Bioinformatics & computational biology
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- Beyond the Final Layer: Evaluating Single-Cell Foundation Model Representations for Molecular Prediction
- rhythmCI: an R package for rhythm detection using harmonic regression amplitude confidence intervals
- TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides
- APOD: reasoning-guided agentic population ordinary differential equation discovery for pharmacological digital twins
- GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem
- Autonomous AI agents discover reverse transcriptases with tandem repeat arrays
- Transcriptomic reconstruction of an interregional molecular connectome in schizophrenia
- Filling the Missing Puzzle: Integrating Interaction and Evolutionary Information to Enhance Protein Fitness Prediction in Inverse Folding
- RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology
- RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction
- phyloDS: phylogeny-aware differential splicing across species, beyond reference annotations
- PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN
- DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features
- Identification of new fucosyltransferase-8 inhibitors: An integrated biochemical, biophysical, and computational approach
- A graph-attentive GAN for rare-cell-aware single-cell RNA-seq data generation
- Sub-consensus haploid variant calling in long-read sequencing technology
- Codon-aware multi-scale feature fusion for metagenomic sequence classification
- Active transcriptome remodeling underlies antimony-induced drug tolerance in persister-like Leishmania parasites
- CausalOdyssey: Multi-Agent Local LLM Reasoning with Per-Patient Causal Structure for Rare Disease Retrieval
- Toxicity by Consortium Revisited: Structural Neighbors and Cross-Family Reach
- An Expert-Curated Benchmark for Frontier and Local LLMs Querying a Biomedical Knowledge Graph
- Understanding when and how knowledge graphs add value to EHR-based clinical prediction across Parkinson's disease, multiple sclerosis, and chronic pain
- Concurrent de novo inference of cell types and gene regulatory networks with NetMap
- CHORUS: A proteome-scale atlas of membrane interaction interfaces constructed using cross-protein language model embeddings from sequences alone
- Benchmarking interface confidence as a selection criterion for computational nanobody design against survivin's BIR-domain groove