Research

  • Genome sequence analysis
    Genome analysis, annotation & interpretation of genomics data • ChIP-seq, RNA-seq, expression analysis of complex genomic sequences • Comparative transcriptomics & proteomics • Metabolic pathway inference from genomic annotation, large-scale methods
  • Comparative genomics
    Whole-genome comparison, metrics for species/strain taxonomy & classification • Metabolic reconstruction, pathway detection & evolutionary history inference • Metabolic innovation, synthetic design of metabolic reaction & pathway variants • Horizontal gene transfer, detection & quantification, the Last Universal Common Ancestor
  • Algorithms & databases
    Genome repository databases, pangenome/paleogenome analysis, ortholog detection • Genome-aware algorithms for phylogenetic profiles, gene clusters, gene fusions • Document clustering & concept discovery, ontology induction • Compositional bias detection & masking, applications for database searches • Sequence matching, network visualization, large-scale sequence comparison • Ancestral state reconstructions: from protein families to genome content
  • Systems biology
    Biological network topology analysis & interpretation, functional module detection • Protein interaction detection, multi-domain decomposition of protein families • Translational bioinformatics, pathological versus physiological stress • Systems radiobiology, low-dose ionizing radiation exposure
  • Science policy
    Science communication: history of science, metaphors in science, ancient science • Community actions for research & training: GEBA, GSC, Mikrobiokosmos, O\HSCB, ISCB • Historical development of a new field: computation in biology, and beyond
  • 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
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