Publications

Master’s Thesis

Understanding the roles of interkingdom microbial interactions, microbial traits, and host factors in the assembly of plant microbiomes. (2021) PDF

Papers

• Bian Z, Wilhoit K, Liber JA, Peer A, Xu Z, Magwene PM, Sun S, Heitman J. (2025) Meiosis-specific genes play roles in ploidy reduction in Cryptococcus neoformans titan cells. bioRxiv. 2025.09. 16.676405

• Guo YS, Liber JA, Morrell-Falvey JL, Bonito G, Retterer ST. (2024) Monitoring the impact of confinement on hyphal penetration and fungal behavior. PloS one. 19(12): e0312855

• Longley R, Robinson A, Liber JA, Bryson AE, Morales, DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. (2023) Comparative Genomics of Mollicutes-related Endobacteria Supports a Late Invasion to Fungi. Communications Biology. 6(1): 1-13.

• Sohrabi R, Paasch BC, Liber JA, He SY (2023) Phyllosphere Microbiome. Annual Review of Plant Biology. 74(1).

• Vande Pol N, Liber JA, Yocca A, Matlock J, Edger P, Bonito G. (2022) Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. PloS one. 17(4): e0261908. PDF

• Liber JA, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. (2022) Leaf litter fungal communities reflect pre-senescent leaf communities in a temperate forest ecosystem. PeerJ. 10(e12701).

• Liber JA, Benucci GMN, Bonito G. (2021) CONSTAX2: Improved taxonomic classification of environmental DNA markers. Bioinformatics. 37(21): 3941-3943. preprint PDF

• Liber JA, Bryson A, Bonito, G, Du Z. (2020) Harvesting microalgae for food and energy products. Small Methods. 2020(2000349): 1-16. PDF

• Vande Pol N, Liber JA, Desirò A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller AN, O’Donnell K, Stajich JE, Bonito G. (2020) Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity. 104: 267–289. https://doi.org/10.1007/s13225-020-00455-5 PDF

• Aime MC, Urbina H, Liber JA, Bonito G, and Oono R. (2018) Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii. Mycologia. 110(1): 136146 PDF

• Desirò A, Hao Z, Liber JA, Benucci GM, Lowry D, Roberson R, Bonito G. (2018) Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle. The ISME journal. 12(7): 1743-1757. PDF

Presentations

• Liber JA, Williams A, Petrucco C, Crocker C, Gladfelter A, He SY (2024) Uncovering genetic bases of phyllosphere commensalism in the biocontrol yeast Aureobasidium pullulans. Microbe-Assisted Crop Production 2024. Schloss Schönbrun. Vienna, Austria. July 17, 2024. Contributed talk & poster.

• Liber JA, He SY (2023) Probing the leaf micro-environment with whole cell yeast biosensors to establish principles of microbiome coexistence. 4th Plant Microbiome Symposium. Universidad San Fransisco de Quito. Quito, Ecuador. Aug. 4, 2023. Contributed talk.

• Liber JA, He SY (2022) Probing phylloplane microbial community physiology and dynamics in situ using whole-cell yeast biosensors. Mycological Society of America. University of Florida, Gainesville, Florida. July 12, 2022. Poster presentation.

• Liber JA, Benucci GMN, Bonito G. (2021) CONSTAXv2: a software for accurate taxonomic classification of environmental DNA markers. Mycological Society of America & Botanical Society of America (Botany 2021). Virtual. July 20, 2021. Poster presentation.

• Liber JA, Golematis N, Cole E, Malmstrom C, Bonito G. (2020) Four-way interactions in the plant holobiont: How does plant viral disease alter fungal and bacterial community assembly? Mycological Society of America. Virtual, July 22, 2020. Poster presentation.

• Liber JA, Bonito G. (2019) Do fungal endophytes facilitate colonization of bacterial endophytes in Brachypodium distachyon? Mycological Society of America. University of Minnesota, Minneapolis, Minnesota, Aug. 13, 2019. Poster presentation.

• Liber JA. (2019) Co-inoculation effects of bacterial and fungal endophytes in Brachypodium distachyon. University Undergraduate Research and Arts Forum. Michigan State University, East Lansing, Michigan, Apr. 5, 2019. Oral presentation.

• Liber JA, Lee J, Uhelski E, Del Rose A, Schultz J, Viola S, Gate C, and Caldwell S. (2018). Transformation of endophyte Enterobacter ludwigii with ACC deaminase related to ethylene stress response. iGEM Giant Jamboree. Hynes Convention Center, Boston, Massachusetts, Oct. 25, 2018. Poster and oral presentation.

• Liber JA, Gall E, Vande Pol N, Silvia D, and Bonito G. (2018). Use of hyphal image analysis and machine learning to classify Mucoromycota soil fungal isolates. International Mycological Congress. San Juan Convention Center, San Juan, Puerto Rico, July 20, 2018. Poster presentation.

• Liber JA, Gall E, Vande Pol N, Silvia D, and Bonito G. (2018). Use of hyphal image analysis and machine learning to classify Mucoromycota soil fungal isolates. University Undergraduate Research and Arts Forum. Michigan State University, East Lansing, Michigan Apr. 13, 2018. Poster presentation.

Press

• Alissa Kocer (2025) The Fungal Fallout of Climate Disasters Duke University School of Medicine Magnify. April 9, 2025.

• Liber JA, Brauer-Delaney B. (2018). Julian Liber: Undergrad research opportunities. MSU Today Student Views. Dec. 5, 2018.

• Liber JA, Houwat I. (2018) MSU team wins bronze at 2018 synthetic biology competition. Michigan State University, Molecular Plant Sciences News. Nov. 27, 2018.