Assistant Professor, UC Riverside

CV + Publications

A PDF of my current CV is available to download here (last updated January 30, 2016).

Click here for my Google Scholar Profile


Submitted or in Preparation

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

Bik HM, Alexiev A, Lang JM, Neufeld J, Sauder L, Jospin G, Eisen JA, Flanagan J, Haggerty M, Shaver A, Bharadwaj L, Aulakh S, Hird S, Sethi A, Coil D. Microbial biogeography and community succession in aquariums, in preparation

Bik HM, Sharma J, Halanych K, Thomas WK. Illumina sequencing reveals long-term community shifts in sediment microbial eukaryote communities impacted by the Deepwater Horizon oil spill, in preparation

2016

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

2015

Adams R#, Bateman AC#, Bik HM#, Meadow JF# (2015) Microbiota of the indoor environment: a meta-analysis, Microbiome, 3:49. doi: 10.1186/s40168-015-0108-3 (# all authors contributed equally) open access PDF

Bik HM, Dove ADM, Goldstein MC, Helm RR, MacPherson R, Martini K, Warneke A, McClain C (2015) Ten Simple Rules for Effective Online Outreach. PLoS Computational Biology, 11(4): e1003906. doi:10.1371/journal.pcbi.1003906 open access PDF

NESCent Working Group on the Evolutionary Biology of the Built Environment, Martin LJ, Adams RI, Bateman A, Bik HM, Hawks J, Hird SM, Hughes D, Kembel SW, Kinney K, Kolokotronis SO, Levy G, McClain C, Meadow JF, Medina RF, Mhuireach G, Moreau CS, Munshi-South J, Nichols LM, Palmer C, Popova L, Schal C, Täubel M, Trautwein M, Ugalde JA, Dunn RR (2015) Evolution of the Indoor Biome, Trends in Ecology and Evolution, 30(4): 223–232. PDF

2014

Bik HM (2014) Deciphering diversity and ecological function from marine metagenomes, Biological Bulletin, 227:107-116. PDF

Bik HM, Coil DA, Eisen JA (2014) microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere. PLoS Biology, 12(6): e1001884. doi:10.1371/journal.pbio.1001884 open access PDF

Morgan MJ, Bass D, Birky CW, Bik H, Blaxter M, Crisp MD, Derycke S, Fitch D, Fontaneto D, Hardy CM, King AJ, Kiontke KC, Moens T, Pawlowski JW, Porazinska D, Tang CQ, Thomas WK, Yeates DK, Creer S (2014) A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proceedings of the Royal Society B, 281: 20133076. PDF

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. PDF

Darling A, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes, PeerJ, 2:e243. open access PDF **Article selected for the PeerJ Picks 2014 Collection**

2013

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. open access PDF

Bik HM, Goldstein MC (2013) An Introduction to Social Media for Scientists, PLoS Biology, 11(4): e1001535. open access PDF

Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O’Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath T, Midford P, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A (2013) Phylotastic! Making Tree-of-Life Knowledge Accessible, Re-usable and Convenient, BMC Bioinformatics, 14(1):158. open access PDF

Ho KT, Chariton AA, Portis LM, Proestou D, Cantwell MG, Baguley JG, Burgess RM, Simpson S, Pelletier MC, Perron MM, Gunsch CK, Bik HM, Katz D, Kamikawa A (2013) Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities. Environmental Toxicology and Chemistry, 32(2):384–92.  PDF

2012

Bik HM, Thomas, WK (2012) Metagenomics will highlight and drive links to taxonomic data: reply to Murray, Trends in Ecology and Evolution, 27 (12), 652-653. doi:10.1016/j.tree.2012.09.005  PDF

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. open access PDF  Data available at  Dryad_button_v1

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. DOI: 10.1016/j.tree.2011.11.010  PDF

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. doi:10.1111/j.1365-294X.2011.05297.x (“From the Cover”)  PDF  Data available at  Dryad_button_v1

2011

Bhadury P#, Bik H#, Lambshead PJD, Austen MC, Smerdon GR, Rogers AD (2011) Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments. PLOS One, 6 (10):e26445. (# joint first author). open access PDF

2010

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. doi:10.1186/1471-2148-10-389  open access PDF

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. doi:10.1186/1471-2148-10-353  open access PDF

Bik HM (2010) Small worms, big ideas: Evolutionary inferences from nematode DNA. Journal of Biogeography. 37(1):1-2. DOI:10.1111/j.1365-2699.2009.02219.x  PDF

2009

Bik HM, Hawkins LE, Hughes JA, Lambshead PJD (2009) Rapid decline of PCR amplification from genomic extracts of DESS-preserved, slide-mounted nematodes. Nematology, 11(6), 827-834.  DOI:100.1163/156854109X422922  PDF

Bik HM (2009) Unraveling post-glacial colonization through molecular techniques: new insight from estuarine invertebrates. Journal of Biogeography, 36, 16-17.  DOI: 10.1111/j.1365-2699.2008.02037.x  PDF


Book Chapters

Bik HM, Thomas WK (in press) Biodiversity and the (data) Beast. In: Hughes J., Cotton, J., and Olson, P. (eds.) Next Generation Systematics: Studying Evolution and Diversity in the Era of Ubiquitous Genomics, Cambridge University Press, UK.

Thaler AD, Zelnio KA, Freitag A, MacPherson R, Shiffman D, Bik H, Goldstein MC, McClain C (2012) Digital Environmentalism: Tools and strategies for the evolving online ecosystem. In: D. Gallagher (ed.) Environmental Leadership: A Reference Handbook, SAGE Publications, London.


PhD Thesis

Bik HM (2010) Resolving phylogenetic relationships within the order Enoplida (Phylum Nematoda). PhD Thesis, University of Southampton, UK.  PDF available on Figshare


Meeting Reports

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Wegener Parfrey L, Stajich JE (2013) Meeting Report: Fungal ITS Workshop (October 2012), Standards in Genomic Sciences, 8(1): doi:10.4056/sigs.3737409 open access PDF

Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA, Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EO, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J. (2012) RCN4GSC Workshop Report: Managing data at the interface of biodiversity and (meta) genomics, March 2011. Standards in Genomic Sciences, 7(1): doi:10.4056/sigs.3156511 open access PDF


Other Publications

NSF RAPID project highlighted, US National Commission on the BP Deepwater Horizon Oil Spill and Offshore Drilling: Report to the President (2011)

Online writing was selected for inclusion in the print anthology “Open Lab 2010: Best Science Writing on the Web”