Bioinformatics and Computational Biology articles for Canada

Time frame: 1 July 2025 - 30 June 2026

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Count: 157

Article ‘Count’ for Bioinformatics and Computational Biology.

Journal Count Share
1 0.13
Rapid Single‐Cell Proteomics Using Nanoconfined Enzyme Reactors on a Microscale Digital Microfluidics Platform 0.13
1 0.18
Plasma metabolites, dietary intakes, and breast cancer incidence: a prospective case-cohort study in NutriNet-Santé 0.18
5 2.28
A next-generation episignature for Kabuki syndrome enables fine mapping of the impact of KMT2D variants to inform precision medicine 0.44
Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases 0.09
Using the ancestral recombination graph to study the history of rare variants in founder populations 1.00
A scalable framework for identifying allelic series from summary statistics 0.15
Toward whole-genome inference of polygenic scores with fast and memory-efficient algorithms 0.60
12 5.68
BAGO: A Self-Optimizing Tool for LC-MS Gradient Design in Metabolomics 0.67
Distinguishing Ile/Leu Variant Ligands in the Immunopeptidome Using Hybrid EAD + CID Fragmentation (ExCID) 0.10
MS-MINT: An Open-Source Data Analysis Software for Large-Scale Metabolomics Studies 1.00
Best Practices in GC–MS and GC × GC–MS-Based Metabolomics and Volatile Analyses: An International Survey 0.13
SPIN: Inkjet-Driven Nanowell Workflow for Scalable and Sensitive Single-Cell Proteomics 1.00
Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum N-Glycoproteome 0.14
Signal Attrition in Whole Cell Cross-Linking Mass Spectrometry 1.00
An Analytical Strategy for Reliable Metabolome Analysis of Clinical Leftover Sera Using Timed Aliquoting 0.40
A Hit Prioritization Strategy for Compound Library Screening Using LiP-MS and Molecular Dynamics Simulations Applied to KRas G12D Inhibitors 0.38
Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset 0.17
Fast and Accurate Charge State Deconvolution of Protein Mass Spectra 0.20
General Screening and Multiple Dissociation Methods for Complementary LC–MS Analysis of Pesticides in Beverages: Potential and Pitfalls 0.50
1 1.00
Building a Bridge Between Ambient MS and LC‐MS by Non‐Exhaustive Microdesorption 1.00
1 0.90
A stem and progenitor cell–derived gene expression signature is prognostic for survival in myelofibrosis 0.90
1 0.05
Multiomic integration reveals tumoral heterogeneity of lipid dependence within lethal group 3 medulloblastoma 0.05
4 1.04
Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects 0.07
D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response 0.07
Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles 0.69
Four centuries of commercial whaling eroded 11,000 years of population stability in bowhead whales 0.21
1 0.09
Genome and Transcriptome-Wide Analyses Identify Multiple Candidate Genes and a Significant Polygenic Contribution in Bicuspid Aortic Valve. 0.09
1 0.61
Obesity- and Lipid-Related Traits May Causally Contribute to Sepsis-Associated Acute Kidney Injury. 0.61
6 3.16
The evolutionary transition from alga to parasite in the sister lineage of apicomplexans 1.00
Adaptive genomic divergence parallels migratory behavior in Atlantic bluefin tuna 0.08
Rapid and repeated evolution of myosin copy number in threespine stickleback 0.08
Paralog interference contributes to the preservation of genetic redundancy 0.95
Discovery of additional ancient genome duplications in yeasts 0.06
Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes 1.00
1 0.11
Gene Family Expansions Provide Molecular Flexibility Required for Context‐Dependent Species Interactions 0.11
1 0.71
Germline and somatic variants in DNMT3A and other clonal haematopoiesis of indeterminate potential genes contribute to pulmonary arterial hypertension 0.71
1 1.00
α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells 1.00
4 2.22
Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit 0.67
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway 0.55
Highly accurate assembly polishing with DeepPolisher 0.01
Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics 1.00
2 0.53
Multiplatform Molecular Testing as an Adjunct to Fine Needle Aspiration in the Evaluation of Pediatric Thyroid Nodules 0.13
Compartment-Specific Metabolic Alterations to Insulin Reflect Adiposity-Driven Variation and Predict Type 2 Diabetes 0.40
1 0.12
The cell-type-specific genetic architecture of chronic pain in brain and dorsal root ganglia 0.12
1 0.20
PALB2 and 53BP1 govern post-resection homologous recombination DNA repair 0.20
4 0.24
Circulating lipids are related to longitudinal changes of ATN biomarkers for Alzheimer’s disease 0.01
Genome-wide association study of delay discounting identifies 11 loci and reveals transdiagnostic associations across mental and physical health 0.03
Genome-wide association studies of lifetime and frequency of cannabis use in 131,895 individuals 0.17
Leveraging transdiagnostic genetic liability to psychiatric disorders to dissect clinical outcomes of anorexia nervosa 0.04
3 0.19
Mapping the genetic landscape across 14 psychiatric disorders 0.03
Novel assembly of a head–trunk interface in the sister group of jawed vertebrates 0.13
Ongoing genome doubling shapes evolvability and immunity in ovarian cancer 0.03
5 1.24
Scoring gene importance by interpreting single-cell foundation models 0.03
Zero-shot de novo peptide sequencing with open posttranslational modification discovery 0.59
TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects 0.50
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets 0.07
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation 0.04
1 0.04
CoCo-ST detects global and local biological structures in spatial transcriptomics datasets 0.04
1 0.75
Polyploidization in diatoms accelerates adaptation to warming 0.75
51 17.89
Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona 0.09
Population-specific heterogeneity in ontogeny of the broadly-conserved blood transcriptional program during the first week of life 0.30
Population-scale chemical response revealed by a barcoded yeast collection 0.06
Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes 0.06
Reticulate leaf venation in Pilea peperomioides is a Voronoi diagram 0.22
SAASI: Sampling Aware Ancestral State Inference 1.00
Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients 0.41
Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta) 0.06
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion 0.02
Experimental assessment of AI-based interactome mapping 0.18
Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function 0.19
The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis 0.20
Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling 0.04
A blueprint for local and distal invasion programs in glioblastoma 0.03
Genetic modifiers of -ε4-associated cognitive decline 0.03
FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models 1.00
Protein-protein interactions are a major source of epistasis in genetic interaction networks 1.00
Integrative functional genomics analysis identifies pleiotropic genes for vascular diseases 0.05
A multi-ancestry genetic reference for the Quebec population 0.96
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle 0.02
A comprehensive tandem repeat catalog of the human genome 1.00
Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics 0.18
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA 0.15
Prostate cancer cells converge to an inflammatory-like state upon metastatic dissemination 0.38
Chromosome-level assembly and analysis of three hydroxy fatty acid-producing Physaria species 0.08
SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbation 0.86
Recessive variants in the intergenic locus cause monogenic kidney disease responsive to anti-proteinuric treatment 0.11
Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology 0.09
scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization 0.50
Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes 1.00
Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation 0.04
Variation in surface protein expression leads to heterogeneous Trypanosoma cruzi populations during host cell infection 1.00
Click-linking: a cell-compatible protein crosslinking method based on click chemistry 1.00
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells 0.20
Computational design and evaluation of optimal bait sets for scalable proximity proteomics 1.00
Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels 0.04
The effect of type 2 diabetes genetic predisposition on non-cardiovascular comorbidities 0.02
Characterization of prevalent genetic variants in the Estonian Biobank body-mass index GWAS 0.01
Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus 0.01
TP53 variant clusters stratify phenotypic diversity in germline carriers and reveal an osteosarcoma-prone subgroup 0.67
Peripheral blood DNA methylation predicts the early onset of primary tumor in mutation carriers 0.64
A draft UAE-based Arab pangenome reference 0.01
Machine learning in Alzheimer’s disease genetics 0.00
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings 0.25
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases 0.14
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells 0.38
DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads 1.00
Shared genetic architecture of posttraumatic stress disorder with cardiovascular imaging, risk, and diagnoses 0.02
Prevalent chromosome fusion in Vibrio cholerae O1 0.22
LassoPred: a tool to predict the 3D structure of lasso peptides 0.14
Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell 0.83
12 2.03
Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation 0.14
Co-expression-based models improve eQTL predictions for transcriptome-wide association studies and highlight new schizophrenia-associated genes 0.01
Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression 0.84
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs 0.73
Empirically determined baseline masking strategies and other considerations for gene-level burden tests 0.04
Genomic, phenomic and geographic associations of leukocyte telomere length in the United States 0.06
A microenvironment-determined risk continuum refines subtyping in meningioma and reveals determinants of machine learning-based tumor classification 0.01
Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion 0.04
Genomic and transcriptomic analyses of aortic stenosis enhance therapeutic target discovery and disease prediction 0.08
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks 0.06
DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution 0.01
Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy 0.02
4 1.06
Circulating metabolites, genetics and lifestyle factors in relation to future risk of type 2 diabetes 0.01
Polygenic prediction of body mass index and obesity through the life course and across ancestries 0.01
Clinical utility of targeted RNA sequencing in cancer molecular diagnostics 1.00
Real-world deployment of a fine-tuned pathology foundation model for lung cancer biomarker detection 0.04
5 0.67
Orthrus: toward evolutionary and functional RNA foundation models 0.58
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads 0.01
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions 0.02
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model 0.02
The Platinum Pedigree: a long-read benchmark for genetic variants 0.03
1 0.04
The mitotic STAG3–cohesin complex shapes male germline nucleome 0.04
2 2.00
Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation 1.00
A cost-effective and scalable barcoded library construction method for deep mutational scanning studies 1.00
6 3.96
Tissue-specific transfer learning improves functional variant and therapeutic target discoveries in breast and prostate cancer 0.50
Topological stratification of continuous genetic variation in large biobanks 0.89
Genomic evidence for a-α heterothallic and α-α unisexual mating and recombination in an environmental Cryptococcus deneoformans population 0.67
Genome-wide association study provides novel insight into the genetic architecture of severe obesity 0.03
On the analysis of genetic association with long-read sequencing data 1.00
Detecting latent interaction effects when analyzing binary traits 0.88
1 0.87
<atl>Haploid Mutation Mapping Identifies a Homoeologous Non‐Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in scp iBrassica napus/i /scp</atl> 0.87
7 3.82
Canonical and variant PRC1 functionally converge on PRC2 targets to regulate transcriptional programs during mouse limb development 0.88
Genome-wide association mapping and targeted loss of function studies identify Shroom3 as a driver of hyperpolyploidy and ventricular dilation 0.11
Reconstructing ancient genomes from gene counts: A robust likelihood framework with sampling bias correction 1.00
Archaeogenetic insights into the demographic history of Late Neanderthals 0.05
Virulence hierarchies within the Mycobacterium tuberculosis complex 0.78
Exceedingly low genetic diversity in snow leopards due to persistently small population size 0.01
A trans-species cytoplasmic polymorphism is associated with seed shape and aridity across multiple species of sunflowers 1.00
1 1.00
Testing the scale dependence of plant community assembly processes using imaging spectroscopy 1.00
4 0.75
Rumen ciliates modulate methane emissions in ruminants 0.04
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis 0.05
FIGNL1 inhibits homologous recombination in BRCA2 deficient cells by dissociating RAD51 filaments 0.10
The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR 0.55
4 1.48
Humpback whale genomes reflect the increased efficiency of commercial whaling 0.25
Structural and epistatic regulatory variants cause hallmark white spotting in cattle 0.26
Pathogenic variants in MAEA disrupt DNA replication fork stability and are associated with developmental abnormalities in humans 0.90
A century of anthropogenic perturbations impact genomic signatures of the iconic migratory Atlantic cod 0.07

Numerical information only (in the tables above) is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International.