Publications

Environmental microbiology. 2022-11-01; 24.11: 5408-5424.
Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations
Koester I, Quinlan ZA, Nothias LF, White ME, Rabines A, Petras D, Brunson JK, Dührkop K, Ludwig M, Böcker S, Azam F, Allen AE, Dorrestein PC, Aluwihare LI
PMID: 36222155
PNAS nexus. 2022-11-01; 1.5: pgac239.
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries
Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL
PMID: 36712365
mSystems. 2022-10-26; 7.5: e0049122.
Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples
Baker JL
PMID: 35993719
Frontiers in bioinformatics. 2022-10-24; 2.1020189.
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation
Wallace ZS, Davis J, Niewiadomska AM, Olson RD, Shukla M, Stevens R, Zhang Y, Zmasek CM, Scheuermann RH
PMID: 36353215
Nature communications. 2022-10-21; 13.1: 6275.
Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model
Rickner HD, Jiang L, Hong R, O'Neill NK, Mojica CA, Snyder BJ, Zhang L, Shaw D, Medalla M, Wolozin B, Cheng CS
PMID: 36271092
Bioinformatics (Oxford, England). 2022-10-14; 38.20: 4735-4744.
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference
Zhang Y, Sun H, Mandava A, Aevermann BD, Kollmann TR, Scheuermann RH, Qiu X, Qian Y
PMID: 36018232
eLife. 2022-10-14; 11.
Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study
Hu Z, van der Ploeg K, Chakraborty S, Arunachalam PS, Mori DAM, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Holubar M, Subramanian A, Khosla C, Maldonado Y, Hedlin H, de la Parte L, Press K, Ty M, Tan GS, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte AJ, Singh U, Pulendran B, Wang TT, Jagannathan P
PMID: 36239699
BMC bioinformatics. 2022-10-12; 23.1: 419.
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Espinoza JL, Dupont CL
PMID: 36224545
Scientific reports. 2022-10-06; 12.1: 16731.
A novel vaccine based on SARS-CoV-2 CD4+ and CD8+ T cell conserved epitopes from variants Alpha to Omicron
Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB
PMID: 36202985
Journal of dental research. 2022-10-01; 101.11: 1274-1288.
A Roadmap for the Human Oral and Craniofacial Cell Atlas
Caetano AJ, Human Cell Atlas Oral and Craniofacial Bionetwork, Sequeira I, Byrd KM
PMID: 36154725

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