Brian J Arnold :: Data Science

Education

Education

  • PhD in Organismic and Evolutionary Biology, Harvard University, 2015
    • Dissertation: “Evolutionary dynamics of a multiple-ploidy system in Arabidopsis arenosa”
    • Advisors: Kirsten Bomblies (primary), Nancy Kleckner (secondary)
    • PhD Committee: John Wakeley, David Reich, Hopi Hoekstra
  • BS in Plant Biology, University of Minnesota – Twin Cities, 2008
    • Honors and High Distinction

Professional Exp

  • Departmental Data Scientist, Princeton University (2023-present)
    • Collaborate with faculty, consult students/postdocs, teach workshops in EEB department
  • Senior Biomedical Data Scientist, Princeton University (2020-2023)
    • Teach workshops, collaborate with faculty, develop software in CS department
  • Senior Bioinformatics Scientist III, Harvard University (2018-2020)
    • Teach workshops, collaborate with faculty, help students analyze large sequencing datasets using high-performance computing
  • Consultant, Day Zero Diagnostics (2018)
    • Bacterial genomics, transmission dynamics within Massachussetts General Hospital

Research Exp

  • Ruth L. Kirschstein Postdoctoral Fellow, Harvard T.H. Chan School of Public Health (2015-2018)
    • Advisors: Bill Hanage, Marc Lipsitch, Yonatan Grad
  • Visiting Scientist, University of Helsinki (2016)
    • Jukka Corander’s group: Bayesian optimization, approximate bayesian computation, machine learning
  • Fulbright Fellow, University of Oulu (2009)
    • Advisor: Outi Savolainen

Skills

  • Programming: proficient in Python/Snakemake, R, Unix/Bash, Perl; familiar with C++
  • Bioinformatics: variant calling, genome assembly, metagenomics, high-performance and cloud computing
  • Teaching and mentoring: passionate about student development, patient with beginners
  • Written and oral communication: 16 scientific publications, 4 successful grant/fellowship applications, 3 invited talks
  • Able to work independently and as part of a team: creative thinker, enjoy collaborations and helping trainees

Academic Awards

  • Postdoctoral Awards (Harvard T.H. Chan School of Public Health)
    • NIH F32 Postdoctoral Fellowship (2016-2018)
  • Graduate Awards (Harvard University)
    • NSF Doctoral Dissertation Improvement Grant (2012)
    • 2X Certificate of Distinction in Teaching (2010, 2012)
    • NSF Graduate Research Fellowship (2010-2015)
    • Herchel Smith Graduate Fellowship (2009-2011)
    • James Mill Peirce Fellowship (2009)
  • Undergraduate Awards (University of Minnesota – Twin Cities)
    • Fulbright Full Grant (2008-2009)
      • Advised by Outi Savolainen at University of Oulu, Finland
    • Merck Index Award (2007)
      • best student in organic chemistry series
    • Prentice Hall Book Prize (2006)
      • highest grade in organic chemistry II

Teaching Exp.

  • As Senior Biomedical Data Scientist
    • Introduction to Machine Learning (2022)
    • Data Vizualization in Python (2022)
    • Best Practices in Python Packaging (2021)
    • Introduction to R (2021)
  • As Senior Bioinformatics Scientist
    • Introduction to R with Tidyverse (2019-2020)
    • Read mapping and variant valling (2019-2020)
  • As Ruth L. Kirschstein Postdoctoral Fellow
    • Mentored Master’s Student (2016-2017)
    • Dept. of Epidemiology summer program (2016)
  • As Graduate teaching fellow
    • Genetics and Genomics, OEB 50 (2012)
    • Coalescent Theory, OEB 252 (2010)
  • As Undergraduate teaching assistant
    • Biochemistry
    • Organic Chemistry
    • General Botany

Publications

  • Peer-reviewed publications

    • Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, and EJ Alm (2022). Metrics to relate COVID-19 wastewater data to clinical testing dynamics. Water Research 212 (2022) 118070.

    • Arnold B, Huang IT, and WP Hanage (2022). Horizontal gene transfer and adaptive evolution in bacteria. Nature Reviews Microbiology 20, 206-218.

    • Campbell-Staton SC†, Arnold B†, Gonçalves D, Granli P, Poole J, Long RA, and Pringle RM (2021). Ivory poaching and the rapid evolution of tusklessness in African elephants. Science 374, 483-487.
      • † these authors contributed equally to this work

    • Cai L, Arnold B,Xi Z, Khost D, Patel N, Hartmann C, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton T, and CC Davis (2021). Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae). Current Biology: 31 (5), 1002-1011.e9.

    • Azarian T, Martinez P, Arnold B, Qiu X, Grant L, Corander J, Fraser C, Croucher N, Hammitt L, Reid R, Santosham M, Weatherholtz R, Bentley S, O’Brien K, Lipsitch M, and WP Hanage (2020). Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biology: https://doi.org/10.1371/journal.pbio.3000878.

    • Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, and Y Grad (2019). Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen. Molecular Biology and Evolution 37(2):417-428.

    • Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees J, Chewapreecha C, Bentley S, Harris S, Parkhill J, Croucher N, and J Corander (2019). Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Research 47(18):e112-e112.

    • Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman C, Marhold K, Slotte T, Bomblies K, and L Yant (2019). Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nature Ecology and Evolution 3(3):457-468

    • Shapiro L, Paulson J, Arnold B, Scully E, Zhaxybayeva O, Pierce N, Rocha J, Klepac-Ceraj V, Holton K, and R Kolter (2018). An introduced crop plant is driving diversification of the virulent plant pathogen Erwinia tracheiphila. mBio 9:e01307-18.

    • Wadsworth C, Arnold B, Sater M, and Y Grad (2018). Azithromycin resistance through interspecific acquisition of an epistasis dependent efflux pump component and transcriptional regulator in Neisseria gonorrhoeae. mBio 9:e01419-18

    • Azarian T, Grant L, Arnold B, Hammitt L, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson C, Bentley S, O’Brien K, Hanage WP, and M Lipsitch (2018). The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathogens: https://doi.org/10.1371/journal.ppat.1006966.

    • Arnold B, Gutmann M, Grad Y, Sheppard S, Corander J, Lipsitch M, and WP Hanage (2018). Weak epistasis may drive adaptation in recombining bacteria. Genetics 208(3):1247-1260.

    • Corander J, Fraser C, Gutmann M, Arnold B, Hanage WP, Bentley S, Lipsitch M, and N Croucher (2017). Frequency-dependent selection in vaccine-associated pheumococcal population dynamics. Nature ecology & evolution 1:1950-1960.

    • Arnold B, Lahner B, DaCosta J, Weisman C, Hollister J, Salt D, Bomblies K, and L Yant (2016). Borrowed alleles and convergence in serpentine adaptation. Proceedings of the National Academy of Sciences of the USA, 113(29): 8320-8325.

    • Baduel P, Arnold B, Weisman C, Hunter B, and K Bomblies (2016). Habitat-associated life history and stress-tolerance variation in Arabidopsis arenosa. Plant physiology, 171(1): 437-451.

    • Arnold B, Kim S, and K Bomblies. (2015). Single origin of autotetraploid Arabidopsis arenosa followed by interploidy admixture. Molecular Biology and Evolution, 32(6):1382-1395.

    • Wright K, Arnold B, Xue K, Šurinová M, O’Connell J, and K Bomblies, (2014). Selection on meiosis genes in diploid and tetraploid Arabidopsis arenosa. Molecular Biology and Evolution, 32(4): 944-955.

    • Arnold B, Corbett-Detig R, Hartl D, and K Bomblies (2013). RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, Vol 22: 3179-3190.

    • Yant L, Hollister JD, Wright K, Arnold B, Higgins JD, Franklin F, and K Bomblies, (2013). Meiotic adaptation to genome duplication in Arabidopsis arenosa. Current Biology. 23, pp. 2151-2156.

    • Hollister J, Arnold B, Svedin E, Xue K, Dilkes B, and K Bomblies, (2012). Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genetics, 8(12): e1003093

    • Arnold B, Bomblies K, and J Wakeley (2012). Extending coalescent theory to autotetraploids. Genetics 192(1):195-204.
Search