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Publications

Sitetack: A deep learning model that improves PTM prediction by using known PTMs.

Gutierrez CS, Kassim AA, Gutierrez BD, Raines RT. Sitetack: A deep learning model that improves PTM prediction by using known PTMs. Bioinformatics (Oxford, England). 2024. doi:10.1093/bioinformatics/btae602

AOP Report: Development of an adverse outcome pathway for deposition of energy leading to bone loss.

Sandhu S, Keyworth M, Karimi-Jashni S, et al. AOP Report: Development of an adverse outcome pathway for deposition of energy leading to bone loss. Environmental and molecular mutagenesis. 2024. doi:10.1002/em.22631

mA modification of mutant huntingtin RNA promotes the biogenesis of pathogenic huntingtin transcripts.

Pupak A, Rodríguez-Navarro I, Sathasivam K, et al. mA modification of mutant huntingtin RNA promotes the biogenesis of pathogenic huntingtin transcripts. EMBO reports. 2024. doi:10.1038/s44319-024-00283-7

Model-directed generation of artificial CRISPR-Cas13a guide RNA sequences improves nucleic acid detection.

Mantena S, Pillai PP, Petros BA, et al. Model-directed generation of artificial CRISPR-Cas13a guide RNA sequences improves nucleic acid detection. Nature biotechnology. 2024. doi:10.1038/s41587-024-02422-w

A community effort to optimize sequence-based deep learning models of gene regulation.

Rafi AM, Nogina D, Penzar D, et al. A community effort to optimize sequence-based deep learning models of gene regulation. Nature biotechnology. 2024. doi:10.1038/s41587-024-02414-w

Single-shot 20-fold expansion microscopy.

Wang S, Shin TW, Yoder HB, et al. Single-shot 20-fold expansion microscopy. Nature methods. 2024. doi:10.1038/s41592-024-02454-9

Breaking the barriers: Overcoming cancer resistance by targeting the NLRP3 inflammasome.

Far NP, Varnousafaderani MH, Faghihkhorasani F, et al. Breaking the barriers: Overcoming cancer resistance by targeting the NLRP3 inflammasome. British journal of pharmacology. 2024. doi:10.1111/bph.17352

Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma.

Gallitto M, Zhang X, Santos GDL, et al. Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma. Neuro-oncology. 2024. doi:10.1093/neuonc/noae215

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.

Branck T, Hu Z, Nickols WA, et al. Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods. The ISME journal. 2024. doi:10.1093/ismejo/wrae201

Same Day Access to Folded Synthetic Proteins.

Callahan AJ, Rondon A, Reja RM, et al. Same Day Access to Folded Synthetic Proteins. Journal of the American Chemical Society. 2024. doi:10.1021/jacs.4c05121