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Publications

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance.

Phan T, Ribeiro RM, Edelstein GE, et al. Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance. bioRxiv : the preprint server for biology. 2024. doi:10.1101/2024.09.13.613000

Socio-medical Factors Associated with Neurodevelopmental Disorders on the Kenyan Coast.

Kipkemoi P, Savage JE, Gona J, et al. Socio-medical Factors Associated with Neurodevelopmental Disorders on the Kenyan Coast. medRxiv : the preprint server for health sciences. 2024. doi:10.1101/2024.09.17.24313844

Cryo-PRO facilitates whole blood cryopreservation for single-cell RNA sequencing of immune cells from clinical samples.

DuBois AK, Ankomah PO, Campbell AC, et al. Cryo-PRO facilitates whole blood cryopreservation for single-cell RNA sequencing of immune cells from clinical samples. medRxiv : the preprint server for health sciences. 2024. doi:10.1101/2024.09.18.24313760

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

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

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