Published in Phys Biol on May 01, 2009
BarMap: RNA folding on dynamic energy landscapes. RNA (2010) 0.91
Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides. Biophys J (2012) 0.81
Studies of RNA Sequence and Structure Using Nanopores. Prog Mol Biol Transl Sci (2016) 0.75
Cooperative translocation dynamics of biopolymer chains through nanopores in a membrane: Slow dynamics limit. Eur Phys J E Soft Matter (2010) 0.75
On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A (2003) 6.02
Transcriptional regulation by the numbers: models. Curr Opin Genet Dev (2005) 5.20
Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev (2005) 3.40
Genome-wide methylation profiling in decitabine-treated patients with acute myeloid leukemia. Blood (2012) 1.97
Nonlinear protein degradation and the function of genetic circuits. Proc Natl Acad Sci U S A (2005) 1.65
Timing and dynamics of single cell gene expression in the arabinose utilization system. Biophys J (2008) 1.41
Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score. J Clin Oncol (2013) 1.34
Mechanically probing the folding pathway of single RNA molecules. Biophys J (2003) 1.23
Regulation of the nucleosome unwrapping rate controls DNA accessibility. Nucleic Acids Res (2012) 1.18
Small RNAs in tomato fruit and leaf development. Biochim Biophys Acta (2007) 1.18
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites. PLoS Comput Biol (2010) 1.14
Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Rep (2012) 1.10
Hybrid alignment: high-performance with universal statistics. Bioinformatics (2002) 1.07
Designing sequential transcription logic: a simple genetic circuit for conditional memory. Syst Synth Biol (2007) 1.07
Dynamics of competitive evolution on a smooth landscape. Phys Rev Lett (2003) 1.05
Contribution of ribosomal residues to P-site tRNA binding. Nucleic Acids Res (2009) 1.01
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res (2011) 1.01
A quantitative model of nucleosome dynamics. Nucleic Acids Res (2011) 0.97
Induction kinetics of a conditional pH stress response system in Escherichia coli. J Mol Biol (2009) 0.97
Triggering enzymatic activity with force. Nano Lett (2009) 0.97
Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences. J Am Chem Soc (2012) 0.97
Coupled dynamics of RNA folding and nanopore translocation. Phys Rev Lett (2005) 0.94
Escalation of polymerization in a thermal gradient. Proc Natl Acad Sci U S A (2013) 0.94
A Scalable, Flexible Workflow for MethylCap-Seq Data Analysis. IEEE Int Workshop Genomic Signal Process Stat (2011) 0.94
Short-read, high-throughput sequencing technology for STR genotyping. Biotech Rapid Dispatches (2012) 0.93
Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucleic Acids Res (2005) 0.93
RAD51 protein ATP cap regulates nucleoprotein filament stability. J Biol Chem (2012) 0.92
Toward a unified physical model of nucleosome patterns flanking transcription start sites. Proc Natl Acad Sci U S A (2013) 0.91
Large scale genotype-phenotype correlation analysis based on phylogenetic trees. Bioinformatics (2007) 0.91
The flexibility of locally melted DNA. Nucleic Acids Res (2009) 0.91
Methods for high-throughput MethylCap-Seq data analysis. BMC Genomics (2012) 0.91
Translocation of structured polynucleotides through nanopores. Phys Biol (2004) 0.90
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. Bioinformatics (2008) 0.90
A practical approach to significance assessment in alignment with gaps. J Comput Biol (2006) 0.89
Model for codon position bias in RNA editing. Phys Rev Lett (2005) 0.88
The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability. J Mol Evol (2013) 0.87
Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy. J Phys Condens Matter (2010) 0.87
Dynamics of force-induced DNA slippage. Phys Rev Lett (2004) 0.87
Formation of the open complex by bacterial RNA polymerase--a quantitative model. Biophys J (2008) 0.86
Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. BMC Genomics (2012) 0.86
A performance enhanced PSI-BLAST based on hybrid alignment. Bioinformatics (2010) 0.86
Kinetic accessibility of buried DNA sites in nucleosomes. Phys Rev Lett (2006) 0.86
Genome annotation in the presence of insertional RNA editing. Bioinformatics (2008) 0.85
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches. Nucleic Acids Res (2009) 0.84
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure. Bioinformatics (2009) 0.84
Emergence of information transmission in a prebiotic RNA reactor. Phys Rev Lett (2011) 0.83
Effects of long-range correlations in DNA on sequence alignment score statistics. J Comput Biol (2007) 0.81
Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides. Biophys J (2012) 0.81
Optimization of collective enzyme activity via spatial localization. J Chem Phys (2013) 0.81
Intermediate phase in DNA melting. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.81
Modeling DNA unzipping in the presence of bound proteins. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.81
Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation. Biophys J (2011) 0.80
Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome. BMC Genomics (2012) 0.80
Deactivation of the E. coli pH stress sensor CadC by cadaverine. J Mol Biol (2012) 0.80
Model for folding and aggregation in RNA secondary structures. Phys Rev Lett (2006) 0.79
Quantification of the differences between quenched and annealed averaging for RNA secondary structures. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.79
DNA as a programmable viscoelastic nanoelement. Biophys J (2005) 0.78
Finite width model sequence comparison. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.78
Simulation of stochastic network dynamics via entropic matching. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.77
Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT). Proteins (2008) 0.77
Target search on a dynamic DNA molecule. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.77
Statistical methods for detecting differentially methylated regions based on MethylCap-seq data. Brief Bioinform (2015) 0.76
A microfluidics approach to study the accumulation of molecules at basal lamina interfaces. Lab Chip (2015) 0.75
Biological signal processing with a genetic toggle switch. PLoS One (2013) 0.75
Comparison of insertional RNA editing in Myxomycetes. PLoS Comput Biol (2012) 0.75
Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.75
Optimal flexibility for conformational transitions in macromolecules. Phys Rev Lett (2007) 0.75
Spontaneous unknotting of a polymer confined in a nanochannel. Nano Lett (2008) 0.75
Detection of charged particles with charge injection devices. Rev Sci Instrum (2007) 0.75
WITHDRAWN: Small RNAs in tomato fruit and leaf development. Biochim Biophys Acta (2007) 0.75
Analytical description of finite size effects for RNA secondary structures. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.75