Published in PLoS One on September 02, 2011
Neighborhood properties are important determinants of temperature sensitive mutations. PLoS One (2011) 0.76
High-Throughput Cloning of Temperature-Sensitive Caenorhabditis elegans Mutants with Adult Syncytial Germline Membrane Architecture Defects. G3 (Bethesda) (2015) 0.75
Robust classification of protein variation using structural modelling and large-scale data integration. Nucleic Acids Res (2016) 0.75
MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes. Genetics (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol (2004) 15.72
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol (1999) 12.09
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science (1989) 8.73
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
What is a support vector machine? Nat Biotechnol (2006) 5.10
Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science (1994) 4.42
MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics (2000) 3.86
Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins (2010) 2.56
A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence. Proc Natl Acad Sci U S A (1996) 1.25
Design of temperature-sensitive mutants solely from amino acid sequence. Proc Natl Acad Sci U S A (2004) 1.15
Relationship between in vivo activity and in vitro measures of function and stability of a protein. Biochemistry (1995) 0.96
Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB. Biochemistry (2008) 0.89
Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Unlocking the secrets of the genome. Nature (2009) 11.80
A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14
A gene expression map of the Arabidopsis root. Science (2003) 9.95
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol (2005) 6.77
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A (2010) 5.59
A validated regulatory network for Th17 cell specification. Cell (2012) 4.82
Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet (2007) 4.69
The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet (2003) 4.34
Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature (2010) 4.32
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell (2007) 4.27
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell (2012) 4.21
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics (2006) 4.05
Protein production and purification. Nat Methods (2008) 3.97
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
The landscape of C. elegans 3'UTRs. Science (2010) 3.32
Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol (2002) 3.30
BioNetBuilder: automatic integration of biological networks. Bioinformatics (2006) 2.76
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue. Cell (2011) 2.64
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol (2005) 2.54
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods (2009) 2.50
Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol (2002) 2.47
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr Protoc Bioinformatics (2008) 2.30
A protein domain-based interactome network for C. elegans early embryogenesis. Cell (2008) 2.23
MINE: Module Identification in Networks. BMC Bioinformatics (2011) 2.08
Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR. RNA (2007) 2.01
An improved protein decoy set for testing energy functions for protein structure prediction. Proteins (2003) 1.94
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PLoS One (2010) 1.89
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One (2007) 1.80
Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res (2004) 1.74
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol (2007) 1.53
Computational design of a PAK1 binding protein. J Mol Biol (2010) 1.51
A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. J Exp Med (2007) 1.51
Electrical activity can impose time of day on the circadian transcriptome of pacemaker neurons. Curr Biol (2012) 1.50
Predicting cellular growth from gene expression signatures. PLoS Comput Biol (2009) 1.50
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One (2013) 1.49
Design and analysis of Bar-seq experiments. G3 (Bethesda) (2014) 1.48
Feo, the Drosophila homolog of PRC1, is required for central-spindle formation and cytokinesis. Curr Biol (2004) 1.48
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol (2006) 1.43
General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A (2007) 1.42
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS One (2010) 1.39
Oligo(N-aryl glycines): a new twist on structured peptoids. J Am Chem Soc (2008) 1.37
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol (2010) 1.34
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinformatics (2013) 1.34
A physical sciences network characterization of non-tumorigenic and metastatic cells. Sci Rep (2013) 1.33
Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol (2003) 1.29
A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell (2007) 1.28
Diverse roles of actin in C. elegans early embryogenesis. BMC Dev Biol (2007) 1.25
Mutation history of the roma/gypsies. Am J Hum Genet (2004) 1.24
Global mapping of transposon location. PLoS Genet (2006) 1.16
Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot (2007) 1.16
Systems biology for the virtual plant. Plant Physiol (2005) 1.11
Autosomal genes of autosomal/X-linked duplicated gene pairs and germ-line proliferation in Caenorhabditis elegans. Genetics (2005) 1.11
UTRome.org: a platform for 3'UTR biology in C. elegans. Nucleic Acids Res (2007) 1.10
Mating induces an immune response and developmental switch in the Drosophila oviduct. Proc Natl Acad Sci U S A (2008) 1.09
Distributions of beta sheets in proteins with application to structure prediction. Proteins (2002) 1.08
Dynamic microRNA gene transcription and processing during T cell development. J Immunol (2012) 1.08
New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res (2005) 1.07
The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis. Mol Microbiol (2009) 1.04
Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. PLoS One (2012) 1.02
Twinstar, the Drosophila homolog of cofilin/ADF, is required for planar cell polarity patterning. Development (2006) 1.00
Multi-species integrative biclustering. Genome Biol (2010) 0.99
High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda) (2011) 0.99
Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. J Biol Chem (2010) 0.99
The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res (2011) 0.98
A preliminary survey of the peptoid folding landscape. J Am Chem Soc (2009) 0.98
The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conf Proc IEEE Eng Med Biol Soc (2009) 0.98
Benzo[a]pyrene diol epoxide stimulates an inflammatory response in normal human lung fibroblasts through a p53 and JNK mediated pathway. Carcinogenesis (2010) 0.97
A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells. Genome Res (2013) 0.97
Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. J Mass Spectrom (2008) 0.97
An assembly model of rift valley Fever virus. Front Microbiol (2012) 0.97
Computational design of the sequence and structure of a protein-binding peptide. J Am Chem Soc (2011) 0.95
SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σ(D) in Bacillus subtilis. Mol Microbiol (2012) 0.95
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PLoS One (2013) 0.94
Diurnally entrained anticipatory behavior in archaea. PLoS One (2009) 0.94
Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation. J Am Chem Soc (2009) 0.93
Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (2006) 0.92
Genetic and nongenetic determinants of cell growth variation assessed by high-throughput microscopy. Mol Biol Evol (2013) 0.91
C. elegans network biology: a beginning. WormBook (2006) 0.91
Learning global models of transcriptional regulatory networks from data. Methods Mol Biol (2009) 0.90
TEXT CLASSIFICATION FOR AUTOMATIC DETECTION OF E-CIGARETTE USE AND USE FOR SMOKING CESSATION FROM TWITTER: A FEASIBILITY PILOT. Pac Symp Biocomput (2016) 0.89
Integrated inference and analysis of regulatory networks from multi-level measurements. Methods Cell Biol (2012) 0.88
Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics (2006) 0.88
Maintaining solvent accessible surface area under rotamer substitution for protein design. J Comput Chem (2007) 0.88