Dr. Victor Kunin |
| Main | Work | Education | Publications | Comments | Co-authors | Presentations | Reviews |
Publications |
| Download | 40. |
Dr Victor Kunin,
Dr Philip Hugenholtz,
PyroTagger: A fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data The Open Journal, Article 1, February 21, 2010.
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| 39. |
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL
Defining the core Arabidopsis thaliana root microbiome. Nature 488:7409p.86-90. August 2012. PMID:22859206 | |
| 38. |
He S, Kunin V, Haynes M, Martin HG, Ivanova N, Rohwer F, Dr Philip Hugenholtz, McMahon KD
Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ. Microbiol. 10:3p. . February 9, 2010. PMID:20148930 | |
| 37. |
Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Dr Philip Hugenholtz
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J p. . January 21, 2010. PMID:20090784 | |
| 36. |
Wu D, Dr Philip Hugenholtz, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Dr Jonathan A Eisen
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:7276p.1056-60. December 2009. PMID:20033048 | |
| Download | 35. |
Kunin V, Engelbrektson A, Ochman H, Dr Philip Hugenholtz
Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 10:3p. . August 27, 2009. PMID:19725865 |
| 34. |
Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P, Brune A, Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P, Brune A
Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl. Environ. Microbiol. 75:9p.2841-9. March 6, 2009. PMID:19270133 | |
| 33. |
Mavromatis K, Dr Natalia Ivanova, Anderson I, Dr Athanasios Lykidis, Hooper SD, Sun H, Kunin V, Lapidus A, Dr Philip Hugenholtz, Patel B, Kyrpides NC
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS ONE 4:1p.e4192. January 15, 2009. PMID:19145256 | |
| Download | 32. |
Kunin V, Copeland A, Lapidus A, Mavromatis K, Dr Philip Hugenholtz
A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72:4p.557-78, Table of Contents. December 2008. PMID:19052320 |
| 31. |
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Dr Philip Hugenholtz, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. U.S.A. 105:23p.8102-7. June 5, 2008. PMID:18535141 | |
| Download | 30. |
Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Dr Philip Hugenholtz
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol. Syst. Biol. 4p.198. June 3, 2008. PMID:18523433 |
| 29. |
Kamburov A, Goldovsky L, Freilich S, Kapazoglou A, Kunin V, Enright AJ, Tsaftaris A, Ouzounis CA
Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics 8p.460. December 14, 2007. PMID:18081932 | |
| 28. |
Sorek R, Kunin V, Dr Philip Hugenholtz
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:3p.181-6. March 2008. PMID:18157154 | |
| Download | 27. |
Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD, Dr Philip Hugenholtz
A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 18:2p.293-7. December 12, 2007. PMID:18077539 |
| 26. |
Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Mr Edward Kirton, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Dr Philip Hugenholtz, Leadbetter JR
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:7169p.560-5. November 2007. PMID:18033299 | |
| Download | 25. |
Kunin V, Sorek R, Dr Philip Hugenholtz
Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8:4p.R61. January 2007. PMID:17442114 |
| 24. |
Gu S, Anderson I, Kunin V, Cipriano M, Minovitsky S, Weber G, Amenta N, Hamann B, Dubchak I
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23:6p.764-6. January 17, 2007. PMID:17234642 | |
| 23. |
Garcia Martin H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Dr Philip Hugenholtz, García Martín H
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 24:10p.1263-9. September 24, 2006. PMID:16998472 | |
| 22. |
Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Dr Athanasios Lykidis, Anderson I, Mavromatis K, Dr Konstantinos Mavrommatis, Kunin V, Garcia Martin H, Dubchak I, Dr Philip Hugenholtz, Kyrpides NC
An experimental metagenome data management and analysis system. Bioinformatics 22:14p.e359-67. July 2006. PMID:16873494 | |
| 21. |
Ouzounis CA, Kunin V, Darzentas N, Goldovsky L
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective. Res. Microbiol. 157:1p.57-68. December 19, 2005. PMID:16431085 | |
| 20. |
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33:19p.6083-9. October 24, 2005. PMID:16246909 | |
| 19. |
Goldovsky L, Janssen P, Ahrén D, Audit B, Cases I, Darzentas N, Enright AJ, López-Bigas N, Peregrin-Alvarez JM, Smith M, Tsoka S, Kunin V, Ouzounis CA
CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics 21:19p.3806-10. October 2005. PMID:16216832 | |
| 18. |
Smith M, Kunin V, Goldovsky L, Enright AJ, Ouzounis CA
MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics 21:16p.3429-30. June 16, 2005. PMID:15961438 | |
| 17. |
Kunin V, Goldovsky L, Darzentas N, Ouzounis CA
The net of life: reconstructing the microbial phylogenetic network. Genome Res. 15:7p.954-9. June 17, 2005. PMID:15965028 | |
| 16. |
Kunin V, Teichmann SA, Huynen MA, Ouzounis CA
The properties of protein family space depend on experimental design. Bioinformatics 21:11p.2618-22. March 15, 2005. PMID:15769834 | |
| 15. |
Janssen P, Goldovsky L, Kunin V, Darzentas N, Ouzounis CA
Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep. 6:5p.397-9. May 2005. PMID:15864286 | |
| 14. |
Kunin V, Ouzounis CA
Clustering the annotation space of proteins. BMC Bioinformatics 6p.24. February 9, 2005. PMID:15703069 | |
| 13. |
Kunin V, Ahrén D, Goldovsky L, Janssen P, Ouzounis CA, Ahren D
Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res. 33:2p.616-21. January 28, 2005. PMID:15681613 | |
| 12. |
Liu Y, Harrison PM, Kunin V, Gerstein M
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 5:9p.R64. August 26, 2004. PMID:15345048 | |
| 11. |
Kunin V, Pereira-Leal JB, Ouzounis CA
Functional evolution of the yeast protein interaction network. Mol. Biol. Evol. 21:7p.1171-6. April 7, 2004. PMID:15071090 | |
| 10. |
Enright AJ, Kunin V, Ouzounis CA
Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31:15p.4632-8. August 2003. PMID:12888524 | |
| 9. |
Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, Harte N, Kunin V, Ouzounis CA
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics 19:11p.1451-2. July 2003. PMID:12874064 | |
| 8. |
Kunin V, Ouzounis CA
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics 19:11p.1412-6. July 2003. PMID:12874054 | |
| 7. |
Kunin V, Ouzounis CA
The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13:7p.1589-94. July 2003. PMID:12840037 | |
| 6. |
Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB
Classification schemes for protein structure and function. Nat. Rev. Genet. 4:7p.508-19. July 2003. PMID:12838343 | |
| 5. |
Janssen P, Audit B, Cases I, Darzentas N, Goldovsky L, Kunin V, López-Bigas N, Peregrin-Alvarez JM, Pereira-Leal JB, Tsoka S, Ouzounis CA, Lopez-Bigas N
Beyond 100 genomes. Genome Biol. 4:5p.402. April 28, 2003. PMID:12734008 | |
| 4. |
Kunin V, Cases I, Enright AJ, de Lorenzo V, Ouzounis CA
Myriads of protein families, and still counting. Genome Biol. 4:2p.401. January 28, 2003. PMID:12620116 | |
| 3. |
Kunin V, Chan B, Sitbon E, Lithwick G, Pietrokovski S
Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol. 307:3p.939-49. March 2001. PMID:11273712 | |
| 2. |
Arons E, Kunin V, Schechter C, Ehrlich R
Organization and functional analysis of the mouse transporter associated with antigen processing 2 promoter. J. Immunol. 166:6p.3942-51. March 2001. PMID:11238639 | |
| Download | 1. |
Kunin V
A system of two polymerases--a model for the origin of life. 30:5p.459-66. October 2000. PMID:11002892 |