software / tool

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome

A static web database proposes 55 305 construct suggestions for 5328 human secreted and cell-surface proteins, using AlphaFold pLDDT and PAE, with ortholog, paralog and BLAST cross-reactivity context.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

Development of py-mea-span for comprehensive analysis of multi-electrode array data and its application to LGI2-deficient neurons

Open-source Python package parses Axion spk files directly and matches NeuralMetric Tool outputs, then reveals burst and network burst hyperexcitability, without synchrony change, in LGI2-knockdown human iPSC neurons.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

In 72,644 matched bioRxiv preprint-publication pairs, LLM-extracted primary abstract claims were unchanged or minorly revised in about 90%; hedging shifted toward caution in 8.4% versus confidence in 4.2%.

CascadeMAP: Autonomous Closed-loop Optimization of Enzyme Cascades via Microfluidics, Machine Learning and Agentic AI

Unattended droplet-microfluidic Bayesian optimization of a glycerol detection cascade matched design of experiments (DoE) with one third of the conditions; a second cascade used DoE with Raman readout.

gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development

gene2fish arranges 53,595 Thisse in situ hybridization images of 8,263 zebrafish genes into a gene-by-stage grid, with anatomy-term search for validating scRNA-seq markers.

Integrating Genetic Domestication and Model-Guided Kill-Switch Engineering in a Non-Model Bacterial Therapeutic

Host-measured parts and inducible systems for Brucella melitensis ΔvjbR guided a modeled Cas9 kill-switch, which cut mouse liver bacterial burden by about 91% at 30 mg/kg doxycycline.

vardictcpp: A C++ reimplementation of VarDict variant caller

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

Reliable and Efficient Agentic Protein Design with Toolset Harnessing

Chaperone, a DataFrame-based framework and agent harness for protein design tools, cut tokens 86% and GPU-hours 64% while raising pass rate from 6% to 12%.

MetaDome 2027: a comprehensively updated resource for aggregating missense variant evidence across homologous human protein domains

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

A Sense of Direction: Detecting Natural Selection Across Non-Stationary Genomes

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

RePurpose: An LLM-Assisted, Source-Traceable Drug Repurposing Tool with Retrospective Validation on Clemastine in Multiple Sclerosis

Large-language-model-assisted repurposing web tool recovered clemastine for multiple sclerosis remyelination only through mechanism-worded, model-dependent queries; its rankings missed later evidence of harm in progressive disease.

Complex enzyme active site scaffolding by iteratively detuned catalytic guidance

CaGE alternates guided structure prediction with sequence redesign, fading guidance each cycle, so sequences recover complex catalytic sites unaided; designed nonheme-iron and PLP-dependent enzymes were active.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

A Framework for Comparing Mouse Neoantigen Immunogenicity

Experimental pMHC melting-temperature stability ranked in vivo CD8+ T cell responses of 25 mouse neoantigens better than affinity assays or nine in silico predictors.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

MtbAIM: AI/ML-guided endpoint-specific prediction of small-molecule activity across drug-susceptible and drug-resistant Mycobacterium tuberculosis

Tree models on RDKit/Morgan features predict M.tb activity and MIC endpoints for drug-susceptible and resistant isolates, slightly beating pretrained embeddings; released as a Colab tool.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Two Comparators May Be All We Need

Random forests on sequence and 2D chemistry pick the favored protein for a molecule, or the favored molecule for a protein, at 0.71 to 0.78 accuracy on unseen compounds.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome

LGTM couples a neural topic model with additive basis-function Gaussian processes, learning microbial co-abundance topics and how covariates relate to their trajectories in longitudinal gut microbiome data.

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.