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List of works by Luis Miguel Rodríguez-R

"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments

scientific article published on 05 April 2019

A user's guide to quantitative and comparative analysis of metagenomic datasets

scientific article published in January 2013

An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1.

scientific article

An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains

scientific article

Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity in Bacillus anthracis

scientific article published on 01 November 2018

Beach sand oil spills select for generalist microbial populations

scientific article published in November 2021

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

scientific article

CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri

scientific article published on 02 December 2019

Computational biology in Colombia

scientific article

Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.

scientific article

Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola

scientific article

Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries

scientific article

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov

scientific article published on 06 May 2019

Estimating coverage in metagenomic data sets and why it matters

scientific article

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

scientific article published on December 2014

Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

scientific article published on 01 March 2020

Genomes-based phylogeny of the genus Xanthomonas

scientific article

Genomic Characterization and Copy Number Variation of Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains

scientific article published on 01 July 2018

Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.

scientific article

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

scientific article published in Nature Communications

How much do rRNA gene surveys underestimate extant bacterial diversity?

scientific article published on 5 January 2018

Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences

scientific article published on 04 June 2020

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

scientific article published on 02 March 2020

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill ⬇️

scientific article published on 17 February 2015

Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications

scientific article

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

scientific article

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database ⬇️

scientific article published in 2022

New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae.

scientific article

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

scientific article published on 10 April 2018

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

scientific article

Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation

scientific article published in 2022

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

scientific article published in 2018

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

scientific article

Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study

scientific article published in June 2013

Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"

publication published on 07 July 2021

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

scientific article

SeqCode: a nomenclatural code for prokaryotes described from sequence data

scientific article published in 2022

Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease.

scientific article published on 29 September 2011

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

scientific article

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

scientific article

Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions

scientific article

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

scientific article published in July 2018

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