In 2009, he started the JGI Fungal Genomics program, which led to the large-scale projects like "1000 Fungal Genomes" or "Fungal mini-ENCODE", and delivered 1500+ annotated fungal genomes and multi-omics datasets integrated in MycoCosm portal with interacting comparative genomics tools. He also leads annotation of a large collection of algal genomes assembled in PhycoCosm portal. Prof. Grigoriev organized more than 50 genomics workshops, engaged several thousand researchers around the world in genome projects, published 250+ papers (46K+ citations, H-index=86), and was recognized by Thomson Reuters and Web of Science as Highly Cited Research (top 1%) in 2014-2019.

Computational genomics: Grigoriev's lab develops computational methods and tools for gene prediction, genome annotation, comparative genomics, and functional multi-omics analyses. These methods were applied to annotation and analysis of a large number of diverse genomes sequenced by JGI and elsewhere. The most recent developments include genome-based prediction of fungal lifestyle using machine learning approaches.

Fungal genomics: There are more than 1.5 million fungal species and they play a critical role in shaping the Earth's ecosystems. A better understanding of pathogens and symbionts is critical for the sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to enable conversion into bioenergy and bioproducts. Many new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical areas of research, including food, medicine, energy, and the environment. (see examples here)

Algal genomics: Algae are a phylogenetically diverse group of eukaryotes that are collectively responsible for 50% of photosynthesis on Earth. The enormous phylogenetic and functional diversity of algae require a systematic genomics exploration to better understand their complex evolution, mechanisms of photosynthesis, and potential for bioenergy, bioproducts, and biomanufacturing. (see examples here)