bold = lab members

2024

Pereira TJ, De Santiago A, Bik HM (2024) Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats. Molecular Ecology, 33(18): e17501. (open access publication)

Perry WB, Seymour M, Orsini L, Jâms IB, Milner N, Edwards F, Harvey R, de Bruyn M, Bista I, Walsh K, Emmett B, Blackman R, Altermatt F, Handley LL, Mächler E, Deiner K, Bik HM, Carvalho G, Colbourne J, Cosby BJ, Durance I, Creer S (2024) An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding, Nature Communications,15: 4372. (open access publication)

Kelly RP, Lodge DM, Lee KN, Theroux S, Sepulveda AJ, Scholin CA, Craine JM, Andruszkiewicz Allan E, Nichols KM, Parsons KM, Goodwin KD, Gold Z, Chavez FP, Noble RT, Abbott CL, Baerwald MR, Naaum AM, Thielen PM, Simons AL, Jerde CL, Duda JJ, Hunter ME, Hagan JA, Meyer RS, Steele JA, Stoeckle MY, Bik HM, Meyer CP, Stein E, James KE, Thomas AC, Demir-Hilton E, Timmers MA, Griffith JF, Weise MJ, Weisberg SB (2024) Toward a national eDNA strategy for the United States, Environmental DNA, 6(1): e432. (open access publication)

2023

Fountain-Jones NM, Giraud T, Zinger L, Bik H, Creer S, Videvall E (2024) Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions. Molecular Ecology, 33(2): e17223. (PDF Download)

Eastwood N, Zhou J, Derelle R, Abdallah MAE, Stubbings WA, Jia Y, Crawford SE, Davidson TA, Colbourne JK, Creer S, Bik H, Holler H, Orsini L (2023) 100 years of anthropogenic impact causes changes in freshwater functional biodiversity. eLife, 12: RP86576. (open access publication)

Pereira TJ, Walters TL, El-Shaffey HM, Bik HM#, Frischer M#. (2023) The microbiome of the pelagic tunicate Dolioletta gegenbauri, a link between the grazing and microbial food web?, Molecular Ecology, 32(23): 6564-6579. (# joint corresponding author; Invited submission for “Insights into Ecological & Evolutionary Processes via Community Metabarcoding” Special Issue; open access publication)

Gillespie RG, Bik HM, Hickerson MJ, Krehenwinkel H, Overcast I, Rominger AJ (2023) Insights into Ecological & Evolutionary Processes via Community Metabarcoding, Molecular Ecology, 32(23), 6083-6092. (Invited editorial for Special Issue; PDF Download)

2022

De Santiago A#, Pereira TJ#, Mincks SL, Bik HM. (2022) Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies, Environmental DNA, 4: 363-384. (# joint first author; open access publication)

Gorneau JA, Ausich WI, Bertolino S, Bik H, Daly M, Demissew S, Donoso DA, Folk R, Freire-Fierro A, Ghazanfar SA, Grace OM, Hu AQ, Kulkarni S, Lichter-Marck IH, Lohmann LG, Malumbres-Olarte J, Muasya AM, Pérez-González A, Singh Y, Siniscalchi CM, Specht CD, Stigall AL, Tank DC, Walker LA, Wright DF, Zamani A, Esposito LA. (2022) Framing the Future for Taxonomic Monography: Improving Recognition, Support, and Access. Bulletin of the Society of Systematic Biologists, 1(1):8328. (open access publication)

2021

Leray M, Wilkins LGE, Apprill A, Bik HM, Clever FK, Connolly SR, De Léon ME, Duffy JE, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan WO, O'Dea A, Pereira TJ, Petersen JM, Petticord DF, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. (2021) Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution, PLoS Biology, 19(8): e3001322. (open access publication)

Bik HM (2021) Just keep it simple? Benchmarking the accuracy of taxonomy assignment software in metabarcoding studies. Molecular Ecology Resources, 21(7): 2187-2189. (invited perspective; PDF Download)

Rodriguez-Ezpeleta N, Zinger L, Kinziger A, Bik H, Bonin A, Coissac E, Emerson B, Lopes C, Pelletier T, Taberlet P, Narum S (2021) Biodiversity monitoring using environmental DNA, Molecular Ecology Resources, 21(5): 1405-1409 (PDF Download)

Mincks SL, Pereira TJ, Sharma J, Blanchard A, Bik HM. (2021) Composition of marine nematode communities across broad longitudinal and bathymetric gradients in the Northeast Chukchi and Beaufort Seas, Polar Biology, 44: 85-103 (PDF Download)

Ingels J, Aronson R, Smith C, Baco A, Bik H, Blake J, Brandt A, Cape M, DeMaster D, Dolan E, Domack E, Fire S, Geisz H, Gigliotti M, Griffiths H, Halanych K, Havermans C, Huettmann F, Ishman S, Kranz S, Leventer A, Mahon A, McClintock J, McCormick M, Mitchell B, Murray A, Peck L, Rogers A, Shoplock. B, Smith K, Steffel B, Stukel M, Sweetman A, Taylor M, Thurber A, Truffer M, Van de Putte A, Vanreusel A, Zamora-Duran M. (2021) Antarctic Ecosystem Responses following Ice Shelf Collapse and Iceberg Calving: Science Review and Future Research, WIREs Climate Change, 12(1): e682. (PDF Download)

2020

Pereira TJ, De Santiago A, Schuelke T, Hardy SM, Bik HM (2020) The impact of intragenomic rRNA variation on metabarcoding‐derived diversity estimates: A case study from marine nematodes, Environmental DNA, 2(4): 519-534 (open access publication)

2019

Qing X#, Bik HM#, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. (2019) Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: implications for phylogeny, species delimitation, and life history inference, Molecular Ecology Resources, 20(1):318-332. (# joint first author; PDF Download)

Wilkins LGE, Leray M, O’Dea A, Yuen B, Peixoto RS, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios HA, Lucey NM, Mejia LC, Rasher DB, Sharp KH, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. (2019) Host-associated microbiomes drive structure and function of marine ecosystems, PLoS Biology, 17(11): e3000533. (open access publication)

Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. (2019) Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure, Communications Biology, 2: 362. (open access publication)

Bik, HM (2019) Microbial Metazoa Are Microbes Too, mSystems, 4: e00109-19. (invited perspective; open access publication)

Zinger L, Bonin A, Alsos I, Bálint M, Bik H, Boyer F, Chariton A, Creer S, Coissac E, Deagle  B, De Barba M, Dickie I, Dumbrell A, Ficetola GF, Fierer N, Fumagalli L, Gilbert T, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen P, Willerslev E, Taberlet P (2019) DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions, Molecular Ecology, 28(8): 1857-1862. (PDF Download)

Bik HM, Alexiev A, Aulakh S, Bharadwaj L, Flanagan J, Haggerty M, Hird S, Jospin G, Lang JM, Sauder L, Neufeld J, Shaver A, Sethi A, Eisen JA, Coil D (2019) Microbial community succession and nutrient cycling responses following perturbations of experimental saltwater aquaria, mSphere, 4 (1): e00043-19. (open access publication)

2018

Katz DS, Allen G, Barba LA, Berg DR, Bik H, Boettiger C, Borgman CL, Brown CT, Buck S, Burd R, de Waard A, Eve MP, Granger BE, Greenberg J, Howe A, Howe B, Khanna M, Killeen TL, Mayernik M, McKiernan E, Mentzel C, Merchant N, Niemeyer KE, Noren L, Nusser SM, Reed DA, Seidel E, Smith M, Spies JR, Turk M, Van Horn JD, Walsh J (2018) The principles of tomorrow’s university, F1000Research, 7: 1926. (open access publication)

Nascimento FJA, Lallias D, Bik HM, Creer S (2018) Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing, Scientific Reports, 8: 11737. (open access publication)

Schuelke T, Pereira TJ, Hardy SM, Bik HM (2018) Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats, Molecular Ecology, 27(8): 1930-1951. (invited submission for “Host-Associated Microbiome” special issue; PDF Download)

Seymour M, Durance I, Cosby BJ, Ransom-Jones E, Deiner K, Ormerod SJ, Colbourne JK, Wilgar G, Carvalho GR, de Bruyn M, Edwards F, Emmett BA, Bik HM, Creer S (2018) Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms, Communications Biology, 1(1):4. (editors’ picks for one year anniversary collection; open access publication)

2017

Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: transforming how we survey animal and plant communities, Molecular Ecology, 26(21): 5872-5895. (invited review; open access publication)

Bik HM (2017) Let’s Rise Up to Unite Taxonomy and Technology, PLoS Biology, 15(8): e2002231. (invited "Research Matters" article; open access publication)

Brannock PM, Sharma J, Bik HM, Thomas WK, Halanych KM. (2017) Spatial and temporal variation of intertidal nematodes in the Northern Gulf of Mexico after the Deepwater Horizon oil spill, Marine Environmental Research, 130:200-212. (PDF Download)

2016

Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM. (2016) Microbial community patterns associated with Automated Teller Machine (ATM) keypads in New York City, mSphere,1(6):e00226-16. (open access publication)

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. (invited review; open access publication)

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. (PDF download)

2015

Adams R#, Bateman AC#, Bik HM#, Meadow JF# (2015) Microbiota of the indoor environment: a meta-analysis, Microbiome, 3:49. (# all authors contributed equally; open access publication)

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 download)

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. (open access publication)

2014

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

Bik HM, Coil D, Eisen JA (2014) microBEnet: Lessons learned from building an interdisciplinary scientific community in the online sphere, PLoS Biology, 12(6): e1001884. (open access publication)

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(1783): 20133076. (PDF download)

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 download)

Darling A, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes, PeerJ, 2:e243. (PeerJ Picks 2015 Collection; open access publication)

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 publication)

Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank CE, Cirranello AL, Cui H, Daly M, Dietterich TG, Gasparich G, Irvine J, Julius M, Kaufman S, Law E, Liu J, Moore LR, O’Leary MA, Passarotti M, Ranade S, Simmons NB, Stevenson DW, Thacker RW, Theriot EC, Todorovic S, Velazco PM, Walls RL, Wolfe JM, Yu A (2013) Next Generation Phenomics for the Tree of Life, PLOS Currents Tree of Life, doi:10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733 (open access publication)

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 publication)

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

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 download)

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. (PDF download)

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 publication)

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. (PDF download)

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. ("From the Cover" paper; PDF download)

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 publication)

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. (open access publication)

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. (open access publication)

Bik HM (2010) Small worms, big ideas: Evolutionary inferences from nematode DNA. Journal of Biogeography. 37(1):1-2. (invited perspective; PDF download)

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):827-34. (PDF download)

Bik HM (2009) Unraveling post-glacial colonization through molecular techniques: new insight from estuarine invertebrates. Journal of Biogeography, 36:16-17. (invited perspective; PDF download)

Book Chapters

Ingels J, Amon D, Bernardino AF, Bhadury P, Bik H, Clark MR, Dahlgren T, Jones DOB, McClain C, Nunnally C, Snelgrove P, Tuhumwire JT, Yasuhara M (2021) Chapter 7M Abyssal Plains, in The Second Global Integrated Marine Assessment: World Ocean Assessment II (United Nations, New York), Vol I, p 453-476. (PDF download)

Bik HM, Thomas WK (2016) Biodiversity and the (data) Beast. In: Olson J, Hughes J, Cotton, J (eds.) Next Generation Systematics: Studying Evolution and Diversity in the Era of Ubiquitous Genomics. Cambridge, UK: Cambridge University Press. pp. 154-174. (PDF download)

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. London: SAGE Publications. pp. 364-372. (PDF download)

Meeting Reports

Arora R, Li X, Hurwitz B, Fay D, Panda DK, Valeev E, Wang S, Moore S, Chandrasekaran S, Cao T, Bik H, Curry M, Islam T (2020) Future Directions of the Cyberinfrastructure for Sustained Scientific Innovation (CSSI) Program, arXiv, DOI: arXiv:2010.15584, https://arxiv.org/abs/2010.15584 (open access publication)

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 publication)

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 publication)