@article {439,
	title = {Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.},
	journal = {BMC Evol Biol},
	volume = {10},
	year = {2010},
	month = {2010},
	pages = {230},
	abstract = {BACKGROUND: Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR) separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences.

RESULTS: CRISPR spacer $\#$1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is unlikely to compensate for interference with hisS. Spacer $\#$1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which the native hisS was replaced with that of P. carbinolicus. The prediction that interference with hisS would result in an attenuated histidyl-tRNA pool insufficient for translation of proteins with multiple closely spaced histidines, predisposing them to mutation and elimination during evolution, was investigated by comparative genomics of P. carbinolicus and related species. Several ancestral genes with high histidine demand have been lost or modified in the P. carbinolicus lineage, providing an explanation for its physiological differences from other Geobacteraceae.

CONCLUSIONS: The disappearance of multiheme c-type cytochromes and other genes typical of a metal-respiring ancestor from the P. carbinolicus lineage may be the consequence of spacer $\#$1 interfering with hisS, a condition that can be reproduced in a heterologous host. This is the first successful co-introduction of an active CRISPR spacer and its target in the same cell, the first application of a chimeric CRISPR construct consisting of a spacer from one species in the context of repeats of another species, and the first report of a potential impact of CRISPR on genome-scale evolution by interference with an essential gene.},
	keywords = {Base Sequence, Comparative Genomic Hybridization, Computational Biology, Deltaproteobacteria, DNA, Bacterial, DNA, Intergenic, Evolution, Molecular, Genes, Bacterial, Genome, Bacterial, Geobacillus, Histidine-tRNA Ligase, Inverted Repeat Sequences, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, DNA},
	issn = {1471-2148},
	doi = {10.1186/1471-2148-10-230},
	author = {Aklujkar, Muktak and Lovley, Derek R}
}
@article {678,
	title = {Epitopia: a web-server for predicting B-cell epitopes.},
	journal = {BMC Bioinformatics},
	volume = {10},
	year = {2009},
	month = {2009},
	pages = {287},
	abstract = {BACKGROUND: Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire protein, a computational tool that predicts the most probable epitope regions is desirable.

RESULTS: The Epitopia server is a web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence. Epitopia implements a machine-learning algorithm that was trained to discern antigenic features within a given protein. The Epitopia algorithm has been compared to other available epitope prediction tools and was found to have higher predictive power. A special emphasis was put on the development of a user-friendly graphical interface for displaying the results.

CONCLUSION: Epitopia is a user-friendly web-server that predicts immunogenic regions for both a protein structure and a protein sequence. Its accuracy and functionality make it a highly useful tool. Epitopia is available at http://epitopia.tau.ac.il and includes extensive explanations and example predictions.},
	keywords = {Algorithms, Artificial Intelligence, Computational Biology, Epitopes, B-Lymphocyte, Internet, Software},
	issn = {1471-2105},
	doi = {10.1186/1471-2105-10-287},
	author = {Rubinstein, Nimrod D and Mayrose, Itay and Martz, Eric and Pupko, Tal}
}
@article {679,
	title = {Proteopedia.Org: a scientific "Wiki" bridging the rift between 3D structure and function of biomacromolecules.},
	journal = {Biopolymers},
	volume = {92},
	year = {2009},
	month = {2009},
	pages = {76-7},
	keywords = {Computational Biology, Imaging, Three-Dimensional, Internet, Models, Molecular, Protein Structure, Quaternary, Protein Structure, Tertiary, Proteins, Structure-Activity Relationship},
	issn = {0006-3525},
	doi = {10.1002/bip.21126},
	author = {Martz, Eric}
}
@article {701,
	title = {Benefits of in-situ synthesized microarrays for analysis of gene expression in understudied microorganisms.},
	journal = {J Microbiol Methods},
	volume = {74},
	year = {2008},
	month = {2008 Jul},
	pages = {26-32},
	abstract = {Although the genome sequences of many microorganisms are now known, whole-genome DNA microarray platforms consisting of PCR amplicon, or oligonucleotide elements printed onto glass slides have been readily available for only a relatively few, highly studied microorganisms. For those microorganisms more recently cultured or studied by fewer investigators it has been difficult to justify the initial time and expense of developing such array platforms especially if only a limited number of gene expression studies are envisioned. However, in-situ synthesized oligonucleotide (ISO) arrays can be inexpensively fabricated on an {\textquoteright}as needed{\textquoteright} basis with a reduced initial investment in time, personnel, resources, and costs. To evaluate the performance of one ISO array platform, gene expression patterns in Geobacter sulfurreducens under nitrogen-fixing conditions were compared with results from quantitative reverse transcriptase PCR (qRT-PCR) and previously published data from a similar experiment using spotted PCR amplicon arrays. There were strong correlations between the results of the ISO arrays and the results from qRT-PCR (r(2)=0.762) and spotted array (r(2)=0.744) analyses. After initial use the ISO arrays could be successfully stripped and reused. The increased flexibility in array design and reusability coupled with a lower initial investment in terms of fabrication time and cost for the ISO arrays suggest that they may be the preferred approach when investigating gene expression in microorganisms, especially when only a few expression studies are required.},
	keywords = {Bacterial Proteins, Computational Biology, Gene Expression, Geobacter, Nitrogen Fixation, Oligonucleotide Array Sequence Analysis, Oligonucleotides, Polymerase Chain Reaction},
	issn = {0167-7012},
	doi = {10.1016/j.mimet.2007.07.004},
	author = {Postier, Bradley and DiDonato, Raymond and Nevin, Kelly P and Liu, Anna and Frank, Bryan and Lovley, Derek and Methe, Barbara A}
}
@article {682,
	title = {Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.},
	journal = {Nucleic Acids Res},
	volume = {35},
	year = {2007},
	month = {2007 Jul},
	pages = {W506-11},
	abstract = {Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (K(s)) and non-synonymous (K(a)) substitutions. This enables the inference of site-specific positive Darwinian selection and purifying selection. We present here Selecton version 2.2 (http://selecton.bioinfo.tau.ac.il), a web server which automatically calculates the ratio between K(a) and K(s) (omega) at each site of the protein. This ratio is graphically displayed on each site using a color-coding scheme, indicating either positive selection, purifying selection or lack of selection. Selecton implements an assembly of different evolutionary models, which allow for statistical testing of the hypothesis that a protein has undergone positive selection. Specifically, the recently developed mechanistic-empirical model is introduced, which takes into account the physicochemical properties of amino acids. Advanced options were introduced to allow maximal fine tuning of the server to the user{\textquoteright}s specific needs, including calculation of statistical support of the omega values, an advanced graphic display of the protein{\textquoteright}s 3-dimensional structure, use of different genetic codes and inputting of a pre-built phylogenetic tree. Selecton version 2.2 is an effective, user-friendly and freely available web server which implements up-to-date methods for computing site-specific selection forces, and the visualization of these forces on the protein{\textquoteright}s sequence and structure.},
	keywords = {Algorithms, Amino Acid Sequence, Amino Acid Substitution, Amino Acids, Animals, Bayes Theorem, Computational Biology, Computer Simulation, Humans, Internet, Models, Molecular, Molecular Sequence Data, Phylogeny, Proteins, Sequence Analysis, Protein, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkm382},
	author = {Stern, Adi and Doron-Faigenboim, Adi and Erez, Elana and Martz, Eric and Bacharach, Eran and Pupko, Tal}
}
@article {512,
	title = {Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.},
	journal = {Gene},
	volume = {384},
	year = {2006},
	month = {2006 Dec 15},
	pages = {73-95},
	abstract = {RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely -35 and -10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative -35/-10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of -35/-10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between -35/-10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Base Sequence, Citrates, Computational Biology, Conserved Sequence, DNA-Directed RNA Polymerases, Escherichia coli, Escherichia coli Proteins, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genome, Bacterial, Geobacter, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Operon, Promoter Regions, Genetic, Sigma Factor, Transcription, Genetic},
	issn = {0378-1119},
	doi = {10.1016/j.gene.2006.06.025},
	author = {Yan, Bin and N{\'u}{\~n}ez, Cinthia and Ueki, Toshiyuki and Esteve-N{\'u}{\~n}ez, Abraham and Puljic, Marko and Adkins, Ronald M and Meth{\'e}, Barbara A and Lovley, Derek R and Krushkal, Julia}
}
@article {539,
	title = {Crystal ball. In silico biology meets in situ phenomenology.},
	journal = {Environ Microbiol},
	volume = {7},
	year = {2005},
	month = {2005 Apr},
	pages = {478-9},
	keywords = {Bacterial Physiological Phenomena, Computational Biology, Models, Biological},
	issn = {1462-2912},
	doi = {10.1111/j.1462-2920.2005.803_8.x},
	author = {Lovley, Derek R}
}
@article {550,
	title = {Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.},
	journal = {J Theor Biol},
	volume = {230},
	year = {2004},
	month = {2004 Sep 7},
	pages = {133-44},
	abstract = {Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae.},
	keywords = {Animals, Computational Biology, Conserved Sequence, DNA Footprinting, Genes, Regulator, Genome, Bacterial, Geobacter, Models, Genetic, Operon, Phylogeny},
	issn = {0022-5193},
	doi = {10.1016/j.jtbi.2004.04.022},
	author = {Yan, Bin and Meth{\'e}, Barbara A and Lovley, Derek R and Krushkal, Julia}
}
@article {685,
	title = {Protein Explorer: easy yet powerful macromolecular visualization.},
	journal = {Trends Biochem Sci},
	volume = {27},
	year = {2002},
	month = {2002 Feb},
	pages = {107-9},
	abstract = {Protein Explorer (PE, http://www.proteinexplorer.org) enables students, educators and other nonspecialists to visualize macromolecular structures easily. It also offers several advanced capabilities useful to protein structure specialists. Great attention has been given to making PE easy to use. Explanations, color keys and troubleshooting information are displayed automatically. There are also {\textquoteright}Frequently Asked Questions{\textquoteright}, a one-hour {\textquoteright}Quick-Tour{\textquoteright}, an alphabetical {\textquoteright}Help/Index/Glossary{\textquoteright}, and a detailed {\textquoteright}Tutorial{\textquoteright}; all making PE much easier to use than either Chime or RasMol. Moreover, it is much more powerful; in addition to basic macromolecular visualization capabilities common to most similar programs, it offers one-click visualization of interfaces between moieties ({\textquoteright}contacts{\textquoteright}), cation-pi interactions and salt bridges, as well as easy-to-use routines to visualize regions of conservation in three-dimensional protein structures based on multiple sequence alignments.},
	keywords = {Computational Biology, DNA, Evolution, Molecular, Macromolecular Substances, Protein Structure, Secondary, Proteins, Sequence Alignment, Software},
	issn = {0968-0004},
	author = {Martz, Eric}
}
