| Year |
Citation |
Score |
| 2023 |
Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. Mbio. e0269623. PMID 38085031 DOI: 10.1128/mbio.02696-23 |
0.352 |
|
| 2023 |
Lindner BG, Gerhardt K, Feistel DJ, Rodriguez-R LM, Hatt JK, Konstantinidis KT. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection. International Journal of Food Microbiology. 410: 110488. PMID 38035404 DOI: 10.1016/j.ijfoodmicro.2023.110488 |
0.316 |
|
| 2023 |
Perez-Quintero AL, Rodriguez-R LM, Cuesta-Morrondo S, Hakalová E, Betancurt-Anzola D, Camelo Valera LC, Chica Cardenas LA, Matiz-Ceron L, Jacobs J, Roman-Reyna V, Reyes Muñoz A, Bernal AJ, Koebnik R. Comparative genomics identifies conserved and variable TAL effectors in African strains of the cotton pathogen Xanthomonas citri pv. malvacearum. Phytopathology. PMID 37081724 DOI: 10.1094/PHYTO-12-22-0477-SC |
0.627 |
|
| 2022 |
Pallen MJ, Rodriguez-R LM, Alikhan NF. Naming the unnamed: over 65,000 names for unnamed and in the Genome Taxonomy Database. International Journal of Systematic and Evolutionary Microbiology. 72. PMID 36125864 DOI: 10.1099/ijsem.0.005482 |
0.338 |
|
| 2022 |
Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, 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. Systematic and Applied Microbiology. 45: 126305. PMID 36049255 DOI: 10.1016/j.syapm.2022.126305 |
0.312 |
|
| 2021 |
Meziti A, Rodriguez-R LM, Hatt JK, Peña-Gonzalez A, Levy K, Konstantinidis KT. How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample. Applied and Environmental Microbiology. PMID 33452027 DOI: 10.1128/AEM.02593-20 |
0.341 |
|
| 2021 |
Montenegro Benavides NA, Alvarez B A, Arrieta-Ortiz ML, Rodriguez-R LM, Botero D, Tabima JF, Castiblanco L, Trujillo C, Restrepo S, Bernal A. The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility. Bmc Microbiology. 21: 14. PMID 33407123 DOI: 10.1186/s12866-020-02066-1 |
0.591 |
|
| 2020 |
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. Environmental Microbiology. PMID 32495495 DOI: 10.1111/1462-2920.15112 |
0.33 |
|
| 2020 |
Campanaro S, Treu L, Rodriguez-R LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. Biotechnology For Biofuels. 13: 25. PMID 32123542 DOI: 10.1186/S13068-020-01679-Y |
0.414 |
|
| 2020 |
Dam P, Rodriguez-R LM, Luo C, Hatt J, Tsementzi D, Konstantinidis KT, Voit EO. Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes. Scientific Reports. 10: 2423. PMID 32051429 DOI: 10.1038/S41598-020-58769-Y |
0.361 |
|
| 2020 |
Suttner BJ, Johnston ER, Orellana LH, Rodriguez-R LM, Hatt JK, Carychao D, Carter MQ, Cooley MB, Konstantinidis KT. Potential and limitations of metagenomics as a public health risk assessment tool in a study of natural creek sediments influenced by agricultural and livestock runoff. Applied and Environmental Microbiology. PMID 31924621 DOI: 10.1128/Aem.02525-19 |
0.351 |
|
| 2019 |
Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. Bmc Genomics. 20: 917. PMID 31791238 DOI: 10.1186/S12864-019-6267-Z |
0.376 |
|
| 2019 |
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. Systematic and Applied Microbiology. PMID 31085022 DOI: 10.1016/J.Syapm.2019.03.007 |
0.395 |
|
| 2019 |
Karthikeyan S, Rodriguez-R LM, Heritier-Robbins P, Kim M, Overholt WA, Gaby JC, Hatt JK, Spain JC, Rosselló-Móra R, Huettel M, Kostka JE, Konstantinidis KT. "Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. The Isme Journal. PMID 30952995 DOI: 10.1038/S41396-019-0400-5 |
0.317 |
|
| 2018 |
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications. 9: 5114. PMID 30504855 DOI: 10.1038/S41467-018-07641-9 |
0.422 |
|
| 2018 |
Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, Konstantinidis KT. imGLAD: accurate detection and quantification of target organisms in metagenomes. Peerj. 6: e5882. PMID 30405973 DOI: 10.7287/Peerj.Preprints.26515V1 |
0.401 |
|
| 2018 |
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. The Isme Journal. PMID 30397261 DOI: 10.1038/S41396-018-0307-6 |
0.385 |
|
| 2018 |
Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, 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. PMID 29905870 DOI: 10.1093/Nar/Gky467 |
0.447 |
|
| 2018 |
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. PMID 29305502 DOI: 10.1128/Aem.00014-18 |
0.475 |
|
| 2017 |
Pena-Gonzalez A, Marston CK, Rodriguez-R LM, Kolton CB, Garcia-Diaz J, Theppote A, Frace M, Konstantinidis KT, Hoffmaster AR. Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids. Genome Announcements. 5. PMID 28428293 DOI: 10.1128/Genomea.00181-17 |
0.413 |
|
| 2017 |
Wang Y, Hatt JK, Tsementzi D, Rodriguez-R LM, Ruiz-Pérez CA, Weigand MR, Kizer H, Maresca G, Krishnan R, Poretsky R, Spain JC, Konstantinidis KT. Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Applied and Environmental Microbiology. PMID 28258138 DOI: 10.1128/Aem.03321-16 |
0.42 |
|
| 2017 |
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: e14. PMID 28180325 DOI: 10.1093/Nar/Gkw900 |
0.364 |
|
| 2016 |
Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. PMID 27487207 DOI: 10.1038/Nature19068 |
0.354 |
|
| 2016 |
Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EA, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Frontiers in Microbiology. 7: 579. PMID 27199914 DOI: 10.3389/Fmicb.2016.00579 |
0.357 |
|
| 2016 |
Soto-Giron MJ, Rodriguez-R LM, Luo C, Elk M, Ryu H, Hoelle J, Santo Domingo JW, Konstantinidis KT. Characterization of biofilms developing on hospital shower hoses and implications for nosocomial infections. Applied and Environmental Microbiology. PMID 26969701 DOI: 10.1128/Aem.03529-15 |
0.42 |
|
| 2015 |
Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Wonni I, Koita O, Pruvost O, Verdier V, Vernière C, et al. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Applied and Environmental Microbiology. 81: 688-98. PMID 25398857 DOI: 10.1128/Aem.02768-14 |
0.364 |
|
| 2014 |
Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT. Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle. Mbio. 5: e01193-14. PMID 24895307 DOI: 10.1128/Mbio.01193-14 |
0.323 |
|
| 2014 |
Rodriguez-R LM, Konstantinidis KT. Estimating coverage in metagenomic data sets and why it matters. The Isme Journal. 8: 2349-51. PMID 24824669 DOI: 10.1038/Ismej.2014.76 |
0.361 |
|
| 2014 |
Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. Plos One. 9: e93827. PMID 24714158 DOI: 10.1371/Journal.Pone.0093827 |
0.402 |
|
| 2014 |
Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Research. 42: e73. PMID 24589583 DOI: 10.1093/Nar/Gku169 |
0.433 |
|
| 2014 |
Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi JZ, Yuan MM, Sherry RA, Li D, Luo Y, Schuur EA, et al. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied and Environmental Microbiology. 80: 1777-86. PMID 24375144 DOI: 10.1128/Aem.03712-13 |
0.319 |
|
| 2014 |
Rodriguez-R LM, Konstantinidis KT. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics (Oxford, England). 30: 629-35. PMID 24123672 DOI: 10.1093/Bioinformatics/Btt584 |
0.364 |
|
| 2014 |
Rodriguez-R. LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species Microbe. 9: 111-118. DOI: 10.1128/Microbe.9.111.1 |
0.388 |
|
| 2013 |
Luo C, Rodriguez-R LM, Konstantinidis KT. A user's guide to quantitative and comparative analysis of metagenomic datasets. Methods in Enzymology. 531: 525-47. PMID 24060135 DOI: 10.1016/B978-0-12-407863-5.00023-X |
0.423 |
|
| 2013 |
Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. Plos One. 8: e68464. PMID 23869221 DOI: 10.1371/Journal.Pone.0068464 |
0.337 |
|
| 2013 |
Jeong K, Bodnar AM, Poulin L, Rojas NA, Rodríguez-R LM, Gagnevin L, Pruvost O, Koebnik R. CRISPR systems in plant pathogens: A new tool for epidemiological surveillance Phytopathology. 103: 67-68. PMID 23676108 DOI: 10.1094/Phyto-103-6-S2.1 |
0.346 |
|
| 2013 |
DeLeon-Rodriguez N, Lathem TL, Rodriguez-R LM, Barazesh JM, Anderson BE, Beyersdorf AJ, Ziemba LD, Bergin M, Nenes A, Konstantinidis KT. Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications. Proceedings of the National Academy of Sciences of the United States of America. 110: 2575-80. PMID 23359712 DOI: 10.1073/Pnas.1212089110 |
0.322 |
|
| 2012 |
Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R. Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. Phytopathology. 102: 948-56. PMID 22957820 DOI: 10.1094/Phyto-04-12-0078-R |
0.363 |
|
| 2012 |
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. PMID 22443110 DOI: 10.1186/1471-2180-12-43 |
0.619 |
|
| 2012 |
Cárdenas A, Rodriguez-R LM, Pizarro V, Cadavid LF, Arévalo-Ferro C. Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease. The Isme Journal. 6: 502-12. PMID 21955993 DOI: 10.1038/Ismej.2011.123 |
0.37 |
|
| 2011 |
Pinzón A, Rodriguez-R LM, González A, Bernal A, Restrepo S. Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. Briefings in Bioinformatics. 12: 151-62. PMID 20353961 DOI: 10.1093/Bib/Bbq009 |
0.613 |
|
| 2010 |
Méndez-Ortega MC, Restrepo S, Rodríguez-R LM, Pérez I, Mendoza JC, Martínez AP, Sierra R, Rey-Benito GJ. An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1. Virology Journal. 7: 369. PMID 21172023 DOI: 10.1186/1743-422X-7-369 |
0.314 |
|
| 2010 |
Sierra R, Rodríguez-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: e9847. PMID 20352100 DOI: 10.1371/Journal.Pone.0009847 |
0.63 |
|
| 2009 |
Restrepo S, Pinzón A, Rodríguez-R LM, Sierra R, Grajales A, Bernal A, Barreto E, Moreno PA, Moreno P, Zambrano MM, Cristancho M, González A, Castro H. Computational biology in Colombia. Plos Computational Biology. 5: e1000535. PMID 19876381 DOI: 10.1371/Journal.Pcbi.1000535 |
0.579 |
|
| 2009 |
Restrepo S, Pinzón A, Rodríguez-R LM, Sierra R, Grajales A, Bernal A, Barreto E, Moreno PA, Zambrano MM, Cristancho M, González A, Castro H. Correction: Computational Biology in Colombia Plos Computational Biology. 5. DOI: 10.1371/Annotation/35Cba0B0-056A-4Dd9-9B67-680D4Bc69243 |
0.552 |
|
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