Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics von Poretsky, Rachel, Rodriguez-R, Luis M, Luo, Chengwei, Tsementzi, Despina, Konstantinidis, Konstantinos T

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Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences von Rodriguez‐R, Luis M., Tsementzi, Despina, Luo, Chengwei, Konstantinidis, Konstantinos T.

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries von Jain, Chirag, Rodriguez-R, Luis M., Phillippy, Adam M., Konstantinidis, Konstantinos T., Aluru, Srinivas

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MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences von Luo, Chengwei, Rodriguez-R, Luis M., Konstantinidis, Konstantinos T.

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The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level von Rodriguez-R, Luis M, Gunturu, Santosh, Harvey, William T, Rosselló-Mora, Ramon, Tiedje, James M, Cole, James R, Konstantinidis, Konstantinos T

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GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs von Zhao, Jianshu, Both, Jean Pierre, Rodriguez-R, Luis M, Konstantinidis, Konstantinos T

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SAR11 bacteria linked to ocean anoxia and nitrogen loss von Tsementzi, Despina, Wu, Jieying, Deutsch, Samuel, Nath, Sangeeta, Rodriguez-R, Luis M., Burns, Andrew S., Ranjan, Piyush, Sarode, Neha, Malmstrom, Rex R., Padilla, Cory C., Stone, Benjamin K., Bristow, Laura A., Larsen, Morten, Glass, Jennifer B., Thamdrup, Bo, Woyke, Tanja, Konstantinidis, Konstantinos T., Stewart, Frank J.

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An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains von Pérez-Quintero, Alvaro L, Rodriguez-R, Luis M, Dereeper, Alexis, López, Camilo, Koebnik, Ralf, Szurek, Boris, Cunnac, Sebastien

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Comparative genomics identifies conserved and variable TAL effectors in African strains of the cotton pathogen Xanthomonas citri pv. malvacearum von Perez-Quintero, Alvaro L, Rodriguez-R, Luis M, Cuesta-Morrondo, Sara, Hakalová, Eliška, Betancurt-Anzola, Daniela, Camelo Valera, Laura Carolina, Chica Cardenas, Luis Alberto, Matiz-Ceron, Luisa, Jacobs, Jonathan, Roman-Reyna, Veronica, Reyes Muñoz, Alejandro, Bernal, Adriana J, Koebnik, Ralf

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Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes von Karthikeyan, Smruthi, Rodriguez‐R, Luis M., Heritier‐Robbins, Patrick, Hatt, Janet K., Huettel, Markus, Kostka, Joel E., Konstantinidis, Konstantinos T.

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Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications von DeLeon-Rodriguez, Natasha, Lathem, Terry L., Rodriguez-R, Luis M., Barazesh, James M., Anderson, Bruce E., Beyersdorf, Andreas J., Ziemba, Luke D., Bergin, Michael, Nenes, Athanasios, Konstantinidis, Konstantinos T.

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Why and how to use the SeqCode von Whitman, William B., Chuvochina, Maria, Hedlund, Brian P., Konstantinidis, Konstantinos T., Palmer, Marike, Rodriguez‐R, Luis M., Sutcliffe, Iain, Wang, Fengping

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An ANI gap within bacterial species that advances the definitions of intra-species units von Rodriguez-R, Luis M, Conrad, Roth E, Viver, Tomeu, Feistel, Dorian J, Lindner, Blake G, Venter, Stephanus N, Orellana, Luis H, Amann, Rudolf, Rossello-Mora, Ramon, Konstantinidis, Konstantinos T

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Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species” von Rodriguez-R, Luis M., Jain, Chirag, Conrad, Roth E., Aluru, Srinivas, Konstantinidis, Konstantinos T.

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

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ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores von Orellana, Luis H, Rodriguez-R, Luis M, Konstantinidis, Konstantinos T

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Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations von Suttner, Brittany, Johnston, Eric R., Orellana, Luis H., Rodriguez-R, Luis M., Hatt, Janet K., Carychao, Diana, Carter, Michelle Q., Cooley, Michael B., Konstantinidis, Konstantinos T.

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Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease von Cárdenas, Anny, Rodriguez-R, Luis M, Pizarro, Valeria, Cadavid, Luis F, Arévalo-Ferro, Catalina

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How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? von Rodriguez-R, Luis M, Castro, Juan C, Kyrpides, Nikos C, Cole, James R, Tiedje, James M, Konstantinidis, Konstantinos T

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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity von Rodriguez-R, Luis M, Gunturu, Santosh, Tiedje, James M, Cole, James R, Konstantinidis, Konstantinos T

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