Candidate: Parul Gupta
Current position: Research Associate
Affiliation: Oregon State University
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
BS (Zoology & Chemistry), 2004, Lucknow University, India
MS (Biochemistry), 2006, Lucknow University, India
Ph.D. (Biochemistry), 2014, Banaras Hindu university, India
Postdoctoral Scholar, 2015-2018, Oregon State University, USA
2018-present – Research Associate, Dept. of Botany & Plant Pathology, Oregon State University
I work as a Research Associate in the Jaiswal Lab at Oregon State University. I have ~6 years of post PhD research experience in the area of plant genomics, bioinformatics, and systems biology. Past 5 years I’m involved in database curation and management. I am the lead curator for Gramene’s Plant Reactome pathway database (plantreactome.gramene.org). I do evidence-based manual biocuration of genes and gene products, reactions, pathways and processes. I have curated more than 100 metabolic, genetic, regulatory and organ development pathways. Based on literature survey, I integrate information about a gene or gene product’s structure-function, sub-cellular location, mutant phenotype, and pathways. I am also a member of a team working on database development, management, quality matrices, testing, and the database release process.
In addition, I am a lead person on the Chia (Salvia hispanica) genome sequencing project, and contributed to the American Beaver (Castor canadensis) genome sequencing and annotation project . I am a lead person for development of mRNA-seq and small RNA-seq based expression atlas for 13 developmental stages and plant parts of Arabidopsis thaliana. I led the project on transcriptome modulation of rice (Oryza sativa) plants upon transition from dark to light, and established the alternatively spliced protein-coding and noncoding transcript sets for dark and light conditions. I am, the only person in international NASA-GeneLab (https://genelab.nasa.gov) plant analysis working group (Plant AWG), leading to decipher the role of alternative splicing on plant growth and development, and nutrition quality in spaceflight grown plants. I am developing methodology and bioinformatics workflows for rice pan-genome project.
- Invited talk on “Alternative splicing and transcriptome modulation under spaceflight response in Arabidopsis thaliana” at American Society for Gravitational and Space Research (ASGSR) virtual conference, (2020)
- Invited talk on “Plant biology in Space” for webinar series on Space Medicine and Life Sciences-An Insight from United States (https://spacegeneration.org/event/smls-usa), (2020)
- Invited talk on “Detection of alternative splicing events in ground control and space flight RNA-Seq data” at NASA-GeneLab Plant Analytical Working Group hack-a-thon, (2020)
- Seminar on “Development of Chia (Salvia hispanica) gene expression atlas and gene regulatory network” at Oregon State University, (2020)
- Invited talk on “Alternative splicing detection from RNA-Seq” at Center for Genome Research and Biocomputing Bioinformatics user group (BUG) meeting, (2019)
- Seminar on “Plant pathway curation using Reactome curator tool” in Pathway curation jamboree at International Conference on Biomedical Ontologies, (2018)
- Seminar on “Biology behind plant pathways” at Department of Botany & Plant Pathology, Oregon State University, (2016)
- Flash talk on “Plant Reactome pathway database” at Center for Genome Research and Biocomputing Spring Conference, Oregon State University, (2016)
- Developed course material and SOPs for Summer STEM camp for DNA Biology and Bioinformatics
- Co-organizer and instructor in Summer STEM camp for DNA Biology and Bioinformatics, Oregon State University, 2016
- Co-organizer and instructor in Summer STEM camp for DNA Biology and Bioinformatics, Oregon State University, 2017
- Co-organized the Pathway curation jamboree on the sidelines of Gene Ontology Consortium Meeting, June 1-5, 2017, Oregon State University
- Co-organized an international conference on biological ontology (ICBO), August 7-10, 2018, Oregon State University
- Co-organized Gene Ontology Consortium Meeting, June 1-5, 2017, Oregon State University
- Co-organized the Pathway curation jamboree in International Conference on Biological Ontology (ICBO), August 7-10, 2018, Oregon State University
- Trained graduates and undergraduate students for implementation of NGS based techniques, gene annotation methods and pathway curation
Motivations for a position on the ISB Executive Committee:
I am very interested in becoming a member of the ISB Executive Committee for variety of reasons. I have six years experience in the field of biocuration which will benefit me to run this position successfully. I manually curate plant metabolic, signaling, genetic, regulatory and plant organ development pathways for Gramene’s Plant Reactome (https://plantreactome.gramene.org ) pathway portal. This process includes curation of genes, gene products (transcripts, microRNAs, proteins), biological processes/reactions (catalysis, transcription, translation, post-translational modifications, association, transport and localization, black box), subcellular location of gene, gene products, reactions, and pathways. As a result of those experiences, I have a keen understanding of the role, function, and importance of biocuration for the scientific community.
Development of automated curation tools leaves manual curation far behind as manual curation is time-intensive process. However, some tasks can be done via manual curation only, for example, development of data standards and data models for new type of data, hypothesis building, integration of diverse data types, and quality control. Therefore, I am interested to promote manual curation when combined with automated curation process by engaging and training the researchers to sustain the biological knowledgebase.
In this era of big data, ensuring the accuracy of the data and its efficient management is very challenging for curating such datasets. For such datasets, long-term sustainable solution is community curation. My experience in organizing biocuration jamborees may help me developing community curation strategies.
If I am selected for the committee, I’ll be dedicated about that responsibility and will do my best to make meaningful contributions.
Thank you for your consideration of my nomination.
Conflicts of interest:
I am a member of Conference Planning Committee of the annual International Society for Biocuration Conference, 2021.
I am the member of following scientific societies:
- Metabolomics Association of North America
- Gamma Sigma Delta, the Honor Society of Agriculture, Oregon State University Chapter
- The National Aeronautics and Space Administration (NASA)-GeneLab Plant AWG
- American Society for Gravitational and Space Research (ASGSR)
- International Society for Biocuration (ISB)
- American Society of Plant Biologist (ASPB)
- All India Society of Cell Biology
I am a member of editorial board of following journals:
- Guest editor and special issue editor for the journal Plants (an Open Access Journal of the MDPI)
- Review editor for Computational Genomics (specialty section of Frontiers in Genetics, Frontiers in Bioengineering and Biotechnology and Frontiers in Plant Science)
- Guest editor for the journal Frontiers in Plant Science