Rick White awarded CCI 2024 Student-Faculty Research Award
The College of Computing and Informatics selected Dr. Richard Allen White as the well deserved recipient of the 2024 Essam El-Kwae Student-Faculty Research Award.
Dr. White, alongside students Madeline Bellanger and Jose Figueroa, has made contributions in the scientific community with the submission of seven papers within a span of 10 months. Five of these papers were submitted in the first quarter of 2024, showcasing their remarkable productivity and dedication.
Their research covers a range of topics, including the development of database-related code for metaomics and metomic annotation, as well as the creation of innovative tools for detecting potato pathogens. Additionally, the team has successfully undertaken the task of quantifying all the viruses in the Great Salt Lake, providing valuable insights into viral ecology.
Their work has not gone unnoticed, with MetaCerberus, a science communication platform, retweeting their findings 91 times. Dr. White and his team’s contributions exemplify the collaborative spirit and commitment to student success through mentorship and advancing scientific knowledge.
Papers published in 2023-2024:
M Bellanger, JL Figueroa III, L Tiemann, ML Friesen, RA White III. (pre-print, in-review at NAR bioinformatics and genomics).
NFixDB (Nitrogen Fixation DataBase)-A Comprehensive Integrated Database for Robust’Omics Analysis of Diazotrophs bioRxiv, 2024.03. 04.583350
Note: Comprehensive database for nitrogenase measurement of nitrogen fixers (i.e., diazotrophs).
Braley LB, Jewell JB, JL Figueroa III, Humann JL, Main D, Mora- Romero GA, Moroz N, Woodhall JW, RA White III, Tanaka K. Nanopore sequencing with GraphMap for comprehensive pathogen detection in potato field soil. (published, 2023) Plant Disease APS. 2023 https://doi.org/10.1094/PDIS-01-23-0052-SR
Note: Pathogen detection pipeline in python that uses nanopore data to detect soil related pathogens for potato agriculture.
JL Figueroa III, E Dhungel, CR Brouwer, RA White III. (pre-print) MetaCerberus: distributed highly parallelized scalable HMM-based implementation for robust functional annotation across the tree of life.
bioRxiv, 2023.08. 10.552700
JL Figueroa, E Dhungel, M Bellanger, C Brouwer, RA White III. (published, 2024) MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life Bioinformatics, btae119
Note: Robust functional annotation for genomes to metacommunities across the tree of life.
X/Twitter states: 22,049 impressions, 1,239 engagements, detail expands 138, 91 reposts, 256 likes, 8 quotes, click likes 687.
GitHub stats: 30 stars.
Anaconda stats: 5253 downloads, https://anaconda.org/bioconda/metacerberus
Altmetric: Score 49 (top 5% of all research outputs), shared in 27 countries, https://oxfordjournals.altmetric.com/details/160230246
MA Bellanger, PT Visscher, RA White III. (published, 2023)
Viral enumeration using cost-effective wet-mount epifluorescence microscopy for aquatic ecosystems and modern microbialites Applied and Environmental Microbiology, 10.1128/aem.01744-23
Note: Measured the amount of viruses within the Great Salt Lake.
JL Figueroa III, A Panyala, S Colby, ML Friesen, L Tiemann, RA White III. (pre-print, in-review at Bioinformatics Advances) MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data bioRxiv, https://doi.org/10.1101/2022.11.22.51756
Just published
https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae061/7657691
Note: Robust microbiome metaomic kmer based counter for diversity measurements.
EpiVirQuant – computer vision code for automatic counting of viruses and their sizes. In review at nature imaging. https://www.biorxiv.org/content/10.1101/2024.04.21.590467v1.abstract