Published in G3 (Bethesda) on June 21, 2013
A differential cargo-loading model of ciliary length regulation by IFT. Curr Biol (2013) 1.92
Decreased FOXJ1 expression and its ciliogenesis programme in aggressive ependymoma and choroid plexus tumours. J Pathol (2016) 1.45
ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6. Am J Hum Genet (2013) 1.24
An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell (2016) 1.06
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell (2014) 1.05
Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii. PLoS Genet (2013) 0.89
New mutations in flagellar motors identified by whole genome sequencing in Chlamydomonas. Cilia (2013) 0.88
High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. Plant Cell (2015) 0.87
Cyclin-Dependent Kinase Regulation of Diurnal Transcription in Chlamydomonas. Plant Cell (2015) 0.84
Subcellular size. Cold Spring Harb Perspect Biol (2015) 0.81
Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol (2015) 0.78
The evolving spectrum of ciliopathies and respiratory disease. Curr Opin Pediatr (2016) 0.75
Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport. PLoS Genet (2016) 0.75
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
A high-resolution root spatiotemporal map reveals dominant expression patterns. Science (2007) 6.60
Proteomic analysis of a eukaryotic cilium. J Cell Biol (2005) 6.54
HEF1-dependent Aurora A activation induces disassembly of the primary cilium. Cell (2007) 6.50
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell (2004) 6.10
Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis. Cell (2004) 5.02
The intraflagellar transport protein IFT20 is associated with the Golgi complex and is required for cilia assembly. Mol Biol Cell (2006) 4.18
A genetic screen in zebrafish identifies cilia genes as a principal cause of cystic kidney. Development (2004) 3.97
ARF family G proteins and their regulators: roles in membrane transport, development and disease. Nat Rev Mol Cell Biol (2011) 3.38
Multiple alpha- and beta-tubulin genes in Chlamydomonas and regulation of tubulin mRNA levels after deflagellation. Cell (1981) 3.02
Coordination of Rab8 and Rab11 in primary ciliogenesis. Proc Natl Acad Sci U S A (2010) 2.88
Human Orc2 localizes to centrosomes, centromeres and heterochromatin during chromosome inheritance. EMBO J (2004) 2.87
Cyclin-dependent kinase control of centrosome duplication. Proc Natl Acad Sci U S A (1999) 2.85
Centriole ciliation is related to quiescence and DNA synthesis in 3T3 cells. Cell (1979) 2.84
The thioredoxin-related redox-regulating protein nucleoredoxin inhibits Wnt-beta-catenin signalling through dishevelled. Nat Cell Biol (2006) 2.83
Regulation of the synthesis and assembly of ciliary and flagellar proteins during regeneration. Annu Rev Cell Biol (1986) 2.63
mRNA abundance changes during flagellar regeneration in Chlamydomonas reinhardtii. Mol Cell Biol (1984) 2.39
The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr Biol (2006) 2.16
Nde1-mediated inhibition of ciliogenesis affects cell cycle re-entry. Nat Cell Biol (2011) 2.15
Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes. Proc Natl Acad Sci U S A (2005) 2.09
Ciliary transition zone activation of phosphorylated Tctex-1 controls ciliary resorption, S-phase entry and fate of neural progenitors. Nat Cell Biol (2011) 2.06
Genetic interactions at the FLA10 locus: suppressors and synthetic phenotypes that affect the cell cycle and flagellar function in Chlamydomonas reinhardtii. Genetics (1991) 1.91
The resorption of primary cilia during mitosis in a vertebrate (PtK1) cell line. J Ultrastruct Res (1979) 1.89
Mutations in axonemal dynein assembly factor DNAAF3 cause primary ciliary dyskinesia. Nat Genet (2012) 1.78
Fat (fat) and tubby (tub): two autosomal recessive mutations causing obesity syndromes in the mouse. J Hered (1991) 1.76
Tissue expression patterns identify mouse cilia genes. Physiol Genomics (2007) 1.69
hPOC5 is a centrin-binding protein required for assembly of full-length centrioles. J Cell Biol (2009) 1.49
Proteomic analysis of mammalian primary cilia. Curr Biol (2012) 1.45
Cochlear and retinal degeneration in the tubby mouse. Neuroreport (1995) 1.40
Centriole reduplication during prolonged interphase requires procentriole maturation governed by Plk1. Curr Biol (2010) 1.34
Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease. PLoS One (2012) 1.32
A Toxoplasma MORN1 null mutant undergoes repeated divisions but is defective in basal assembly, apicoplast division and cytokinesis. PLoS One (2010) 1.21
A multifunctional lentiviral-based gene knockdown with concurrent rescue that controls for off-target effects of RNAi. Genomics Proteomics Bioinformatics (2010) 1.20
Pitchfork regulates primary cilia disassembly and left-right asymmetry. Dev Cell (2010) 1.18
Allele loss and epigenetic inactivation of 3p21.3 in malignant liver tumors. Int J Cancer (2005) 1.13
The tubby family proteins. Genome Biol (2011) 1.07
RASSF1A, BLU, NORE1A, PTEN and MGMT expression and promoter methylation in gliomas and glioma cell lines and evidence of deregulated expression of de novo DNMTs. Brain Pathol (2008) 1.05
Nucleoredoxin sustains Wnt/β-catenin signaling by retaining a pool of inactive dishevelled protein. Curr Biol (2010) 1.04
Cilia, Wnt signaling, and the cytoskeleton. Cilia (2012) 0.99
A role for Tctex-1 (DYNLT1) in controlling primary cilium length. Eur J Cell Biol (2011) 0.97
Cloning and characterization of the nucleoredoxin gene that encodes a novel nuclear protein related to thioredoxin. Genomics (1997) 0.95
Conservation of ciliary proteins in plants with no cilia. BMC Plant Biol (2011) 0.91
Evolutionarily conserved Delta(25(27))-olefin ergosterol biosynthesis pathway in the alga Chlamydomonas reinhardtii. J Lipid Res (2012) 0.89
Molecular enzymology of the glyoxalase system. Drug Metabol Drug Interact (2008) 0.89
Frequent epigenetic inactivation of chromosome 3p candidate tumor suppressor genes in gallbladder carcinoma. Cancer Lett (2006) 0.88
Hypermethylation of two consecutive tumor suppressor genes, BLU and RASSF1A, located at 3p21.3 in cervical neoplasias. Gynecol Oncol (2006) 0.88
Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration. Invest Ophthalmol Vis Sci (2010) 0.86
Nucleoredoxin regulates the Wnt/planar cell polarity pathway in Xenopus. Genes Cells (2008) 0.86
Expression of candidate chromosome 3p21.3 tumor suppressor genes and down-regulation of BLU in some esophageal squamous cell carcinomas. Cancer Lett (2006) 0.86
Alterations of BLU, a candidate tumor suppressor gene on chromosome 3p21.3, in human nasopharyngeal carcinoma. Int J Cancer (2003) 0.85
Centrosome amplification in CHO and DT40 cells by inactivation of cyclin-dependent kinases. Cytoskeleton (Hoboken) (2011) 0.84
Cloning and characterization of testis-specific spermatogenesis associated gene homologous to human SPATA4 in rat. Biol Pharm Bull (2004) 0.82
Cloning of a full-length cDNA of human testis-specific spermatogenic cell apoptosis inhibitor TSARG2 as a candidate oncogene. Biochem Biophys Res Commun (2004) 0.80
Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. Proc IEEE Int Symp Bioinformatics Bioeng (2010) 0.79
A yeast two hybrid screen identifies SPATA4 as a TRAPP interactor. FEBS Lett (2011) 0.77
High-resolution melting analysis of BLU methylation levels in gastric, colorectal, and pancreatic cancers. Cancer Invest (2010) 0.77
Cloning and expression analysis of gonadogenesis-associated gene SPATA4 from rainbow trout (Oncorhynchus mykiss). J Biochem Mol Biol (2005) 0.76
Cloning and characterization of zebra fish SPATA4 gene and analysis of its gonad specific expression. Biochemistry (Mosc) (2005) 0.76
Cloning and characterization of chicken SPATA4 gene and analysis of its specific expression. Mol Cell Biochem (2007) 0.76
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell (2004) 6.10
Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics (2003) 5.99
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
The AP-1 transcription factor Batf controls T(H)17 differentiation. Nature (2009) 3.75
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol (2011) 2.58
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics (2005) 2.43
The neuropeptide pigment-dispersing factor coordinates pacemaker interactions in the Drosophila circadian system. J Neurosci (2004) 2.42
Target selectivity of vertebrate notch proteins. Collaboration between discrete domains and CSL-binding site architecture determines activation probability. J Biol Chem (2005) 2.33
Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc Natl Acad Sci U S A (2002) 2.33
Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol (2002) 2.23
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . . Bioessays (2002) 2.17
Direct, androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element. Endocrinology (2005) 2.04
Early sexual origins of homeoprotein heterodimerization and evolution of the plant KNOX/BELL family. Cell (2008) 1.90
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics (2004) 1.89
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res (2002) 1.87
An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods (2012) 1.84
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. Genome Res (2006) 1.78
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci U S A (2005) 1.72
A revised nomenclature for the human and rodent alpha-tubulin gene family. Genomics (2007) 1.68
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
Three-dimensional organization of basal bodies from wild-type and delta-tubulin deletion strains of Chlamydomonas reinhardtii. Mol Biol Cell (2003) 1.59
Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia. Am J Hum Genet (2012) 1.53
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc (2004) 1.53
Retrograde intraflagellar transport mutants identify complex A proteins with multiple genetic interactions in Chlamydomonas reinhardtii. Genetics (2009) 1.52
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Katanin localization requires triplet microtubules in Chlamydomonas reinhardtii. PLoS One (2013) 1.43
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics (2008) 1.42
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res (2011) 1.37
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics (2004) 1.35
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics (2007) 1.32
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics (2005) 1.31
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res (2005) 1.27
Sex determination in Chlamydomonas. Semin Cell Dev Biol (2007) 1.27
Plus and minus sexual agglutinins from Chlamydomonas reinhardtii. Plant Cell (2005) 1.26
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res (2005) 1.22
RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites. Proc Natl Acad Sci U S A (2004) 1.22
Two flagellar genes, AGG2 and AGG3, mediate orientation to light in Chlamydomonas. Curr Biol (2006) 1.18
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol Syst Biol (2009) 1.17
Making connections between novel transcription factors and their DNA motifs. Genome Res (2005) 1.16
PromoLign: a database for upstream region analysis and SNPs. Hum Mutat (2004) 1.15
Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major. Mol Biochem Parasitol (2004) 1.14
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. Genome Res (2004) 1.13
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol (2008) 1.12
PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat (2005) 1.12
CCDC65 mutation causes primary ciliary dyskinesia with normal ultrastructure and hyperkinetic cilia. PLoS One (2013) 1.12
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res (2007) 1.11
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics (2012) 1.09
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res (2013) 1.07
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res (2007) 1.07
A unified taxonomy for ciliary dyneins. Cytoskeleton (Hoboken) (2011) 1.04
LRRC6 mutation causes primary ciliary dyskinesia with dynein arm defects. PLoS One (2013) 1.04
Molecular diagnostics in sepsis: from bedside to bench. J Am Coll Surg (2006) 1.02
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02
Whole-Genome Sequencing to Identify Mutants and Polymorphisms in Chlamydomonas reinhardtii. G3 (Bethesda) (2012) 1.02
Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J Eukaryot Microbiol (2003) 1.01
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. Genome Res (2007) 1.01
Mutant kinesin-2 motor subunits increase chromosome loss. Mol Biol Cell (2005) 0.98
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics (2010) 0.98
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res (2011) 0.97
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 0.97
The cis-regulatory map of Shewanella genomes. Nucleic Acids Res (2008) 0.96
ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res (2004) 0.96
Site-specific basal body duplication in Chlamydomonas. Cytoskeleton (Hoboken) (2013) 0.95
Synthesizing and salvaging NAD: lessons learned from Chlamydomonas reinhardtii. PLoS Genet (2010) 0.94
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor. Nucleic Acids Res (2004) 0.92
Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays. Crit Care Med (2002) 0.92
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics (2007) 0.92
Editing efficiency of a Drosophila gene correlates with a distant splice site selection. RNA (2005) 0.92
Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria. Nucleic Acids Res (2003) 0.92
A nutrient-sensitive interaction between Sirt1 and HNF-1α regulates Crp expression. Aging Cell (2011) 0.91
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res (2013) 0.91
Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PLoS One (2009) 0.91
Transcriptional profiles of human epithelial cells in response to heat: computational evidence for novel heat shock proteins. Shock (2008) 0.90
Understanding microtubule organizing centers by comparing mutant and wild-type structures with electron tomography. Methods Cell Biol (2007) 0.90
Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii. PLoS Genet (2013) 0.89
Molecular markers for rapidly identifying candidate genes in Chlamydomonas reinhardtii. Ery1 and ery2 encode chloroplast ribosomal proteins. Genetics (2003) 0.89
New mutations in flagellar motors identified by whole genome sequencing in Chlamydomonas. Cilia (2013) 0.88
Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2. BMC Genomics (2009) 0.88
Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines. PLoS Comput Biol (2009) 0.88
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res (2002) 0.88
Procom: a web-based tool to compare multiple eukaryotic proteomes. Bioinformatics (2004) 0.87
Cilia and models for studying structure and function. Proc Am Thorac Soc (2011) 0.87
An axonemal PP2A B-subunit is required for PP2A localization and flagellar motility. Cytoskeleton (Hoboken) (2011) 0.87
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic Acids Res (2007) 0.87
Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling. Philos Trans R Soc Lond B Biol Sci (2002) 0.87
Mutations in alpha-tubulin promote basal body maturation and flagellar assembly in the absence of delta-tubulin. J Cell Sci (2004) 0.86
bop5 Mutations reveal new roles for the IC138 phosphoprotein in the regulation of flagellar motility and asymmetric waveforms. Mol Biol Cell (2011) 0.86