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PixelDeck organizes and manages large biomedical image and video libraries with duplicate detection and metadata extraction, enabling efficient curation and preparation for downstream analysis.

ProtAff predicts protein-protein binding affinity using sequence data, outperforming existing methods on an EGFR benchmark but underperforming structural methods in cross-target discrimination.

The paper identifies four nucleosomal DNA classes and shows their association with TF binding, revealing DNA-encoded codes for nucleosome positioning and interaction modes.

RNARL is a reinforcement learning framework for RNA codon design that generates high-performance sequences across multiple species and RNA types.

The paper evaluates genomic language models as DNA compressors, finds smaller vocabularies perform better, and maps information content across the human genome.

This paper introduces a mathematical framework to analyze allostery in proteins, showing how mutations affect pathway correlations and communication through intermediary residues.

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

This study investigates the pervasiveness and variation of genomic signatures across eukaryotic genomes using k-mer-based FCGR analysis, identifying localized exceptions and developing tools for improved taxonomic classification.

The paper develops FuncZymeDB-BAHD and FuncPred tools to systematically annotate BAHD acyltransferase functions in plants using LLMs and phylogenomics, achieving high prediction accuracy and expanding existing databases.

Phi-Space ST identifies continuous cell states in spatial transcriptomics data using scRNA-seq references, revealing niche-specific cell types and patterns in cancer tissues.

The paper identifies phosphopyruvate hydratase (PPH) as a drug target in kinetoplastid parasites through proteome mining, structural modeling, and experimental validation, and identifies hinokinin as a promising antiparasitic compound.

The paper identifies BAN as a novel HIV-1 protease inhibitor with binding affinity comparable to 3TL but through a distinct mechanism involving stronger polar interactions and increased protein flexibility.

PertFlow jointly predicts gene expression and cellular morphology from drug perturbations, achieving high correlation and expert-rated image similarity.

ProMiSE evaluates protein multi-state prediction models using a curated dataset of biological conformational changes, revealing limitations in capturing functionally relevant dynamics.

The paper shows that protein language models can exploit taxonomic information rather than true interaction features in PPI datasets, leading to inflated performance.

This paper introduces ISC, a framework to evaluate cell type annotations in single-cell RNA-seq without ground truth, revealing reproducibility gaps and enabling tool benchmarking.

The paper investigates human transcripts enriched in PTMD codons and finds they have longer half-lives, suggesting PTMD selectively destabilizes otherwise stable mRNAs.

This paper introduces STAMO, a spatially aware integration method for unpaired spatial multi-omics data, showing improved alignment and domain detection compared to existing methods.

Amylo-Pipe integrates mechanistic and kinetic prediction tools for protein and peptide aggregation, offering a web interface for assessing aggregation behavior and supporting protein engineering.

GHIST+ reconstructs tissue-wide molecular maps from H&E histology, enabling cohort-scale molecular reconstruction from sparse spatial transcriptomic data.