Research and Software


Here you can find a list of research topics that I am currently interested in:
  • Pattern Discovery:
           Varun: Extensible motif discovery
           Subtle Motif Finder: Detection of consensus motifs
           www.research.ibm.com/computationalgenomics
  • Pattern Filtering, Classification and Alignment-Free Measures
           Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords
           Underlying Subwords
           Filtering Degenerate Motifs with Application to Protein Sequence Analysis
           Pattern Filtering
           Alignment-free comparison of regulatory sequences (cis-regulatory modules)
           UnderII - regulatory sequences comparison
           Assembly-free Genome Comparison based on Next-Generation Sequencing Reads and Variable Length Patterns
           Assembly-free Genome Comparison
           QCluster: Extending Alignment-free Measures with Quality Values for Reads Clustering
           QCluster
           Alignment-free genome comparison based on Sequencing Reads and Quality Values
           c2q
  • MetaGenomics
           MetaProb: Accurate Metagenomics Sequence Classification based on Probabilistic Sequence Signatures
           MetaProb
           Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads
           CIOR
           SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on filtering uninformative k-mers
           SKraken
  • Sequence Entropy
           Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes
           Fast Entropic Profiler
           EP-sim: Multiple-resolution alignment-free measure based on Entropic Profiles
           EP-sim
  • Phylogenetic
           Ultrametric Networks: A New Tool For Phylogenetic Analysis
           Ultranet
  • String Hashing
  •        Fast Spaced Seed Hashing
           FSSH
  • Data Compression
  • Grammatical Inference
  • Structural Proteomics - a web-service version of this work is currently available: PROuST
  • GRID Computing