The Epigenomic Landscape of Prokaryotes.

Autor: Matthew J Blow, Tyson A Clark, Chris G Daum, Adam M Deutschbauer, Alexey Fomenkov, Roxanne Fries, Jeff Froula, Dongwan D Kang, Rex R Malmstrom, Richard D Morgan, Janos Posfai, Kanwar Singh, Axel Visel, Kelly Wetmore, Zhiying Zhao, Edward M Rubin, Jonas Korlach, Len A Pennacchio, Richard J Roberts

Publikováno v: PLoS Genetics, Vol 12, Iss 2, p e1005854 (2016)

DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and prop

Externí odkaz: https://doaj.org/article/611a8e3186b0460990c4d6a70850c22d

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Autor: Tanja Woyke, Daniel Barich, Joan L. Slonczewski, Rob Egan, Volkan Sevim, Dongwan D. Kang, Derek N. Macklin, Rachael M. Morgan-Kiss, Jeff Froula, Harrison Ho, Frederik Schulz, Wei Li, Zhong Wang, Kayla McCue, Shijie Yao, Rachel Orsini, Christopher J. Sedlacek, Jackie E. Shay

Classifying taxa, including those that have not previously been identified, is a key task in characterizing the microbial communities of under-described habitats, including permanently ice-covered lakes in the dry valleys of the Antarctic. Current su

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::033506eb5ab89f18b15a66df268b54c6

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

Autor: Weibing Shi, Priya Soni, Jeff Froula, William J. Kelly, Janine Kamke, Graeme T. Attwood, Sinead C. Leahy, Yang Li, Edward M. Rubin, Siva Ganesh

Publikováno v: BMC Research Notes
BMC Research Notes, Vol 10, Iss 1, Pp 1-14 (2017)

Background Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71b8b596a28aea1e6102f5b5511589aa
http://europepmc.org/articles/PMC5549432

Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software

Autor: Andreas Bremges, Charles Deltel, Jeff Froula, Marc Strous, Tue Sparholt Jørgensen, Alexander Sczyrba, Søren J. Sørensen, Michael D. Barton, Hsin-Hung Lin, Aaron E. Darling, Nikos C. Kyrpides, Surya Saha, Claire Lemaitre, Ivan Gregor, Julia A. Vorholt, Chirag Jain, David Koslicki, Alexey Gurevich, Lars Hestbjerg Hansen, Dominique Lavenier, Steven W. Singer, Peter Hofmann, Philip D. Blood, Peter Belmann, Stephan Majda, Jeffrey J. Cook, Dongwan Don Kang, Peter Meinicke, Genivaldo G. Z. Silva, Michael Beckstette, Matthew Z. DeMaere, Yang Bai, Zhong Wang, Monika Balvočiūtė, Alice C. McHardy, Hans-Peter Klenk, Yu Wei Wu, Burton Kuan Hui Chia, Markus Göker, Nicole Shapiro, Rayan Chikhi, Thomas Rattei, Christopher Quince, Edward M. Rubin, Niranjan Nagarajan, Paul Schulze-Lefert, Thomas Lingner, Tanja Woyke, Bernhard Y. Renard, Eik Dahms, Robert Egan, Pierre Peterlongo, Yu-Chieh Liao, Daniel A. Cuevas, Mihai Pop, Dmitrij Turaev, Robert Edwards, Vitor C. Piro, Guillaume Rizk, Fernando Meyer, Jessika Fiedler, Adrian Fritz, Ruben Garrido-Oter, Bertrand Denis, Johannes Dröge, Stefan Janssen, Heiner Klingenberg

Publikováno v: Nature Methods, 14 (11)
Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Dröge, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jørgensen, T S, Shapiro, N, Blood, P D, Gurevich, A, Bai, Y, Turaev, D, DeMaere, M Z, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvociute, M, Hansen, L H, Sørensen, S J, Chia, B K H, Denis, B, Froula, J L, Wang, Z, Egan, R, Kang, D D, Cook, J J, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, S W, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, M D, Lingner, T, Lin, H-H, Liao, Y-C, Silva, G G Z, Cuevas, D A, Edwards, R A, Saha, S, Piro, V C, Renard, B Y, Pop, M, Klenk, H-P, Göker, M, Kyrpides, N C, Woyke, T, Vorholt, J A, Schulze-Lefert, P, Rubin, E M, Darling, A E, Rattei, T & McHardy, A C 2017, ' Critical Assessment of Metagenome Interpretation : a benchmark of metagenomics software ', Nature Methods, vol. 14, no. 11, pp. 1063-1071 . https://doi.org/10.1038/NMETH.4458
Nature Methods
Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Droege, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jorgensen, T S, Shapiro, N, Blood, P D, Gurevich, A, Bai, Y, Turaev, D, DeMaere, M Z, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvociute, M, Hansen, L H, Sorensen, S J, Chia, B K H, Denis, B, Froula, J L, Wang, Z, Egan, R, Kang, D D, Cook, J J, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, S W, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, M D, Lingner, T, Lin, H-H, Liao, Y-C, Silva, G G Z, Cuevas, D A, Edwards, R A, Saha, S, Piro, V C, Renard, B Y, Pop, M, Klenk, H-P, Goeker, M, Kyrpides, N C, Woyke, T, Vorholt, J A, Schulze-Lefert, P, Rubin, E M, Darling, A E, Rattei, T & McHardy, A C 2017, ' Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software ', Nature Methods, vol. 14, no. 11, pp. 1063-1071 . https://doi.org/10.1038/NMETH.4458
Nature methods, vol 14, iss 11
Nature methods

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has en

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d6edbef3576f41e42f08c76da345c095
https://hdl.handle.net/20.500.11850/206823

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation

Autor: Matthias Hess, Erik R. Hawley, Jeff Froula, Douglas S. Clark, Changbin Du, Hans-Peter Klenk, Nathalia Ivanova, Stefan Bauer, Tae-Wan Kim, Zhong Wang, Hailan Piao

Publikováno v: Biotechnology and Bioengineering. 111:1550-1565

Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2719619d9280691fe61b0a9b74a7eba6
https://doi.org/10.1002/bit.25250