Publications

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
Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study.
eLife. 2022-10-14; 11.
PMID: 36239699
Espinoza JL, Dupont CL
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.
BMC bioinformatics. 2022-10-12; 23.1: 419.
PMID: 36224545
Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB
A novel vaccine based on SARS-CoV-2 CD4+ and CD8+ T cell conserved epitopes from variants Alpha to Omicron.
Scientific reports. 2022-10-06; 12.1: 16731.
PMID: 36202985
Caetano AJ, Human Cell Atlas Oral and Craniofacial Bionetwork, Sequeira I, Byrd KM
A Roadmap for the Human Oral and Craniofacial Cell Atlas.
Journal of dental research. 2022-10-01; 101.11: 1274-1288.
PMID: 36154725
Le H, Peng B, Uy J, Carrillo D, Zhang Y, Aevermann BD, Scheuermann RH
Machine learning for cell type classification from single nucleus RNA sequencing data.
PloS one. 2022-09-23; 17.9: e0275070.
PMID: 36149937
Bianchi DM, Pelletier JF, Hutchison CA, Glass JI, Luthey-Schulten Z
Toward the Complete Functional Characterization of a Minimal Bacterial Proteome.
The journal of physical chemistry. B. 2022-09-15; 126.36: 6820-6834.
PMID: 36048731
McGrath ME, Xue Y, Dillen C, Oldfield L, Assad-Garcia N, Zaveri J, Singh N, Baracco L, Taylor LJ, Vashee S, Frieman MB
SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis.
Proceedings of the National Academy of Sciences of the United States of America. 2022-09-13; 119.37: e2204717119.
PMID: 36040867
Abkallo HM, Hemmink JD, Oduor B, Khazalwa EM, Svitek N, Assad-Garcia N, Khayumbi J, Fuchs W, Vashee S, Steinaa L
Co-Deletion of A238L and EP402R Genes from a Genotype IX African Swine Fever Virus Results in Partial Attenuation and Protection in Swine.
Viruses. 2022-09-13; 14.9:
PMID: 36146830
Haas D, Thamm AM, Sun J, Huang L, Sun L, Beaudoin GAW, Wise KS, Lerma-Ortiz C, Bruner SD, Breuer M, Luthey-Schulten Z, Lin J, Wilson MA, Brown G, Yakunin AF, Kurilyak I, Folz J, Fiehn O, Glass JI, Hanson AD, Henry CS, de Crécy-Lagard V
Metabolite Damage and Damage Control in a Minimal Genome.
mBio. 2022-08-30; 13.4: e0163022.
PMID: 35862786
Kirkland TN, Stevens DA, Hung CY, Beyhan S, Taylor JW, Shubitz LF, Duttke SH, Heidari A, Johnson RH, Deresinski SC, Lauer A, Fierer J
Coccidioides Species: A Review of Basic Research: 2022.
Journal of fungi (Basel, Switzerland). 2022-08-16; 8.8:
PMID: 36012847

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