Published in FEBS Lett on March 20, 2008
Gene expression regulation by upstream open reading frames and human disease. PLoS Genet (2013) 1.76
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions. BMC Genomics (2013) 1.38
Stress-inducible alternative translation initiation of human cytomegalovirus latency protein pUL138. J Virol (2010) 1.29
An upstream open reading frame modulates ebola virus polymerase translation and virus replication. PLoS Pathog (2013) 1.12
New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol (2013) 1.09
N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics (2014) 1.07
Ribosomal scanning on the 5'-untranslated region of the human immunodeficiency virus RNA genome. Nucleic Acids Res (2011) 0.99
Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J (2016) 0.94
Transcripts from a novel BMPR2 termination mutation escape nonsense mediated decay by downstream translation re-initiation: implications for treating pulmonary hypertension. Clin Genet (2010) 0.92
Conserved upstream open reading frames in higher plants. BMC Genomics (2008) 0.90
Extensive translatome remodeling during ER stress response in mammalian cells. PLoS One (2012) 0.89
5' UTR control of native ERG and of Tmprss2:ERG variants activity in prostate cancer. PLoS One (2013) 0.88
Alternative splicing within the elk-1 5' untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2. Mol Cell Biol (2012) 0.88
The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes. BMC Bioinformatics (2011) 0.81
Identification of the salmonid IL-17A/F1a/b, IL-17A/F2b, IL-17A/F3 and IL-17N genes and analysis of their expression following in vitro stimulation and infection. Immunogenetics (2015) 0.78
Selective constraint on the upstream open reading frames that overlap with coding sequences in animals. PLoS One (2012) 0.78
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts. Plant Cell (2015) 0.78
Tandem termination signal in plant mRNAs. Gene (2011) 0.76
Sequence and Expression Analysis of Interferon Regulatory Factor 10 (IRF10) in Three Diverse Teleost Fish Reveals Its Role in Antiviral Defense. PLoS One (2016) 0.75
Upstream ORF affects MYCN translation depending on exon 1b alternative splicing. BMC Cancer (2009) 0.75
Alternative splicing of the human gene SYBL1 modulates protein domain architecture of Longin VAMP7/TI-VAMP, showing both non-SNARE and synaptobrevin-like isoforms. BMC Mol Biol (2011) 0.75
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. Nucleic Acids Res (2017) 0.75
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics (2004) 3.45
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res (2006) 2.81
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res (2004) 2.65
PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics (2005) 2.51
PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics (2009) 2.07
ASAView: database and tool for solvent accessibility representation in proteins. BMC Bioinformatics (2004) 1.94
Real value prediction of solvent accessibility from amino acid sequence. Proteins (2003) 1.86
Moment-based prediction of DNA-binding proteins. J Mol Biol (2004) 1.79
Introductory note for BGRS\SB-2014 special issue. J Bioinform Comput Biol (2015) 1.73
Classification of protein-DNA complexes based on structural descriptors. Structure (2006) 1.71
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J Mol Biol (2004) 1.69
Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network. BMC Struct Biol (2007) 1.45
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0. Nucleic Acids Res (2002) 1.43
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. Bioinformatics (2003) 1.42
Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res (2007) 1.41
Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J Comput Chem (2004) 1.33
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res (2004) 1.32
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding. J Mol Biol (2002) 1.28
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Res (2013) 1.21
The Diamond STING server. Nucleic Acids Res (2005) 1.18
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. J Am Chem Soc (2005) 1.18
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. BMC Bioinformatics (2007) 1.15
The role of alternative translation start sites in the generation of human protein diversity. Mol Genet Genomics (2005) 1.14
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res (2005) 1.06
Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations. Biopolymers (2002) 1.05
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res (2008) 1.04
Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry (2002) 1.03
Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression. Proteins (2005) 1.01
SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine. Proteins (2007) 0.98
Structural analysis of cation-pi interactions in DNA binding proteins. Int J Biol Macromol (2004) 0.97
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. BMC Genomics (2009) 0.94
Role of inter and intramolecular interactions in protein-DNA recognition. Gene (2005) 0.93
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Nucleic Acids Res (2006) 0.93
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. BMC Struct Biol (2009) 0.93
Characterization of BRCAA1 and its novel antigen epitope identification. Cancer Epidemiol Biomarkers Prev (2004) 0.93
NotI flanking sequences: a tool for gene discovery and verification of the human genome. Nucleic Acids Res (2002) 0.92
Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif. Structure (2003) 0.92
Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics (2011) 0.91
Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. BMC Struct Biol (2011) 0.89
Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis. Biopolymers (2004) 0.88
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics (2007) 0.88
PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools. Adv Bioinformatics (2010) 0.87
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res (2002) 0.86
Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis. BMC Struct Biol (2009) 0.86
NPRD: Nucleosome Positioning Region Database. Nucleic Acids Res (2005) 0.86
Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters. BMC Genomics (2015) 0.86
A signature-based method for indexing cell cycle phase distribution from microarray profiles. BMC Genomics (2009) 0.86
Thermodynamic database for proteins: features and applications. Methods Mol Biol (2010) 0.86
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network. Gene (2008) 0.86
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. Nucleic Acids Res (2011) 0.86
Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability. Biophys Chem (2004) 0.85
Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput Biol Chem (2005) 0.85
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. BMC Genomics (2015) 0.85
Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Mol Divers (2010) 0.85
Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochem (2011) 0.84
CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Res (2010) 0.84
The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain. BMC Genomics (2015) 0.84
Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application. BMC Genomics (2014) 0.84
On nucleotide solvent accessibility in RNA structure. Gene (2010) 0.83
Contribution of a single hydrogen bond between betaHis81 of MHC class II I-E(k) and the bound peptide to the pH-dependent thermal stability. Microbiol Immunol (2004) 0.83
Insights into pathophysiology of dystropy through the analysis of gene networks: an example of bronchial asthma and tuberculosis. Immunogenetics (2014) 0.83
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. Nucleic Acids Res (2013) 0.82
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Nucleic Acids Res (2007) 0.82
Atom-wise statistics and prediction of solvent accessibility in proteins. Biophys Chem (2006) 0.81
Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin. J Mol Model (2010) 0.81
Visualization and analysis of a cardio vascular disease- and MUPP1-related biological network combining text mining and data warehouse approaches. J Integr Bioinform (2010) 0.81
DeltaG-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome. FEBS J (2008) 0.81
NF-E2 p45 is important for establishing normal function of platelets. Mol Cell Biol (2013) 0.81
Construction of stochastic context trees for genetic texts. In Silico Biol (2002) 0.80
Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. Comput Biol Chem (2012) 0.80
Subcellular localization charts: a new visual methodology for the semi-automatic localization of protein-related data sets. J Bioinform Comput Biol (2013) 0.80
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. Nucleic Acids Res (2004) 0.80
A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen. Int J Biol Macromol (2008) 0.80
A generalized conformational energy function of DNA derived from molecular dynamics simulations. Nucleic Acids Res (2009) 0.80
A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea). Biophys Chem (2007) 0.80
Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett (2004) 0.80
A new method for evaluating the specificity of indirect readout in protein-DNA recognition. Nucleic Acids Res (2012) 0.79
How multiple auxin responsive elements may interact in plant promoters: a reverse problem solution. J Bioinform Comput Biol (2013) 0.79
Studying the non-thermal effects of terahertz radiation on E. coli/pKatG-GFP biosensor cells. Bioelectromagnetics (2012) 0.79
Databases and QSAR for cancer research. Cancer Inform (2007) 0.79
Role of non-covalent interactions for determining the folding rate of two-state proteins. Biophys Chem (2004) 0.79
Recognition of interferon-inducible sites, promoters, and enhancers. BMC Bioinformatics (2007) 0.78
Dimensionality of amino acid space and solvent accessibility prediction with neural networks. Comput Biol Chem (2006) 0.78
Time-course human urine proteomics in space-flight simulation experiments. BMC Genomics (2014) 0.78
Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. Bioinformatics (2004) 0.78
Molecular evolution of cyclin proteins in animals and fungi. BMC Evol Biol (2011) 0.78
Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia). BMC Genomics (2014) 0.78
Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines. J Chem Inf Model (2010) 0.77
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. BMC Res Notes (2014) 0.77
SNPs in the HIV-1 TATA box and the AIDS pandemic. J Bioinform Comput Biol (2010) 0.77