Son K. Pham




Contact information:

Son Kim Pham, Ph.D
LOG-G Department, Salk Institute for Biological Studies
10010 North Torrey Pines Rd, San Diego, CA 92037, USA.

Tel: +1 - 858-436-4073
E-mail: spham--at--salk.edu
Curriculum vitae


Research interests:

Son Pham finished his Ph.D in bioinformatics under the supervision of Pavel Pevzner and is currently working in Rusty Gage’s lab, studying the genetic code of schizophrenia, bipolar diseases.

Publications:

  • Mikhail Kolmogorov, Brian Raney, Benedict Paten, Son Pham. "Complete Assembly of Common Bacterial Genomes Using Only Short Reads": ISMB2014
  • Ilya Minkin, Hoa Pham, Ekaterina Starostina, Nikolay Vyahhi, and Son Pham. Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison (F1000Research)
  • Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, and Son Pham. Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes (WABI2013 - Corresponding author)
  • Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna, Cerulean: A hybrid assembly using high throughput short and long reads (WABI2013)
  • Ilya Minkin, Nikolay Vyahhi and Son Pham. "Sibelia: A Synteny Blocks Generation and Genome Comparison Tool (Poster in WABI2012)"
  • From de Bruijn Graphs to Rectangle Graphs for Genome Assembly -- With Nikolay Vyahhi, Alex Pyshkin, and Pavel Pevzner
  • Son Pham, Paul Medvedev, Pavel Pevzner " Mate-pair Consistency and Generating Problems". RECOMB-AB 2012
  • Son Pham*, Dmitry Antipov*, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner, and Max Alekseyev "Pathset Graphs: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly". Journal of Computational Biology 2012
  • Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler and Pavel Pevzner, Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. Journal of Computational Biology
  • Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander Kulikov, Valery Lesin, Sergey Nikolenko, Son Pham, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max Alekseyev, and Pavel Pevzner "SPAdes: a New Genome Assembly Algorithm and its Applications to Single-Cell Sequencing". Journal of Computational Biology, 2012. (to appear)
  • Son Pham*, Dmitry Antipov*, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner, and Max Alekseyev "Pathset Graphs: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly". The 16th Annual Conference on Research in Computational Molecular Biology (RECOMB), 2012. (to appear)
  • Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler and Pavel Pevzner, Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers, RECOMB 2011.
  • Son K. Pham and Pavel A. Pevzner, DRIMM-Synteny: Decomposing Genomes into Evolutionary Conserved Segments (accepted)
  • K. Avrachenkov, N. Litvak, S. Pham, A Singular Pertubation Approach for Choosing the PageRank Damping Factor. Journal: Internet Mathematics 2009
  • K. Avrachenkov, D. Nemirovsky, Son K. Pham, R. Cascella, R. Battiti, M. Brunato, Eigenvector based reputation measures. Journal: Paradigms for Biologically--Inspired Autonomic Networks and Services 2008
  • K. Avrachenkov, V. Dobrynin, D. Nemirovsky, S.K. Pham and E. Smirnova, PageRank Based Clustering of Hypertext Document Collections . Proceedings of ACM SIGIR 2008.
  • K. Avrachenkov, N. Litvak, and K.S. Pham, Distribution of PageRank Mass Among Principle Components of the Web .Proceedings of the 5th Workshop on Algorithms and Models for the Web-Graph (WAW2007, Lecture notes in computer science 2007-Springer)
  • K. Avrachenkov, D. Nemirovsky and S. Pham, A survey on distributed approaches to graph based reputation measures. Proceedings of International Workshop on Tools for Solving Structured Markov Chains: SMCtools 2007.
  • V Dobrynin, S Pham, D Patterson, N Rooney, M. Galushka, SOPHIA in Enterprise Track .The Fifteenth Text REtrieval Conference (TREC 2006) Proceedings. 2006


  • Some Videos

    Read-Pair Assembly (Coursera)
    String Reconstruction Problem (Coursera)
    String Reconstruction Problem, Hamiltonion Approach (Coursera)
    Trie (Coursera)
    BWT for compression (Coursera)
    BWT for pattern matching (Coursera)
    Further Applications of Read Mapping (Coursera)
    My Defense

    Teaching Activities


    Book for the current year:

    TAoCP - Vol 4a
    Combinatorial Problems and Excercises

    Software:

  • DRIMM Synteny
  • Sibelia
  • Etool.Me: Sibelia’s web server
  • Cerulean: Hybrid Genome Assembler
  • I am now living with the sound of pacific waves crashing against the shore in dreams, with the San Diego gentle sea breezes rustle through hair every afternoon on the beach, with slow and peaceful steps at night and deeply indebted to my wife and daughter for their love and sacrifices.
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