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27 de febrero: Reference databases for taxonomic assignment in metagenomics.

13 febrero, 2013

Santamaria, M., Fosso, B., Consiglio, A., De Caro, G., Grillo, G., Licciulli, F., Liuni, S., et al. (2012). Reference databases for taxonomic assignment in metagenomics. Briefings in bioinformatics, 13(6), 682–695. doi:10.1093/bib/bbs036   Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus…
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27 de febrero, ejemplo de microbioma: Microbiome of the upper troposphere Species composition and prevalence effects of tropical storms and atmospheric implications.

13 febrero, 2013

DeLeon-Rodriguez, N., Lathem, T. L., Rodriguez-r, L. M., Barazesh, J. M., Anderson, B. E., Beyersdorf, A. J., Ziemba, L. D., et al. (2013). Microbiome of the upper troposphere Species composition and prevalence effects of tropical storms and atmospheric implications. PNAS, 1212089110–. doi:10.1073/pnas.1212089110 The composition and prevalence of microorganisms in the middle-to-upper troposphere (8-15 km altitude)…
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27 de febrero: Genoma de ejemplo: Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1

13 febrero, 2013

Mykytczuk, N. C., Foote, S. J., Omelon, C. R., Southam, G., Greer, C. W., & Whyte, L. G. (2013). Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. The ISME Journal, 1–16. doi:10.1038/ismej.2013.8 Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at ~15 °C, the lowest…
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25 de febrero: The metagenomics RAST server

13 febrero, 2013

Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., et al. (2008).The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics, 9, 386. doi:10.1186/1471-2105-9-386 BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the…
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25 de febrero: Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective

13 febrero, 2013

Teeling, H., & Glöckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective. Briefings in bioinformatics, 13(6), 728–742. doi:10.1093/bib/bbs039 Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large…
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25 de febrero: Bioinformatic approaches for functional annotation and pathway inference in metagenomics

13 febrero, 2013

De Filippo, C., Ramazzotti, M., Fontana, P., & Cavalieri, D. (2012). Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics, 13(6), 696–710. doi:10.1093/bib/bbs070 Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems.The development ofmethods for pathway inference frommetagenomics data is of paramount…
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20 de Febrero: High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

13 febrero, 2013

Loman, N. J., Constantinidou, C., Chan, J. Z. M., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R., et al. (2012). High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nature reviews. Microbiology, 10(9), 599–606. doi:10.1038/nrmicro2850 Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical…
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20 de febrero: A primer on metagenomics.

13 febrero, 2013

Wooley, J. C. J., Godzik, A., & Friedberg, I. (2010). A primer on metagenomics. PLoS computational biology, 6(2), e1000667. doi:10.1371/journal.pcbi.1000667 Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of…
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20 de Febrero: The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist.

13 febrero, 2013

Gilbert, J. a, O’Dor, R., King, N., & Vogel, T. M. (2011). The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial informatics and experimentation, 1(1), 5. doi:10.1186/2042-5783-1-5 ABSTRACT: Scientific discovery is incremental. The Merriam-Webster definition of ‘Scientific Method’ is «principles and procedures for the systematic pursuit…
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18 de Febrero: Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.

13 febrero, 2013

Alcaraz, L.D., et al. (2010). Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC genomics, 11(1), 332. doi:10.1186/1471-2164-11-332 BACKGROUND:The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus…
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18 de Febrero: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”.

13 febrero, 2013

Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V, et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A, 102(39), 13950–13955. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16172379 The development of efficient and inexpensive genome sequencing methods…
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18 de Febrero: Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.

13 febrero, 2013

Konstantinidis, K. T., & Tiedje, J. M. (2007). Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current opinion in microbiology, 10(5), 504–9. doi:10.1016/j.mib.2007.08.006 Advancing prokaryotic taxonomy constitutes a contemporary academic challenge as well as practical necessity. Genome sequencing has greatly facilitated the evaluation of the current taxonomic system and the development…
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13 de Febrero: The Neolithic revolution of bacterial genomes.

7 febrero, 2013

Mira, A., Pushker, R., & Rodriguez-Valera, F. (2006). The Neolithic revolution of bacterial genomes. Trends Microbiol, 14(5), 200–206. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16569502 Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the…
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13 de febrero: Deletional bias and the evolution of bacterial genomes

7 febrero, 2013

Mira, A., Ochman, H., & Moran, N. A. (2001). Deletional bias and the evolution of bacterial genomes, 17(10), 589–596. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11585665 Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards…
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13 de Febrero: Comparative genomics of gene-family size in closely related bacteria.

7 febrero, 2013

Pushker, R., Mira, A., & Rodriguez-Valera, F. (2004). Comparative genomics of gene-family size in closely related bacteria. Genome Biol, 5(4), 0. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15059260 BACKGROUND: The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a…
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Edificio A Segundo Piso Laboratiorio de Biología Molecular y Genómica Facultad de Ciencias Universidad Nacional Autónoma de México 04510 Coyoacán Ciudad de México

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