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Pankaj Jaiswal Assistant Professor,
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Comparative Plant Genomics, Functional genomics, Systems Biology, Bioinformatics, Genome Annotation, Biochemical and Regulatory Pathway Databases, Genome Databases, Ontology Development.
Databases and bioinformatics projects
Gramene database: 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: 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 thsi model to include regulatory gene networks and pathways. The databse website also mirrors pathways from 8-9 plant species for comparative analysis.
Rice 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 Ontology Consortium: 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.
Biomedical Ontologies: Ontologies are structured controlled vocabularies that are used in annotation of gene function, expression and phenotypes in a standardized way by various plant and model organism databases. These vocabularies are organized using a mathematical model Directed Acyclic Graph (DAG) and are key to any successful query to find similarities in function, spatial and temporal expression and phenotypes across databases. Some of the ontologies amy group works on are:
Justin Elser (Postdoc)
Palitha Dharmawardhana (Postdoc)
BOT331 Plant Physiology
Lab Projects
Gramene Database
The Plant Ontology
Azevedo, J., F. Courtois, et al. (2008). "Intraplastidial trafficking of a phage-type RNA polymerase is mediated by a thylakoid RING-H2 protein." Proc Natl Acad Sci USA 105(26): 9123-8.
Bruskiewich, R., M. Senger, et al. (2008). "The generation challenge programme platform: semantic standards and workbench for crop science." Int J Plant Genomics 2008: 369601.
Avraham, S., C. W. Tung, et al. (2008). "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations." Nucleic Acids Res 36(Database issue): D449-54.
Liang, C., P. Jaiswal, et al. (2008). "Gramene: a growing plant comparative genomics resource." Nucleic Acids Res 36(Database issue): D947-53.
Rice Annotation Project (Multiple Authors) Curated Genome Annotation of Oryza sativa ssp. japonica and Comparative Genome Analysis with Arabidopsis thaliana. Genome Research 2007 Feb;17(2):175-83
Katica Illic*, Elizabeth Kellogg*, Pankaj Jaiswal*, et al. Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology. 2007 Dec 1 DOI:10.1104/pp.106.092825
Anuradha Pujar*, Pankaj Jaiswal*, et al. Whole Plant Growth Stage Ontology for Angiosperms and its Application in Plant Biology. Plant Physiology 2006, 142(2):414-28
Pankaj Jaiswal, et al. Gramene: A bird’s eye view of cereal genomes. Nucleic Acids Research 2006 Jan 1;34:D717-23.
Gene Ontology Consortium (Multiple Authors). The Gene Ontology (GO) Project in 2006. Nucleic Acids Research. 2006 Jan 1;34:D322-6
Pankaj Jaiswal, et al. Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397
Yamazaki Y and Jaiswal P. Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiology 2005 Jan;46(1):63-8.
Gene Ontology Consortium, The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research. 2004; 32: D258-261
Ware DH*, Jaiswal P*, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR. Gramene, a tool for grass genomics. Plant Physiology. 2002; 130(4): 1606-13.
Beardslee TA, Roy-Chowdhury S, Jaiswal P, Buhot L, Lerbs-Mache S, Stern DB, Allison LA. A nucleus encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts. Plant J. 2002; 31(2): 199-209
Pankaj Jaiswal, Doreen Ware, Junjian Ni, Kuan Chang, Wei Zhao, Steve Schmidt, Xiaokang Pan, Kenneth Clark, Leonid Teytelman, Samuel Cartinhour, Lincoln Stein and Susan McCouch, Gramene: Development and Integration of Trait and Gene ontologies for rice, Comparative and Functional Genomics, 2002, vol.3(2), pp132-136.
Bruskiewich R, Coe E H, Jaiswal P, McCouch S, Polacco M, Stein L, Vincent L, Ware D; The Plant Ontology (TM) Consortium and plant ontologies; Comparative and Functional Genomics, 2002, vol.3(2), pp137-142
Doreen Ware, Pankaj Jaiswal, Junjian Ni, Xiaokang Pan, Kuan Chang, Kenneth Clark, Leonid Teytelman, Steve Schmidt, Wei Zhao, Samuel Cartinhour, Susan McCouch and Lincoln Stein; Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 2002, Vol. 30, No. 1 103-105.
Jaiswal P, Sane AP, Ranade SA, Nath P and Sane PV, Mitochondrial and total DNA RAPD patterns can distinguish restorers of CMS lines in sorghum. Theor Appl Genet, 1998, 96: 791-796.
Sane AP, Jaiswal P, Nath P, Dabholkar AR and Sane PV; Mitochondrial Plasmids in Sorghum: Presence of Linear Plasmids in Indian Male Sterile and Milo 296 lines; J. Plant Biochem and Biotech, 1994, Vol. 3(2), 121-124.
