Rising — Salient

EZSolver: Template-free prediction of polar enzymatic mechanisms via bidirectional flow matching and search

1d · Kuo, L.-H., Yang, J., Arnold, F. · biorxiv

method development benchmarked top 6% novel

Surfaced because: benchmarked against baselines.

💬 3 discussion

Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts

1d · Regimbeau, A., Tian, F., Smith, G., et al. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

💬 1 discussion

Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data

1d · Eder, B., Rigato, I., Dietrich, A., et al. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 3 discussion

Machine learning guided cell-free expression maps the biochemical landscape of carbonic anhydrase

2d · Lazar, J. T., Komp, E., Martinez, I., et al. · biorxiv

method development benchmarked top 9% novel

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 4 discussion

MicroGrowAgents: An Agentic AI System for Microbial Cultivation Engineering

1d · Naseem, S., Miller, M. A., Martinez-Gomez, N. C., et al. · biorxiv

method development top 3% novel

Surfaced because: matches the platform's topic region.

scJET: Full-gene Space Single-cell Expression Generation with Patch-based Transformer Modeling

1d · Liang, Q., Lyu, Q. R. · biorxiv

method development

Surfaced because: matches the platform's topic region.

💬 2 discussion

SpliSync: Genomic language model-driven splice site correction of long RNA sequencing reads

4d · Lui, W. W., Florea, L. D. · biorxiv

method development code benchmarked top 3% open

Surfaced because: unusual independent discussion, open code, benchmarked against baselines.

💬 4 discussion

A genetically encoded local learning rule enables physical learning in engineered bacteria

2d · Prakash, S., Varela, C., Walsh, M., et al. · biorxiv

method development top 5% novel

Surfaced because: unusual independent discussion.

💬 4 discussion

VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance

1d · Tsuda, Y., Tanizawa, Y., Vu, T. M. H., et al. · biorxiv

method development top 10% novel

Surfaced because: matches the platform's topic region.

Coding agents author interpretable single-cell embedding models from the literature

1d · Brunn, N., Krissmer, S. M., Frosch, M., et al. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 2 discussion

FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

1d · Zhu, J., Shi, Y., Bi, R., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

💬 1 discussion

CSGDA: A Cell State-Guided Graph Domain Adaptation Network for Single-Cell Drug Response Prediction

2d · Yan, F., Cao, X., Mao, F., et al. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 4 discussion

A deep-learning-informed prior and Bayesian model for differential AP-MS interactome analysis

1d · Seefelder, M. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 4 discussion

Calibration standards and sensitivity limits for fluorescence measurements with the Chi.Bio open-source bioreactor platform

1d · Sambruna, A., Tallarico, G., Cosentino Lagomarsino, M. · biorxiv

method development top 3% novel

Surfaced because: matches the platform's topic region.

BertST: BERT-based Spatial Domain Identification in Patient Data

1d · Nnadi, G. O. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

💬 3 discussion

Benchmarking biochemical networks generated by large language models

2d · Tewari, J., Dahl, B. W., Bates, B. A., et al. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

Models trained with noisy genomes extend bacterial phenotype prediction into deep time

8d · Koldaeva, A., Szollosi, G., Bagrova, O., et al. · biorxiv

method development top 1% discussedtop 1% novel

Surfaced because: unusual independent discussion.

💬 5 discussion 👁 1 reader

2d · Bohutskyi, P., DiMura, R., Johnson, Z., et al. · biorxiv

method development top 1% novel

Surfaced because: matches the platform's topic region.

💬 2 discussion

Emergence of Biological Structural Discovery in General-Purpose Language Models

1d · Wang, L. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

💬 1 discussion

Cross-architecture ensembling of DNA foundation models improves the precision and stability of chimera detection in long-read metagenomic bins

3d · MinSeo, K., Jae-Ho, S. · biorxiv

method development benchmarked top 5% novel

Surfaced because: benchmarked against baselines.

💬 3 discussion

PHI: A Galaxy-based workflow for reproducible prophage-host interaction analysis and standardized viral-genomics reporting

3d · Saraiva, J. P., Borim Correa, F., Bernt, M., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

👁 1 reader

MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities

9d · He, C., Zhang, J., Dahleh, M. A., et al. · biorxiv

method development top 1% discussed

Surfaced because: unusual independent discussion.

💬 6 discussion

SELECT-seq allows Pre-Sequencing Enrichment of SNP Edits in One-Pot Single-Cell Whole-Transcriptome Sequencing

2d · Iwama, S., Gitterman, D., Brendler-Spaeth, T., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

💬 3 discussion

EpiBinder: a multimodal framework for cell-type-specific prediction and interpretation of transcription factor binding

2d · Solozabal, R., Baichorov, A., Miodownik, I., et al. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 3 discussion

Biological Network Organization, Not Generic Graph Topology, Drives Graph-Based Gene Essentiality Prediction

1d · Rahimi, S., Bonner, S., Afzal, A., et al. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

💬 2 discussion

Integrating morphology and gene expression of neural cells in unpaired single-cell data using GeoAdvAE

10d · Du, J. T., Chartrand, T., Jayadev, S., et al. · biorxiv

method development code benchmarked top 9% noveltop 3% open

Surfaced because: unusual independent discussion, open code, benchmarked against baselines.

💬 5 discussion

Characterising AlphaFold 3s ability to predict T cellantigen specificity

1d · McMaster, B., Elmoselhy, A., Ilievski, I., et al. · biorxiv

method development benchmarked

Surfaced because: benchmarked against baselines.

Weak form Scientific Machine Learning for Systems Biology: A Tutorial on WENDy

1d · Heitzman-Breen, N., Lyons, R., Jain, P., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

💬 2 discussion

ThermoFusion: A Multimodal Deep Learning Framework for Generalizable Prediction of Enzyme Thermostability

3d · Wei, Y., Eberini, I., Meyer, F. · biorxiv

method development benchmarked

Surfaced because: unusual independent discussion, benchmarked against baselines.

💬 3 discussion 👁 1 reader

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

6d · Malovichko, Y. V., Bein, B., Gonzales-Irribarren, A., et al. · biorxiv

method development top 4% novel

Surfaced because: unusual independent discussion.

💬 4 discussion