Search Results - "Ardell, David H."

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores by Illergård, Kristoffer, Ardell, David H., Elofsson, Arne

“…Protein structures change during evolution in response to mutations. Here, we analyze the mapping between sequence and structure in a set of structurally…”
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Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens by Kelly, Paul, Hadi-Nezhad, Fatemeh, Liu, Dennis Y, Lawrence, Travis J, Linington, Roger G, Ibba, Michael, Ardell, David H

“…The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between…”
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Computational analysis of tRNA identity by Ardell, David H.

“…I review recent developments in computational analysis of tRNA identity. I suggest that the tRNA–protein interaction network is hierarchically organized, and…”
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Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line by Weinholdt, Claus, Wichmann, Henri, Kotrba, Johanna, Ardell, David H, Kappler, Matthias, Eckert, Alexander W, Vordermark, Dirk, Grosse, Ivo

“…The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with…”
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tRNA functional signatures classify plastids as late-branching cyanobacteria by Lawrence, Travis J, Amrine, Katherine Ch, Swingley, Wesley D, Ardell, David H

“…Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances…”
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Eye movements during listening reveal spontaneous grammatical processing by Huette, Stephanie, Winter, Bodo, Matlock, Teenie, Ardell, David H, Spivey, Michael

“…Recent research using eye-tracking typically relies on constrained visual contexts in particular goal-oriented contexts, viewing a small array of objects on a…”
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Dynamic regulation of mRNA decay during neural development by Burow, Dana A, Umeh-Garcia, Maxine C, True, Marie B, Bakhaj, Crystal D, Ardell, David H, Cleary, Michael D

“…Gene expression patterns are determined by rates of mRNA transcription and decay. While transcription is known to regulate many developmental processes, the…”
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tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria by Amrine, Katherine C H, Swingley, Wesley D, Ardell, David H

“…Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions…”
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The Louse-Borne Human Pathogen Bartonella quintana Is a Genomic Derivative of the Zoonotic Agent Bartonella henselae by Alsmark, Cecilia M., Frank, A. Carolin, Karlberg, E. Olof, Legault, Boris-Antoine, Ardell, David H., Canbäck, Björn, Eriksson, Ann-Sofie, Näslund, A. Kristina, Handley, Scott A., Huvet, Maxime, La Scola, Bernard, Holmberg, Martin, Siv G. E. Andersson, Falkow, Stanley

“…We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain…”
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FAST: FAST Analysis of Sequences Toolbox by Lawrence, Travis J, Kauffman, Kyle T, Amrine, Katherine C H, Carper, Dana L, Lee, Raymond S, Becich, Peter J, Canales, Claudia J, Ardell, David H

“…FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological…”
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Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure–Function Map by Phillips, Julie Baker, Ardell, David H.

“…The evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon…”
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tSFM 1.0: tRNA Structure–Function Mapper by Lawrence, Travis J, Hadi-Nezhad, Fatemeh, Grosse, Ivo, Ardell, David H

“…Abstract Motivation Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their…”
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No accident: genetic codes freeze in error–correcting patterns of the standard genetic code by Johnstone, R. A., Dall, S. R. X., Ardell, David H., Sella, Guy

“…The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic…”
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Match fitness landscapes for macromolecular interaction networks: Selection for translational accuracy and rate can displace tRNA-binding interfaces of non-cognate aminoacyl-tRNA synthetases by Collins-Hed, Andrea I., Ardell, David H.

“…Advances in structural biology of aminoacyl-tRNA synthetases (aaRSs) have revealed incredible diversity in how aaRSs bind their tRNA substrates. The causes of…”
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SNP-SVant: A Computational Workflow to Predict and Annotate Genomic Variants in Organisms Lacking Benchmarked Variants by Gunasekaran, Deepika, Ardell, David H, Nobile, Clarissa J

“…Whole-genome sequencing is widely used to investigate population genomic variation in organisms of interest. Assorted tools have been independently developed…”
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Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria by Ardell, David H, Hou, Ya-Ming

“…While the CCA sequence at the mature 3' end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always…”
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Influences on gene expression in vivo by a Shine–Dalgarno sequence by Jin, Haining, Zhao, Qing, Gonzalez de Valdivia, Ernesto I., Ardell, David H., Stenström, Magnus, Isaksson, Leif A.

“…Summary The Shine–Dalgarno (SD+: 5′‐AAGGAGG‐3′) sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation…”
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CMCpy: Genetic Code-Message Coevolution Models in Python by Becich, Peter J., Stark, Brian P., Bhat, Harish S., Ardell, David H.

“…Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”)- Formally, CMC models are…”
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Transient Erythromycin Resistance Phenotype Associated with Peptidyl-tRNA Drop-Off on Early UGG and GGG Codons by MACVANIN, Mirjana, GONZALEZ DE VALDIVIA, Ernesto I, ARDELL, David H, ISAKSSON, Leif A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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The coevolution of genes and genetic codes: Crick's frozen accident revisited by Sella, Guy, Ardell, David H

“…The standard genetic code is the nearly universal system for the translation of genes into proteins. The code exhibits two salient structural characteristics:…”
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