The following list includes the published works where I am the leading author (including equal contributions). For a comprehensive list of my publications and citation statistics see my Google Scholar profile. For a list of my journal reviews see my Publons profile.
- Lignocellulolytic consortium
Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation ISME Comms., 2022.
- 65,000 names
Pallen MJ, Rodriguez-R LM, Alikhan NF. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database Int. J. Syst. Appl. Microbiol., 2022.
- SeqCode
Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst PJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN, Whitman WB. SeqCode: a nomenclatural code for prokaryotes described from sequence data Nat. Microbiol., 2022.
- Development of the SeqCode
Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst PJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type Syst. Applied Microbiol., 2022.
- Maputo children: comparative fecal microbiome
Kim M, Rodriguez-R LM, Hatt JK, Kayali O, Nalá R, Dunlop AL, Brennan PA, Corwin E, Smith AK, Brown J, Konstantinidis KT. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling ISME Comms., 2022.
- RecruitPlotEasy Announcement
Gerhardt K•, Ruiz-Perez CA•, Rodriguez-R LM•, Conrad RE, Konstantinidis KT. RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity Front. Bioinform., 2022. • Equal contribution.
- ANI debate reply
Rodriguez-R LM, Jain C, Conrad RE, Aluru S, Konstantinidis KT. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species” Nat Comm, 2021.
- Specialization-Disturbance Hypothesis tested in a mesocosm
Heritier-Robbins P, Karthikeyan S, Hatt JK, Kim M, Huettel M, Kostka JE, Konstantinidis KT, Rodriguez-R LM. Beach sand oil spills select for generalist microbial populations ISME J, 2021.
- Fecal MAG quality
Meziti A•, Rodriguez-R LM•, Hatt JK, Peña-Gonzalez A, Levy K, Konstantinidis KT. The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample Appl Env Microbiol, 87(6):e02593-20. 2021. • Equal contribution.
- Genome classification
Rodriguez-R LM, Rosselló-Mora R, Konstantinidis KT. Identification and Classification of Prokaryotes using Whole-genome Sequences. Trends in the Systematics of Bacteria and Fungi. Chapter 13. 2021.
- Using MiGA
Rodriguez-R LM, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT. Classifying prokaryotic genomes using the Microbial Genomes Atlas (MiGA) webserver. Bergey's Manual of Systematics of Archaea and Bacteria. 2020.
- Freshwater Iterative Subtractive Binning
Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences Env Micro, 22(8):3394-3412. 2020.
- Fonsibacter lacus
Tsementzi D•, Rodriguez-R LM•, Ruiz-Perez CA, Meziti A, Hatt JK, Konstantinidis KT. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov. Sys App Micro 42(4):495-505. 2019. • Equal contribution.
- Kalamas Genome diversity
Meziti A•, Tsementzi D•, Rodriguez-R LM•, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. ISME J 13:767-779. 2018. • Equal contribution.
- MiGA Webserver
Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Cole JR, Tiedje JM, Konstantinidis KT. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Research 46(W1):W282-W288. 2018.
- Nonpareil 3
Rodriguez-R LM•, Gunturu S•, Cole JR, Tiedje JM, Konstantinidis KT. Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity. mSystems 3(3):e00039-18. 2018. • Equal contribution.
- 16S vs ANI
Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT. How much do rRNA gene surveys underestimate extant bacterial diversity? Applied and Environmental Microbiology 84(6):e00014-18. 2018.
- ROCker
Orellana LH•, Rodriguez-R LM•, Konstantinidis KT. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Research 45(3):e14. 2017. • Equal contribution.
- Bioinformatics and Microbial Ecology
Rodriguez-R LM. Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics. Dissertation, Doctor of Philosophy in Bioinformatics, Georgia Institute of Technology, School of Biological Sciences. 2016.
- Enveomics Collection
Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900. 2016.
- Macondo Oil Spill
Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME Journal 9:1928-1940. 2015.
- Metagenomic Coverage
Rodriguez-R LM, Konstantinidis KT. Estimating coverage in metagenomic data sets and why it matters. ISME Journal 8(11):2349. 2014.
- Bypassing cultivation
Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 9(3):111-118. 2014.
- Nonpareil
Rodriguez-R LM, Konstantinidis KT. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics 30(5):629-635. 2013.
- Analysis of Metagenomes
Luo C•, Rodriguez-R LM•, Konstantinidis KT. A user’s guide to quantitative and comparative analysis of metagenomic datasets. Methods in Enzymology 531:525-547. 2013. • Equal contribution.
- Phylogeny of Xanthomonas
Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A. Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiology 12:43. 2012.
- Polloc
Rodriguez-R LM. Polloc – A Perl library for polymorphic loci analyses in bacterial molecular typing studies. Thesis, Master in Computer Sciences – Skills integration, Université Montpellier II, College of Sciences. 2011.
- Phytophthora infestans expression in planta
Sierra R•, Rodriguez-R LM•, Chaves D, Pinzón A, Grajales A, Rojas A, Mutis G, Cárdenas M, Burbano D, Jiménez P, Bernal A, Restrepo S. Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries. PLoS ONE 5(3): e9847. 2010. • Equal contribution.