Momi3 accelerates complex demographic model inference from large allele frequency spectra by up to an unspecified speedup, enabling analysis of multiple populations and samples.
- Open access
- 3 cites
Bioinformatics
Oxford University Press · Genomics & Bioinformatics · ISSN 1367-4803, 1460-2059
- Impact (2-yr)
- 6.3
- h-index
- 575
- Open access
- 82%
- Works
- 19.8K
- Papers this month
- 33
Rebuilt
Moved this week
Agentomics autonomously develops state-of-the-art biomedical machine learning models, outperforming existing agentic systems and matching human expertise on 11 of 20 datasets.
- Open access
- 2 cites
Collaborative graphical lasso improves multi-omics network reconstruction by integrating data across layers, recovering known interactions and revealing new biological connections.
- Open access
- 1 cites
WILDkCAT retrieves extensive enzyme turnover numbers for Escherichia coli and human models, covering a wide range of enzymes under specified conditions.
- Open access
MoESurv achieves a 4% higher C-index than existing models in predicting survival for seven rare cancer types using a zero-sample, transfer learning approach.
- 2 cites
ECLIPSE uncovers 120,985 dark proteins in the ESKAPE pathogens' proteomes, revealing conserved, structurally characterized targets for combating antimicrobial resistance.
- 1 cites
PCIM-DTA achieves state-of-the-art performance in drug-target affinity prediction under various cold-start scenarios, including cold-drug and cold-target conditions.
- 2 cites
NCFlow enables the placement of any non-canonical amino acid into proteins, outperforming existing methods in structure prediction for unseen ncAAs.
- 7 cites
Deep learning models trained on a novel microbiome-specific corpus achieved 96% F1-score for NER and 91% accuracy for entity linking, significantly outperforming traditional pipelines.
- 1 opens in JClub
- Open access
FIERCE accurately reconstructs cellular differentiation trajectories without prior assumptions, outperforming existing methods in complex systems.
- 1 opens in JClub
- Open access
Latest in Bioinformatics
Newest first · last 60 days
GROMTools enables nearly identical GReX predictions for mega-biobank cohorts with 100-fold faster computation and 33-fold less memory than existing tools.
Interaction-weighted network topology predicts absolute stability of natural and de novo proteins with high accuracy, outperforming existing models on mutational stability tests.
CSGDA achieves approximately 6 percentage points higher accuracy and AUPR than the previous best method in predicting single-cell drug responses across diverse biological conditions.
OrchAlign achieves state-of-the-art gene expression prediction by explicitly modeling fine-grained cross-modal and intra-modal relationships in DNA and epigenomic data.
AcrSeek achieves a significant increase in AUPRC from 0.017 to 0.355 under extreme class imbalance in anti-CRISPR protein detection.
PRISM-GEP uncovers overlapping gene-expression programs in single-cell RNA-seq data with performance comparable to specialized methods across 15 datasets.
scURL achieves superior clustering accuracy and robustness in single-cell multi-omics data, outperforming existing methods across ten datasets with improved biological relevance.
ShadoNet achieves improved cell detection and classification accuracy in Ki-67-stained histopathology images, enhancing tumor grading for pancreatic neuroendocrine tumors.
scLDM accurately predicts single-cell responses to perturbations with over 90% accuracy across diverse biological datasets, outperforming existing methods.
pileup-hi is an ultra-high-throughput, customizable pileup program that is up to 13 times faster than samtools mpileup for large sequencing datasets.
COCOA.jl enables scalable, high-performance analysis of biochemical network modules, handling genome-scale networks with multithreaded Julia implementation.
CircadiOmics is the largest comprehensive bioinformatics platform with 704 circadian omic datasets across 18 species, enabling advanced analysis of molecular rhythms.
DESTIN predicts genome-wide compound-protein interactions with high accuracy by utilizing 3D structural information, achieving strong results even for membrane proteins.
Nextstrain automates real-time phylogenetic analysis of 21 viruses and Mycobacterium tuberculosis, providing continually updated insights into pathogen evolution using open data.
DesignMaster achieves superior, constraint-aware PROTAC molecule generation by explicitly controlling linker length and physicochemical properties with a diffusion-based framework.
FAIDR-Desi enables non-technical design of IDRs by optimizing 127 sequence features, surpassing existing methods in complexity and functionality.
CrossMol achieves state-of-the-art performance on molecular tasks by effectively integrating 3D structures and SMILES modalities through cross-modal mask-predict pre-training.
massMatchR automates glycan identification and semi-quantitative analysis in MALDI-TOF mass spectrometry, enhancing efficiency for large-scale glycomics studies.
DeepGVS achieves 87.50% accuracy in bacterial virulence factor prediction by integrating coding sequences and protein structures, outperforming existing models by up to 6.30 percentage points.
GlycoViz improves glycopeptide validation accuracy by 30% and enhances site-specific analysis in mass spectrometry-based glycoproteomics.
HD-AIP achieves superior anti-inflammatory peptide prediction accuracy by integrating dual-stream, alignment-free features from language models and CT-Net, outperforming baseline models.
Fine-tuned protein language models can be interpreted to reveal biophysical principles of nanobody thermostability, with sparse autoencoders extracting meaningful features from embeddings.
CDVGL-PDA achieves high accuracy in predicting phosphorylation site-disease associations by integrating multi-modal biological data with contrastive dual-view graph learning.
Regulatory-prior-guided attention in scHPGT enhances biological structure preservation during unpaired RNA and ATAC data integration, outperforming existing methods across multiple benchmarks.
VCCV enhances drug-target interaction predictions by conservatively integrating perturbational transcriptomics, improving discrimination and reducing ambiguity across five models.
Deconvolution of chimeric MS/MS spectra enhances lipid identification accuracy in LC-MS/MS workflows, reducing false positives by over 50%.
VirPLM accurately predicts antigenic evolution of influenza A/H3N2 viruses, outperforming existing methods with high robustness across seasons and evaluations.
Convex optimization with Clorinn accurately isolates shared and unique genetic components across complex traits, recovering 200 latent factors from GWAS data.
Coolsecture enables streamlined, reproducible cross-species Hi-C contact map comparisons with high accuracy and diagnostic support.
- Open access
Perseus reduces false taxonomic assignments by up to 50% in long-read metagenomic data through lineage-aware confidence modeling.
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Journals this month
- bioRxiv5569
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- Environ Res483
- PNAS463
- Sci Adv439
- JAMA255
- Cell Rep210
- BMJ199
- Nat Commun177
- Environ Pollution170
- Lancet149
- Science138
- NEJM119
- Applied & Environ Microbio116
- J Exp Bot115
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- Nature104
Moving areas, week to 3 Oct 2026
- Single-cell and spatial transcriptomics10
- Artificial Intelligence in Healthcare and Education8
- CAR-T cell therapy research7
- Neuroinflammation and Neurodegeneration Mechanisms6
- Lung Cancer Treatments and Mutations5
- Diabetes Treatment and Management4
- Pancreatic and Hepatic Oncology Research4
- Photosynthetic Processes and Mechanisms4
- Genomics and Chromatin Dynamics4
- Gut microbiota and health4