Our research is currently supported by the NSF CAREER award (DBI-1652164), the NIH R01 award (R01GM140370) and the UNL startup grant
1. Bioinformatics tool development:
ORFan study (NIH 1R15GM114706): We develop new bioinformatics tools for studying orphan genes and horizontaly transferred genes in plant, microbial and meta-genomes to understand their evolution
- We developed ORFanFinder, a software and web server to identify taxonomically restricted orphan genes and classify genes of a genome into different age groups
- We developed HGT-Finder, a software to identify horizontaly transferred genes in fungi
CAZyme study (NSF DBI-1652164 and NIH R01GM140370): We develop new bioinformatics tools to allow automated annotation of genomes for CAZymes
- We developed and maintain the web resource dbCAN, dedicated to functional domain-based CAZyme annotation for newly sequenced genomes/metagenomes.
- We developed and maintain the PlantCAZyme database to provide pre-computed CAZyme sequence and annotation data for all sequenced plant and algal genomes
2. Evolution of plant cell walls:
- We are sequencing a charophyote green alga zygnma circumcarinatum to understand how plant cell walls have evolved from algae to land plants
- We study the phylogeny of cell wall-related genes (encoding enzymes, transcription factors, transporters, ncRNAs etc.) involved in plant cell wall synthesis and degradation to understand how plant cell walls have evolved.
- Carbohydrate active enzymes (CAZymes): these enzymes are responsible for the synthesis, degradation, modification and recognition of all carbohydrates on Earth.
- We identify important industrial interested enzymes, e.g. CAZymes by bioinformatics mining of genomic and metagenomic data