Rising — Salient

HESTIA: Scalable Multimodal Integration of Histology and High-Resolution Spatial Transcriptomics for Robust Spatial Domain Identification

1d · Zhong, Z., Zhu, X., Guo, J., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

A self-supervised DNA foundation model with collapse-resistant multimodal fusion

1d · Chen, Y. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Accurate and efficient prediction of protein conformations with ProtMonomer

1d · Si, Y., Zhang, S., Chen, L. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Universal physical principles of protein structural genesis emerge in language-model representation space

1d · Chuanyang, L., Liu, J., Qiu, X., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Topologically-based parameter inference for agent-based model selection from spatiotemporal cellular data

3d · Wenzel, A. R., Haughey, P. M., Nguyen, K. C., et al. · biorxiv

method development code benchmarked top 10% noveltop 1% open

Surfaced because: open code, benchmarked against baselines.

S2F-Agent: Harnessing sequence-to-function models for verifiable genome interpretation

1d · Li, J., Qin, T., Li, J. G., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

scPyviewer: a Python-native interactive viewer from AnnData single-cell data

1d · Xuan, H., Huang, Y., Bian, J., et al. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.

Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm

1d · Su, X., Peng, Y., Yang, X., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Vipsania: Unsupervised Deep Gene Finding

2d · Krieg, R., Becker, F., Saenko, S., et al. · biorxiv

method development code top 2% open

Surfaced because: open code.

LRSPAT: A low-rank framework for spatial omics statistics

1d · Frost, H. R. · biorxiv

method development

Surfaced because: matches the platform's topic region.

OmniSplice: detection of non-canonical splicing events from RNA-seq

1d · Lannes, R., Li, R. Y., Fingerhut, J. M., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Chemi-Proteome Language Attention Network Empowers Fragment-Based Ligand Interactome and Binding Sites Discovery with Evidence

2d · Liao, B., He, J., zhao, M., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

RegimeFormer: A Large Protein Model of Global Perturbation Regimes

2d · Ma, S., Chai, Y., Wu, Y., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

3d · Potter, L. A., Trull, A., Kumar, N., et al. · biorxiv

method development top 3% novel

Surfaced because: matches the platform's topic region.

PhageTransformer - scalable and accurate host assignments for bacteriophages

2d · Siemers, M., Lopez, J. L., Dutilh, B. E. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

FlexiTAC enables controllable PROTAC linker generation across diverse structural settings using a Bayesian flow network with posterior guidance

2d · Li, Y., Zhao, Y., Zhou, L., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Dynamic Hierarchical Interleaved Bloom Filter: An Updatable Index for Large-Scale Fast Sequence Search

2d · Seiler, E., Willemsen, M., Piro, V. C., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

OmniScore: Universal Scoring of Diverse Biomolecular Complexes via Equivariant Geometry-Aware Discrete Representation Learning

3d · Bui, T.-C., Lee, J., Ko, J. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

PMPNN-DDG: an accurate machine learning-based {triangleup}{triangleup}G prediction pipeline trained on a novel interpretable feature set extracted from ProteinMPNN

5d · Jani, R., Ahmed, S. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.

OmicsFM brings proteomics into the foundation model era

4d · Heyndrickx, S., Gabriels, R., Ramadasan, H., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

A pretrained unified model enables cellular functional profile prediction and multi-objective virtual drug screening

4d · Chen, R., Huang, L., Qiao, Y., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Gene expression inference from cell-free DNA using uncertainty-aware deep learning

4d · Patton, R. D., McDeed, A. P., Netzley, A., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

SPC-Clean: A napari Plugin for Reducing Speckle and Isolated Pixel Noise in Fluorescence Microscopy Images

5d · Alirezazadeh, P., Kirsch, E. M., Tian, Y., et al. · biorxiv

method development top 2% novel

Surfaced because: matches the platform's topic region.

Evaluating the performance of splicing predictors on thousands of synthetic gene variants

5d · Bellido Molias, F., Kudla, G. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

BatchRefiner: fast, significant improvement in batch integration of single-cell embeddings with ensemble refinement

6d · Schäffer, D. E., Kang, H., Aksu, E. D., et al. · biorxiv

method development benchmarked top 1% noveltop 2% open

Surfaced because: benchmarked against baselines.

Label Noise Limits TCR-pMHC Specificity Prediction: Improved Performance Through AlphaFold3-Based Structural Modeling and Data Denoising

4d · Ballesteros-Cuartero, P., Lund, J., Nielsen, M. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Quantifying the Rearrangement Complexity of Pangenomes

3d · Bohnenkaemper, L., Stoye, J. · biorxiv

method development

Surfaced because: matches the platform's topic region.

scDisent: regulatory-aware disentangled representation learning for multi-omic single-cell analysis

6d · Xi, G. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.

G2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching

4d · Birk, S., Theis, F. J., Lotfollahi, M. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

AntiSite: Modality Dropout Enables Antibody Paratope Prediction With or Without Structure From a Single Model

5d · Papadopoulos, A. M., Alvarez, F., Daras, P. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.