime without loss of accuracy.

Sparse Tensor Decomposition For Haplotype Assembly Of Diploids And Polyploids

The paper introduces AltHap, a method for haplotype assembly in diploids and polyploids using sparse tensor decomposition, showing improved performance over existing techniques for polyploids.

Characterizing and Managing Missing Structured Data in Electronic Health Records

The paper evaluates imputation methods for missing structured data in EHRs using clinical lab measures from 602,366 patients, showing some methods perform well while others are unsuitable for multiple imputation.

Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework

This paper compares E-PCA and I-PCA methods on chromosome and protein contact matrices to reveal structural dynamics and differences across cell types and protein complexes.

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

The paper integrates chromatin accessibility and DNA methylation data from human pancreatic islets to refine regulatory mechanisms at Type 2 Diabetes susceptibility loci.

Methods in Description and Validation of Local Metagenetic Microbial Communities

The paper compares MinHash and NMF methods for metagenetic sample similarity and evaluates clustering quality using ecological metadata.

Genomic dissection of Systemic Lupus Erythematosus: Distinct Susceptibility, Activity and Severity Signatures

This study identifies distinct susceptibility and activity/severity signatures in SLE using transcriptomics and genetics, enabling improved diagnosis and personalized therapy.

netSmooth: Network-smoothing based imputation for single cell RNA-seq

netSmooth improves scRNA-seq clustering by smoothing expression values using network diffusion and gene expression priors.

Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism

This study investigates the relationship between Jacobian and modal matrices in metabolic kinetic models, showing how network structure and reaction kinetics determine modal sparsity and complexity.

New insights on the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation

This study identifies two SNPs associated with antidepressant response in GENDEP and STAR*D studies but finds limited replication in independent cohorts.

Identification of key pathways and metabolic fingerprints of longevity in C. elegans

This study identifies shared metabolic pathways and signatures of longevity in C. elegans by integrating transcriptomics and metabolomics data from IIS and CR models.

K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity

The paper introduces a MapReduce-based k-mer clustering method to parallelize the Inchworm module of Trinity, reducing runtime and memory usage in transcriptome assembly.

Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava

The paper evaluates genomic prediction models for Cassava Brown Streak Disease using transcriptomics and GWAS data, finding only marginal improvements in prediction accuracy.

A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information

This paper introduces DTINet, a network integration method for predicting drug-target interactions and repositioning drugs, showing improved performance and validated novel COX inhibitor applications.

Acceleration Of Nucleotide Semi-Global Alignment With Adaptive Banded Dynamic Programming

The paper introduces an adaptive banded dynamic programming algorithm for faster nucleotide sequence alignment, achieving 5x speedup over BLAST+ while maintaining similar sensitivity.

MELD: Mixed Effects for Large Datasets

MELD combines mixed effects models with dimensionality reduction and permutation testing to efficiently analyze large neural datasets, improving sensitivity and computational efficiency.

Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing

This paper introduces a matrix factorization method that accounts for censored data in scRNA-Seq to improve clustering accuracy.

Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Suite2p processes two-photon calcium movies faster than real time on desktop workstations, roughly doubling curated cell yield over CNMF and recovering 13,451 neurons in one session.

Pan-genome and phylogeny of Bacillus cereus sensu lato

The paper characterizes the pan-genome of Bacillus cereus sensu lato using public genomes and performs phylogenetic and population genetic analyses, identifying genes linked to phenotypes and quantifying phylogenetic clustering of taxa with shared traits.

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

The paper introduces matrix-clustering, a tool that reduces redundancy and clusters transcription factor binding motifs from multiple sources, improving interpretation of motif collections.

Rainbowfish: A Succinct Colored de Bruijn Graph Representation

Grouping k-mer color sets into equivalence classes and entropy-compressing them shrinks colored de Bruijn graph color storage up to 20-fold versus VARI, keeping BOSS for topology.

LEAP: A Generalization Of The Landau-Vishkin Algorithm With Custom Gap Penalties

The paper introduces LEAP, a generalized algorithm for approximate string matching that outperforms existing methods in speed under various scoring schemes.

Comparison of Principal Component Analysis and t-Stochastic Neighbor Embedding with Distance Metric Modifications for Single-cell RNA-sequencing Data Analysis

This study compares PCA and t-SNE with distance metric modifications for visualizing and classifying single-cell RNA-seq data, finding that variable gene selection is critical for reliable classification.