Me

< Nam Pho />

Data Scientist and HPC Systems Administrator





Analytics

Over 10 years of research experience analyzing data of all scales and formats. Well published in a wide variety of fields.


IT

Maintained a 7,000+ core Linux high-performance compute (HPC) cluster using automation and virtualization technologies (e.g., Cobbler, Ansible, KVM).


Consulting

Available as an independent consultant on select projects as my schedule allows.


I started my career as a research fellow at the National Institutes of Health studying insertional mutagenesis in Zebrafish. At the Broad Institute I was a data analyst on The Cancer Genome Atlas project, processing next-generation sequencing data on tumors. I'm currently a senior consultant in the research computing group at Harvard Medical School where I configure and maintain a HPC cluster for biomedical research. I also pursue independent research studying large-scale EHR data.

I graduated from Johns Hopkins University and the University of Maryland. I also trained in graduate-level computer science at Harvard University and the Georgia Institute of Technology. I possess several technical credentials including a graduate certificate in data science from Harvard University.

I'm grateful to have had my work supported with grants, scholarships, or other funding through the years by the University of Maryland, the National Institutes of Health, the Johns Hopkins University, Clemson University, the Linux Foundation, ACM-SIGHPC, the Open Science Data Cloud, and many others.




Projects


Detailed information coming soon.




Blog


No current blog entries.




Publications


Journals

  1. Glicksberg BS, Li Li, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT. "Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks." Bioinformatics, 2016 32(12):i101-i110. [PubMed]
  2. Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S. "A chromatin-based mechanism for limiting divergent noncoding transcription." Cell, 2014 157(7):1712-23 [PubMed]
  3. Francis JM, Kiezun A, Ramos AH, Serra S, Pedamallu CS, Qian ZR, Banck MS, Kanwar R, Kulkarni AA, Karpathakis A, Manzo V, Contractor T, Philips J, Nickerson E, Pho N, Hooshmand SM, Brais LK, Lawrence MS, Pugh T, McKenna A, Sivachenko A, Cibulskis K, Carter SL, Ojesina AI, Freeman S, Jones RT, Voet D, Saksena G, Auclair D, Onofrio R, Shefler E, Sougnez C, Grimsby J, Green L, Lennon N, Meyer T, Caplin M, Chung DC, Beutler AS, Ogino S, Thirlwell C, Shivdasani R, Asa SL, Harris CR, Getz G, Kulke M, Meyerson M. "Somatic mutation of CDKN1B in small intestine neuroendocrine tumors." Nature Genetics, 2013 45(12):1483-6 [PubMed]
  4. Varshney GK, Lu J, Gildea DE, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld D, Pho NH, Casero D, Hirase T, Mosbrook-Davis D, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg TG, Pellegrini M, Burgess SM, Lin S. "A large-scale zebrafish gene knockout resource for the genome-wide study of gene function." Genome Research, 2013 23(4):727-35 [PubMed]
  5. The Cancer Genome Atlas Network. "Comprehensive molecular portraits of human breast tumours." Nature, 2012 490:61-70 [PubMed]
  6. The Cancer Genome Atlas Network. "Comprehensive genomic characterization of squamous cell lung cancers." Nature, 2012 489:519-25 [PubMed]
  7. Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M. "Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2." Proc. Natl. Acad. Sci., 2012 109:14476-81 [PubMed]
  8. The Cancer Genome Atlas Network. "Comprehensive molecular characterization of human colon and rectal cancer." Nature, 2012 487:330-7 [PubMed]
  9. Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodriguez-Cuevas S, Romero-Cordoba SL, Schumacher SE, Stransky N, Thompson KM, Uribe-Figueroa L, Baselga J, Beroukhim R, Polyak K, Sgroi DC, Richardson AL, Jimenez-Sanchez G, Lander ES, Gabriel SB, Garraway LA, Golub TR, Melendez-Zajgla J, Toker A, Getz G, Hidalgo-Miranda A, Meyerson M. "Sequence analysis of mutations and translocations across breast cancer subtypes." Nature, 2012 486:405-9 [PubMed]

Papers

  1. Pho N, Magri DRC, Redigolo FF, Kim BD, Feeney T, Morgan HL, Patel CJ, Botka C, and Carvalho TCMB. "Data Transfer in a Science DMZ using SDN with Applications for Precision Medicine in Cloud and High-performance Computing." Supercomputing '15 SDN Workshop, Austin, TX. November 2015. [PDF]

Abstracts

  1. Colby DJ, Pho NH, Quang VM, Chau NV, Chinh NT, Nguyen TT, Lu D, Ferreira LC, Libman H. "Tenofovir Associated Nephrotoxicity in an HIV Positive Vietnamese Cohort." The 10th Int’l Congress on AIDS in Asia and the Pacific, 2011. Busan, South Korea.
  2. He Bo, Son SJ, Pho N, Lee SB. "Shape-differentiated silica nanotubes for biosensing." American Chemical Society National Meeting, 2005. Washington, DC.
  3. He Bo, Son SJ, Pho N, Lee SB. "Bio-coding silica nanotubes: Synthesis and application." American Chemical Society National Meeting, 2005. Washington, DC.

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