Curated papers with reproducible code and real impact
Auto-updated from arXiv & bioRxiv · Last sync: 3/16/2026
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.
Lee, H., Segae, V. S., Garcia-Abadillo, J., de Oliveira Bussiman, F., Trujano Chavez, M. Z., Hidalgo, J., Jarquin, D.
Genotype-by-environment interaction (GEI) has been studied to identify environment-stable/favorable genotypes. The GEI simulation could help refine the inference by incorporating tangible factors s...
Flanagan, K., Xu, S., Yeo, G. W.
Motivation: Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess ...
Pose-Lagoa, I., Urda-Garcia, B., Olvera, N., Sanchez-Valle, J., Faner, R., Valencia, A., Carbonell-Caballero, J.
Complex and clinically heterogeneous diseases pose significant challenges for gene prioritisation and patient stratification, as relevant genes often show weak or context-specific signals and trans...
Stroh, D., Zilio, N., Pabba, M. K., Roukos, V., Cardoso, M. C., Ulrich, H. D., Zarnack, K.
During S phase, the genome is replicated in a tightly regulated spatiotemporal order described as DNA replication timing (RT). Discontinuous lagging-strand synthesis produces Okazaki fragments whos...
Hsu, S.-Y., Ryu, Y. J., Nepiyushchikh, Z., Jeong, K., Yu, J., Dixon, J. B.
Lymphedema, a chronic and incurable condition with limited therapeutic options, has limited options to quantitatively assess functional changes during its development; as a result, a deeper underst...
Yin, Z., Wang, S., Moraros, J.
Background: Scalp electroencephalography (EEG) based seizure prediction plays a critical role in improving the quality of life for patients with drug-resistant epilepsy, offering the potential for ...
Shantong, H., Zhang, G., Wang, J., Zhu, L., Menghan, J., Song, J., Webb, G., Pan, T., Yee Koh, H., Wang, Z., Zhang, Y.
The acid activity of enzymes, characterized by the minimum pH at which enzymes remain active (pHmin), is crucial for industrial applications in acidic environments. However, the rational design of ...
De la Rosa Santamaria, R., Ruiz Perez, D. G., Lopez Rosas, I., Cadena Villegas, S., Rodas Trejo, J., Izquierdo Reyes, F., Vargas Villamil, L. M.
The objective of this research was to characterize the proteome of the Apis mellifera royal pupae to evaluate its potential as a nutraceutical and functional food. Six pupal instars (E1 to E6) were...
Liu, X., Zheng, H., Halmos, P., Gold, J., Storrs, E., Ding, L., Raphael, B.
Recent efforts to build comprehensive tissue and tumor atlases leverage diverse spatial technologies to measure transcriptomic, proteomic, epigenetic, and other modalities with hundreds to thousand...
Shtengel, D., Shtengel, G., Xu, C. S., Hess, H. F.
Electron Microscopy (EM) is widely used in many scientific fields, particularly in life sciences, offering high-resolution information on the ultrastructure of biological organisms. Accurate charac...
Koeksal, R., Fritz, A., Kumar, A., Schmidts, M., Tran, V. D., Backofen, R.
Identifying genes associated with human diseases is essential for effective diagnosis and treatment. Experimentally identifying disease-causing genes is time-consuming and expensive. Computational ...
Weng, Y., Moyne, O., Walker, C., Haddad, E., Lieng, C., Chin, L., Rahman, G., McDonald, D., Knight, R., Zengler, K.
Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of th...
Xu, X., Feng, C., Zha, C., He, W., He, M., Xiao, B., Gao, X.
Computational protein design is often constrained by slow, complex, inaccessible, and highly sophiscated and expert-dependent workflows that hinder its transferrability and generalization power for...
Liu, T., Lv, J., Wang, S., Liu, Y., Chen, Y., Li, J., Wang, L., Shi, Y., Li, N., Ding, W., Piao, Y.
Post-transcriptional processing has a crucial yet largely unresolved dynamic change and role during the malignant progression of ovarian cancer, especially due to the limited read length of short-r...
Smith, J. J., Wang, X., McPheeters, M., Widjaja-Adhi, M. A., Littleton, S., Saban, D., Golczak, M., Jenkins, M. W.
Spatial transcriptomics enables high-resolution mapping of gene expression in intact tissues but remains challenging due to complex computational workflows that limit accessibility and reproducibil...
Wang, F., Wang, C., Teng, J., Fang, L., Ionita-Laza, I.
Production livestock provide a natural system for studying gene regulation under physiologically demanding conditions shaped by rapid growth, environmental exposure, and immune challenges. Using fa...
Amineni, V. P. S., Cedden, D.
RNA interference (RNAi) has emerged as an eco-friendly approach to pest management and relies on the processing of exogenous double-stranded RNA (dsRNA). RNAi-based pest management is highly effect...
Paz, I., Ley, R. E., Enav, H.
Background: Microbiomes contain multiple conspecific strains whose genomic differences arise from both single nucleotide variants (SNVs) and structural variation (insertions, deletions, recombinati...
Khabbaz, R., Mateos, J., Antonini, M., Kas Hanna, S.
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS)...
Lyu, Y., Huang, X., Lin, S. H., Li, Z.
This paper introduces SuperSurv, a user-friendly R package for building, evaluating, and interpreting ensemble models for right-censored survival data. Although many survival modeling methods are a...