Published in Mol Cell on January 30, 2004
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
Prp8 protein: at the heart of the spliceosome. RNA (2005) 2.89
Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics (2013) 2.70
Identification of cross-linked peptides from complex samples. Nat Methods (2012) 2.70
Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol (2012) 2.55
Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev (2006) 2.52
RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev (2004) 2.48
Powering through ribosome assembly. RNA (2009) 2.19
IMP dehydrogenase: structure, mechanism, and inhibition. Chem Rev (2009) 1.99
PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA. RNA (2004) 1.94
Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J (2005) 1.92
Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev (2005) 1.90
Biogenesis of cytosolic ribosomes requires the essential iron-sulphur protein Rli1p and mitochondria. EMBO J (2005) 1.87
The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell (2004) 1.84
The splicing ATPase prp43p is a component of multiple preribosomal particles. Mol Cell Biol (2005) 1.82
The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism. Mol Cell Biol (2007) 1.82
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics (2008) 1.81
Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol (2009) 1.81
When ribosomes go bad: diseases of ribosome biogenesis. Mol Biosyst (2010) 1.76
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Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev (2007) 1.71
The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol Cell Biol (2006) 1.70
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The small subunit processome in ribosome biogenesis—progress and prospects. Wiley Interdiscip Rev RNA (2011) 1.66
A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J Cell Biol (2006) 1.64
Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Mol Cell Biol (2006) 1.64
Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells. Genes Dev (2007) 1.57
Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res (2008) 1.55
Confirmation of organized modularity in the yeast interactome. PLoS Biol (2007) 1.52
5-fluorouracil enhances exosome-dependent accumulation of polyadenylated rRNAs. Mol Cell Biol (2004) 1.46
Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol (2008) 1.44
All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol (2007) 1.41
Tor1 and CK2 kinases control a switch between alternative ribosome biogenesis pathways in a growth-dependent manner. PLoS Biol (2017) 1.39
Ytm1, Nop7, and Erb1 form a complex necessary for maturation of yeast 66S preribosomes. Mol Cell Biol (2005) 1.39
TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. J Biol Chem (2009) 1.39
The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Mol Cell (2011) 1.38
The DEAD-box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies. Mol Biol Cell (2007) 1.35
Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci. Mol Biol Cell (2006) 1.33
Interdependence of Pes1, Bop1, and WDR12 controls nucleolar localization and assembly of the PeBoW complex required for maturation of the 60S ribosomal subunit. Mol Cell Biol (2007) 1.31
The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation. Proc Natl Acad Sci U S A (2006) 1.31
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Potential interface between ribosomal protein production and pre-rRNA processing. Mol Cell Biol (2007) 1.30
A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing. Mol Cell Biol (2008) 1.30
GTP-independent tRNA delivery to the ribosomal P-site by a novel eukaryotic translation factor. J Biol Chem (2010) 1.29
Widespread correlations between dominance and homozygous effects of mutations: implications for theories of dominance. Genetics (2005) 1.28
Autosomal dominant retinitis pigmentosa mutations in inosine 5'-monophosphate dehydrogenase type I disrupt nucleic acid binding. Biochem J (2005) 1.27
Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly. Mol Cell Biol (2005) 1.26
The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA (2009) 1.24
The SUMO system controls nucleolar partitioning of a novel mammalian ribosome biogenesis complex. EMBO J (2011) 1.24
Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet (2008) 1.23
Inside the 40S ribosome assembly machinery. Curr Opin Chem Biol (2011) 1.23
A survey of essential gene function in the yeast cell division cycle. Mol Biol Cell (2006) 1.23
Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics (2013) 1.23
A toolbox for epitope-tagging and genome-wide location analysis in Candida albicans. BMC Genomics (2008) 1.23
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res (2008) 1.22
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol (2009) 1.22
Human ovarian cancer stem/progenitor cells are stimulated by doxorubicin but inhibited by Mullerian inhibiting substance. Proc Natl Acad Sci U S A (2012) 1.21
Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis. Genetics (2008) 1.19
Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell (2012) 1.18
A novel small-subunit processome assembly intermediate that contains the U3 snoRNP, nucleolin, RRP5, and DBP4. Mol Cell Biol (2009) 1.17
Making the most of high-throughput protein-interaction data. Genome Biol (2007) 1.17
Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PLoS One (2008) 1.16
Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol (2007) 1.15
Change in nutritional status modulates the abundance of critical pre-initiation intermediate complexes during translation initiation in vivo. J Mol Biol (2007) 1.13
The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis. Nucleic Acids Res (2006) 1.13
Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res (2012) 1.12
Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis. Mol Cell Biol (2006) 1.11
The C-terminus of Utp4, mutated in childhood cirrhosis, is essential for ribosome biogenesis. Nucleic Acids Res (2010) 1.10
Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 1.09
Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. Mol Biol Cell (2008) 1.09
Role and dynamics of the ribosomal protein P0 and its related trans-acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae. Nucleic Acids Res (2009) 1.09
Arabidopsis nucleolin affects plant development and patterning. Plant Physiol (2007) 1.08
NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. PLoS Genet (2012) 1.07
Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes. Nucleic Acids Res (2011) 1.07
Protein-protein interactions within late pre-40S ribosomes. PLoS One (2011) 1.07
Trm112 is required for Bud23-mediated methylation of the 18S rRNA at position G1575. Mol Cell Biol (2012) 1.07
Replication stress checkpoint signaling controls tRNA gene transcription. Nat Struct Mol Biol (2010) 1.06
Roles of the HEAT repeat proteins Utp10 and Utp20 in 40S ribosome maturation. RNA (2007) 1.06
Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics (2006) 1.05
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PLoS Genet (2013) 1.05
The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits. Nucleic Acids Res (2005) 1.05
Core exosome-independent roles for Rrp6 in cell cycle progression. Mol Biol Cell (2009) 1.05
The DEAD-box RNA helicase-like Utp25 is an SSU processome component. RNA (2010) 1.04
Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction. Mol Cell Biol (2005) 1.04
60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes. Nucleic Acids Res (2008) 1.04
LAS1L interacts with the mammalian Rix1 complex to regulate ribosome biogenesis. Mol Biol Cell (2011) 1.03
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Syst Biol (2008) 1.02
Characterization of Saccharomyces cerevisiae Npa2p (Urb2p) reveals a low-molecular-mass complex containing Dbp6p, Npa1p (Urb1p), Nop8p, and Rsa3p involved in early steps of 60S ribosomal subunit biogenesis. Mol Cell Biol (2006) 1.01
A role for the Saccharomyces cerevisiae regulation of Ace2 and polarized morphogenesis signaling network in cell integrity. Genetics (2005) 1.01
DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol (2012) 0.99
Human diseases of the SSU processome. Biochim Biophys Acta (2013) 0.99
Las1L is a nucleolar protein required for cell proliferation and ribosome biogenesis. Mol Cell Biol (2010) 0.99
Conservation of a masked nuclear export activity of La proteins and its effects on tRNA maturation. Mol Cell Biol (2007) 0.98
The exozyme model: a continuum of functionally distinct complexes. RNA (2010) 0.98
Exploring functional roles of multibinding protein interfaces. Protein Sci (2009) 0.97
The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing. Nucleic Acids Res (2006) 0.97
Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation. Mol Cell Proteomics (2012) 0.97
Mrd1p binds to pre-rRNA early during transcription independent of U3 snoRNA and is required for compaction of the pre-rRNA into small subunit processomes. Nucleic Acids Res (2008) 0.96
Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res (2012) 0.94
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Structures of the bacterial ribosome at 3.5 A resolution. Science (2005) 12.63
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01
The first metal-organic framework (MOF) of Imazethapyr and its SHG, piezoelectric and ferroelectric properties. Dalton Trans (2008) 8.86
WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell (2005) 8.86
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell (2007) 8.43
Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments. Brief Bioinform (2007) 8.26
Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics (2007) 7.93
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell (2003) 7.47
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79
Hydrogen-bonded ferroelectrics based on metal-organic coordination. J Am Chem Soc (2009) 6.69
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell (2006) 5.72
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2003) 5.60
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell (2003) 5.57
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
DNA-binding specificities of human transcription factors. Cell (2013) 5.14
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol (2002) 5.04
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell (2005) 4.95
A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91
Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Supramolecular bola-like ferroelectric: 4-methoxyanilinium tetrafluoroborate-18-crown-6. J Am Chem Soc (2011) 4.73
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet (2002) 4.68
The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature (2004) 4.65
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell (2003) 4.49
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature (2005) 4.33
Diisopropylammonium chloride: a ferroelectric organic salt with a high phase transition temperature and practical utilization level of spontaneous polarization. Adv Mater (2011) 4.30
Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog (2009) 4.24
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Aurora B phosphorylates centromeric MCAK and regulates its localization and microtubule depolymerization activity. Curr Biol (2004) 4.20