Rosen Center for Advanced Computing

Yucheng Zhang

Yucheng Zhang's Profile Photo

Senior Life Science Scientist

Yucheng joined RCAC Support team in August 2021. Prior to joining RCAC, Yucheng was a bioinformatician working on genomics, epigeanomics and transcriptomics in Indiana University Melvin and Bren Simon Cancer Center. Besides cancer bioinformatics, he also has extensive research experience in plant and microbe genomics and transcriptomics. His interests include computational biology, gene regulation, machine learning, and deep learning. Details about his research can be found in his Google Scholar Profile. In RCAC, Yucheng provides support for life science related and containerized applications.

Education

  • Bsc, Viticulture & Enology, Northwest A&F University, China (2009).
  • Msc, Viticulture & Enology, Northwest A&F University, China (2012).
  • PhD, Plant Pathology, University of Florida (2016).

Selected Publications

  • "BioContainers on Purdue Clusters ", Y Zhang, L Gorestein, In Practice and Experience in Advanced Research Computing (PEARC '22), July 10–14, 2022, Boston, MA, USA. ACM, New York, NY, USA. 2 Pages. https://doi.org/10.1145/3491418.3535152
  • "Caspases Switch off the m6A RNA Modification Pathway to Foster the Replication of a Ubiquitous Human Tumor Virus", K Zhang, Y Zhang, Y Maharjan, FG Sugiokto, J Wan, R Li, Mbio, 12(4), e01706-21(2021).
  • "LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells", J Liu, S Liu, L Han, Y Sheng, Y Zhang, IM Kim, J Wan, L Yang, Development, 148(13), dev199628(2021).
  • "Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type", AG Yow, Y Zhang, K Bansal, SM Eacker, S Sullivan, I Liachko, MA Cubeta, JA Rollins, H Ashrafi, G3, 11(2), jkaa052(2021).
  • "Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis", Y Zhang, J Zhang, D Vanderpool, JA Smith, JA Rollins, BMC genomics, 21(1), 1-23(2020).
  • "Functional genomics insights into the pathogenicity, habitat fitness, and mechanisms modifying plant development of Rhodococcus sp. PBTS1 and PBTS2", D Vereecke, Y Zhang, IM Francis, PQ Lambert, J Venneman, RA Stamler, J Kilcrease, JJ Randall, Frontiers in microbiology, 11, 14(2020).
  • "Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces", Y Zhang, G Jiang, Y Ding, R Loria, Molecular plant pathology, 19(7), 1733-1741(2018).
  • "High-yield production of herbicidal thaxtomins and thaxtomin analogs in a nonpathogenic Streptomyces strain", G Jiang, Y Zhang, MM Powell, P Zhang, R Zuo, Y Zhang, D Kallifidas, AM Tieu, H Luesch, R Loria, Y Ding, Applied and environmental microbiology, 84(11), e00164-18(2018).
  • "Emergence of novel pathogenic Streptomyces species by site-specific accretion and cis-mobilization of pathogenicity islands", Y Zhang, R Loria, Molecular Plant-Microbe Interactions, 30(1), 72-82(2017).
  • "Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp.", Y Zhang, DRD Bignell, R Zuo, Q Fan, JC Huguet-Tapia, Y Ding, R Loria, Molecular Plant-Microbe Interactions, 29(8), 640-650(2016).
  • "A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data", Y Zhang, Q Fan, R Loria, Systematic and applied microbiology, 39(4), 252-259(2016).
  • "Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes", Y Zhang, S Qiu, Antonie Van Leeuwenhoek, 109(1), 71-82(2016).

Workshop

  • "Containers 101", Y Zhang, L Gorenstein, Purdue IT Research Computing Virtual Workshop Series, Purdue University(2021).
  • "Next Generation Sequencing Data Analysis", S Liu, S Utturkar, Y Zhang, N Lanman, The 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), virtue due to COVID-19(2021).

Presentations

  • "BioContainers on Purdue Clusters ", Y Zhang, L Gorestein, Practice and Experience in Advanced Research Computing (PEARC '22), Boston, MA, USA(222).
  • "Towards Understanding Virulence in Clavibacter michiganensis subsp. nebraskensis", Y Zhang, J Huguet, F White, American Phytopathological Society Annual Meeting, Cleveland, OH, USA(2019).
  • "Genomic backgrounds and mobilization of pathogenicity islands are determinants of novel pathogenic Streptomyces species", Y Zhang, D Bignell, Y Ding, R Loria, 18th International Symposium on the Biology of Actinomycetes (ISBA), Jeju Island, South Korea(2017).
  • "Evolution of plant pathogenicity in Streptomyces", Y Zhang, D Bignell, R Zuo, Q Fan, J Huguet, Y Ding, R Loria, American Phytopathological Society Annual Meeting, Tampa, FL, USA(2016).
  • "In vivo and in vitro investigation of the mobilization of pathogenicity islands of Streptomyces", Y Zhang, D Bignell, R Zuo, Q Fan, J Huguet, Y Ding, R Loria, American Phytopathological Society Southern Division Meeting, Balm, FL, USA(2016).

Other Activities and Fun Facts

  • Award: Bravo Award for extraordinary employee achievement, Purdue University - 2022.