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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Nature biotechnology

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.
PMID: 31341288
Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9.

No abstract available.

Cite
Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852-857doi: 10.1038/s41587-019-0209-9.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R., & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9
Bolyen, Evan, et al. "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature biotechnology vol. 37,8 (2019): 852-857. doi: https://doi.org/10.1038/s41587-019-0209-9
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. PMID: 31341288; PMCID: PMC7015180.
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Qiita: rapid, web-enabled microbiome meta-analysis.

Nature methods

Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R.
PMID: 30275573
Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 01.

Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses...

Cite
Gonzalez A, Navas-Molina JA, Kosciolek T, et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018;15(10):796-798doi: 10.1038/s41592-018-0141-9.
Gonzalez, A., Navas-Molina, J. A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A. D., Orchanian, S. B., Sanders, J. G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C. J., Wang, M., Rideout, J. R., Bolyen, E., Dillon, M., Caporaso, J. G., Dorrestein, P. C., & Knight, R. (2018). Qiita: rapid, web-enabled microbiome meta-analysis. Nature methods, 15(10), 796-798. https://doi.org/10.1038/s41592-018-0141-9
Gonzalez, Antonio, et al. "Qiita: rapid, web-enabled microbiome meta-analysis." Nature methods vol. 15,10 (2018): 796-798. doi: https://doi.org/10.1038/s41592-018-0141-9
Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 01. PMID: 30275573; PMCID: PMC6235622.
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Enhanced Impact Strength of Recycled PET/Glass Fiber Composites.

Polymers

Monti M, Scrivani MT, Kociolek I, Larsen ÅG, Olafsen K, Lambertini V.
PMID: 34062861
Polymers (Basel). 2021 May 01;13(9). doi: 10.3390/polym13091471.

In this paper, we report a study on the effects of different ethylene copolymers in improving the impact strength of a fiber-reinforced composite based on a recycled poly(ethylene terephthalate) (rPET) from post-consumer bottles. Different ethylene copolymers have been selected...

Cite
Monti M, Scrivani MT, Kociolek I, et al. Enhanced Impact Strength of Recycled PET/Glass Fiber Composites. Polymers (Basel). 2021;13(9)doi: 10.3390/polym13091471.
Monti, M., Scrivani, M. T., Kociolek, I., Larsen, �. �. G., Olafsen, K., & Lambertini, V. (2021). Enhanced Impact Strength of Recycled PET/Glass Fiber Composites. Polymers, 13(9), . https://doi.org/10.3390/polym13091471
Monti, Marco, et al. "Enhanced Impact Strength of Recycled PET/Glass Fiber Composites." Polymers vol. 13,9 (2021). doi: https://doi.org/10.3390/polym13091471
Monti M, Scrivani MT, Kociolek I, Larsen ÅG, Olafsen K, Lambertini V. Enhanced Impact Strength of Recycled PET/Glass Fiber Composites. Polymers (Basel). 2021 May 01;13(9). doi: 10.3390/polym13091471. PMID: 34062861; PMCID: PMC8124343.
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COVID-19-Related Submission Priorities From the Journal of the Pediatric Infectious Diseases Society.

Journal of the Pediatric Infectious Diseases Society

Green M, Adler-Shohet FC, Blyth CC, Chiotos K, Gerber JS, Jhaveri R, Kociolek L, Martin-Blais R, Palazzi D, Shane AL, Schuster JE, Shulman ST, Storch GA, Weinberg GA, Zaoutis T.
PMID: 34608936
J Pediatric Infect Dis Soc. 2021 Oct 05; doi: 10.1093/jpids/piab093. Epub 2021 Oct 05.

No abstract available.

Cite
Green M, Adler-Shohet FC, Blyth CC, et al. COVID-19-Related Submission Priorities From the Journal of the Pediatric Infectious Diseases Society. J Pediatric Infect Dis Soc. 2021;doi: 10.1093/jpids/piab093.
Green, M., Adler-Shohet, F. C., Blyth, C. C., Chiotos, K., Gerber, J. S., Jhaveri, R., Kociolek, L., Martin-Blais, R., Palazzi, D., Shane, A. L., Schuster, J. E., Shulman, S. T., Storch, G. A., Weinberg, G. A., & Zaoutis, T. (2021). COVID-19-Related Submission Priorities From the Journal of the Pediatric Infectious Diseases Society. Journal of the Pediatric Infectious Diseases Society, . https://doi.org/10.1093/jpids/piab093
Green, Michael, et al. "COVID-19-Related Submission Priorities From the Journal of the Pediatric Infectious Diseases Society." Journal of the Pediatric Infectious Diseases Society vol. (2021). doi: https://doi.org/10.1093/jpids/piab093
Green M, Adler-Shohet FC, Blyth CC, Chiotos K, Gerber JS, Jhaveri R, Kociolek L, Martin-Blais R, Palazzi D, Shane AL, Schuster JE, Shulman ST, Storch GA, Weinberg GA, Zaoutis T. COVID-19-Related Submission Priorities From the Journal of the Pediatric Infectious Diseases Society. J Pediatric Infect Dis Soc. 2021 Oct 05; doi: 10.1093/jpids/piab093. Epub 2021 Oct 05. PMID: 34608936; PMCID: PMC8500135.
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The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

Standards in genomic sciences

Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley ST, Kirkup BC, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert J.
PMID: 23961316
Stand Genomic Sci. 2013 Apr 15;8(1):112-7. doi: 10.4056/sigs.3717348. eCollection 2013 Apr 15.

This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science...

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Smith D, Alverdy J, An G, et al. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci. 2013;8(1):112-7doi: 10.4056/sigs.3717348.
Smith, D., Alverdy, J., An, G., Coleman, M., Garcia-Houchins, S., Green, J., Keegan, K., Kelley, S. T., Kirkup, B. C., Kociolek, L., Levin, H., Landon, E., Olsiewski, P., Knight, R., Siegel, J., Weber, S., & Gilbert, J. (2013). The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Standards in genomic sciences, 8(1), 112-7. https://doi.org/10.4056/sigs.3717348
Smith, Daniel, et al. "The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012." Standards in genomic sciences vol. 8,1 (2013): 112-7. doi: https://doi.org/10.4056/sigs.3717348
Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley ST, Kirkup BC, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci. 2013 Apr 15;8(1):112-7. doi: 10.4056/sigs.3717348. eCollection 2013 Apr 15. PMID: 23961316; PMCID: PMC3739179.
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Individuals with substance use disorders have a distinct oral microbiome pattern.

Brain, behavior, & immunity - health

Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Knight R, Paulus MP.
PMID: 34589776
Brain Behav Immun Health. 2021 May 29;15:100271. doi: 10.1016/j.bbih.2021.100271. eCollection 2021 Aug.

BACKGROUND: Substance use disorder emerges from a complex interaction between genetic predisposition, life experiences, exposure, and subsequent adaptation of biological systems to the repeated use of drugs. Recently, investigators have proposed that the human microbiota may play a role...

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Kosciolek T, Victor TA, Kuplicki R, et al. Individuals with substance use disorders have a distinct oral microbiome pattern. Brain Behav Immun Health. 2021;15:100271doi: 10.1016/j.bbih.2021.100271.
Kosciolek, T., Victor, T. A., Kuplicki, R., Rossi, M., Estaki, M., Ackermann, G., Knight, R., & Paulus, M. P. (2021). Individuals with substance use disorders have a distinct oral microbiome pattern. Brain, behavior, & immunity - health, 15100271. https://doi.org/10.1016/j.bbih.2021.100271
Kosciolek, Tomasz, et al. "Individuals with substance use disorders have a distinct oral microbiome pattern." Brain, behavior, & immunity - health vol. 15 (2021): 100271. doi: https://doi.org/10.1016/j.bbih.2021.100271
Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Knight R, Paulus MP. Individuals with substance use disorders have a distinct oral microbiome pattern. Brain Behav Immun Health. 2021 May 29;15:100271. doi: 10.1016/j.bbih.2021.100271. eCollection 2021 Aug. PMID: 34589776; PMCID: PMC8474247.
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A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data.

Biometrics

Liu J, Zhang X, Chen T, Wu T, Lin T, Jiang L, Lang S, Liu L, Natarajan L, Tu JX, Kosciolek T, Morton J, Nguyen TT, Schnabl B, Knight R, Feng C, Zhong Y, Tu XM.
PMID: 34010477
Biometrics. 2021 May 19; doi: 10.1111/biom.13487. Epub 2021 May 19.

The human microbiome plays an important role in our health and identifying factors associated with microbiome composition provides insights into inherent disease mechanisms. By amplifying and sequencing the marker genes in high-throughput sequencing, with highly similar sequences binned together,...

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Liu J, Zhang X, Chen T, et al. A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data. Biometrics. 2021;doi: 10.1111/biom.13487.
Liu, J., Zhang, X., Chen, T., Wu, T., Lin, T., Jiang, L., Lang, S., Liu, L., Natarajan, L., Tu, J. X., Kosciolek, T., Morton, J., Nguyen, T. T., Schnabl, B., Knight, R., Feng, C., Zhong, Y., & Tu, X. M. (2021). A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data. Biometrics, . https://doi.org/10.1111/biom.13487
Liu, J, et al. "A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data." Biometrics vol. (2021). doi: https://doi.org/10.1111/biom.13487
Liu J, Zhang X, Chen T, Wu T, Lin T, Jiang L, Lang S, Liu L, Natarajan L, Tu JX, Kosciolek T, Morton J, Nguyen TT, Schnabl B, Knight R, Feng C, Zhong Y, Tu XM. A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data. Biometrics. 2021 May 19; doi: 10.1111/biom.13487. Epub 2021 May 19. PMID: 34010477; PMCID: PMC8602427.
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American Gut: an Open Platform for Citizen Science Microbiome Research.

mSystems

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R.
PMID: 29795809
mSystems. 2018 May 15;3(3). doi: 10.1128/mSystems.00031-18. eCollection 2018.

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols...

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McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3)doi: 10.1128/mSystems.00031-18.
McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., Humphrey, G., Huttenhower, C., Jackson, M. A., Janssen, S., Jeste, D. V., Jiang, L., Kelley, S. T., Knights, D., Kosciolek, T., Ladau, J., Leach, J., Marotz, C., Meleshko, D., Melnik, A. V., Metcalf, J. L., Mohimani, H., Montassier, E., Navas-Molina, J., Nguyen, T. T., Peddada, S., Pevzner, P., Pollard, K. S., Rahnavard, G., Robbins-Pianka, A., Sangwan, N., Shorenstein, J., Smarr, L., Song, S. J., Spector, T., Swafford, A. D., Thackray, V. G., Thompson, L. R., Tripathi, A., Vázquez-Baeza, Y., Vrbanac, A., Wischmeyer, P., Wolfe, E., Zhu, Q., & Knight, R. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), . https://doi.org/10.1128/mSystems.00031-18
McDonald, Daniel, et al. "American Gut: an Open Platform for Citizen Science Microbiome Research." mSystems vol. 3,3 (2018). doi: https://doi.org/10.1128/mSystems.00031-18
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May 15;3(3). doi: 10.1128/mSystems.00031-18. eCollection 2018. PMID: 29795809; PMCID: PMC5954204.
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The Microbiome and Its Potential for Pharmacology.

Handbook of experimental pharmacology

Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R.
PMID: 31820171
Handb Exp Pharmacol. 2019;260:301-326. doi: 10.1007/164_2019_317.

The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-"omics" techniques have dramatically improved our understanding of the constituents of the microbiome and their functions....

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Chavira A, Belda-Ferre P, Kosciolek T, et al. The Microbiome and Its Potential for Pharmacology. Handb Exp Pharmacol. 2019;260:301-326doi: 10.1007/164_2019_317.
Chavira, A., Belda-Ferre, P., Kosciolek, T., Ali, F., Dorrestein, P. C., & Knight, R. (2019). The Microbiome and Its Potential for Pharmacology. Handbook of experimental pharmacology, 260301-326. https://doi.org/10.1007/164_2019_317
Chavira, Aries, et al. "The Microbiome and Its Potential for Pharmacology." Handbook of experimental pharmacology vol. 260 (2019): 301-326. doi: https://doi.org/10.1007/164_2019_317
Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R. The Microbiome and Its Potential for Pharmacology. Handb Exp Pharmacol. 2019;260:301-326. doi: 10.1007/164_2019_317. PMID: 31820171.
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The notes from nature tool for unlocking biodiversity records from museum records through citizen science.

ZooKeys

Hill A, Guralnick R, Smith A, Sallans A, Rosemary Gillespie, Denslow M, Gross J, Murrell Z, Tim Conyers, Oboyski P, Ball J, Thomer A, Prys-Jones R, de Torre J, Kociolek P, Fortson L.
PMID: 22859890
Zookeys. 2012;(209):219-33. doi: 10.3897/zookeys.209.3472. Epub 2012 Jul 20.

Legacy data from natural history collections contain invaluable and irreplaceable information about biodiversity in the recent past, providing a baseline for detecting change and forecasting the future of biodiversity on a human-dominated planet. However, these data are often not...

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Hill A, Guralnick R, Smith A, et al. The notes from nature tool for unlocking biodiversity records from museum records through citizen science. Zookeys. 2012;(209):219-33doi: 10.3897/zookeys.209.3472.
Hill, A., Guralnick, R., Smith, A., Sallans, A., Rosemary Gillespie, Denslow, M., Gross, J., Murrell, Z., Tim Conyers, Oboyski, P., Ball, J., Thomer, A., Prys-Jones, R., de Torre, J., Kociolek, P., & Fortson, L. (2012). The notes from nature tool for unlocking biodiversity records from museum records through citizen science. ZooKeys, (209), 219-33. https://doi.org/10.3897/zookeys.209.3472
Hill, Andrew, et al. "The notes from nature tool for unlocking biodiversity records from museum records through citizen science." ZooKeys vol. ,209 (2012): 219-33. doi: https://doi.org/10.3897/zookeys.209.3472
Hill A, Guralnick R, Smith A, Sallans A, Rosemary Gillespie, Denslow M, Gross J, Murrell Z, Tim Conyers, Oboyski P, Ball J, Thomer A, Prys-Jones R, de Torre J, Kociolek P, Fortson L. The notes from nature tool for unlocking biodiversity records from museum records through citizen science. Zookeys. 2012;(209):219-33. doi: 10.3897/zookeys.209.3472. Epub 2012 Jul 20. PMID: 22859890; PMCID: PMC3406478.
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Rehabilitation counsellor perceived importance and competence in assistive technology.

Disability and rehabilitation. Assistive technology

Kuo HJ, Kosciulek J.
PMID: 34752717
Disabil Rehabil Assist Technol. 2021 Nov 09;1-7. doi: 10.1080/17483107.2021.2001062. Epub 2021 Nov 09.

PURPOSE: Assistive technology (AT) has received much attention for its capacity to improve quality of life for individuals with disabilities. While AT can be promising, the high AT abandonment issue persists. Rehabilitation counsellors are considered important in solving such...

Cite
Kuo HJ, Kosciulek J. Rehabilitation counsellor perceived importance and competence in assistive technology. Disabil Rehabil Assist Technol. 2021;1-7doi: 10.1080/17483107.2021.2001062.
Kuo, H. J., & Kosciulek, J. (2021). Rehabilitation counsellor perceived importance and competence in assistive technology. Disability and rehabilitation. Assistive technology, 1-7. https://doi.org/10.1080/17483107.2021.2001062
Kuo, Hung Jen, and Kosciulek, John. "Rehabilitation counsellor perceived importance and competence in assistive technology." Disability and rehabilitation. Assistive technology vol. (2021): 1-7. doi: https://doi.org/10.1080/17483107.2021.2001062
Kuo HJ, Kosciulek J. Rehabilitation counsellor perceived importance and competence in assistive technology. Disabil Rehabil Assist Technol. 2021 Nov 09;1-7. doi: 10.1080/17483107.2021.2001062. Epub 2021 Nov 09. PMID: 34752717.
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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Nature biotechnology

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.
PMID: 31399723
Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Cite
Bolyen E, Rideout JR, Dillon MR, et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(9):1091doi: 10.1038/s41587-019-0252-6.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R., & Caporaso, J. G. (2019). Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(9), 1091. https://doi.org/10.1038/s41587-019-0252-6
Bolyen, Evan, et al. "Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature biotechnology vol. 37,9 (2019): 1091. doi: https://doi.org/10.1038/s41587-019-0252-6
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6. PMID: 31399723.
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