Published in FEBS J on May 21, 2012
Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition. BMC Bioinformatics (2012) 0.93
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. Bioinformatics (2014) 0.89
Dynamic transcriptional response of Escherichia coli to inclusion body formation. Biotechnol Bioeng (2014) 0.83
Discrimination of soluble and aggregation-prone proteins based on sequence information. Mol Biosyst (2013) 0.81
Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genomics (2015) 0.80
A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli. BMC Bioinformatics (2014) 0.77
A method to predict edge strands in beta-sheets from protein sequences. Comput Struct Biotechnol J (2013) 0.75
The effects of protein solubility on the RNA Integrity Number (RIN) for recombinant Escherichia coli. Biochem Eng J (2013) 0.75
ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli. Bioinformatics (2014) 0.75
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean. EXCLI J (2015) 0.75
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res (2004) 3.71
Illuminating the evolutionary history of chlamydiae. Science (2004) 3.39
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS (2004) 1.92
The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78
Mining sequence annotation databanks for association patterns. Bioinformatics (2005) 1.62
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet (2004) 1.55
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49
TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics (2010) 1.43
Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell (2013) 1.43
A domain interaction map based on phylogenetic profiling. J Mol Biol (2004) 1.35
Pitfalls of supervised feature selection. Bioinformatics (2009) 1.33
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res (2004) 1.31
PROMPT: a protein mapping and comparison tool. BMC Bioinformatics (2006) 1.31
Will my protein crystallize? A sequence-based predictor. Proteins (2006) 1.30
SNAPper: gene order predicts gene function. Bioinformatics (2002) 1.27
Co-evolving residues in membrane proteins. Bioinformatics (2007) 1.25
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res (2012) 1.24
Protein solubility: sequence based prediction and experimental verification. Bioinformatics (2006) 1.23
PEDANT genome database: 10 years online. Nucleic Acids Res (2006) 1.20
DIMA 3.0: Domain Interaction Map. Nucleic Acids Res (2010) 1.19
MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res (2010) 1.19
Applying negative rule mining to improve genome annotation. BMC Bioinformatics (2007) 1.18
Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett (2006) 1.15
Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs. J Mol Biol (2007) 1.12
An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics (2008) 1.03
Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i. J Mol Biol (2010) 1.02
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res (2013) 1.01
Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Comput Biol (2010) 1.00
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res (2006) 0.99
Phosphorylation variation during the cell cycle scales with structural propensities of proteins. PLoS Comput Biol (2013) 0.99
Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN). Gene (2008) 0.97
Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks. Proteins (2009) 0.97
The DIMA web resource--exploring the protein domain network. Bioinformatics (2006) 0.96
Importance of mRNA secondary structural elements for the expression of influenza virus genes. OMICS (2009) 0.96
Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics (2013) 0.91
Designability, aggregation propensity and duplication of disease-associated proteins. Protein Eng Des Sel (2005) 0.91
Telemonitoring of blood pressure self measurement in the OLMETEL study. Blood Press Monit (2004) 0.90
Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor. Cold Spring Harb Protoc (2011) 0.90
Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biol (2008) 0.89
Current status of membrane protein structure classification. Proteins (2010) 0.88
DIMA 2.0--predicted and known domain interactions. Nucleic Acids Res (2007) 0.87
QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis. Nucleic Acids Res (2013) 0.87
Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus. RNA Biol (2012) 0.87
Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res (2011) 0.86
RNAtips: Analysis of temperature-induced changes of RNA secondary structure. Nucleic Acids Res (2013) 0.84
Complex principal component and correlation structure of 16 yeast genomic variables. Mol Biol Evol (2011) 0.84
Defining the fold space of membrane proteins: the CAMPS database. Proteins (2006) 0.83
Reproducibility: In praise of open research measures. Nature (2013) 0.83
Atypical RNAs in the coelacanth transcriptome. J Exp Zool B Mol Dev Evol (2013) 0.82
Unexpected diversity of signal peptides in prokaryotes. MBio (2012) 0.82
HALO--a Java framework for precise transcript half-life determination. Bioinformatics (2010) 0.81
Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins. Proteins (2011) 0.81
Predicting experimental properties of integral membrane proteins by a naive Bayes approach. Proteins (2008) 0.81
Ionic interactions promote transmembrane helix-helix association depending on sequence context. J Mol Biol (2009) 0.81
Complex patterns of histidine, hydroxylated amino acids and the GxxxG motif mediate high-affinity transmembrane domain interactions. J Mol Biol (2008) 0.81
Predicting experimental properties of proteins from sequence by machine learning techniques. Curr Protein Pept Sci (2007) 0.81
Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms. J Food Prot (2008) 0.81
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinformatics (2004) 0.80
Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution. Nucleic Acids Res (2013) 0.80
Fold designability, distribution, and disease. PLoS Comput Biol (2006) 0.80
How many signal peptides are there in bacteria? Environ Microbiol (2013) 0.80
Prediction of protein interaction types based on sequence and network features. BMC Syst Biol (2013) 0.79
Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution. BMC Evol Biol (2011) 0.78
Computational prediction of domain interactions. Methods Mol Biol (2007) 0.77
Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns. Proteins (2010) 0.77
Classification of α-helical membrane proteins using predicted helix architectures. PLoS One (2013) 0.75
Protein crystallizability. Methods Mol Biol (2010) 0.75
Phylogenetic web profiler. Bioinformatics (2003) 0.75
Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep (2017) 0.75
Designability and disease. Methods Mol Biol (2008) 0.75