About me

Son Kim Pham, Ph.D

I'm a research associate in Fred Gage's lab at Salk Institute, currently focusing on finding the genetic code of bipolar, schizophrenia, and autism spectrum disorder.
I'm still active in developing algorithms for genome assembly and comparative genomics.

Address: 10010 North Torrey Pines Rd, San Diego, CA 92037, USA.
Email: kspham@eng.ucsd.edu
Phone: +1-858-436-4073
Curriculum vitae


The opportunity to teach, be it lecturing or mentoring students, is an important reason why I want to pursue my career in academia. Below is my coursera video lectures with Pavel Pevzner and Phillip Compeau (with more than 200.000 students registered for the last 2 years)...



My research interest includes:

  • Neuroscience
  • Graph Theory
  • Bioinformatics

The highlights of my research can be seen in my publications:

Recomb bioinformatics ISMP

A full list of my recent publications is available here. You may also check the following databases:

DBLP| Google Scholar


My former student Ilia Minkin got the best poster award at RECOMB2016, Congratulations!
Ragout2: Pseudo-chromosome assembly of large and complex genomes using multiple references will be presented in RECOMB 2016. Poster is available here.
Our pre-beta release for Mobile Element Atlas is now online.
Our post-mortem neuron single cell paper appeared in Nature Protocol.
Our paper about Bipolar Disease appeared in Nature, Volume 527 Number 7576 pp7-128 , 5 November 2015.

Ragout2 Ragout2
Ragout2: a reference-assisted tool for mammalian genome assembly” has been chosen as a default pipeline for Sanger/UCSC to assemble 22 mouse wild-strains into complete chromosomes. (Mikhail Kolmogorov, Brian Raney, Duncan Odom, Paul Flicek, David Thybert, Benedict Paten, and Son Pham).
The source code is now available under GPL license.
"Ragout: a reference-assisted assembly tool for bacterial genomes" has been accepted to ISMB 2014, Bioinformatics 2014 and featured by Genomeweb.

Genomic Medicine 2015 conference in Vietnam.

I am the organizer and program chair of Genomic Medicine 2015, and also served as a Program Committee Member for: RECOMB-BE 2009, RECOMB-BE 2010, RECOMB-BE 2011; Referee for Bioinformatics, BMC Bioinformatics, Nucleic Acids Research, Frontiers in Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics; Sub-reviewer for Nature, Nature Communication, Cell.