Computational Genomics

Publications

Publications

2009

  • Briegel, A, Ortega DR, Tocheva EI, Wuichet K, Li Z, Chen S, Muller A, Iancu CV, Murphy GE, Dobro MJ, Zhulin IB, Jensen GJ. Universal architecture of bacterial chemoreceptor arrays. Proceedings of the National Academy of Sciences of the USA 2009 published online before print September 23, 2009, doi:10.1073/pnas.0905181106. Press release.
  • Rekapalli B, Halloy C, Zhulin IB. HSP-HMMER: a tool for protein domain identification on a large scale. Proceedings of the 24 Annual ACM Symposium on Advanced Computing 2009, p. 677-670.
  • Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 2009, 10:145. openAccess
  • Zhulin IB. It is computation time for bacteriology! Journal of Bacteriololgy 2009, 191:20-22. openAccess
  • Elliott KT, Zhulin IB, Stuckey JA, DiRita VJ. Conserved residues in the HAMP domain define a new family of proposed bipartite energy taxis receptors. Journal of Bacteriololgy 2009, 191:375-387. openAccess

2008

  • Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. Towards environmental systems biology of Shewanella. Nature Reviews Microbiology 2008, 6:592-603.
  • Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genetics 2008, 4:e1000087. openAccess
  • Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N. Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. Journal of Bacteriology 2008, 190:2957-65. openAccess
  • Belas R, Zhulin IB, Yang Z. Bacterial signaling and motility: sure bets. Journal of Bacteriology 2008, 190:1849-56. openAccess

2007

  • Borziak K, Zhulin IB., FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. Bioinformatics . 2007, 23:2518-21. openAccess
  • Alexander, R.P. and I.B. Zhulin. 2007. From the Cover: Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proceedings of the National Academy of Sciences of the USA 104, 2885-2890 openAccess PNAS In This Issue PNAS commentary. Press release
  • Wuichet, K., R.P. Alexander, and I.B. Zhulin. 2007. Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods in Enzymology 422, 3-31. openAccess
  • Ulrich, L.E and I.B. Zhulin. 2007. MiST: a Microbial Signal Transduction database. Nucleic Acids Research 35, D386-D390 openAccesssf1000biology.gif

2006

  • Chain, P.S.G., V.J. Denef, K. Konstantinidis, L.M.Vergez, L. Agullo, V.L.Reyes, L. Hauser, M. Cordova, L. Gomez, M. Gonzalez, M. Land, V. Lao, F. Larimer, J.J. LiPuma, E. Mahenthiralingam, S.A. Malfatti, C.J. Marx, J.J. Parnell, A. Ramette, P. Richardson, M. Seeger, D. Smith, T. Spilker, W.J. Sul, T.V. Tsoi, L.E. Ulrich, I.B. Zhulin, and J.M. Tiedje. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 M bp genome shaped for versatility. Proceedings of the National Academy of Sciences of the USA 103, 15280-15287 openAccesss

2005

  • Ulrich, L.E. and I.B. Zhulin. 2005. Four-helical bundle: a ubiquitous sensory module in prokaryotic signal transduction. Bioinformatics 21 Suppl 3, iii45-iii48. openAccesss
  • Wu, M., Q. Ren, A. S. Durkin, S. C. Daugherty, L. M. Brinkac, R. J. Dodson, R. Madupu, S. A. Sullivan, J. F. Kolonay, W. Nelson, L. J. Tallon, K. M. Jones, L. E. Ulrich, J. M. Gonzalez, I. B. Zhulin, F. T. Robb and J. A. Eisen*. 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genetics 1, e65 openAccesss Press release
  • Ulrich, L.E., E.V. Koonin and I.B. Zhulin. 2005. From the Cover: One-component regulators dominate signal transduction in prokaryotes. Trends in Microbiology 13, 52-56. openAccess

2004

  • Alexandre, G. and I.B. Zhulin. 2004. Ecological role of energy taxis. FEMS Microbiology Reviews 28, 113-126
  • Zhulin, I.B. 2004. Digging with experimental pick and computational shovel: a new addition to the histidine kinase superfamily. Journal of Bacteriology 186, 267-269 openAccesss

2003

  • Mazzag, B., I.B. Zhulin and A. Mogilner. 2003. Model of bacterial band formation in aerotaxis. Biophysical Journal 85, 3558-3574 openAccesss
  • Phillips-Greer, S.E., Alexandre, G., Taylor, B.L. and I.B. Zhulin. 2003. Aer and Tsr guide Escherichia coli in spatial gradients of oxidizable substrates. Microbiology 149, 2661-2667 openAccesss f1000biology.gif
  • Wuichet, K. and I.B. Zhulin. 2003. Molecular evolution of sensory domains in cyanobacterial chemoreceptors. Trends in Microbiology 11, 200-203
  • Shu, C.J., L.E. Ulrich and I.B. Zhulin. 2003. The NIT domain: a predicted nitrate responsive module in bacterial sensory receptors. Trends in Biochemical Sciences 28, 121-124
  • Alexandre, G. and I. B. Zhulin. 2003. Different evolutionary constraints on CheW and CheY proteins revealed by heterologous expression studies and protein sequence analysis. Journal of Bacteriology 185, 544-552 openAccesss
  • Zhulin, I.B., A. Nikolskaya and M. Y. Galperin. 2003. Common sensory domains in transmembrane receptors for diverse signal transduction pathways in Bacteria and Archaea. Journal of Bacteriology 185, 285-294 openAccesss

2002

  • Shiomi, D., I. B. Zhulin, M. Homma and I. Kawagishi. 2002. Dual recognition of the bacterial chemoreceptor by chemotaxis-specific domains of the CheR methyltransferase. Journal of Biological Chemistry 277, 42325-42333 openAccesss
  • Sun, X., I. Zhulin and R. M. Wartell. 2002. Predicted structure and phyletic distribution of the RNA binding protein Hfq. Nucleic Acids Research 30: 3662-3671openAccesss
  • Perelygin, A.A., S.V. Scherbik, I.B. Zhulin, B.M. Stockman, Y. Li and M.A. Brinton. 2002. Positioning cloning of the murine flavivirus resistance gene. Proceedings of the National Academy of Sciences of the USA 99, 9322-9327 openAccesss f1000biology.gif PNAS commentary
  • Hauwaerts, D., G. Alexandre, S. Das, J. Vanderleyden and I.B. Zhulin. 2002. A major chemotaxis gene cluster in Azospirillum brasilense and relationships between chemotaxis operons in ?-proteobacteria. FEMS Microbiology Letters 208, 61-67
  • Shu, C.J. and I.B. Zhulin. 2002. ANTAR: an RNA-binding domain in transcription antitermination regulatory proteins. Trends in Biochemical Sciences 27, 3-5
  • Aizawa, S.-I., I. B. Zhulin, L. Marquez-Magana and G. W. Ordal. 2002. Chemotaxis and Motility, pp. 437-452. In A. L. Sonenshein et al. (Ed.). Bacillus subtilis and Its Closest Relatives: from Genes to Cells. ASM Press, Washington, DC.

2001

  • Iyer, L. M., L. Aravind, P. Bork, K. Hoffmann, A. R. Mushegian, I. B. Zhulin, and E. V. Koonin. 2001. Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biology 2, research0051.1-0051.11
  • Kirby, J. R., C. J. Kristich, M. M. Saulmon, L. F. Garrity, I. B. Zhulin, and G. W. Ordal. 2001. CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Molecular Microbiology 42, 573-585
  • Mougel, C. and I. B. Zhulin. 2001. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends in Biochemical Sciences 26, 582-584
  • Alexandre, G. and I. B. Zhulin. 2001. More than one way to sense chemicals. Journal of Bacteriology 183, 4681-4686
  • Zhulin, I. B. 2001. The superfamily of chemotaxis transducers: from physiology to genomics and back. Advances in Microbial Physiology 45, 157-198

2000

  • Alexandre, G., S. E. Greer, and I. B. Zhulin. 2000. Energy taxis is the dominant behavior in Azospirillum brasilense. Journal of Bacteriology 182, 6042-6048 openAccesss
  • Repik, A. V., A. Rebbapragada, M. S. Johnson, J. O. Haznedar, I. B. Zhulin and B. L. Taylor. 2000. PAS domain residues involved in signal transduction by the Aer redox sensor of Escherichia coli. Molecular Microbiology 36, 806-816 openAccesss
  • Zhulin, I. B. 2000. Novel phototaxis receptor hidden in the cyanobacterial genome. Journal of Molecular Microbiology and Biotechnology 2, 491-493
  • Alexandre, G., and I. B. Zhulin. 2000. Laccases are widespread in bacteria. Trends in Biotechnology 18, 41-42

1999

  • Alexandre, G., R. Bally, B. L. Taylor and I. B. Zhulin. 1999. Loss of cytochrome c oxidase activity and acquisition of resistance to exogenous quinones in a laccase-positive variant of Azospirillum lipoferum. Journal of Bacteriology 181, 6730-6738 openAccesss
  • Taylor, B. L., I. B. Zhulin, and M. S. Johnson. 1999. Aerotaxis and related responses in bacteria. Annual Reviews in Microbiology 53, 103-128
  • Taylor, B. L., and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential and light. Microbiology and Molecular Biology Reviews 63, 479-506 openAccesss
    • Featured in a book “Quest: The Essence of Humanity” by Charles A. Pasternak as an important scientific contribution to our understanding of evolution
    • More than 600 citations

For publications prior to 1999, please download Igor Zhulin’s CV