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Sequence motif analysis

Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16

Ron X. Yu, Jie Liu, Nick True, Wei Wang

The Plasmodium Export Element Revisited

Jan Alexander Hiss, Jude Marek Przyborski, [ ... ], Gisbert Schneider

Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome

Shicai Fan, Fang Fang, Xuegong Zhang, Michael Q. Zhang

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

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

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

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

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

Selection against Spurious Promoter Motifs Correlates with Translational Efficiency across Bacteria

Jeffrey L. Froula, M. Pilar Francino

Prediction of Cyclin-Dependent Kinase Phosphorylation Substrates

Emmanuel J. Chang, Rashida Begum, Brian T. Chait, Terry Gaasterland

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