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Bioinformatics

Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks

Jeffrey L. Blanchard, Wei-Yun Wholey, Erin M. Conlon, Pablo J. Pomposiello

NF-κB/Rel-Mediated Regulation of the Neural Fate in Drosophila

Savita Ayyar, Daniela Pistillo, [ ... ], Pat Simpson

DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

Chodon Sass, Damon P. Little, Dennis Wm. Stevenson, Chelsea D. Specht

Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes

Stein Aerts, Jacques van Helden, Olivier Sand, Bassem A. Hassan

Identification and Classification of Hubs in Brain Networks

Olaf Sporns, Christopher J. Honey, Rolf Kötter

Nullomers: Really a Matter of Natural Selection?

Claudia Acquisti, George Poste, David Curtiss, Sudhir Kumar

Conservation, Variability and the Modeling of Active Protein Kinases

James D. R. Knight, Bin Qian, David Baker, Rashmi Kothary

SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards, Norman E. Davey, Denis C. Shields

Complete Genomic Characterization of a Pathogenic A.II Strain of Francisella tularensis Subspecies tularensis

Stephen M. Beckstrom-Sternberg, Raymond K. Auerbach, [ ... ], Paul S. Keim

Mammalian MicroRNA Prediction through a Support Vector Machine Model of Sequence and Structure

Ying Sheng, Pär G. Engström, Boris Lenhard

Early Evolution of Ionotropic GABA Receptors and Selective Regimes Acting on the Mammalian-Specific Theta and Epsilon Subunits

Christopher J. Martyniuk, Stéphane Aris-Brosou, [ ... ], Vance L. Trudeau

Structural and Functional Analyses of Five Conserved Positively Charged Residues in the L1 and N-Terminal DNA Binding Motifs of Archaeal RadA Protein

Li-Tzu Chen, Tzu-Ping Ko, [ ... ], Ting-Fang Wang

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

Yuval Tabach, Ran Brosh, [ ... ], Eytan Domany

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