Brian J Arnold

CV

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Personal Summary

Highly adaptive computational biologist with 9+ years of professional data-science experience, specializing in software (Python), machine learning, and detailed analysis of diverse data modalities. Successfully led projects from conception to completion and significantly improved analytical capabilities of research teams by managing large datasets with scalable software. Learns fast, works hard, and navigates uncertainty well.

Skills

  • Software: proficient in Python, R, Bash; familiar with C/C++; comfortable reading code in any language
  • Machine learning: proficient in scipy, scikit-learn, scikit-image, PyTorch, Keras, numpy, Statsmodels
  • Bioinformatics: adept at genomics (short-/long-read), spatial/single-cell transcriptomics, images/videos analyses
  • Large datasets: adept at parallelizing tasks via Snakemake workflows, Python multiprocessing libraries
  • Computing: adept at high-performance computing (SLURM), experience with cloud computing (GCP, AWS)
  • Data visualization: proficient with Matplotlib and Seaborn; experience with Plotly for interactive 3D figures
  • Communication: authored 25 scientific publications, 4 successful grant/fellowship applications
  • Teaching and mentoring: taught 11 highly acclaimed workshops, designed 7 of these from scratch; patient with beginners

Experience

Departmental Data Scientist (2023-present)
Princeton University, Ecology and Evolutionary Biology

  • Segmented 3D 2-photon microscopy videos of brains and directed statistical analyses to decode animal behavior
  • Led machine-/deep-learning analyses of 40+ enhancer-readout datasets to characterize cis-regulatory motifs
  • Managed 2 trainees on large scale sequencing projects involving 700+ samples and 10+ TB of data
  • Gave 2 workshops on machine learning and Snakemake workflows for computational biology

Biomedical Data Scientist (2020-2023)
Princeton University, Computer Science

  • Packaged new software to optimize neural networks that segment tissues in spatial transcriptomics data and run at scale
  • Authored two modules of new software to detect copy-number variants in bulk tumor sequencing data
  • Managed Conda releases and developed software that characterizes evolutionary history of somatic mutations
  • Authored Science paper (co-first) on the evolutionary genetics of tusklessness in African elephants
  • Taught 4 workshops on Python Packaging, data visualization, machine learning, and R

Senior Bioinformatics Scientist (2018-2020)
Harvard University

  • Created and published Snakemake workflow to massively parallelize variant calling
  • Designed machine learning classifier to quantify scale of horizontal gene transfer in world’s largest flower species
  • Authored highly cited review (cover article) in Nature Reviews Microbiology on horizontal gene transfer in bacteria
  • Taught 2 workshops on R and genomics

Consultant (2018)
Day Zero Diagnostics

  • Disentangled unexpected transmission dynamics within Massachusetts General Hospital using bacterial genomes

Postdoctoral Fellow (2015-2018)
Harvard T.H. Chan School of Public Health

  • Inferred recombination parameters from bacterial genomes via Bayesian optimization with Gaussian Process regression
  • Designed fast, memory-efficient population genetic simulators in C++ to test novel analyses of bacterial genomes
  • Mentored 1 Master’s student, 2 undergraduates

PhD Candidate (2009-2015)
Harvard University

  • Bomblies lab: generated a variety of genomic data to study the evolutionary origins of tetraploid Arabidopsis arenosa
  • Kleckner lab: used immunofluorescence cytology to explore meiotic cell cycle delays in tetraploid yeast
  • Wakeley group: developed new population genetic theory for tetraploids using probability theory and Markov chains

Fulbright Fellow (2009)
University of Oulu – Finland

  • Sequenced candidate genes to identify mutations associated with hairlessness in the plant Arabidopsis lyrata

Education

Harvard University
PhD, Organismic and Evolutionary Biology (2015)

  • Dissertation: “Evolutionary dynamics of a multiple-ploidy system in Arabidopsis arenosa”
  • Primary advisor: Kirsten Bomblies
  • Secondary advisor: Nancy Kleckner
  • Committee members: John Wakeley, David Reich, Hopi Hoekstra

University of Minnesota – Twin Cities
BS (Honors and High Distinction), Plant Biology (2008)

Awards And Honors

  • NIH F32 Postdoctoral Fellowship (2016-2018)
  • NSF Doctoral Dissertation Improvement Grant (2012)
  • Two Certificate of Distinction in Teaching (2010, 2012)
  • NSF Graduate Research Fellowship (2010-2015)
  • Herchel Smith Graduate Fellowship (2009-2011)
  • James Mill Peirce Fellowship (2009)
  • Fulbright Full Grant (2008-2009)
  • Merck Index Award (2007)
    • best student in organic chemistry series
  • Prentice Hall Book Prize (2006)
    • highest grade in organic chemistry II

Selected Publications

*authors contributed equally to this work

  • Chitra U*, Arnold B *, B Raphael (2024). “Quantifying higher-order epistasis: beware the chimera” (in review).

  • Chitra U, Arnold B, Sarkar H, Ma C, Lopez-Darwin S, Sanno K, Raphael B (2024). Mapping the topography of spatial gene expression with interpretable deep learning. RECOMB 2024.

  • Myers M, Arnold B, Bansal V, Balaban M, Mullen K, Zaccaria S, B Raphael (2024). HATCHet2: clone-and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biology 25 (1):1-28.

  • Mirchandani C, Shultz A, Thomas G, Smith S, Baylis M, Arnold B, Corbett-Detig R, Enbody E, T Sackton (2024). A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Molecular Biology and Evolution 41 (1): msad270.

  • Arnold B, Huang IT, and WP Hanage (2022). Horizontal gene transfer and adaptive evolution in bacteria. Nature Reviews Microbiology 20, 206-218.
    • highlighted as the cover article for April issue of Nature Reviews Microbiology
  • 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.
    • featured in over 40 media interviews including New York Times, Science magazine, and Nature magazine

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

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

Teaching Exp.

Princeton University workshops

  • Introduction to computational biology workflows (2024; GitHub)
    • Designed and taught three 2-hour sessions
    • 26 attendees
  • Introduction to machine learning for Ecology and Evolutionary Biology (2023; GitHub)
    • Designed and taught two 1-hour sessions
    • 45 attendees
  • Introduction to machine learning (2023; GitHub)
    • Designed and taught one of five 1-hour sessions
    • 90+ attendees
  • Data visualization python (2022; GitHub)
    • Designed and taught one 2-hour session
    • 20+ attendees
  • Level up your python (2022)
    • Assisted instructor for one 2-hour session
    • 20+ attendees
  • Best practices in python packaging (2021)
    • Designed and co-taught one 3-hour session
    • 10+ attendees
  • Introduction to data analysis with R (2021)
    • Designed and taught one 2-hour session
    • 10+ attendees

Harvard University workshops

  • Introduction to R and tidyverse (2019-2020)
    • Taught three 2-hour sessions
    • 15+ attendees
  • Read mapping and variant calling (2019-2020)
    • Taught one 3-hour session
    • 5+ attendees

Harvard University classes

  • Genetics and Genomics (2012)
    • Taught weekly recitations, graded homework and exams; received teaching award
  • Coalescent Theory (2010)
    • Taught weekly recitations, graded homework and exams; received teaching award

University of Minnesota classes

  • Biochemistry (2008)
    • Taught weekly recitations, graded exams
  • Organic Chemistry (2007)
    • Supervised lab experiments, graded exams
  • General Botany (2007)
    • Supervised lab experiments, graded exams

Selected Presentations

Contributed Talk – “New analyses for copy number, tumor evolution, and spatial transcriptomics” – 2022 National Cancer Institute’s Genomic Data Analysis Network

Invited Talk – “Characterizing copy number aberrations and intratumor heterogeneity with machine learning” – 2022 University of Edinburgh

Invited Talk – “Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen” – 2019 University of Nottingham Departmental Seminar

Invited Talk – “Genomic landscape of linked selection in N. gonorrhoeae” – 2018 Society for Molecular Biology and Evolution Satellite Workshop on “Genome Evolution in Pathogen Transmission and Disease”

Contributed Talk – “Weak epistasis may drive adaptation in recombining bacteria” – 2017 Society for Molecular Biology and Evolution

Invited Talk – “Evolutionary dynamics of a multiple ploidy system in A. arenosa” – 2015 University of Oslo Departmental Seminar Series

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