Published in Proteins on August 01, 2004
Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc Natl Acad Sci U S A (2012) 1.83
PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. J Struct Funct Genomics (2011) 1.26
Natively unstructured loops differ from other loops. PLoS Comput Biol (2007) 1.19
RDC-assisted modeling of symmetric protein homo-oligomers. Protein Sci (2008) 1.18
Comparative analysis of carboxysome shell proteins. Photosynth Res (2011) 1.10
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. Protein Sci (2005) 1.03
The application of FAST-NMR for the identification of novel drug discovery targets. Drug Discov Today (2008) 0.93
Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins (2009) 0.92
The accurate assessment of small-angle X-ray scattering data. Acta Crystallogr D Biol Crystallogr (2015) 0.86
Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). Protein Sci (2009) 0.84
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci (2003) 0.84
Engineering of a wheat germ expression system to provide compatibility with a high throughput pET-based cloning platform. J Struct Funct Genomics (2010) 0.83
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. Protein Sci (2005) 0.83
Resonance assignments for the 18 kDa protein CC1736 from Caulobacter crescentus. J Biomol NMR (2004) 0.77
1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family. J Biomol NMR (2005) 0.75
1H, 13C, and 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica. J Biomol NMR (2005) 0.75
Automatic target selection for structural genomics on eukaryotes. Proteins (2004) 2.34
The structural genomics experimental pipeline: insights from global target lists. Proteins (2004) 1.98
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
SNAP predicts effect of mutations on protein function. Bioinformatics (2008) 15.39
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2012) 11.31
The PredictProtein server. Nucleic Acids Res (2004) 10.89
The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Non-canonical inflammasome activation targets caspase-11. Nature (2011) 8.85
SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res (2007) 8.46
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Evaluating protein structures determined by structural genomics consortia. Proteins (2007) 5.45
Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7. Nature (2011) 5.32
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res (2002) 4.58
A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet (2011) 4.52
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc (2005) 4.43
Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival. Nature (2009) 4.12
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Protein production and purification. Nat Methods (2008) 3.97
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (2013) 3.60
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol (2005) 3.21
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
Analysing six types of protein-protein interfaces. J Mol Biol (2003) 2.96
Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95
Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A (2011) 2.92
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Genomics. Defining genes in the genomics era. Science (2003) 2.73
The PredictProtein server. Nucleic Acids Res (2003) 2.72
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins (2002) 2.72
Loss of the tumor suppressor BAP1 causes myeloid transformation. Science (2012) 2.69
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66