University of California, Riverside

Department of Nematology



Holly Bik's Faculty Page


holly bik  Holly Bik
Assistant Professor
Department of Nematology

Office: 2202A Genomics 
Lab: 2126 Genomics Building
Office phone: (951) 827-4230
email: holly.bik@ucr.edu
Lab Website: https://biklab.github.io

 

 

Research Areas

Research in the Bik Lab is intensely interdisciplinary, using high-throughput sequencing and diverse –Omics approaches to explore broad patterns in microbial eukaryote assemblages (biodiversity and phylogeography, functional roles for microbial taxa, and the relationship between species and environmental parameters), with an emphasis on free-living nematodes in marine sediments. Our long-term research interests lie at the interface between biology and computer science, using biological questions and evolutionary hypotheses to drive the development and refinement of –Omic approaches focused on marine microbial eukaryotes. Microbial eukaryotes (organisms <1mm, such as nematodes, fungi, protists, and other ‘minor’ metazoan phyla) are abundant and ubiquitous across every ecosystem on earth, performing key functions such as nutrient cycling and sediment stability in marine habitats. Yet, their unexplored diversity represents one of the major challenges in biology and currently limits our capacity to understand, mitigate and remediate the consequences of environmental change. Given this knowledge gap, the lab research themes span three key areas: 1) "Is Everything Everywhere?": Testing seminal biodiversity & biogeography hypotheses using –Omics, 2) “Systems Ecology” to investigate ecosystem function and species interactions, with an emphasis on microbial eukaryotes in marine sediments, and 3) Comparative phylogenomics and targeted genome sequencing of microbial eukaryotes as a complement to environmental –Omics

 

Selected Publications

Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WKT, Potter C, Bik HM. (2016) The ecologist’s field guide to sequence-based identification of biodiversity, Methods in Ecology and Evolution, 7(9): 1008-1018.
http://dx.doi.org/10.1111/2041-210X.12574

Derycke S, De Meester N, Rigaux A, Creer S, Bik H, Thomas WK, Moens T. (2016) Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability, Molecular Ecology, 25(9):2093-2110
http://dx.doi.org/10.1111/mec.13597

Bik HM (2014) Deciphering diversity and ecological function from marine metagenomes, The Biological Bulletin, 227:107-116. https://www.ncbi.nlm.nih.gov/pubmed/25411370

Bik HM, Pitch Interactive (2014) Phinch: An interactive, exploratory data visualization framework for –Omic datasets, bioRxiv, doi: http://dx.doi.org/10.1101/009944 (preprint)

Chariton A, Ho K, Proestou D, Bik H, Simpson S, Portis L, Cantwell M, Baguley J, Burgess R, Pelletier M, Perron M, Gunsch C (2014) A molecular-based approach for examining responses of microcosm-contained eukaryotes to contaminant-spiked estuarine sediments, Environmental Toxicology and Chemistry, 33(2): 359-369. http://dx.doi.org/10.1002/etc.2450

Darling A, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes, PeerJ, 2:e243. http://dx.doi.org/10.7717/peerj.243

Bik HM, Fournier D, Bergeron RD, Sung W, Thomas WK (2013) Intra-Genomic Variation in the Ribosomal Repeats of Nematodes, PLoS ONE, 8(10): e78230 http://dx.doi.org/10.1371/journal.pone.0078230

Bik HM, Halanych KM, Sharma J, Thomas WK (2012) Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. PLoS ONE, 7(6):e38550. http://dx.doi.org/10.1371/journal.pone.0038550

Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution, 27(4):233-243. http://dx.doi.org/10.1016/j.tree.2011.11.010

Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK (2012) Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Molecular Ecology, 21(5):1048-1059. http://dx.doi.org/10.1111/j.1365-294X.2011.05297.x

Bik HM, Lunt DH, Thomas WK, Lambshead PJD (2010) Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evolutionary Biology, 10:389. http://dx.doi.org/10.1186/1471-2148-10-389

Bik HM, Thomas WKT, Lambshead PJD, Lunt DH (2010) Moving towards a complete molecular framework of the Nematoda: A focus on the Enoplida and early-branching clades. BMC Evolutionary Biology, 10:353. http://dx.doi.org/10.1186/1471-2148-10-353

 

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Department Information

Department of Nematology
Margarita Flores
1447 Boyce Hall

Tel: (951) 827-3598
Fax: (951) 827-2364
E-mail: mverd003@ucr.edu

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