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Students:

Working with smart students is one of the joys of academia, and I have been particularly fortunate to have worked with some excellent ones over the years:

• Thao Truong, University of Science, Vietnam
• Tan Phan, University of Science, Vietnam
• Ilia Minkin, Master thesis: "Genome comparision with de Bruijn graphs", Now Ph.D with Paul Medvedev
  Publications with me
  • Ilia Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham, "Sibelia: a scalable and comprehensive synteny block generation tool for closely related microbial genomes", WABI2013
  • Ilia Minkin, Hoa Pham, Ekaterina Starostina, Nikolay Vyahhi, Son Pham, "C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison", F1000Research
  • Ilia Minkin, Son Pham, Paul Medvedev, "An efficient algorithm to build the compacted de Bruijn graph from many complete genomes"
• Mikhail Kolmogorov, Master thesis: "Multiple reference assisted assembly", Now Ph.D with Pavel Pevzner
  Publications with me
  • Mikhail Kolmogorov, Brian Raney, Benedict Paten, Son Pham, "Ragout—a reference-assisted assembly tool for bacterial genomes", ISMB2014, Bioinformatics 2014
  • Mikhail Kolmogorov, Brian Raney, Duncan Odom, Paul Flicek, David Thybert, Benedict Paten, and Son Pham "Ragout2: a reference-assisted rearrangement-based tool for mammalian genome assembly" (In Revision)
• Dmitrii Meleshko, Master thesis: "Assembly-based contig copy number estimation", Now Ph.D student at Cornell
  Publications with me
  • Dmitrii Meleshko, Vera Bushmanova, Son Pham, "CNVera: an assembly-based tool for contig copy number estimation" (In Revision)