Curated papers with reproducible code and real impact
Auto-updated from arXiv & bioRxiv · Last sync: 5/30/2026
Zambaldi et al.
AlphaProteo generates novel protein binders with state-of-the-art binding affinities across diverse targets.
Hayes et al.
A multimodal generative language model that reasons over the sequence, structure, and function of proteins.
Abramson et al.
AlphaFold 3 can predict the joint structure of complexes including proteins, nucleic acids, small molecules, ions, and modified residues.
Watson et al.
A structure denoising diffusion probabilistic model for protein backbone generation.
Corso et al.
A diffusion generative model over the non-Euclidean manifold of ligand poses for molecular docking.
Joy, M. N. H., Hasan, M. K. E., Hossan, M. S., Sourov, M. M. H., Shahriar, S., Hasan, M. F., Dutta, A. K., Haque, M. E.
Cholera, caused by Vibrio cholerae, continues to pose a serious global public health challenge, with its impact worsened by rising antibiotic resistance associated with bacterial biofilm formation....
Mendez-Riosalido, V., Gohl, P., Bota, P. M., Kramer, E., Meseguer, A., Gallego, O., Fernandez-Fuentes, N., Oliva, B.
We present ModCRE-NN, a machine-learning framework and server for predicting transcription-factor (TF) DNA-binding motifs through the integration of structural and evolutionary information. The met...
Wang, J. R., Li, H.
We introduce a reimplementation of the widely used mapping tool minimap2 in Rust called rammap. We demonstrate perfect concordance with minimap2, enabling its backwards compatibility as a drop-in r...
Choi, M., Bauermeister, S., Kim, D.-G.
Alzheimer's disease (AD) progression involves systemic network transitions. To capture these using ROSMAP bulk RNA-seq (n=624), we focused on the geometry of the covariance structure, performing a ...
Maynard, T. M.
Background The emergence of accessible spatial transcriptomic platforms such as 10x Genomics Visium HD and Xenium has created demand for analysis tools that can handle the complexity and scale of s...
Long, M., Hu, T., Sountoulidis, A., Samakovlis, C., Nilsson, M.
The spatial organization of tissues emerges from cell interactions across multiple scales, yet current spatial omics analysis tools often emphasize local neighborhoods and may not summarize broader...
Alibutud, R. F., Kumar, S.
Phylogenetic inference is a common task in molecular and evolutionary biology and has conventionally required a multiple sequence alignment (MSA), a statistical model of amino acid substitutions, a...
Griebel, B. T., Ma, S.
We present MetworkPy, a python package for investigating in silico genome-scale models of metabolism (GSMM). By using novel graph- and information-theoretic methods to explore the feasible reaction...
Meimetis, N., Magliacane, S., Hoang, T. N., Lauffenburger, D. A.
Observations from pre-clinical models rarely generalize to human patients, leading to many failures in clinical trials. Most existing methods cannot handle domains with non-overlapping features and...
Palem, R. R., Chen, H., Yue, Z.
Background: The biomedical literature is expanding at an unprecedented rate, with over 4,000 new articles indexed on PubMed each day. Clinicians and researchers frequently lack the time to review t...
Goodall-Halliwell, I., DeKraker, J., Bautin, P., Mendelson, D., Cabalo, D. G., Sahlas, E., Ngo, A., Xie, K., Lam, J., Smith, M., Hwang, Y., Vavassori, L., Milano, P., Chen, J., Dascal, A., Ding, R., Zhou, G., Naish, M., Mo, J., Fadaie, F., Cruces, R. R., Bernhardt, B. C.
MICAFlow is a fully automated MRI preprocessing pipeline designed to translate advanced neuroimaging workflows from research into routine clinical practice. The pipeline emphasizes speed, robustnes...
Shaw, J., Riisgaard-Jensen, M., Andersen, K. S., Kirkegaard, R., Dueholm, M. K. D., Li, H.
Long-read amplicon sequencing can profile longer sequences compared to short reads, but recovering amplicon sequence variants (ASVs) is a challenge for long, noisy reads. We present savont, an algo...
Vlachas, P., Nonchev, K., Koelzer, V., Ratsch, G.
Spatial transcriptomics couples hematoxylin and eosin (H&E) tissue morphology with spatially resolved gene expression (GE). However, generative models that exploit this coupling to synthesize tissu...
Loh, Y. H. E., Lieber, M. R., Hsieh, C.-L., Manojlovic, Z.
In contrast to simple deletions and simple insertions, most complex indels involve both deletions and insertions, often with base changes within a few nucleotides of the indel's left and right boun...
De Agro, M., Caradonna, D., Pande, A., Falotico, E., Sumner-Rooney, L.
The measurement of visual fields in arachnology has a long-standing history. Given the wide variety of eye positions, orientation and structure, the topic is fundamental for studies of taxonomy, ev...
Ge, Z., Liu, S., Dou, W.
Background and Objective: Normative modeling is a key tool for understanding brain alterations in neurodegenerative diseases, such as cerebellar-type multiple system atrophy. However, existing meth...
Nabijiang, A., Shahriyari, L.
Cell-type extraction is an important task in biomedical text mining because biomedical literature contains evidence about cell types and cell-type-related biological interactions that supports stud...
Deane, C., Cagiada, M., Qurat-ul-ain, Q., Whye Teh, Y., Outeiral Rubiera, C.
Accurate in silico prediction of protein properties, functional fitness, and mutational effects remains a central challenge in protein engineering and therapeutic design. While Protein Language Mod...
Xu, Z., Wang, W., Li, Y., Zhang, Y., Chen, J., Du, W., Yang, T.
Background Human organogenesis is orchestrated by precise spatiotemporal gene expression. Mapping these dynamic processes requires transcriptomic data that preserve native anatomical context across...
Van Riper, J., Corsaro, B. J., Pillon, M. C.
The central challenge of the post-AlphaFold era is the "functional gap". Despite having structure predictions for nearly every human protein, we remain unable to systematically distinguish residues...