Works matching AU Rodriguez-R, Luis M.

Results: 32

Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrae215

By:

Bustos-Caparros, Esteban;
Viver, Tomeu;
Gago, Juan F;
Rodriguez-R, Luis M;
Hatt, Janet K;
Venter, Stephanus N;
Fuchs, Bernhard M;
Amann, Rudolf;
Bosch, Rafael;
Konstantinidis, Konstantinos T;
Rossello-Mora, Ramon

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 5, p. 629, doi. 10.1093/bioinformatics/btt584

By:

Rodriguez-R, Luis M.;
Konstantinidis, Konstantinos T.

Publication type:

Article

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.

Published in:

Environmental Microbiology, 2020, v. 22, n. 8, p. 3394, doi. 10.1111/1462-2920.15112

By:

Rodriguez‐R, Luis M.;
Tsementzi, Despina;
Luo, Chengwei;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

Environmental Microbiology, 2020, v. 22, n. 6, p. 2094, doi. 10.1111/1462-2920.14966

By:

Karthikeyan, Smruthi;
Rodriguez‐R, Luis M.;
Heritier‐Robbins, Patrick;
Hatt, Janet K.;
Huettel, Markus;
Kostka, Joel E.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

2021

By:

Rodriguez-R, Luis M.;
Jain, Chirag;
Conrad, Roth E.;
Aluru, Srinivas;
Konstantinidis, Konstantinos T.

Publication type:

Letter

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics.

Published in:

PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0093827

By:

Poretsky, Rachel;
Rodriguez-R, Luis M.;
Luo, Chengwei;
Tsementzi, Despina;
Konstantinidis, Konstantinos T.

Publication type:

Article

Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen <i>Xanthomonas axonopodis</i> pv. Manihotis Strain CIO151.

Published in:

PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079704

By:

Arrieta-Ortiz, Mario L.;
Rodríguez-R, Luis M.;
Pérez-Quintero, Álvaro L.;
Poulin, Lucie;
Díaz, Ana C.;
Arias Rojas, Nathalia;
Trujillo, Cesar;
Restrepo Benavides, Mariana;
Bart, Rebecca;
Boch, Jens;
Boureau, Tristan;
Darrasse, Armelle;
David, Perrine;
Dugé de Bernonville, Thomas;
Fontanilla, Paula;
Gagnevin, Lionel;
Guérin, Fabien;
Jacques, Marie-Agnès;
Lauber, Emmanuelle;
Lefeuvre, Pierre

Publication type:

Article

An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of <i>Xanthomonas oryzae</i> Strains.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0068464

By:

Pérez-Quintero, Alvaro L.;
Rodriguez-R, Luis M.;
Dereeper, Alexis;
López, Camilo;
Koebnik, Ralf;
Szurek, Boris;
Cunnac, Sebastien

Publication type:

Article

Discovery of Phytophthora infestans Genes Expressed in Planta through Mining of cDNA Libraries.

Published in:

PLoS ONE, 2010, v. 5, n. 3, p. 1, doi. 10.1371/journal.pone.0009847

By:

Sierra, Roberto;
Rodríguez-R, Luis M.;
Chaves, Diego;
Pinzón, André s;
Grajales, Alejandro;
Rojas, Alejandro;
Mutis, Gabriel;
Cárdenas, Martha;
Burbano, Daniel;
Jiménez, Pedro;
Bernal, Adriana;
Restrepo, Silvia

Publication type:

Article

Beach sand oil spills select for generalist microbial populations.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2021, v. 15, n. 11, p. 3418, doi. 10.1038/s41396-021-01017-6

By:

Heritier-Robbins, Patrick;
Karthikeyan, Smruthi;
Hatt, Janet K.;
Kim, Minjae;
Huettel, Markus;
Kostka, Joel E.;
Konstantinidis, Konstantinos T.;
Rodriguez-R, Luis M.

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2019, v. 13, n. 8, p. 2129, doi. 10.1038/s41396-019-0400-5

By:

Karthikeyan, Smruthi;
Rodriguez-R, Luis M.;
Heritier-Robbins, Patrick;
Kim, Minjae;
Overholt, Will A.;
Gaby, John C.;
Hatt, Janet K.;
Spain, Jim C.;
Rosselló-Móra, Ramon;
Huettel, Markus;
Kostka, Joel E.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2019, v. 13, n. 3, p. 767, doi. 10.1038/s41396-018-0307-6

By:

Meziti, Alexandra;
Tsementzi, Despina;
Rodriguez-R, Luis M.;
Hatt, Janet K.;
Karayanni, Hera;
Kormas, Konstantinos A.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 9, p. 1928, doi. 10.1038/ismej.2015.5

By:

Rodriguez-R, Luis M;
Overholt, Will A;
Hagan, Christopher;
Huettel, Markus;
Kostka, Joel E;
Konstantinidis, Konstantinos T

Publication type:

Article

Estimating coverage in metagenomic data sets and why it matters.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2014, v. 8, n. 11, p. 2349, doi. 10.1038/ismej.2014.76

By:

Rodriguez-R, Luis M;
Konstantinidis, Konstantinos T

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 3, p. 502, doi. 10.1038/ismej.2011.123

By:

Cárdenas, Anny;
Rodriguez-R, Luis M;
Pizarro, Valeria;
Cadavid, Luis F;
Arévalo-Ferro, Catalina

Publication type:

Article

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

Published in:

Virology Journal, 2010, v. 7, p. 369, doi. 10.1186/1743-422X-7-369

By:

Méndez-Ortega, María C.;
Restrepo, Silvia;
Rodríguez-R, Luis M.;
Pérez, Iván;
Mendoza, Juan C.;
Martínez, Andrés P.;
Sierra, Roberto;
Rey-Benito, Gloria J.

Publication type:

Article

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

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07641-9

By:

Jain, Chirag;
Rodriguez-R, Luis M.;
Phillippy, Adam M.;
Konstantinidis, Konstantinos T.;
Aluru, Srinivas

Publication type:

Article

imGLAD: accurate detection and quantification of target organisms in metagenomes.

Published in:

PeerJ, 2018, p. 1, doi. 10.7717/peerj.5882

By:

Castro, Juan C.;
Rodriguez-R, Luis M.;
Harvey, William T.;
Weigand, Michael R.;
Hatt, Janet K.;
Carter, Michelle Q.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2011, v. 12, n. 2, p. 151, doi. 10.1093/bib/bbq009

By:

Pinzón, Andrés;
Rodriguez-R., Luis M.;
González, Andrés;
Bernal, Adriana;
Restrepo, Silvia

Publication type:

Article

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00579

By:

Johnston, Eric R.;
Rodriguez-R., Luis M.;
Chengwei Luo;
Mengting M. Yuan;
Liyou Wu;
Zhili He;
Schuur, Edward A. G.;
Yiqi Luo;
Tiedje, James M.;
Jizhong Zhou;
Konstantinidis, Konstantinos T.

Publication type:

Article

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53787-0

By:

Conrad, Roth E.;
Brink, Catherine E.;
Viver, Tomeu;
Rodriguez-R, Luis M.;
Aldeguer-Riquelme, Borja;
Hatt, Janet K.;
Venter, Stephanus N.;
Rossello-Mora, Ramon;
Amann, Rudolf;
Konstantinidis, Konstantinos T.

Publication type:

Article

FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf348

By:

Gerhardt, Kenji;
Ruiz-Perez, Carlos A;
Rodriguez-R, Luis M;
Jain, Chirag;
Tiedje, James M;
Cole, James R;
Konstantinidis, Konstantinos T

Publication type:

Article

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 16, p. e74, doi. 10.1093/nar/gkae609

By:

Zhao, Jianshu;
Both, Jean Pierre;
Rodriguez-R, Luis M;
Konstantinidis, Konstantinos T

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. W1, p. W282, doi. 10.1093/nar/gky467

By:

Rodriguez-R, Luis M.;
Gunturu, Santosh;
Harvey, William T.;
Rosselló-Mora, Ramon;
Tiedje, James M.;
Cole, James R.;
Konstantinidis, Konstantinos T.

Publication type:

Article

Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-58769-y

By:

Dam, Phuongan;
Rodriguez-R, Luis M.;
Luo, Chengwei;
Hatt, Janet;
Tsementzi, Despina;
Konstantinidis, Konstantinos T.;
Voit, Eberhard O.

Publication type:

Article

Towards estimating the number of strains that make up a natural bacterial population.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44622-z

By:

Viver, Tomeu;
Conrad, Roth E.;
Rodriguez-R, Luis M.;
Ramírez, Ana S.;
Venter, Stephanus N.;
Rocha-Cárdenas, Jairo;
Llabrés, Mercè;
Amann, Rudolf;
Konstantinidis, Konstantinos T.;
Rossello-Mora, Ramon

Publication type:

Article

Towards estimating the number of strains that make up a natural bacterial population.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44622-z

By:

Viver, Tomeu;
Conrad, Roth E.;
Rodriguez-R, Luis M.;
Ramírez, Ana S.;
Venter, Stephanus N.;
Rocha-Cárdenas, Jairo;
Llabrés, Mercè;
Amann, Rudolf;
Konstantinidis, Konstantinos T.;
Rossello-Mora, Ramon

Publication type:

Article

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters.

Published in:

Biotechnology for Biofuels, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s13068-020-01679-y

By:

Campanaro, Stefano;
Treu, Laura;
Rodriguez-R, Luis M.;
Kovalovszki, Adam;
Ziels, Ryan M.;
Maus, Irena;
Zhu, Xinyu;
Kougias, Panagiotis G.;
Basile, Arianna;
Luo, Gang;
Schlüter, Andreas;
Konstantinidis, Konstantinos T.;
Angelidaki, Irini

Publication type:

Article

Why and how to use the SeqCode.

Published in:

mLife, 2024, v. 3, n. 1, p. 1, doi. 10.1002/mlf2.12092

By:

Whitman, William B.;
Chuvochina, Maria;
Hedlund, Brian P.;
Konstantinidis, Konstantinos T.;
Palmer, Marike;
Rodriguez‐R, Luis M.;
Sutcliffe, Iain;
Wang, Fengping

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. 3, p. 1, doi. 10.1093/nar/gkw900

By:

Orellana, Luis H.;
Rodriguez-R., Luis M.;
Konstantinidis, Konstantinos T.

Publication type:

Article

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 8, p. e73, doi. 10.1093/nar/gku169

By:

Luo, Chengwei;
Rodriguez-R, Luis M.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

Environmental Microbiology Reports, 2014, v. 6, n. 6, p. 640, doi. 10.1111/1758-2229.12180

By:

Tsementzi, Despina;
Poretsky, Rachel;
Rodriguez-R, Luis M.;
Luo, Chengwei;
Konstantinidis, Konstantinos T.

Publication type:

Article