ORCID Profile
0000-0001-5410-1518
Current Organisation
University of California, San Diego
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Publisher: Cold Spring Harbor Laboratory
Date: 20-12-2022
DOI: 10.1101/2022.12.19.520774
Abstract: 16S rRNA and shotgun metagenomics studies typically yield different results, usually attributed to biases in PCR lification of 16S rRNA genes. Here, we introduce Greengenes2 and show that differences in reference phylogeny are more important. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same s les agree in principal coordinates space, taxonomy, and in phenotype effect size when analyzed with the same tree.
Publisher: Springer Science and Business Media LLC
Date: 11-11-2020
Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24621
Abstract: Our growing awareness of the microbial world’s importance and ersity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community s les collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of ersity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial ersity.
Publisher: Oxford University Press (OUP)
Date: 12-02-2015
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-12-2014
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first ergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of erse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Publisher: Springer Science and Business Media LLC
Date: 27-07-2023
DOI: 10.1038/S41587-023-01845-1
Abstract: Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR lification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same s les agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
Publisher: Elsevier BV
Date: 11-2018
Publisher: Springer Science and Business Media LLC
Date: 08-04-2021
DOI: 10.1038/S41586-021-03473-8
Abstract: A Correction to this paper has been published: 0.1038/s41586-021-03473-8.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-06-2019
Abstract: The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat ersity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
Publisher: Springer Science and Business Media LLC
Date: 18-10-2023
Location: United States of America
No related grants have been discovered for Siavash Mirarab.