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Items: 37

1.

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov.

Tsementzi D, Rodriguez-R LM, Ruiz-Perez CA, Meziti A, Hatt JK, Konstantinidis KT.

Syst Appl Microbiol. 2019 Jul;42(4):495-505. doi: 10.1016/j.syapm.2019.03.007. Epub 2019 May 6.

PMID:
31085022
2.

"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments.

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.

ISME J. 2019 Aug;13(8):2129-2134. doi: 10.1038/s41396-019-0400-5. Epub 2019 Apr 5.

PMID:
30952995
3.

Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity in Bacillus anthracis.

Gargis AS, McLaughlin HP, Conley AB, Lascols C, Michel PA, Gee JE, Marston CK, Kolton CB, Rodriguez-R LM, Hoffmaster AR, Weigel LM, Sue D.

mSystems. 2018 Dec 11;3(6). pii: e00154-18. doi: 10.1128/mSystems.00154-18. eCollection 2018 Nov-Dec.

4.

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S.

Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.

5.

imGLAD: accurate detection and quantification of target organisms in metagenomes.

Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, Konstantinidis KT.

PeerJ. 2018 Nov 2;6:e5882. doi: 10.7717/peerj.5882. eCollection 2018.

6.

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.

Meziti A, Tsementzi D, Rodriguez-R LM, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT.

ISME J. 2019 Mar;13(3):767-779. doi: 10.1038/s41396-018-0307-6. Epub 2018 Nov 5.

PMID:
30397261
7.

Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.

Pena-Gonzalez A, Rodriguez-R LM, Marston CK, Gee JE, Gulvik CA, Kolton CB, Saile E, Frace M, Hoffmaster AR, Konstantinidis KT.

mSystems. 2018 Aug 14;3(4). pii: e00065-18. doi: 10.1128/mSystems.00065-18. eCollection 2018 Jul-Aug.

8.

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT.

Nucleic Acids Res. 2018 Jul 2;46(W1):W282-W288. doi: 10.1093/nar/gky467.

9.

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT.

mSystems. 2018 Apr 10;3(3). pii: e00039-18. doi: 10.1128/mSystems.00039-18. eCollection 2018 May-Jun.

10.

How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT.

Appl Environ Microbiol. 2018 Mar 1;84(6). pii: e00014-18. doi: 10.1128/AEM.00014-18. Print 2018 Mar 15.

11.

Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.

Pena-Gonzalez A, Marston CK, Rodriguez-R LM, Kolton CB, Garcia-Diaz J, Theppote A, Frace M, Konstantinidis KT, Hoffmaster AR.

Genome Announc. 2017 Apr 20;5(16). pii: e00181-17. doi: 10.1128/genomeA.00181-17.

12.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

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.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03321-16. doi: 10.1128/AEM.03321-16. Print 2017 Apr 15.

13.

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores.

Orellana LH, Rodriguez-R LM, Konstantinidis KT.

Nucleic Acids Res. 2017 Feb 17;45(3):e14. doi: 10.1093/nar/gkw900.

14.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

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, Woyke T, Konstantinidis KT, Stewart FJ.

Nature. 2016 Aug 11;536(7615):179-83. Epub 2016 Aug 3.

15.

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EA, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT.

Front Microbiol. 2016 Apr 25;7:579. doi: 10.3389/fmicb.2016.00579. eCollection 2016.

16.

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections.

Soto-Giron MJ, Rodriguez-R LM, Luo C, Elk M, Ryu H, Hoelle J, Santo Domingo JW, Konstantinidis KT.

Appl Environ Microbiol. 2016 Apr 18;82(9):2872-2883. doi: 10.1128/AEM.03529-15. Print 2016 May.

17.

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities.

Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT.

Environ Microbiol Rep. 2014 Dec;6(6):640-55.

PMID:
25756118
18.

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill.

Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT.

ISME J. 2015 Sep;9(9):1928-40. doi: 10.1038/ismej.2015.5. Epub 2015 Feb 17.

19.

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.

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, Koebnik R.

Appl Environ Microbiol. 2015 Jan;81(2):688-98. doi: 10.1128/AEM.02768-14. Epub 2014 Nov 14.

20.

Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.

Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT.

MBio. 2014 Jun 3;5(3):e01193-14. doi: 10.1128/mBio.01193-14.

21.

Estimating coverage in metagenomic data sets and why it matters.

Rodriguez-R LM, Konstantinidis KT.

ISME J. 2014 Nov;8(11):2349-51. doi: 10.1038/ismej.2014.76. Epub 2014 May 13. No abstract available.

22.

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT.

PLoS One. 2014 Apr 8;9(4):e93827. doi: 10.1371/journal.pone.0093827. eCollection 2014.

23.

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.

Luo C, Rodriguez-R LM, Konstantinidis KT.

Nucleic Acids Res. 2014 Apr;42(8):e73. doi: 10.1093/nar/gku169. Epub 2014 Mar 3.

24.

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics.

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, Chain P, Tiedje JM, Zhou J, Konstantinidis KT.

Appl Environ Microbiol. 2014 Mar;80(5):1777-86. doi: 10.1128/AEM.03712-13. Epub 2013 Dec 27.

25.

Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.

Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero Á, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A.

PLoS One. 2013 Nov 22;8(11):e79704. doi: 10.1371/journal.pone.0079704. eCollection 2013.

26.

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.

Rodriguez-R LM, Konstantinidis KT.

Bioinformatics. 2014 Mar 1;30(5):629-35. doi: 10.1093/bioinformatics/btt584. Epub 2013 Oct 11.

PMID:
24123672
27.

A user's guide to quantitative and comparative analysis of metagenomic datasets.

Luo C, Rodriguez-R LM, Konstantinidis KT.

Methods Enzymol. 2013;531:525-47. doi: 10.1016/B978-0-12-407863-5.00023-X.

PMID:
24060135
28.

Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study.

DeLeon-Rodriguez N, Lathem TL, Rodriguez-R LM, Barazesh JM, Anderson BE, Beyersdorf AJ, Ziemba LD, Bergin M, Nenes A, Konstantinidis KT.

Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):E2085. No abstract available.

29.

An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains.

Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S.

PLoS One. 2013 Jul 15;8(7):e68464. doi: 10.1371/journal.pone.0068464. Print 2013.

30.

Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.

DeLeon-Rodriguez N, Lathem TL, Rodriguez-R LM, Barazesh JM, Anderson BE, Beyersdorf AJ, Ziemba LD, Bergin M, Nenes A, Konstantinidis KT.

Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2575-80. doi: 10.1073/pnas.1212089110. Epub 2013 Jan 28.

31.

Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola.

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.

Phytopathology. 2012 Oct;102(10):948-56. doi: 10.1094/PHYTO-04-12-0078-R.

32.

Genomes-based phylogeny of the genus Xanthomonas.

Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A.

BMC Microbiol. 2012 Mar 23;12:43. doi: 10.1186/1471-2180-12-43.

33.

Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease.

Cárdenas A, Rodriguez-R LM, Pizarro V, Cadavid LF, Arévalo-Ferro C.

ISME J. 2012 Mar;6(3):502-12. doi: 10.1038/ismej.2011.123. Epub 2011 Sep 29.

34.

An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1.

Méndez-Ortega MC, Restrepo S, Rodríguez-R LM, Pérez I, Mendoza JC, Martínez AP, Sierra R, Rey-Benito GJ.

Virol J. 2010 Dec 20;7:369. doi: 10.1186/1743-422X-7-369.

35.

Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions.

Pinzón A, Rodriguez-R LM, González A, Bernal A, Restrepo S.

Brief Bioinform. 2011 Mar;12(2):151-62. doi: 10.1093/bib/bbq009. Epub 2010 Mar 29.

PMID:
20353961
36.

Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries.

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.

PLoS One. 2010 Mar 24;5(3):e9847. doi: 10.1371/journal.pone.0009847.

37.

Computational biology in Colombia.

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.

PLoS Comput Biol. 2009 Oct;5(10):e1000535. doi: 10.1371/journal.pcbi.1000535. Epub 2009 Oct 30. Review. No abstract available. Erratum in: PLoS Comput Biol. 2009 Oct;5(11). doi: 10.1371/annotation/35cba0b0-056a-4dd9-9b67-680d4bc69243.

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