New papers on Bioinformatics
191 new papers on bioinformatics in the last 7 days, within Biology. These are the 50 Pipette rates most worth reading, with the main result in the authors' own words.
The best of the week
Simulation and Analysis of Solute Transport in Multi-Lymphangion Lymphatic Vessels
Overall, the proposed PBS framework provides a first quantitative basis for solute transport modeling in the LS and several concrete application scenarios for MC in this underexplored domain.
PreprintARCHER-LD: Rapid Long-Range Linkage Disequilibrium Calculations at Biobank Scale using GPU Acceleration
We present a novel approach that uses multi-GPU distributed computing to compute R2 for every variant pair in a dataset.
PreprintReal-world useSpeciesformer learns conserved cellular states for cross-species generative virtual cell modeling
Here we present Speciesformer, a cross-species generative single-cell foundation model that integrates evolutionary representation learning with virtual cell-state generation.
PreprintAn integrated platform for genome-wide functional analysis in Aspergillus niger through Ac/Ds insertion profiling and metabolic modeling
Here, we establish a unified experimental and computational platform in Aspergillus niger ATCC1015 by combining curated metabolic reconstruction, Ac/Ds transposon mutagenesis and machine-learning-based essentiality prediction.
PreprintWILSON - a pathology foundation model framework for patient-level analysis and diagnostic text generation
Here we present WILSON, a vision--language foundation model that represents whole-slide images and multi-slide cases as single multi-magnification composite images, trained on approximately 189k slides from Mayo Clinic spanning 42 organs and 829 diagnostic entities using pathology reports as supervision.
PreprintReal-world useARSA: an autonomous research scientist for target nomination in Alzheimer's disease and related dementias
To address this challenge, we present ARSA, an autonomous research scientist that transforms natural-language research interests and molecular data into prioritized, evidence-grounded target shortlists.
PreprintReal-world useGapDream: Active Synthetic Evidence Acquisition for Long-Tailed Medical Imaging
Across a multi-modality protocol spanning long-tailed chest radiography, dermoscopy, clinical dermatology, and histopathology, GAPDREAM reaches stronger held-out real-data performance with substantially fewer generated samples than random,class-balanced, uncertainty-only, and static targeted augmentation.
PreprintReal-world usePredictors Recover Most of the Metagenomic Signal for Antibiotic Resistance Gene Occurrence: A Cross-City Test of Geographic Transferability in Urban Wastewater
These findings demonstrate that freely available environmental reanalysis predictors - spanning meteorological, hydrological, radiative, geospatial, and temporal domains - recover 78% of the predictive signal for antibiotic resistance gene occurrence in urban wastewater, allowing scarce sequencing capacity to be directed to the catchments where it changes a decision.
PreprintReal-world useA dependency-free, streamable format and cross-language toolkit for scalable LC-MS feature detection: reading only what you need
We present Ionic (.ion), an open-source, compact, streamable binary format, and Quant{middle dot}ion, a processing toolkit built on the former.
PreprintReal-world useSurfGraphPro: Integrating Protein Language Models with Geometric Deep Learning On Coarse Protein Surfaces for Binding Site Prediction
To our knowledge, this represents the first approach to integrate protein language model embeddings with coarse geometric surface representations for binding site prediction, demonstrating that learned evolutionary features coupled with geometric transformers can replace traditional feature engineering without sacrificing performance.
PreprintBold claims, read criticallyStressNET: an adaptable deep-learning model for mechanical stress inference in tissues
Here we present StressNET, a Graph Neural Network (GNN) that infers intercellular mechanical stresses directly from tissue geometry, without assuming any underlying physical model.
PreprintBold claims, read criticallyA World Model of Molecular Organization Detects Cryptic Pockets from Apo Structure
Here we present a novel detector that reads cryptic pockets directly from a structural world-model latent representation of a single apo structure, without conformational sampling or external pocket finders.
PreprintReal-world useAn open imaging and AI resource enabling unbiased quantification of extrachromosomal DNA at scale
Here we establish an open resource for computational ecDNA imaging, integrating 2,986 native-resolution metaphase FISH image sets with manual annotations, standardized benchmarks and open-source quantification frameworks.
PreprintCMAC: A deep learning framework for absolute cardiomyocyte transcriptional age estimation
Together, these results establish CMAC as a quantitative, deep learning framework for assigning absolute transcriptional maturation age and quantifying deviations from normal cardiomyocyte development.
PreprintDe novo design of small cyclic peptide inhibitors from non-canonical amino acids by cofolding-guided search
Here, we present nCycle-Forge, a simulated annealing framework that designs cyclic peptide binders by iteratively substituting building blocks and scoring each proposal by cofolding with the target.
PreprintBold claims, read criticallyPepSpace: An Automated, Physics-Driven Directed Evolution Platform for the De Novo Design of Specific Peptide Binders and Condensate Modulators
Evaluated alongside deep-learning generative models across multiple targets, PepSpace-designed peptides achieve predicted interaction strengths up to two orders of magnitude greater than machine-learning designs, while reproducing experimentally observed binding hierarchies and revealing distinct binding modes.
PreprintBold claims, read criticallyNeural Learning as a Game Induced by Spike-Timing-Dependent Plasticity
Here, we develop a game-theoretic description for a canonical, convergent neural circuit with general STDP and postsynaptic-potential (PSP) kernels.
PreprintGravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq
We show that these relations form a statistic that is sufficient for such consumers, and we design a compact, seekable, content-authenticated archive that stores them while deferring every annotation-dependent decision to analysis time.
PreprintCode availablePRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments
Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments.
PreprintLanguage-Model-Based Detection of Genetic Editing in Bacteria
After training the model on our datasets, it is able to accurately detect genes artificially added to bacterial genomes due to their unnatural context.
PreprintReal-world useCorrelation-aware discovery of co-occurring mutational signatures in cancer
Here we present Cornet (CORrelated NMF ExTraction), a framework for mutational signature discovery that explicitly models co-occurring processes and jointly infers signatures and their correlation structure.
PreprintA unified intermediate-resolution framework for modeling biomolecular condensates at near-cellular complexity
Here, we present a unified, physics-based intermediate-resolution framework for efficient and quantitative simulation of biomolecular phase separation at near-cellular complexity.
PreprintOpenCRS: an open-source regulated human cardiorespiratory model with large-scale calibration and global sensitivity analysis at rest and during exercise
We present OpenCRS, an open-source Python cardiorespiratory model coupling closed-loop 0D lumped-parameter circulation with gas exchange and integrated autonomic and respiratory control.
PreprintRetracing the Process of Translation: Proteome-wide mapping of stable transcriptomic predictors of protein abundance in cancer cell lines
Our analysis revealed both globally predictive and context-specific gene features.
PreprintImproving racial fairness in brain age models using style-transfer synthesis
We present an approach to improve accuracy and reduce racial disparities using synthetic T1 images generated via style-transfer with SuperSynth, an open-source FreeSurfer tool that produces intensity harmonized isotropic images regardless of the input's contrast or resolution.
PreprintReal-world useDeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference
Here, we present DeepSCENIC, a deep learning framework that enables causal GRN inference by performing transfer learning from S2F models to single-cell multiome atlases.
PreprintComputational Framework for Identifying Ion Channel Mutation-Compensating Interventions
We present an automated pipeline for finding therapeutic interventions in channelopathies.
PreprintReal-world useGenerative Access to Make-on-Demand Chemical Space Enables Ultra-Large Virtual Screening
Here, we present REAL-SWIT, a generative ULVS framework that learns Enamine REAL Space as a synthesizable molecular distribution and couples this generator with a target-specific scoring model to enable docking-guided exploration of REAL Space at the level of complete molecule.
PreprintReal-world useExtracting interpretable single-cell metabolic states with graph-guided representation learning
Our results establish MeRN as a unified method for metabolic analysis of single-cell transcriptomes.
PreprintReal-world usePathEdit: Diagnostic-Preserving Counterfactual Medical Image Editing through State-Factorized Generative Intervention
We introduce PATHEDIT, a state-factorized counterfactual editing framework that decomposes an abdominal CT representation into pathology, anatomy, acquisition, and residual context before performing a clinically specified latent intervention.
PreprintReal-world usemiRstring: An RNA language model enables mature miRNA decoding and artificial small RNA design across species
Here, we present miRstring, a biogenesis-aware RNA language framework that decodes the four boundaries defining the miRNA/miRNA duplex.
PreprintBold claims, read criticallyReal-world useReaction-aware hypergraph learning of chemical representations with LARK
Here we introduce LARK, a unified framework for learning atom-molecule-reaction knowledge from chemical transformations.
PreprintEnabling predictive modeling of molecular connections between fermented foods and human inflammation through a paired dataset of cell-based models and multi-omics approaches
By generating sample-matched multi-omics data, our work aims to lay the scientific groundwork that will enable scientists to generate predictive models and testable hypotheses about the molecular mechanisms underlying the anti-inflammatory effects of fermented foods.
PreprintMINT infers the latent single-cell spatial transcriptome from paired histology
Here, we present MINT (Morphological Integrative Network for Transcriptomics), which combines this latent cellular organisation with sample-specific spatial measurements to infer tissue-wide, cell-resolved transcriptomes without an external single-cell reference.
PreprintFoundation-model-based multi-label phenotyping of combined hyperkinetic movement disorders
This frozen foundation-model backbone with light per-site calibration yields transferable, interpretable, conservative multi-label phenotyping of co-occurring hyperkinetic MDs across ages and from standardized to routine video, adding robustness on high-confidence, clinician-agreed labels.
PreprintBold claims, read criticallyReal-world useCode availableAn AI-ready compositional framework for mechanistic aging research and in silico intervention testing
We present hallsim, a JAX-native compositional simulation framework designed as the mechanistic substrate for agent-orchestrated research.
PreprintBold claims, read criticallystEDGE enables edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics
Here we present stEDGE, an edge-guided and interpretable framework for multiscale reconstruction of spatial domain hierarchies and transition-associated states in spatial transcriptomics.
PreprintAnewDDE: An Agentic Drug Discovery Engine for Biomolecular Interaction Modelling and Closed-Loop Design
We introduce AnewDDE, an agentic Drug Discovery Engine that connects these capabilities into a closed-loop system for biomolecular interaction modelling and design.
PreprintBold claims, read criticallyReal-world usefastACCORD enables ultrahigh-dimensional partial correlation modeling for multi-omic data integration
Together, these analyses establish fastACCORD as a practical framework for ultrahigh-dimensional multi-omic partial correlation modeling and demonstrate how joint modeling of transcriptomic and epigenomic measurements can refine the interpretation of gene co-expression networks.
PreprintEPIC: An open community challenge for sequence-based prediction of transcription initiation in five non-model metazoans
Here we introduce EPIC, the Eukaryotic Promoter and transcription Initiation prediction Challenge.
PreprintPutative Cyclospora cayetanensis detection in wastewater metagenomic datasets
Applying that threshold to 2,333 public runs from BioProject PRJNA1247874 yielded putative C. cayetanensis reads in 81 runs, or 3.5%, and in 24 of the 30 longitudinally sampled sewersheds.
PreprintReal-world useTraffickome infers directed, compartment-resolved membrane trafficking from proteomic data
We present Traffickome, a deterministic method organizing 754 trafficking proteins into 11 directed transitions across seven compartments and 1,837 signaling proteins across 22 pathways.
PreprintRapid classification of β-lactamase activity through AI-based structure prediction and electric field analysis
Here, we propose a computational protocol for rapid estimation of {beta}-lactamase activity towards carbapenem antibiotics from sequence alone.
PreprintReal-world useAgentic campaign control for high-throughput de novo binder design
Here, we introduce Target-adaptive Rescue-Explore-eXploit (T-REX), an agentic protein binder design framework that orchestrates multiple state-of-the-art protein generative models and structure evaluators.
PreprintANIMA: predicting protein-protein interactions across species
Results: We present ANIMA (Artificial Neural Interaction Model for Animals), an AI supported cross-species PPI prediction model trained on popular species to predict PPIs in under-researched species.
PreprintCoevolutionary mining of prokaryotic non-coding elements with a genome language model
Here, we introduce Minerva, a framework for coevolutionary mining that uses genome language models to predict local interactions directly from sequence as two-dimensional maps.
PreprintBold claims, read criticallyAn interpretable open platform for sequence-based antibody developability prediction
We present DELPHI, open software for training developability predictors from labelled antibody assay data, together with ready-to-run, retrainable models.
PreprintReal-world useCell-Lens: Advancing LLM Reasoning at Single-Cell Resolution
These results show that a better cell representation can improve single-cell reasoning without retraining the model.
PreprintCode availableMeasurement reliability bounds functional benchmarks and relocates where variant effect prediction fails
Territory-resolved benchmarks should report a per-stratum reliability estimate, or state that the assay permits none.
PreprintCardioChrom Reconstructs the Human Cardiac Virtual Epigenome from Single-Nucleus Transcriptomes
Conclusions: CardioChrom extends RNA-only human heart failure cohorts toward cell-type-resolved virtual epigenomic and regulatory analysis while distinguishing predictions from direct measurements.
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