Works by Rodriguez-R, Luis M.

Results: 30

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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