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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.

Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB.

PLoS Comput Biol. 2016 Apr 6;12(4):e1004862. doi: 10.1371/journal.pcbi.1004862. eCollection 2016 Apr.


Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex.

Ortega DR, Zhulin IB.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004723. doi: 10.1371/journal.pcbi.1004723. eCollection 2016 Feb.


Joint mouse-human phenome-wide association to test gene function and disease risk.

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW.

Nat Commun. 2016 Feb 2;7:10464. doi: 10.1038/ncomms10464.


Databases for Microbiologists.

Zhulin IB.

J Bacteriol. 2015 Aug 1;197(15):2458-67. doi: 10.1128/JB.00330-15. Epub 2015 May 26. Review.


CDvist: a webserver for identification and visualization of conserved domains in protein sequences.

Adebali O, Ortega DR, Zhulin IB.

Bioinformatics. 2015 May 1;31(9):1475-7. doi: 10.1093/bioinformatics/btu836. Epub 2014 Dec 18.


Sisters unbound is required for meiotic centromeric cohesion in Drosophila melanogaster.

Krishnan B, Thomas SE, Yan R, Yamada H, Zhulin IB, McKee BD.

Genetics. 2014 Nov;198(3):947-65. doi: 10.1534/genetics.114.166009. Epub 2014 Sep 5.


A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors.

Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB.

Nat Commun. 2013;4:2881. doi: 10.1038/ncomms3881.


Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein.

Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB.

PLoS Comput Biol. 2013;9(11):e1003337. doi: 10.1371/journal.pcbi.1003337. Epub 2013 Nov 14.


SeqDepot: streamlined database of biological sequences and precomputed features.

Ulrich LE, Zhulin IB.

Bioinformatics. 2014 Jan 15;30(2):295-7. doi: 10.1093/bioinformatics/btt658. Epub 2013 Nov 13.


Homology modeling of the CheW coupling protein of the chemotaxis signaling complex.

Cashman DJ, Ortega DR, Zhulin IB, Baudry J.

PLoS One. 2013 Aug 7;8(8):e70705. doi: 10.1371/journal.pone.0070705. eCollection 2013.


Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli.

Borziak K, Fleetwood AD, Zhulin IB.

J Bacteriol. 2013 Aug;195(16):3596-602. doi: 10.1128/JB.00421-13. Epub 2013 Jun 7.


The 3.2 Å resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays.

Li X, Fleetwood AD, Bayas C, Bilwes AM, Ortega DR, Falke JJ, Zhulin IB, Crane BR.

Biochemistry. 2013 Jun 4;52(22):3852-65. doi: 10.1021/bi400383e. Epub 2013 May 23.


Dynamics of domain coverage of the protein sequence universe.

Rekapalli B, Wuichet K, Peterson GD, Zhulin IB.

BMC Genomics. 2012 Nov 16;13:634. doi: 10.1186/1471-2164-13-634.


Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48.

Sukharnikov LO, Alahuhta M, Brunecky R, Upadhyay A, Himmel ME, Lunin VV, Zhulin IB.

J Biol Chem. 2012 Nov 30;287(49):41068-77. doi: 10.1074/jbc.M112.405720. Epub 2012 Oct 10.


Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB.

PLoS Genet. 2011 Dec;7(12):e1002430. doi: 10.1371/journal.pgen.1002430. Epub 2011 Dec 22.


Cellulases: ambiguous nonhomologous enzymes in a genomic perspective.

Sukharnikov LO, Cantwell BJ, Podar M, Zhulin IB.

Trends Biotechnol. 2011 Oct;29(10):473-9. doi: 10.1016/j.tibtech.2011.04.008. Epub 2011 Jun 16.


Origins and diversification of a complex signal transduction system in prokaryotes.

Wuichet K, Zhulin IB.

Sci Signal. 2010 Jun 29;3(128):ra50. doi: 10.1126/scisignal.2000724.


PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis.

Xie Z, Ulrich LE, Zhulin IB, Alexandre G.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2235-40. doi: 10.1073/pnas.0910055107. Epub 2010 Jan 19.


Evolution and phyletic distribution of two-component signal transduction systems.

Wuichet K, Cantwell BJ, Zhulin IB.

Curr Opin Microbiol. 2010 Apr;13(2):219-25. doi: 10.1016/j.mib.2009.12.011. Epub 2010 Feb 3. Review.

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