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Holly Bik - Publications

Affiliations: 
University of California, Davis, Davis, CA 
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Fountain-Jones NM, Giraud T, Zinger L, Bik H, Creer S, Videvall E. Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions. Molecular Ecology. PMID 38014746 DOI: 10.1111/mec.17223  0.393
2023 Gillespie RG, Bik HM, Hickerson MJ, Krehenwinkel H, Overcast I, Rominger AJ. Insights into Ecological & Evolutionary Processes via community metabarcoding. Molecular Ecology. 32: 6083-6092. PMID 37999451 DOI: 10.1111/mec.17208  0.324
2023 Eastwood N, Zhou J, Derelle R, Abdallah MA, Stubbings WA, Jia Y, Crawford SE, Davidson TA, Colbourne JK, Creer S, Bik H, Hollert H, Orsini L. 100 years of anthropogenic impact causes changes in freshwater functional biodiversity. Elife. 12. PMID 37933221 DOI: 10.7554/eLife.86576  0.34
2022 Pereira TJ, Walters TL, El-Shaffey HM, Bik HM, Frischer ME. The microbiome of the pelagic tunicate Dolioletta gegenbauri: A potential link between the grazing and microbial food web. Molecular Ecology. PMID 35989550 DOI: 10.1111/mec.16668  0.419
2021 Leray M, Wilkins LGE, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy JE, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, et al. Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. Plos Biology. 19: e3001322. PMID 34411089 DOI: 10.1371/journal.pbio.3001322  0.593
2019 Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure. Communications Biology. 2: 362. PMID 31925166 DOI: 10.1038/s42003-019-0610-4  0.391
2019 Xue Q, Bik H, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation, and life history inference. Molecular Ecology Resources. PMID 31721426 DOI: 10.1111/1755-0998.13118  0.511
2019 Wilkins LGE, Leray M, O'Dea A, Yuen B, Peixoto R, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios H, Lucey NM, Mejia LC, Rasher DB, Sharp K, et al. Host-associated microbiomes drive structure and function of marine ecosystems. Plos Biology. 17: e3000533. PMID 31710600 DOI: 10.1371/Journal.Pbio.3000533  0.718
2019 Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure. Communications Biology. 2: 362. PMID 31602411 DOI: 10.1038/s42003-019-0610-4  0.391
2019 Bik HM. Microbial Metazoa Are Microbes Too. Msystems. 4. PMID 31164404 DOI: 10.1128/mSystems.00109-19  0.314
2019 Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, et al. DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology. PMID 31033079 DOI: 10.1111/Mec.15060  0.301
2019 Bik HM, Alexiev A, Aulakh SK, Bharadwaj L, Flanagan J, Haggerty JM, Hird SM, Jospin G, Lang JM, Sauder LA, Neufeld JD, Shaver A, Sethi A, Eisen JA, Coil DA. Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria. Msphere. 4. PMID 30787117 DOI: 10.1128/mSphere.00043-19  0.704
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, et al. The principles of tomorrow's university. F1000research. 7: 1926. PMID 30687499 DOI: 10.12688/F1000Research.17425.1  0.321
2018 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. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Communications Biology. 1: 4. PMID 30271891 DOI: 10.1038/s42003-017-0005-3  0.322
2018 Nascimento FJA, Lallias D, Bik HM, Creer S. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Scientific Reports. 8: 11737. PMID 30082688 DOI: 10.1038/s41598-018-30179-1  0.311
2018 Nascimento FJA, Lallias D, Bik HM, Creer S. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Scientific Reports. 8: 11737. PMID 30082688 DOI: 10.1038/s41598-018-30179-1  0.311
2018 Schuelke T, Pereira TJ, Hardy SM, Bik HM. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Molecular Ecology. PMID 29600535 DOI: 10.1111/mec.14539  0.492
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. Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Molecular Ecology. PMID 28921802 DOI: 10.1111/Mec.14350  0.383
2017 Brannock PM, Sharma J, Bik HM, Thomas WK, Halanych KM. Spatial and temporal variation of intertidal nematodes in the northern Gulf of Mexico after the Deepwater Horizon oil spill. Marine Environmental Research. PMID 28781067 DOI: 10.1016/J.Marenvres.2017.07.008  0.312
2016 Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM. Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City. Msphere. 1. PMID 27904880 DOI: 10.1128/mSphere.00226-16  0.438
2016 Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM, Freckleton R. The ecologist's field guide to sequence-based identification of biodiversity Methods in Ecology and Evolution. 7: 1008-1018. DOI: 10.1111/2041-210X.12574  0.38
2015 Adams RI, Bateman AC, Bik HM, Meadow JF. Microbiota of the indoor environment: a meta-analysis. Microbiome. 3: 49. PMID 26459172 DOI: 10.1186/s40168-015-0108-3  0.391
2015 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, et al. Evolution of the indoor biome. Trends in Ecology & Evolution. 30: 223-32. PMID 25770744 DOI: 10.1016/J.Tree.2015.02.001  0.671
2014 Bik HM. Deciphering diversity and ecological function from marine metagenomes. The Biological Bulletin. 227: 107-16. PMID 25411370 DOI: 10.1086/BBLv227n2p107  0.429
2014 Bik HM, Coil DA, Eisen JA. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. Plos Biology. 12: e1001884. PMID 24937755 DOI: 10.1371/Journal.Pbio.1001884  0.447
2014 Morgan MJ, Bass D, Bik H, Birky CW, Blaxter M, Crisp MD, Derycke S, Fitch D, Fontaneto D, Hardy CM, King AJ, Kiontke KC, Moens T, Pawlowski JW, Porazinska D, et al. A critique of Rossberg et al.: Noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proceedings. Biological Sciences / the Royal Society. 281: 20133076. PMID 24671969 DOI: 10.1098/Rspb.2013.3076  0.394
2014 Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. Peerj. 2: e243. PMID 24482762 DOI: 10.7717/Peerj.243  0.677
2014 Chariton AA, Ho KT, Proestou D, Bik H, Simpson SL, Portis LM, Cantwell MG, Baguley JG, Burgess RM, Pelletier MM, Perron M, Gunsch C, Matthews RA. A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments. Environmental Toxicology and Chemistry / Setac. 33: 359-69. PMID 24399368 DOI: 10.1002/Etc.2450  0.454
2013 Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK. Intra-genomic variation in the ribosomal repeats of nematodes. Plos One. 8: e78230. PMID 24147124 DOI: 10.1371/journal.pone.0078230  0.325
2013 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, et al. Meeting report: fungal its workshop (october 2012). Standards in Genomic Sciences. 8: 118-23. PMID 23961317 DOI: 10.4056/Sigs.3737409  0.322
2013 Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank C, Cirranello AL, Cui H, Daly M, Dietterich TG, Gasparich G, Irvine J, Julius M, Kaufman S, Law E, Liu J, et al. Next-generation phenomics for the Tree of Life. Plos Currents. 5. PMID 23827969 DOI: 10.1371/Currents.Tol.085C713Acafc8711B2Ff7010A4B03733  0.321
2012 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 EÓ, Parr C, et al. RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. Standards in Genomic Sciences. 7: 159-65. PMID 23451294 DOI: 10.4056/Sigs.3156511  0.435
2012 Bik HM, Halanych KM, Sharma J, Thomas WK. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. Plos One. 7: e38550. PMID 22701662 DOI: 10.1371/Journal.Pone.0038550  0.397
2012 Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution. 27: 233-43. PMID 22244672 DOI: 10.1016/j.tree.2011.11.010  0.36
2012 Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Molecular Ecology. 21: 1048-59. PMID 21985648 DOI: 10.1111/J.1365-294X.2011.05297.X  0.502
2011 Bhadury P, Bik H, Lambshead JD, Austen MC, Smerdon GR, Rogers AD. Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments. Plos One. 6: e26445. PMID 22046287 DOI: 10.1371/Journal.Pone.0026445  0.516
2010 Bik HM, Thomas WK, Lunt DH, Lambshead PJD. Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida) Bmc Evolutionary Biology. 10. PMID 21167065 DOI: 10.1186/1471-2148-10-389  0.498
2010 Bik HM, Lambshead PJD, Thomas WK, Lunt DH. Moving towards a complete molecular framework of the Nematoda: A focus on the Enoplida and early-branching clades Bmc Evolutionary Biology. 10. PMID 21073704 DOI: 10.1186/1471-2148-10-353  0.38
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