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• Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction. PeerJ 14, e20706 (2026).
• Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2. Current protocols 6, e70307 (2026).
• Machine learning reveals sequence and methylation determinants of SaCas9-PAM interactions in bacteria. Nucleic acids research 54, (2026).
• Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2. NAR genomics and bioinformatics 7, lqaf108 (2025).
• Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization. Genome biology 26, 139 (2025).
• The impact of progressive chronic kidney disease on hepatic drug metabolism. Drug metabolism and disposition: the biological fate of chemicals 53, 100085 (2025).
• Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance. Animal microbiome 7, 11 (2025).
• Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies. Microbiome 12, 271 (2024).
• Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis. bioRxiv : the preprint server for biology (2024).
• De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials. ACS synthetic biology 12, 3578-3590 (2023).
• Multi-site microbiota alteration is a hallmark of kidney stone formation. Microbiome 11, 263 (2023).
• A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets. Nature communications 14, 5514 (2023).
• Metabolically-targeted dCas9 expression in bacteria. Nucleic acids research 51, 982-996 (2023).
• Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi. Biodesign research 2022, 9802168 (2022).
• Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10, e13607 (2022).
• Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics. Scientific reports 12, 7010 (2022).
• Preen gland microbiota of songbirds differ across populations but not sexes. The Journal of animal ecology 90, 2202-2212 (2021).
• Editorial: Compositional data analysis and related methods applied to genomics-a first special issue from NAR Genomics and Bioinformatics. NAR genomics and bioinformatics 2, lqaa103 (2020).
• Pannexin 1 mutation found in melanoma tumor reduces phosphorylation, glycosylation, and trafficking of the channel-forming protein. Molecular biology of the cell 32, 376-390 (2021).