Research

• I core activities
  • Genome sequence analysis
    Genome analysis, annotation & interpretation of genomics data • ChIP-seq, RNA-seq, expression analysis of complex genomic sequences • Protein sequence motif discovery • Comparative transcriptomics & proteomics • Metagenomics • Metabolic pathway inference from genomic annotation
  • Comparative genomics
    Whole-genome comparison, metrics for taxonomy & classification • Metabolic reconstruction, pathway detection & evolutionary history inference • Metabolic innovation, reaction & pathway variants • Evolution of transcription • Deep phylogeny, horizontal gene transfer, detection & quantification • The Last Universal Common Ancestor
  • Algorithms & databases
    Genome repository databases, pangenome/paleogenome analysis, ortholog detection • Document clustering & concept discovery, ontology induction • Compositional bias detection & masking • Sequence matching, network visualization, large-scale sequence comparison • Ancestral state reconstructions: from protein families to genome content • Genome-aware algorithms for phylogenetic profiles, gene clusters, gene fusions
• II collaborative activities
  • Systems biology
    Biological network analysis & interpretation, functional module detection • Protein interaction detection, multi-domain decomposition of proteins • Translational bioinformatics, pathological vs. physiological stress, systems biomedicine • Systems radiobiology, low-dose ionizing radiation exposure
  • Synthetic biology
    Context-free module detection via evolutionary comparison • Ancestral state reconstructions: from genome content to genomic sequences • Astrobiology (exobiology): life detection protocols, universal reactions
  • Science policy
    Science communication: history of science, metaphors in science, ancient science, epistemology • Community actions for research & training: GEBA, GSC, Mikrobiokosmos*, MetaSUB, Monumentome*, HSCBB*, HBio*, ISCB* • Impact metrics • Development of a field: computation in biology

* founder