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Items: 35

1.

Microbial Metazoa Are Microbes Too.

Bik HM.

mSystems. 2019 Jun 4;4(3). pii: e00109-19. doi: 10.1128/mSystems.00109-19.

2.

DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions.

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, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P.

Mol Ecol. 2019 Apr;28(8):1857-1862. doi: 10.1111/mec.15060. Epub 2019 Apr 29. No abstract available.

3.

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria.

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.

mSphere. 2019 Feb 20;4(1). pii: e00043-19. doi: 10.1128/mSphere.00043-19.

4.

The principles of tomorrow's university.

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.

F1000Res. 2018 Dec 11;7:1926. doi: 10.12688/f1000research.17425.1. eCollection 2018.

5.

Corrigendum.

Schuelke T, Pereira TJ, Hardy SM, Bik HM.

Mol Ecol. 2018 Dec;27(23):4972. doi: 10.1111/mec.14915. No abstract available.

PMID:
30562842
6.

Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms.

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.

Commun Biol. 2018 Jan 22;1:4. doi: 10.1038/s42003-017-0005-3. eCollection 2018.

7.

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.

Nascimento FJA, Lallias D, Bik HM, Creer S.

Sci Rep. 2018 Aug 6;8(1):11737. doi: 10.1038/s41598-018-30179-1.

8.

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats.

Schuelke T, Pereira TJ, Hardy SM, Bik HM.

Mol Ecol. 2018 Apr;27(8):1930-1951. doi: 10.1111/mec.14539. Epub 2018 Mar 29. Erratum in: Mol Ecol. 2018 Dec;27(23):4972.

PMID:
29600535
9.

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities.

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.

Mol Ecol. 2017 Nov;26(21):5872-5895. doi: 10.1111/mec.14350. Epub 2017 Oct 26. Review.

10.

Let's rise up to unite taxonomy and technology.

Bik HM.

PLoS Biol. 2017 Aug 18;15(8):e2002231. doi: 10.1371/journal.pbio.2002231. eCollection 2017 Aug.

11.

Spatial and temporal variation of intertidal nematodes in the northern Gulf of Mexico after the Deepwater Horizon oil spill.

Brannock PM, Sharma J, Bik HM, Thomas WK, Halanych KM.

Mar Environ Res. 2017 Sep;130:200-212. doi: 10.1016/j.marenvres.2017.07.008. Epub 2017 Jul 6.

PMID:
28781067
12.

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City.

Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM.

mSphere. 2016 Nov 16;1(6). pii: e00226-16. eCollection 2016 Nov-Dec.

13.

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability.

Derycke S, De Meester N, Rigaux A, Creer S, Bik H, Thomas WK, Moens T.

Mol Ecol. 2016 May;25(9):2093-110. doi: 10.1111/mec.13597. Epub 2016 Mar 28.

14.

Microbiota of the indoor environment: a meta-analysis.

Adams RI, Bateman AC, Bik HM, Meadow JF.

Microbiome. 2015 Oct 13;3:49. doi: 10.1186/s40168-015-0108-3.

15.

Ten simple rules for effective online outreach.

Bik HM, Dove AD, Goldstein MC, Helm RR, MacPherson R, Martini K, Warneke A, McClain C.

PLoS Comput Biol. 2015 Apr 16;11(4):e1003906. doi: 10.1371/journal.pcbi.1003906. eCollection 2015 Apr. No abstract available.

16.

Evolution of the indoor biome.

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.

Trends Ecol Evol. 2015 Apr;30(4):223-32. doi: 10.1016/j.tree.2015.02.001. Epub 2015 Mar 11. Review.

PMID:
25770744
17.

Deciphering diversity and ecological function from marine metagenomes.

Bik HM.

Biol Bull. 2014 Oct;227(2):107-16. Review.

PMID:
25411370
18.

microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere.

Bik HM, Coil DA, Eisen JA.

PLoS Biol. 2014 Jun 17;12(6):e1001884. doi: 10.1371/journal.pbio.1001884. eCollection 2014 Jun. No abstract available.

19.

A critique of Rossberg et al.: Noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets.

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, Tang CQ, Thomas WK, Yeates DK, Creer S.

Proc Biol Sci. 2014 Mar 26;281(1783):20133076. doi: 10.1098/rspb.2013.3076. Print 2014 May 22. No abstract available.

20.

PhyloSift: phylogenetic analysis of genomes and metagenomes.

Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.

PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243. eCollection 2014.

21.

A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments.

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.

Environ Toxicol Chem. 2014 Feb;33(2):359-69.

PMID:
24399368
22.

Intra-genomic variation in the ribosomal repeats of nematodes.

Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK.

PLoS One. 2013 Oct 11;8(10):e78230. doi: 10.1371/journal.pone.0078230. eCollection 2013.

23.

Meeting report: fungal its workshop (october 2012).

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, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.

24.

Next-generation phenomics for the Tree of Life.

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, Moore L, O'Leary MA, Passarotti M, Ranade S, Simmons NB, Stevenson DW, Thacker RW, Theriot EC, Todorovic S, Velazco PM, Walls RL, Wolfe JM, Yu M.

PLoS Curr. 2013 Jun 26;5. pii: ecurrents.tol.085c713acafc8711b2ff7010a4b03733. doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733.

25.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

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 TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

26.

An introduction to social media for scientists.

Bik HM, Goldstein MC.

PLoS Biol. 2013;11(4):e1001535. doi: 10.1371/journal.pbio.1001535. Epub 2013 Apr 23.

27.

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

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, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J.

Stand Genomic Sci. 2012 Oct 10;7(1):159-65. doi: 10.4056/sigs.3156511. Epub 2012 Jul 28.

28.

Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities.

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.

Environ Toxicol Chem. 2013 Feb;32(2):384-92. doi: 10.1002/etc.2067. Epub 2012 Dec 10.

PMID:
23161706
29.

Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill.

Bik HM, Halanych KM, Sharma J, Thomas WK.

PLoS One. 2012;7(6):e38550. doi: 10.1371/journal.pone.0038550. Epub 2012 Jun 6.

30.

Sequencing our way towards understanding global eukaryotic biodiversity.

Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK.

Trends Ecol Evol. 2012 Apr;27(4):233-43. doi: 10.1016/j.tree.2011.11.010. Epub 2012 Jan 11. Review.

31.

Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments.

Bhadury P, Bik H, Lambshead JD, Austen MC, Smerdon GR, Rogers AD.

PLoS One. 2011;6(10):e26445. doi: 10.1371/journal.pone.0026445. Epub 2011 Oct 26.

32.

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments.

Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK.

Mol Ecol. 2012 Mar;21(5):1048-59. doi: 10.1111/j.1365-294X.2011.05297.x. Epub 2011 Oct 10.

33.

Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida).

Bik HM, Thomas WK, Lunt DH, Lambshead PJ.

BMC Evol Biol. 2010 Dec 18;10:389. doi: 10.1186/1471-2148-10-389.

34.

Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades.

Bik HM, Lambshead PJ, Thomas WK, Lunt DH.

BMC Evol Biol. 2010 Nov 12;10:353. doi: 10.1186/1471-2148-10-353.

35.

Phase II metabolism of hesperetin by individual UDP-glucuronosyltransferases and sulfotransferases and rat and human tissue samples.

Brand W, Boersma MG, Bik H, Hoek-van den Hil EF, Vervoort J, Barron D, Meinl W, Glatt H, Williamson G, van Bladeren PJ, Rietjens IM.

Drug Metab Dispos. 2010 Apr;38(4):617-25. doi: 10.1124/dmd.109.031047. Epub 2010 Jan 7.

PMID:
20056724

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