Son Pham

Publications

2015-today

• Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder
  Jerome Mertens, Qiu-Wen Wang, Yongsung Kim, X Yu Diana, Son Pham, Bo Yang, Yi Zheng, Kenneth E Diffenderfer, Jian Zhang, Sheila Soltani, Tameji Eames, Simon T Schafer, Leah Boyer, Maria C Marchetto, John I Nurnberger, Joseph R Calabrese, Ketil J Oedegaard, Michael J McCarthy, Peter P Zandi, Martin Alda, Caroline M Nievergelt, Shuangli Mi, Kristen J Brennand, John R Kelsoe, Fred H Gage, Jun Yao.
  Nature 527 (7576), 95-99, 2015/11/5.
  
  
  
• RNA-Seq from single nuclei: capturing the transcriptome of postmortem neurons
  Suguna Rani Krishnaswami, Rashel V. Grindberg, Mark Novotny, Pratap Venepally, Benjamin Lacar, Kunal Bhutani, Sara B. Linker, Son Pham, Jennifer A. Erwin, Jeremy A. Miller, Rebecca Hodge, James K. McCarthy, Martijn Kelder, Jamison McCorrison, Jun Lee, Ed S. Lein, Nicholas Schork, Michael J. McConnell, Fred H. Gage, Roger S. Lasken.
  Accepted to Nature Protocols, 2015
  
  
• Ragout2: a reference-assisted rearrangement-based tool for mammalian genome assembly
  Mikhail Kolmogorov, Brian Raney, Duncan Odom, Paul Flicek, David Thybert, Benedict Paten, and Son Pham. (Corresponding author)
  In Submission
  
  
  
• An efficient algorithm to build the compacted de Bruijn graph from many complete genomes
  Ilia Minkin, Son Pham, and Paul Medvedev
  In Submission
  
  
• The Pharmacogenomics of Bipolar Disorder study (PGBD): identification of genes for lithium response in a prospective sample
  Ketil J. Oedegaard, Martin Alda, Yokesh Balaraman, Wade H. Berrettini, Abesh Bhattacharjee; Kristen J. Brennand, Katherine E. Burdick, Joseph R. Calabrese, Cynthia V. Calkin, William H. Coryell, David Craig, Anna DeModena, Mark Frye, Fred H. Gage, Julie Garnham, Elliot Gershon, Michael J. McCarthy, Melvin G. McInnis, Adam X. Meihofer, Jerome Mertens, Caroline M Nievergelt, John Nurnberger, Son Pham, Tatyana Shekhtman, Paul D. Shilling, Szabolcs Szelinger, Bruce Tarwater, Jun Yao, Peter P. Zandi, John R. Kelsoe.
  In Submission
  
  
• INIGO: A Fast and Highly Accurate Tool for Detecting Mobile Element Insertions from High-Throughput Sequencing Data.
  Son Pham and Fred Gage et. al., In Preparation for Submission
  
  

2014

• Ragout—a reference-assisted assembly tool for bacterial genomes
  Mikhail Kolmogorov, Brian Raney, Benedict Paten, Son Pham. (Corresponding author).
  ISMB2014 and Bioinformatics 30 (12), i302-309, 2014/6/15. [pdf]
  
  
  
• ExSPAnder: a universal repeat resolver for DNA fragment assembly
  Andrey D Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus, Pavel A Pevzner.
  ISMB2014 and Bioinformatics 30 (12), i293-301, 2014/6/15. (Best ISMB Paper Award) [pdf]
  
  
  

2013

• Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly
  Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A Pevzner, Max A Alekseyev.
  RECOMB2013 and Journal of Computational Biology 20 (4), 359-371, 2013/4/1.
  
  
  
• C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison
  Ilya Minkin, Hoa Pham, Ekaterina Starostina, Nikolay Vyahhi, Son Pham. (Corresponding author).
  F1000Research 2, 2013. [pdf]
  
  
  
• Sibelia: a scalable and comprehensive synteny block generation tool for closely related microbial genomes
  Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham. (Corresponding Author).
  Algorithms in Bioinformatics, 215-229, 2013/1/1. [pdf]
  
  
  
• Cerulean: a hybrid assembly using high throughput short and long reads
  Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna.
  Algorithms in Bioinformatics, 349-363, 2013/1/1 [pdf]
  
  
  

2012

• SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
  Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski, Alexey V Pyshkin, Alexander V Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A Alekseyev, Pavel A Pevzner.
  Journal of Computational Biology 19 (5), 455-477, 2012/5/1. [pdf]
  
  
  
• Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly
  Son K Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A Pevzner, Max A Alekseyev.
  RECOMB2012 and Research in Computational Molecular Biology, 200-212, 2012/1/1.
  
  
• From de Bruijn Graphs to Rectangle Graphs for Genome Assembly.
  Nikolay Vyahhi, Alex Pyshkin, Son K Pham, Pavel A Pevzner. (Corresponding Author)
  WABI, 249-261, 2012/1/1.
  
  
  

2011

• Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers
  Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler, Pavel Pevzner.(Co-first author)
  Journal of Computational Biology 8 (11), 1625-1634, 2011/11/1.
  
  
  

2010

• DRIMM-Synteny: decomposing genomes into evolutionary conserved segments
  Son Pham, Pavel A Pevzner.
  Bioinformatics 26 (20), 2509-2516, 2010/10/15. [pdf]
  
  

2008

• Eigenvector based reputation measures
  AK Avrachenkov, D Nemirovsky, S Pham, RG Cascella, R Battiti, M Brunato.
  WP 2.1–PARADIGMS COLLECTION AND FOUNDATIONS, 225, 2008/11/5. [pdf]
  
  
• Pagerank based clustering of hypertext document collections
  Konstantin Avrachenkov, Vladimir Dobrynin, Danil Nemirovsky, Son Kim Pham, Elena Smirnova.
  Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval, 873-874, 2008/7/20. [pdf]
  
  
• A singular perturbation approach for choosing the PageRank damping factor
  Konstantin Avrachenkov, Nelly Litvak, Kim Son Pham.
  Internet Mathematics 5 (1-2), 47-69, 2008/1/1. [pdf]
  
  
  

2007

• A survey on distributed approaches to graph based reputation measures
  Konstantin Avrachenkov, Danil Nemirovsky, Kim Son Pham.
  Proceedings of the 2nd international conference on Performance evaluation methodologies and tools, 82, 2007/10/22. [pdf]
  
  
• Distribution of PageRank mass among principle components of the web
  Konstantin Avrachenkov, Nelly Litvak, Kim Pham.
  Algorithms and Models for the Web-Graph, 16-29, 2007. [pdf]
  
  

2006

• SOPHIA in Enterprise Track.
  Vladimir Dobrynin, Son Kim Pham, David Patterson, Niall Rooney, Mykola Galushka.
  TREC, 2006. [pdf]