Browsing by Author "Marks, Debora"
Now showing items 1-14 of 14
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Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors
Hopf, Thomas A.; Morinaga, Satoshi; Ihara, Sayoko; Touhara, Kazushige; Marks, Debora S.; Benton, Richard (2015)Insect Odorant Receptors (ORs) comprise an enormous protein family that translates environmental chemical signals into neuronal electrical activity. These heptahelical receptors are proposed to function as ligand-gated ion ... -
Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4
Nicoludis, John M; Vogt, Bennett E; Green, Anna G; Schärfe, Charlotta PI; Marks, Debora S; Gaudet, Rachelle (eLife Sciences Publications, Ltd, 2016)Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. ... -
Computational Analysis of Mouse piRNA Sequence and Biogenesis
Betel, Doron; Sheridan, Robert L.; Marks, Debora; Sander, Chris (Public Library of Science, 2007)The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs (rasiRNAs), has raised ... -
Erratum: mRNA Turnover Rate Limits siRNA and microRNA Efficacy
Larsson, Erik; Sander, Chris; Marks, Debora (Nature Publishing Group, 2010)Erratum -
FreeContact: fast and free software for protein contact prediction from residue co-evolution
Kaján, László; Hopf, Thomas A; Kalaš, Matúš; Marks, Debora S; Rost, Burkhard (BioMed Central, 2014)Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ... -
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models
Stein, Richard R.; Marks, Debora S.; Sander, Chris (Public Library of Science, 2015)Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy ... -
The MicroRNA.org Resource: Targets and Expression
Betel, Doron; Wilson, Manda; Gabow, Aaron; Marks, Debora S.; Sander, Chris (Oxford University Press, 2008)MicroRNA.org (http://www.microrna.org) is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current ... -
miRcode: A map of putative microRNA target sites in the long non-coding transcriptome
Jeggari, Ashwini; Marks, Debora; Larsson, Erik (Oxford University Press, 2012)Summary: Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell, long non-coding RNAs (lncRNAs) have only recently started to emerge as abundant regulators of cell physiology, and ... -
mRNA Turnover Rate Limits siRNA and microRNA Efficacy
Larsson, Erik; Sander, Chris; Marks, Debora (Nature Publishing Group, 2010)Based on a simple model of the mRNA life cycle, we predict that mRNAs with high turnover rates in the cell are more difficult to perturb with RNAi. We test this hypothesis using a luciferase reporter system and obtain ... -
PconsFold: improved contact predictions improve protein models
Michel, Mirco; Hayat, Sikander; Skwark, Marcin J.; Sander, Chris; Marks, Debora S.; Elofsson, Arne (Oxford University Press, 2014)Motivation: Recently it has been shown that the quality of protein contact prediction from evolutionary information can be improved significantly if direct and indirect information is separated. Given sufficiently large ... -
Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans
Romero-Aristizabal, Catalina; Marks, Debora S.; Fontana, Walter; Apfeld, Javier (2014)Cells adjust their behavior in response to redox events by regulating protein activity through the reversible formation of disulfide bridges between cysteine thiols. However, the spatial and temporal control of these ... -
Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity
Nicoludis, John Michael; Lau, Sze-Yi; Scharfe, Charlotta; Marks, Debora; Weihofen, Wilhelm; Gaudet, Rachelle (Elsevier BV, 2015)Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1–EC3, containing ... -
Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel
Gofman, Yana; Schärfe, Charlotta; Marks, Debora S.; Haliloglu, Turkan; Ben-Tal, Nir (Public Library of Science, 2014)Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought ... -
Target MRNA Abundance Dilutes MicroRNA and SiRNA Activity
Arvey, Aaron; Larsson, Erik; Sander, Chris; Leslie, Christina S.; Marks, Debora S. (Nature Publishing Group, 2010)Post-transcriptional regulation by microRNAs and siRNAs depends not only on characteristics of individual binding sites in target mRNA molecules, but also on system-level properties such as overall molecular concentrations. ...