Chris Berthiaume

I support reproducible computational research in the Armbrust Lab. My primary focus is working with the SeaFlow instrument, our in-house continuous flow cytometer. I write software to analyze SeaFlow data (seaflowpy, popcycle), manage the data itself, and create systems for realtime collection, processing, and monitoring of SeaFlow data while at sea. I’ve also worked on a number of genomics projects in the Armbrust Lab involving RNA microarrays, Sanger and 454 EST library creation, SOLiD and Illumina short-read transcriptomes and genomes, and de novo SOLiD short-read metagenomic assemblies.

github: https://github.com/ctberthiaume

Publications

2019

  1. SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific
    François Ribalet, Chris Berthiaume, Annette Hynes, Jarred Swalwell, Michael Carlson, Sophie Clayton, Gwenn Hennon, Camille Poirier, Eric Shimabukuro, Angelicque White, and E. Virginia Armbrust
    Scientific Data, Nov 2019
    DOI: 10.1038/s41597-019-0292-2
  2. Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana
    Johanna AL Goldman, Megan J. Schatz, Chris T. Berthiaume, Sacha N. Coesel, Mónica V. Orellana, and E. Virginia Armbrust
    PloS one, 2019
    DOI: 10.1371/journal.pone.0222325

2018

  1. Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana
    Julie A. Koester, Chris T. Berthiaume, Naozumi Hiranuma, Micaela S. Parker, Vaughn Iverson, Rhonda Morales, Walter L. Ruzzo, and E. Virginia Armbrust
    Scientific reports, 2018
    DOI: 10.1038/s41598-018-28630-4

2016

  1. Genomic evidence of adaptive evolution in emergent Vibrio parahaemolyticus ecotypes
    Jeffrey W. Turner, Chris T. Berthiaume, Rhonda Morales, E. Virginia Armbrust, and Mark S. Strom
    Elementa: Science of the Anthropocene, Jul 2016
    DOI: 10.12952/journal.elementa.000117

2015

  1. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria
    S. A. Amin, L. R. Hmelo, H. M. Tol, B. P. Durham, L. T. Carlson, K. R. Heal, R. L. Morales, C. T. Berthiaume, M. S. Parker, B. Djunaedi, A. E. Ingalls, M. R. Parsek, M. A. Moran, and E. V. Armbrust
    Nature, Jun 2015
    DOI: 10.1038/nature14488
  2. Diatom acclimation to elevated CO 2 via cAMP signalling and coordinated gene expression
    Gwenn MM Hennon, Justin Ashworth, Ryan D. Groussman, Chris Berthiaume, Rhonda L. Morales, Nitin S. Baliga, Mónica V. Orellana, and E. V. Armbrust
    Nature Climate Change, 2015
    DOI: 10.1038/nclimate2683

2014

  1. Transcriptional responses of three model diatoms to nitrate limitation of growth
    Sara J. Bender, Colleen A. Durkin, Chris T. Berthiaume, Rhonda LM Morales, and E. Virginia Armbrust
    Frontiers in Marine Science, 2014
    DOI: 10.3389/fmars.2014.00003
  2. The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis
    Jeff S. Bowman, Chris T. Berthiaume, E. Virginia Armbrust, and Jody W. Deming
    FEMS microbiology ecology, 2014
    DOI: 10.1111/1574-6941.12331

2012

  1. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability
    Adrian Marchetti, David M. Schruth, Colleen A. Durkin, Micaela S. Parker, Robin B. Kodner, Chris T. Berthiaume, Rhonda Morales, Andrew E. Allen, and E. Virginia Armbrust
    Proceedings of the National Academy of Sciences, Feb 2012
    DOI: 10.1073/pnas.1118408109
  2. Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
    Vaughn Iverson, Robert M. Morris, Christian D. Frazar, Chris T. Berthiaume, Rhonda L. Morales, and E. Virginia Armbrust
    Science, Feb 2012
    DOI: 10.1126/science.1212665

2008

  1. Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses
    Thomas Mock, Manoj Pratim Samanta, Vaughn Iverson, Chris Berthiaume, Matthew Robison, Karie Holtermann, Colleen Durkin, Sandra Splinter BonDurant, Kathryn Richmond, Matthew Rodesch, Toivo Kallas, Edward L. Huttlin, Francesco Cerrina, Michael R. Sussman, and E. Virginia Armbrust
    Proceedings of the National Academy of Sciences, Feb 2008
    DOI: 10.1073/pnas.0707946105

2004