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      LM Rodriguez-R

      Bioinformatics & Microbial Ecology

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Published Works

Google Scholar

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.