Holly Bik

Assistant Professor (Bioinformatics and computational biology not elsewhere classified)

University of California, Riverside

My work utilizes high-throughput sequencing approaches to explore broad patterns in microbial eukaryote assemblages (biodiversity and biogeography, functional roles for microbial taxa, and the relationship between species and environmental parameters), with a specific focus on benthic marine habitats. I am particularly interested in the integration of different data types (metagenomics, marker gene amplicons, and metatranscriptomics), and assessing data processing tools using a combination of environmental and simulated datasets. Biological questions thus drive the development and refinement of computational analysis specifically focused on eukaryotes, where specific research questions include: • How do different OTU pickers affect the biological interpretation of rRNA amplicon data derived from eukaryotic taxa, where genomes contain multiple rRNA gene copies and intragenomic variation across these gene sequences? • What new and novel biological insights can be gained through the development of innovative, exploratory data visualization tools? • How can we link disparate types of eukaryotic –omic data to better inform our understanding of ecosystem function? • How can we improve taxonomic assignments and increase our confidence in species presence/abundance for high-throughput environmental sequence data? (e.g. through tree placement, more robust mathematical/statistical approaches)


  • Metagenomics will highlight and drive links to taxonomic data: reply to Murray DOI: 10.1016/j.tree.2012.09.005
  • RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011 DOI: 10.4056/sigs.3156511
  • Sequencing our way towards understanding global eukaryotic biodiversity DOI: 10.1016/j.tree.2011.11.010
  • Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments DOI: 10.1111/j.1365-294X.2011.05297.x
  • Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida) DOI: 10.1186/1471-2148-10-389
  • Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades DOI: 10.1186/1471-2148-10-353
  • Rapid decline of PCR amplification from genomic extracts of DESS-preserved, slide-mounted nematodes DOI: 10.1163/156854109X422922
  • Small worms, big ideas: evolutionary inferences from nematode DNA DOI: 10.1111/j.1365-2699.2009.02219.x
  • Unravelling post-glacial colonization through molecular techniques: new insight from estuarine invertebrates DOI: 10.1111/j.1365-2699.2008.02037.x
  • Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill DOI: 10.1371/journal.pone.0038550
  • Molecular Diversity of Fungal Phylotypes Co-Amplified Alongside Nematodes from Coastal and Deep-Sea Marine Environments DOI: 10.1371/journal.pone.0026445
  • Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades DOI: 10.1186/1471-2148-10-353
  • Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities DOI: 10.1002/etc.2067

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Co-workers & collaborators

Jonathan Eisen

Professor - Davis, CA

Jonathan Eisen

Miriam Goldstein

Knauss Sea Grant Fellow - Washington DC

Miriam Goldstein

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