Pankaj Jaiswal

Professor, Comparative Plant Genomics
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Office: 541-737-8471

Cordley Hall

Cordley Hall 3082/3087

2701 SW Campus Way

2701 SW Campus Way
Corvallis, OR 97331

Flowering Time, Seed Development, Comparative Plant Genomics, Functional genomics, Systems Biology, Bioinformatics, Genome Annotation, Biochemical and Regulatory Pathway Databases, Genome Databases, Ontology Development.

RiceCyc metabolic pathwaysMy primary research focus is on studying the processes of flowering time and seed development in plants. These two developmental features of a plant determine how a plant reproduces on time and generate fruit/seeds thus contributing to our nutritional needs by way of quality and global food security by way of yield. We are interested in studying these two developmental features and their response to abiotic stresses like salt, drought and photoperiod.

The project includes genome-wide mapping of genomic/genetic loci (genes) in rice that regulate gene expression and gene to gene interactions influencing changes in the flowering time and seed development. We use molecular and genetic applications such as the genetic diversity, mutant phenotypes, genome sequences, gene expression and bioinformatics approaches, to provide mechanistic insights into the plant development and its adaptation to the global climate change (abiotic stress).

The lab encourages young scientists and students to use cutting edge technologies on genome sequencing, gene expression, plant development, and bioinformatics. The lab has an interdisciplinary program on training in computational biology /bioinformatics and plant biology. We collaborate extensively with computational biology scientists at the OSU, Plant and Gene Ontology projects, Gramene database and iPlantCollaborative (iPlant) lead by the University of Arizona and Cold Spring Harbor Laboratory.

The lab works on number of genomics aspects including the Comparative Plant Genomics, Functional Genomics, Systems Biology, Genome Annotation, Biochemical and Regulatory Pathways, Genome Databases and Ontology Development. Besides large scale genomics projects, we also have a wetlab work bench laboratory to work on biology of plants with respect to flowering time pathway, seed development and organelle (chloroplast and mitochondrial) function. Therefore we think its a great place to work with facilities available for a wet-lab work bench that uses molecular Biology and Biochemistry and seamlessly integrates the dry-lab components involving Computational Biology and Bioinformatics approaches to study the fundamental processes of plant gene function(s).

Various lab projects include:

Gramene Database

    • Project Website:

http://www.gramene.org

  • It is a comparative plant genomics platform and a Systems Biology database. This is the first such database that allows researchers to carryout in-silico investigation using either or both the forward and reverse genetics approaches to find the genes, proteins, phenotypes, function, expression, gene-gene interaction, metabolic pathways and polymorphic markers in the region of interest. It also allows researchers to make comparisons across genetic maps, genomes and gene orthologs.

RiceCyc

    • Project Website:

http://www.gramene.org/pathway

  • A database of metabolic pathways in Rice. This is a first of its kind pathway database dedicated to rice pathways. It allows researchers to find the rice genes and their role in given biochemical pathways. We are also looking at extending this model to include regulatory gene networks and pathways. The database website also mirrors pathways from 8-9 plant species for comparative analysis.

Plant Ontology

    • Website:

http://www.plantontology.org

  • It is a project on development of structured common set of plant anatomy and growth stage vocabularies for use in Genomics data sets, gene and phenotype annotations. The project also provides standard protocols and the database for ontology based annotations.

WikiPathways

    • Project Website:

http://www.wikipathways.org

  • An open, public platform for curation of biological pathways by and for the scientific community. We collaborate on plant pathways.

Planteome

  • Predicted interactome of genes for several species (not available yet). It includes Plant Genome Annotations and functional characterization of the genes using in-silico and manual curation driven by homology (orthologs and paralogs), and assignment of functional domains and Gene Ontology annotations

Plant Genome Annotation

We routinely collaborate on performing functional annotation of plant genomes such as those of following species. These annotations include, phylogenetic analysis of gene orthologs and paralogs, Gene Ontology based functional assignments to genes and developing metabolic and regulatory networks of genes.

  • Fragaria vesca (strawberry)
  • Vitis vinifera (grape)
  • Eucalyptus grandis (Eucalyptus)
  • Zea mays (maize/corn)
  • Brachypodium
  • Sorghum

Research Group Members

Postdoctoral Fellows and Research Associates (Bioinformatics and Biology lab)

  • Justin Elser
  • Parul Gupta
  • Laurel Cooper
  • Past:
    • Austin Meier
    • Samuel Fox
    • Palitha Dharmawardhana
    • Vindhya Amarasinghe
    • Mamatha Hanumappa

Research Assistants: Bioinformatics and Software Development

Graduate student(s)

  • Rachel Baschieri (Botany and Plant Pathology)
  • Past:
    • Noor Al-Bader (Molecular and Cellular Biology)
    • Matthew Geniza (Molecular and Cellular Biology)
    • Nikhil TL Venkata (Software development)- Computer Science
    • Balaji Athreya (Software development)- Computer Science

Undergraduate student(s)

  • Laura Rathbun (2018-2019)
  • Aaron Cohen (2017-2018) Computer Science and Engineering
  • Spencer Moss (2017) Computer Science and Engineering
  • Nick Ames (2015-2018) Computer Science and Engineering
  • Megan Seymour (2014-2016) Botany major
  • Ethan Johnson (2014-2016) Biology major-Honors College Thesis
  • Jeremy Levi Phillips (2013-2014) Environmental Sciences
  • Miles Van de Wetering (2013-2014) Computer Science and Engineering Major
  • Alexander Roos (2013-2014) Construction Engineering Mgt. Major
  • Teague Green (2013-2014) Biology and International Degree Major
  • Dylan Beorchia (2012-2014) Botany Major
  • Kindra Amos (2012-2015) Botany Major
  • Ebaad Haq (2013) Biology Major
  • Laura Moore (2012-2013) Enology and Viticulture Major
  • Keshav Menon (2010-2012) Biology Major
  • Kenny Wu (2010-2012): Biology Major
  • Gina Bono (2009-2011): Botany Major

Profile Field Tabs

At OSU
Affiliated with: 
Ag Botany / Plant Path
Do you accept grad students?: 
I accept graduate students for the Botany and Plant Pathology Department
Courses Taught: 

BOT331 Plant Physiology

My Publications
Proceedings and Conference Presentations: 
  1. Qu, B., P. Kumar, E. Zhang, Jaiswal P, L. Cooper, J. Elser, and Y. Zhang, Interactive design and visualization of N-ary relationships, in SIGGRAPH Asia 2017 Symposium on Visualization. 2017, ACM: Bangkok, Thailand.
  2. Cooper L, Meier A, Elser J, Preece J, Xu X, Kitchen R, Qu B, Zhang E, Todorovic S, Jaiswal P, Laporte M-A, Arnaud E, Carbon S, Mungall C, Smith B, Gkoutos G, Doonan J. he Planteome Project. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  3. Meier A, Cooper L, Elser J, Jaiswal P, Laporte M-A. Annotating germplasm to Planteome reference ontologies. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  4. Preece J, Elser J, Jaiswal P, Kvilekval K, Fedorov D, Manjunath B.S., Kitchen R, Xu X, Trigkakis D, Todorovic S, Carbon S. Plant Image Segmentation and Annotation with Ontologies in BisQue. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  5. Naithani S, Preece J, Gupta P, D’Eustachio P, Elser J, Mundao A, Weiser J, McKay S, Stein L, Ware D, Jaiswal P. Plant Reactome: A Resource for Comparative Plant Pathway Analysis. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  6. Qu B, Diefenbaugh J, Zhang E, Elser J, Jaiswal P, Carbon S, Mungall C. Planteome Gene Annotation Enrichment Analysis. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 201
  7. Xu W, Gupta A, Jaiswal P, Taylor C, Lockhart P. A Web Application for Extracting Key Domain Information for Scientific Publications using Ontology. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  8. Laporte M-A, Valette L, Cooper L, Mungall C, Meier A, Jaiswal P, Arnaud E. Comparison of ontology mapping techniques to map plant trait ontologies. Proceedings of the International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  9. Weijia X, Gupta A, Jaiswal P, Taylor C and Lockhart P (2016) Enhancing Information Accessibility of Publications with Text Mining and Ontology. International Conference on Biomedical Ontologies, Corvallis, USA, August 1-4, 2016.
  10. Jaiswal P; (2013). WikiPathways for Plants: An Online Pathway Editing & Visualisation Portal for Plant Biologists. GARNish Edition 20.
  11. Arnaud E, Cooper L, Shreshtha R, Menda N, Nelson RT, Matteis L, Skofic M, Bastow R, Jaiswal P, Mueller L, McLaren G; (2012). Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype. International Conference on Knowledge Discovery and Information Retrieval (IC3K2012): Barcelona, Spain, October 4-7th, 2012.  
  12. Walls R, Cui H, Macklin J, Mungall C, Cooper L,  Stevenson DW, Jaiswal P; (2012); Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. ICBO 2012: 3rd International Conference on Biomedical Ontology Proceedings.  
  13. Walls R, Smith B, Elser J, Goldfain A, Stevenson DW, Jaiswal P; (2012); A plant disease extension of the Infectious Disease Ontology. ICBO 2012: 3rd International Conference on Biomedical Ontology Proceedings.
  14. Preece J, Elser J, Jaiswal P (2011); Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes. Semantic Web Applications and Tools for Life Sciences (SWAT4LS-2011) Proceedings.
  15. Chen C, Casstevens T, Youens-Clark K, Zhang J, Ware D, Jaiswal P, McCouch S, Buckler E (2010); The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species. Nature Precedings. hdl:10101/npre.2010.4645.1
  16. Preece J, Elser J, Jaiswal P (2010); A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species. NETTAB-BBCC 2010 Biological Wikis Proceedings, Pages 109-112. http://www.molgen.mpg.de/~lappe/stehr/NETTAB-BBCC-2010-Proceedings.pdf