Curriculum Vitae

Luis Miquel Rodriquez-Rojas

Research Engineer
Environmental Engineering
Ford Environmental Science & Technology Building 3324


Dr. Rodriguez-R earned his B.Sc. (Biology) degree from the National University of Colombia, following the concentration lines on Conservation Ecology and Molecular Plant Pathology. Next, he pursuit a M.Sc. (Microbiology) from Los Andes University, also in his native Colombia, followed by a second M.Sc. (Applied Informatics) from the University of Montpellier, in France, where he also worked as a researcher at the Research Institute for Development (IRD) with the sponsorship of the Region Languedoc-Rosillon (now Occitanie). After completing his degree, Dr. Rodriguez-R earned a Ph.D. in Bioinformatics from the Georgia Institute of Technology, after which he completed a 1.5-year postdoctoral fellowship. He now serves as Research Engineer for the School of Civil and Environmental Engineering of Georgia Tech.

He is the author of over three dozen papers and book chapters (about a third as first author) with over two thousand citations and an h-index of 23, has presented multiple workshops, seminars, and symposia on microbiome analysis for researchers and undergraduate educators, and has served as reviewer for several international journals. In addition, he has produced tens of bioinformatic tools and web interfaces including grid and cloud computing in a variety of programming languages and frameworks with over 6,000 downloads or online queries per month.


  • Ph.D. Bioinformatics, Georgia Institute of Technology, 2016
  • M.Sc. Applied Informatics, University of Montpellier (France), 2011
  • M.Sc. Microbiology, Los Andes University (Colombia), 2010
  • B.Sc. Biology, National University of Colombia (Colombia), 2009

Research Interests

  • Microbial Ecology & Evolution
  • Microbiome Analysis
  • Bioinformatics and Computational Biology
  • Genomics and Metagenomics


  • Sigma Xi, Georgia Tech Chapter 2017, Atlanta, USA 2017 Best Ph.D. Thesis Award
  • International Society for Microbial Ecology (ISME) 2016, Montréal, Canada ISME Travel Award, ISME 16
  • Georgia Institute of Technology, School of Biology 2015, Atlanta, USA School of Biology Graduate Excellence Award 2015
  • Région Languedoc Roussillon (now Occitanie), France 2010, Montpellier, France Fellowship granted by the region to outstanding international students
  • Evaluation-Orientation of Scientific Cooperation Program (ECOS) 2009, Montpellier, France Scientific Mission to Institut de Recherche pour le Développement (IRD)
  • Universidad Nacional de Colombia 2004, Bogotá, Colombia Award Matrícula de Honor




  1. Tsementzi•, Rodriguez-R LM•, et al. 2019. Ecogenomic characterization of widespread, closely- related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov. Systematic and Applied Microbiology. • Equal contribution.
  2. Meziti A•, Tsementzi D•, Rodriguez-R LM•, et al. 2019. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. The ISME Journal (in press). • Equal contribution.
  3. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Cole JR, Tiedje JM, Konstantinidis KT. 2018. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucl. Acids Res. 46(W1).
  4. Rodriguez-R LM•, Gunturu S•, Cole JR, Tiedje JM, Konstantinidis KT. 2018. Nonpareil 3: Fast estimation of metagenomic coverage and sequence diversity. mSystems 3(3). • Equal contrib.
  5. Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT. 2018. How much do rRNA gene surveys underestimate extant bacterial diversity? Appl. Env. Microbiol. 84(6).
  6. Orellana LH•, Rodriguez-R LM•, Konstantinidis KT. 2017. 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. • Equal contribution.
  7. Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, et al. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536(7615): 179-183.
  8. Rodriguez-R LM, Konstantinidis KT. 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints: e1900v1.
  9. Johnston ER, Rodriguez-R LM, et al. 2016. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem. Front. Microbiol. 7:579.
  10. Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT. 2015. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. The ISME Journal 9(9): 1928-1940.
  11. Rodriguez-R LM, Konstantinidis KT. 2014. Estimating coverage in metagenomic data sets and why it matters. The ISME Journal 8: 2349-2351.
  12. Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT. 2014. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. Environmental Microbiology Reports 6(6): 640-655.
  13. Rodriguez-R LM, Konstantinidis KT. 2014. Bypassing cultivation to identify bacterial species. Microbe 9(3): 111-118.
  14. Rodriguez-R LM, Konstantinidis KT. 2014. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics 30(5): 629-635.
  15. Luo C•, Rodriguez-R LM•, Konstantinidis KT. 2013. Chapter 23: A user’s guide to quantitative and comparative analysis of metagenomic datasets. In: DeLong EF (ed.). Microbial metagenomics, metatranscriptomics, and metaproteomics. Methods in enzymology 531. • Equal contribution.
  16. DeLeon-Rodriguez N, Lathem TL, Rodriguez-R LM, et al. 2013. Microbiome of the upper troposphere: species composition, effects of tropical storms, and atmospheric implications. PNAS 110(7): 2575-2580.
  17. Cárdenas A, Rodriguez-R LM, Pizarro V, Cadavid LF, Arévalo-Ferro C. 2012. Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease. The ISME Journal 6: 502-512.
  18. Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A. 2012. Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiology 12:43.
  19. Pinzón A, Rodriguez-R LM, González A, Bernal A, Restrepo S. 2011. Targeted Metabolic Reconstruction: a novel approach for the characterization of plant pathogen interactions. Briefings in Bioinformatics 12(2): 151-62.
  20. Sierra R•, Rodriguez-R LM•, Chaves D, Pinzon A, Grajales A, Rojas A, Mutis G, Cárdenas M, Burbano D, Jiménez P, Bernal A, Restrepo S. 2010. Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries. PLoS ONE 5(3): e9847. • Equal contribution.
  21. Burbano Sefair DA, Castro Barrera HE, Pérez Cabarcas MA, Restrepo Restrepo S, Rodríguez LM. 2009. Grid-enabled HMMER (G-HMMER): A Uniandes contribution to the biology community. In: Mayo R, et al (eds.). 2009. Proceedings of EELA-2. Ed. CIEMAT. Madrid. ISBN: 978-84-7834-627-1.




  1. American Society for Microbiology (ASM) Microbe 2018; Atlanta, USA, 2018 Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes recovers nearly complete genomes from over four hundred novel species. Symposium.
  2. American Society for Microbiology (ASM) Microbe 2018; Atlanta, USA, 2018 Rodriguez-R LM, Gunturu S, Jain C, Tiedje JM, Cole JR, Konstantinidis KT. MiGA – The Microbial Genomes Atlas: Expanding the catalogued diversity of Archaea and Bacteria. Poster presentation and Poster Talk.
  3. American Society for Microbiology (ASM) Microbe 2016; Boston, USA, 2016 Rodriguez-R LM, Gunturu S, Luo C, Tiedje JM, Cole JR, Konstantinidis KT. Microbial Genomes Atlas: Standardizing Genome-based Taxonomic Analyses for Archaea and Bacteria. Oral presentation.
  4. 16th International Symposium on Microbial Ecology – ISME16; Montréal, Canada, 2016 Rodriguez-R LM, Tsementzi D, Luo C, Hatt JK, Konstantinidis KT. Biogeography and seasonal variation disentangled in microbial meta-communities of five connected lakes. Oral presentation.
  5. CDC, Division of High-consequence pathogens and pathology science seminar; Atlanta, USA, 2015 Rodriguez-R LM, Pena-Gonzalez A, Gee J, Konstantinidis K, Hoffmaster A. Increased utilization of WGS for molecular epidemiology investigations of anthrax and melioidosis. Invited talk.
  6. IUMS XIV International Congress of Bacteriology & Applied Microbiology; Montréal, Canada, 2014 Rodriguez-R LM, Luo C, Konstantinidis KT. Expanding the bioinformatics toolbox for the analysis of genomes and metagenomes. Oral presentation.
  7. American Society for Microbiology General Meeting; Boston (MA), USA, 2014 Rodriguez-R LM, et al. Metagenomics insights into the effects of the Deepwater Horizon oil spill on indigenous communities in beach sands. Oral presentation.
  8. ASM Conference for Undergraduate Educators (ASMCUE); Danvers (MA), USA, 2014 Course-Integrated Research by J Tiedje, KT Konstantinidis, J Cole, and LM Rodriguez-R. Hands-on bioinformatics exercises for the analysis of complex microbiomes in the classroom. Workshop.


Updated date: January 8, 2020 - 11:34