Publications

Jha N, Kravitz J, West-Roberts J, Camargo AP, Roux S, Cornman AL*, Hwang Y*, “Gaia: A Context-Aware Sequence Search and Discovery Tool for Microbial Proteins”, Science Advances, https://doi.org/10.1126/sciadv.adv5109

Cornman AL*, West-Roberts J, Camargo AP, Roux Simon, Beracochea M, Mirdita M, Ovchinnikov S, Hwang Y* , “The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling”, International Conference on Learning Representations (ICLR) 2025, 2024.08. https://doi.org/10.1101/2024.08.14.607850

West-Roberts J, Kravitz J, Jha N, Cornman AL*, Hwang Y*, “Diverse Genomic Embedding Benchmark for Functional Evaluation Across the Tree of Life”, Biorxiv (in review), 2024.07. 10.602933, 2024. https://doi.org/10.1101/2024.07.10.602933

Hwang Y*,  Cornman AL, Kellogg E, Ovchinnikov S*, Girguis PR*, “Genomic language model predicts protein co-regulation and function”, Nature Communications 15, 2880. 2024. https://doi.org/10.1038/s41467-024-46947-9

Hwang Y*, Roux S, Coclet C, Krause SJE, Girguis PR*, Host-virus interactions cross-cutting microbial phyla and domains in a dense syntrophic microbial mat. Nature Microbiology. 2023. https://doi.org/10.1038/s41564-023-01347-5

Hwang Y*, Girguis PR*, “Differentiated evolutionary strategies of atlantic and pacific thaumarchaeal populations”. mSystems. 2022. Vol.7, No.3  https://doi.org/10.1128/msystems.01477-21

Hwang Y, Schulze-Makuch D*, Arens FL , Saenz JS, Adam PS, Sager C, Bornemann TLV, Zhao W, Zhang Y, Airo A, Schloter M and Probst AJ*, “Leave no stone unturned: Individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core” Microbiome. 2021. 9, 234 ; https://doi.org/10.1186/s40168-021-01177-9

Hwang Y*, Rahlff J, Schulze-Makuch D, Schloter M, Probst AJ*, “Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil” mSystems. 2021. Vol. 6, No. 3 https://doi.org/10.1128/mSystems.00385-21