Publications

CAGEF has contributed to over 280 publications.

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies

Posted by on Aug 11, 2016 in Publications | Comments Off on A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies

Thakur S, Guttman DS BMC Bioinformatics 2016;17(1):260 PMID: 27363390
Abstract: BACKGROUND: Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. RESULTS: We have developed a de-novo...

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Genomic screens identify a new phytobacterial microbe-associated molecular pattern and the cognate Arabidopsis receptor-like kinase that mediates its immune elicitation

Posted by on Aug 11, 2016 in Publications | Comments Off on Genomic screens identify a new phytobacterial microbe-associated molecular pattern and the cognate Arabidopsis receptor-like kinase that mediates its immune elicitation

Mott GA, Thakur S, Smakowska E, Wang PW, Belkhadir Y, Desveaux D, Guttman DS Genome Biol. 2016;17:98 PMID: 27160854
Abstract: BACKGROUND: The recognition of microbe-associated molecular patterns during infection is central to the mounting of an effective immune response. In spite of their importance, it remains difficult to identify these molecules and the host receptors required for their perception, ultimately limiting our understanding of the role of these molecules in the evolution of host-pathogen relationships. RESULTS: We employ a...

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The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes

Posted by on Aug 11, 2016 in Publications | Comments Off on The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes

Krogan NT, Marcos D, Weiner AI, Berleth T New Phytol. 2016 Jul; PMID: 27441727
Abstract: The regulatory effect auxin has on its own transport is critical in numerous self-organizing plant patterning processes. However, our understanding of the molecular mechanisms linking auxin signal transduction and auxin transport is still fragmentary, and important regulatory genes remain to be identified. To track a key link between auxin signaling and auxin transport in development, we established an Arabidopsis thaliana genetic background in which...

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High fecal IgA is associated with reduced Clostridium difficile colonization in infants

Posted by on Aug 11, 2016 in Publications | Comments Off on High fecal IgA is associated with reduced Clostridium difficile colonization in infants

Bridgman SL, Konya T, Azad MB, Guttman DS, Sears MR, Becker AB, Turvey SE, Mandhane PJ, Subbarao P, , Scott JA, Field CJ, Kozyrskyj AL Microbes Infect. 2016 May; PMID: 27235197
Abstract: Colonization of infants with Clostridium difficile is on the rise. Although better tolerated by infants than adults, it is a risk factor for future allergic disease. The present study describes associations between infant fecal immunoglobulin A (IgA) and colonization with C. difficile in 47 infants enrolled in the Canadian Healthy Infant Longitudinal...

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Prophages mediate defense against phage infection through diverse mechanisms

Posted by on Aug 11, 2016 in Publications | Comments Off on Prophages mediate defense against phage infection through diverse mechanisms

Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL ISME J 2016 Jun; PMID: 27258950
Abstract: The activity of bacteriophages poses a major threat to bacterial survival. Upon infection, a temperate phage can either kill the host cell or be maintained as a prophage. In this state, the bacteria carrying the prophage is at risk of superinfection, where another phage injects its genetic material and competes for host cell resources. To avoid this, many phages have evolved mechanisms that alter the bacteria and make it...

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New BAR Tools for Mining Expression Data and Exploring Cis-Elements in Arabidopsis thaliana

Posted by on Aug 11, 2016 in Publications | Comments Off on New BAR Tools for Mining Expression Data and Exploring Cis-Elements in Arabidopsis thaliana

Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang T, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ Plant J. 2016 Jul; PMID: 27401965
Abstract: Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which...

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Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana

Posted by on Aug 11, 2016 in Publications | Comments Off on Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana

Gould BA, Stinchcombe JR Mol. Ecol. 2016 Apr; PMID: 27064998
Abstract: A long-standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common variants of large effect on flowering time in the native range do not appear...

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The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling

Posted by on Aug 11, 2016 in Publications | Comments Off on The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling

Zhou X, Zhang ZL, Park J, Tyler L, Yusuke J, Qiu K, Nam EA, Lumba S, Desveaux D, McCourt P, Kamiya Y, Sun TP Plant Physiol. 2016 Aug;171(4):2760-70 PMID: 27255484
Abstract: The phytohormone gibberellin (GA) plays a key role in promoting stem elongation in plants. Previous studies show that GA activates its signaling pathway by inducing rapid degradation of DELLA proteins, GA signaling repressors. Using an activation-tagging screen in a reduced-GA mutant ga1-6 background, we identified AtERF11 to be a novel positive regulator of both GA...

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The HopF family of Pseudomonas syringae type III secreted effectors

Posted by on Aug 11, 2016 in Publications | Comments Off on The HopF family of Pseudomonas syringae type III secreted effectors

Lo T, Koulena N, Seto D, Guttman DS, Desveaux D Mol. Plant Pathol. 2016 Apr; PMID: 27061875
Abstract: Pseudomonas syringae is a bacterial phytopathogen that utilizes the type III secretion system to inject effector proteins into plant host cells. P. syringae can infect a wide range of plant hosts including agronomically-important crops such as tomatoes and beans. The ability of P. syringae to infect such numerous hosts is due, in part, to the diversity of effectors employed by this phytopathogen. Over 60 different effector families exist in P....

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A Human “eFP” Browser for Generating Gene Expression Anatograms

Posted by on Aug 11, 2016 in Publications | Comments Off on A Human “eFP” Browser for Generating Gene Expression Anatograms

Patel RV, Hamanishi ET, Provart NJ PLoS ONE 2016;11(3):e0150982 PMID: 26954504
Abstract: Transcriptomic studies help to further our understanding of gene function. Human transcriptomic studies tend to focus on a particular subset of tissue types or a particular disease state; however, it is possible to collate into a compendium multiple studies that have been profiled using the same expression analysis platform to provide an overview of gene expression levels in many different tissues or under different conditions. In order to increase the...

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