Michael Snyder
Publications
- An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; (7414): 57-74
- Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012; (9): 1790-7
- Architecture of the human regulatory network derived from ENCODE data. Nature. 2012; (7414): 91-100
- Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol. 2012; (3): 226-9
- Extensive genetic variation in somatic human tissues. Proc Natl Acad Sci U S A. 2012; (44): 18018-23
- Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012; (1-2): 84-98
- Linking disease associations with regulatory information in the human genome. Genome Res. 2012; (9): 1748-59
- Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012; (6): 1293-307
- Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001; (6819): 533-8
- Promise of personalized omics to precision medicine. Wiley Interdiscip Rev Syst Biol Med. 2013 Jan-Feb; (1): 73-82
- A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res. 2013; (1): 45-57
- A major epigenetic programming mechanism guided by piRNAs. Dev Cell. 2013; (5): 502-16
- Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013; (3): 387-97
- Centromere-like regions in the budding yeast genome. PLoS Genet. 2013; (1): e1003209
- Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res. 2013; (8): 4423-4432
- Exome sequencing by targeted enrichment. Curr Protoc Mol Biol. 2013: Unit7.12
- Extensive transcript diversity and novel upstream open reading frame regulation in yeast. G3 (Bethesda). 2013; (2): 343-52
- Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. J Proteome Res. 2013
- High-throughput sequencing for biology and medicine. Mol Syst Biol. 2013: 640
- Identification of Potential Glycan Cancer Markers with Sialic Acid Attached to Sialic Acid and Up-regulated Fucosylated Galactose Structures in Epidermal Growth Factor Receptor Secreted from A431 Cell Line. Mol Cell Proteomics. 2013; (5): 1239-49
- Multimodal dynamic profiling of healthy and diseased states for future personalized health care. Clin Pharmacol Ther. 2013; (1): 29-32
- Preparation of recombinant protein spotted arrays for proteome-wide identification of kinase targets. Curr Protoc Protein Sci. 2013: Unit 27.4
- Proteogenomic Analysis of Human Colon Carcinoma Cell Lines LIM1215, LIM1899, and LIM2405. J Proteome Res. 2013
- SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res. 2013; (2): 377-87
- Systematic investigation of protein-small molecule interactions. IUBMB Life. 2013; (1): 2-8
- The variable somatic genome. Cell Cycle. 2013; (1): 5-6
- Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 2013; (1): R5
- Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A. 2013; (2): 594-9
- Variation and genetic control of protein abundance in humans. Nature. 2013
- A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proc Natl Acad Sci U S A. 2012; (10): 3832-7
- A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012; (4): 855-66
- A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. Genome Res. 2012; (9): 1668-79
- An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012; (8): 418
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012; (9): 1813-31
- Characterization of enhancer function from genome-wide analyses. Annu Rev Genomics Hum Genet. 2012: 29-57
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012; (9): R48
- Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. BMC Bioinformatics. 2012: 305
- Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype. G3 (Bethesda). 2012; (2): 279-86
- Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 2012; (9): 1616-25
- Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One. 2012; (8): e43198
- Genome interpretation and assembly-recent progress and next steps. Nat Biotechnol. 2012; (11): 1081-3
- Interpretome: a freely available, modular, and secure personal genome interpretation engine. Pac Symp Biocomput. 2012: 339-50
- Investigating metabolite-protein interactions: an overview of available techniques. Methods. 2012; (4): 459-66
- Michael Snyder. Interview by Asher Mullard. Nat Rev Drug Discov. 2012; (10): 744
- Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med. 2012; (130): 130ra47
- Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function. J Proteome Res. 2012; (1): 261-8
- Q & A: the Snyderome. Genome Biol. 2012; (3): 147
- SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. J Biol Chem. 2012; (37): 30897-905
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012; (9): 1798-812
- Systems biology: personalized medicine for the future? Curr Opin Pharmacol. 2012; (5): 623-8
- Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. PLoS Genet. 2012; (3): e1002565
- The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol. 2012; (3): 221-3
- Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012; (9): 1735-47
- Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012; (9): 1658-67
- VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics. 2012; (17): 2267-2269
- A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011; (8): e1002236
- A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. PLoS Genet. 2011; (12): e1002380
- A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. PLoS Genet. 2011; (6): e1001392
- AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011: 522
- Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor. Plant Cell. 2011; (9): 3374-91
- CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011; (6): 974-84
- Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol. 2011; (11): e1002190
- Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A. 2011; (32): 13353-8
- Dissecting phosphorylation networks: lessons learned from yeast. Expert Rev Proteomics. 2011; (6): 775-86
- Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. 2011; (7): 767-78
- Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet. 2011; (3): e1002008
- Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011; (2): 245-54
- Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. Nucleic Acids Res. 2011; (11): 4628-39
- Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. PLoS One. 2011; (11): e27859
- Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011: 375
- Kinase substrate interactions. Methods Mol Biol. 2011: 201-12
- Landscape of next-generation sequencing technologies. Anal Chem. 2011; (12): 4327-41
- Mapping copy number variation by population-scale genome sequencing. Nature. 2011; (7332): 59-65
- Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 2011; (1): e1001050
- Metabolites as global regulators: a new view of protein regulation: systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies. Bioessays. 2011; (7): 485-9
- Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011; (10): 908-14
- Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011; (9): e1002280
- Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011; (2): 276-85
- RNA sequencing. Methods Mol Biol. 2011: 125-32
- RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics. 2011; (2): 281-3
- Regulatory variation within and between species. Annu Rev Genomics Hum Genet. 2011: 327-46
- The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biol. 2011; (3): R32
- The human proteome project: Current state and future direction. Mol Cell Proteomics. 2011
- The human proteome project: current state and future direction. Mol Cell Proteomics. 2011; (7): M111.009993
- Annotating non-coding regions of the genome. Nat Rev Genet. 2010; (8): 559-71
- ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites. Methods Enzymol. 2010: 77-104
- Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010; (8): 3639-44
- Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res. 2010; (10): 1451-8
- Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal. 2010; (109): ra12
- 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; (11): 5254-9
- Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell. 2010; (4): 639-50
- Genetic analysis of variation in transcription factor binding in yeast. Nature. 2010; (7292): 1187-91
- Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010; (2): e1000848
- Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010; (6012): 1775-87
- MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics. 2010: 243
- Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 2010; (4): e1000834
- Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol. 2010; (1): 47-55
- Personal genome sequencing: current approaches and challenges. Genes Dev. 2010; (5): 423-31
- RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol. 2010: Unit 4.11.1-13
- Systems biology approaches to disease marker discovery. Dis Markers. 2010; (4): 209-24
- Variation in transcription factor binding among humans. Science. 2010; (5975): 232-5
- X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U S A. 2010; (8): 3704-9
- Yeast proteomics and protein microarrays. J Proteomics. 2010; (11): 2147-57
- A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. Genes Dev. 2009; (5): 575-88
- Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev. 2009; (11): 1351-63
- EBNA1 regulates cellular gene expression by binding cellular promoters. Proc Natl Acad Sci U S A. 2009; (52): 22421-6
- Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics. 2009: 37
- Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol. 2009: 308
- Global identification of protein kinase substrates by protein microarray analysis. Nat Protoc. 2009; (12): 1820-7
- Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol. 2009; (7): e1000432
- MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev. 2009; (1): 80-92
- MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res. 2009; (1): 106-17
- Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009; (35): 14926-31
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009; (1): 66-75
- Protein microarrays. Methods Mol Biol. 2009: 209-22
- Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS One. 2009; (1): e4221
- Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009; (5): 1374-9
- RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009; (1): 57-63
- The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A. 2009; (29): 12031-6
- A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res. 2008; (8): 1224-37
- A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci U S A. 2008; (40): 15499-504
- Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 2008; (12): 1865-74
- Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet. 2008; (7): e1000133
- Leptin affects endocardial cushion formation by modulating EMT and migration via Akt signaling cascades. J Cell Biol. 2008; (2): 367-80
- Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays. BMC Genomics. 2008: 635
- Modeling ChIP sequencing in silico with applications. PLoS Comput Biol. 2008; (8): e1000158
- Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body. RNA. 2008; (3): 491-502
- RNA polymerase II stalling: loading at the start prepares genes for a sprint. Genome Biol. 2008; (5): 220
- Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 2008; (1): R3
- The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol. 2008; (3): 366-74
- The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant. 2008; (1): 27-41
- The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008; (5881): 1344-9
- Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions. Plant Signal Behav. 2007; (5): 416-20
- Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007; (6): 886-97
- Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A. 2007; (11): 4730-5
- Divergence of transcription factor binding sites across related yeast species. Science. 2007; (5839): 815-9
- Getting connected: analysis and principles of biological networks. Genes Dev. 2007; (9): 1010-24
- Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci U S A. 2007; (44): 17494-9
- Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007; (6): 720-31
- Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007; (6): 898-909
- New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 2007; (5): 601-14
- Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007; (5849): 420-6
- Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Res. 2007; (2): e8
- Protein microarray technology. Mech Ageing Dev. 2007; (1): 161-7
- Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007; (6): 839-51
- Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007; (6): 787-97
- Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A. 2007; (24): 10110-5
- The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007; (6): 732-45
- Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 2007; (5): R81
- Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007; (4): 335-45
- What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007; (6): 669-81
- A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics. 2006; (24): 3016-24
- Charging it up: global analysis of protein phosphorylation. Trends Genet. 2006; (10): 545-54
- Defined culture conditions of human embryonic stem cells. Proc Natl Acad Sci U S A. 2006; (15): 5688-93
- Design optimization methods for genomic DNA tiling arrays. Genome Res. 2006; (2): 271-81
- Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods Enzymol. 2006: 282-311
- Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Res. 2006; (8): e57
- HTRA1 promoter polymorphism in wet age-related macular degeneration. Science. 2006; (5801): 989-92
- High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A. 2006; (12): 4534-9
- High-throughput methods of regulatory element discovery. Biotechniques. 2006; (6): 673, 675, 677 passim
- Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol. 2006: 111-6
- Predicting essential genes in fungal genomes. Genome Res. 2006; (9): 1126-35
- ProCAT: a data analysis approach for protein microarrays. Genome Biol. 2006; (11): R110
- Proteome chips for whole-organism assays. Nat Rev Mol Cell Biol. 2006; (8): 617-22
- Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc Natl Acad Sci U S A. 2006; (11): 4011-6
- Target hub proteins serve as master regulators of development in yeast. Genes Dev. 2006; (4): 435-48
- Yeast as a model for human disease. Curr Protoc Hum Genet. 2006: Unit 15.6
- A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol. 2005; (1): 137-49
- Advances in functional protein microarray technology. FEBS J. 2005; (21): 5400-11
- Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res. 2005; (3): 259-74
- Global analysis of protein function using protein microarrays. Mech Ageing Dev. 2005; (1): 171-5
- Global analysis of protein phosphorylation in yeast. Nature. 2005; (7068): 679-84
- Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes Dev. 2005; (24): 2953-68
- Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 2005; (8): 466-75
- Prospects and challenges in proteomics. Plant Physiol. 2005; (2): 560-2
- Sexual dimorphism in mammalian gene expression. Trends Genet. 2005; (5): 298-305
- CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004; (9): 3804-14
- DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A. 2004; (51): 17771-6
- Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004; (7006): 308-12
- Global identification of human transcribed sequences with genome tiling arrays. Science. 2004; (5705): 2242-6
- Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res. 2004; (10A): 1975-86
- Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell. 2004; (6): 791-800
- Microbial synergy via an ethanol-triggered pathway. Mol Cell Biol. 2004; (9): 3874-84
- Regulation of gene expression by a metabolic enzyme. Science. 2004; (5695): 482-4
- Regulation of polarized growth initiation and termination cycles by the polarisome and Cdc42 regulators. J Cell Biol. 2004; (2): 207-18
- A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003; (5644): 449-53
- Cytoskeletal activation of a checkpoint kinase. Mol Cell. 2003; (3): 663-73
- Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003; (21): 12247-52
- ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res. 2003; (13): 3477-82
- Genomics. Defining genes in the genomics era. Science. 2003; (5617): 258-60
- Identification of novel functional elements in the human genome. Cold Spring Harb Symp Quant Biol. 2003: 317-22
- Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function. Mol Cell Biol. 2003; (8): 2762-77
- Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes Dev. 2003; (21): 2698-708
- Protein chip technology. Curr Opin Chem Biol. 2003; (1): 55-63
- Proteomics. Annu Rev Biochem. 2003: 783-812
- Recent developments in analytical and functional protein microarrays. Curr Opin Mol Ther. 2003; (3): 271-7
- Specific protein targeting during cell differentiation: polarized localization of Fus1p during mating depends on Chs5p in Saccharomyces cerevisiae. Eukaryot Cell. 2003; (4): 821-5
- The transcriptional activity of human Chromosome 22. Genes Dev. 2003; (4): 529-40
- A dynamic approach to mapping coordinates between microplates and microarrays. J Biomed Inform. 2002 Oct-Dec; (5-6): 306-12
- "Omic" approaches for unraveling signaling networks. Curr Opin Cell Biol. 2002; (2): 173-9
- A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 2002; (21): 2755-60
- A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 2002; (5): 1083-90
- A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol. 2002; (3): 409-19
- An integrated approach for finding overlooked genes in yeast. Nat Biotechnol. 2002; (1): 58-63
- Bud-site selection and cell polarity in budding yeast. Curr Opin Microbiol. 2002; (2): 179-86
- Carbohydrate analysis prepares to enter the "Omics" era. Chem Biol. 2002; (4): 400-1
- ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol. 2002: 469-83
- Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002; (6896): 387-91
- GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A. 2002; (5): 2924-9
- Global analysis of gene expression in yeast. Funct Integr Genomics. 2002; (4-5): 171-80
- Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast. Methods Enzymol. 2002: 219-29
- Large-scale identification of genes important for apical growth in Saccharomyces cerevisiae by directed allele replacement technology (DART) screening. Funct Integr Genomics. 2002; (6): 345-56
- Proteomic approaches for the global analysis of proteins. Biotechniques. 2002; (6): 1308-16
- Subcellular localization of the yeast proteome. Genes Dev. 2002; (6): 707-19
- The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Res. 2002; (1): 73-5
- The alpha-factor receptor C-terminus is important for mating projection formation and orientation in Saccharomyces cerevisiae. Cell Motil Cytoskeleton. 2002; (4): 251-66
- YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002: 140-4
- A filamentous growth response mediated by the yeast mating pathway. Genetics. 2001; (3): 919-28
- A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell. 2001; (7): 2147-70
- A metadata framework for interoperating heterogeneous genome data using XML. Proc AMIA Symp. 2001: 110-4
- Emerging technologies in yeast genomics. Nat Rev Genet. 2001; (4): 302-12
- Genome-wide transposon mutagenesis in yeast. Curr Protoc Mol Biol. 2001: Unit13.3
- Global analysis of protein activities using proteome chips. Science. 2001; (5537): 2101-5
- Large-scale mutagenesis: yeast genetics in the genome era. Curr Opin Biotechnol. 2001; (1): 28-34
- Phosphorylation of gamma-tubulin regulates microtubule organization in budding yeast. Dev Cell. 2001; (5): 621-31
- Protein arrays and microarrays. Curr Opin Chem Biol. 2001; (1): 40-5
- The Cbk1p pathway is important for polarized cell growth and cell separation in Saccharomyces cerevisiae. Mol Cell Biol. 2001; (7): 2449-62
- An integrated web interface for large-scale characterization of sequence data. Funct Integr Genomics. 2000; (1): 70-5
- Analysis of yeast protein kinases using protein chips. Nat Genet. 2000; (3): 283-9
- Compartmentalization of the cell cortex by septins is required for maintenance of cell polarity in yeast. Mol Cell. 2000; (5): 841-51
- Drivers and passengers wanted! the role of kinesin-associated proteins. Trends Cell Biol. 2000; (7): 281-9
- Genome-wide mutant collections: toolboxes for functional genomics. Curr Opin Microbiol. 2000; (3): 309-15
- Graphically-enabled integration of bioinformatics tools allowing parallel execution. Proc AMIA Symp. 2000: 141-5
- High-throughput methods for the large-scale analysis of gene function by transposon tagging. Methods Enzymol. 2000: 550-74
- Polarized growth controls cell shape and bipolar bud site selection in Saccharomyces cerevisiae. Mol Cell Biol. 2000; (14): 5235-47
- Sbe2p and sbe22p, two homologous Golgi proteins involved in yeast cell wall formation. Mol Biol Cell. 2000; (2): 435-52
- TRIPLES: a database of gene function in Saccharomyces cerevisiae. Nucleic Acids Res. 2000; (1): 81-4
- The Kar3p kinesin-related protein forms a novel heterodimeric structure with its associated protein Cik1p. Mol Biol Cell. 2000; (7): 2373-85
- The carboxy terminus of Tub4p is required for gamma-tubulin function in budding yeast. J Cell Sci. 2000: 3871-82
- gamma-Tubulin of budding yeast. Curr Top Dev Biol. 2000: 75-104
- Differential regulation of the Kar3p kinesin-related protein by two associated proteins, Cik1p and Vik1p. J Cell Biol. 1999; (6): 1219-33
- Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999; (5429): 901-6
- Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 1999; (6760): 413-8
- Nim1-related kinases coordinate cell cycle progression with the organization of the peripheral cytoskeleton in yeast. Genes Dev. 1999; (2): 176-87
- Transposon mutagenesis for the analysis of protein production, function, and localization. Methods Enzymol. 1999: 512-32
- Cell polarity and morphogenesis in budding yeast. Annu Rev Microbiol. 1998: 687-744
- Pheromone-regulated genes required for yeast mating differentiation. J Cell Biol. 1998; (3): 461-83
- Spa2p interacts with cell polarity proteins and signaling components involved in yeast cell morphogenesis. Mol Cell Biol. 1998; (7): 4053-69
- The Spa2-related protein, Sph1p, is important for polarized growth in yeast. J Cell Sci. 1998: 479-94
- A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1997; (1): 190-5
- Human dishevelled genes constitute a DHR-containing multigene family. Genomics. 1997; (2): 302-10
- SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathway. Science. 1997; (5307): 1781-4
- Targeting of chitin synthase 3 to polarized growth sites in yeast requires Chs5p and Myo2p. J Cell Biol. 1997; (1): 95-110
- The Rho-GEF Rom2p localizes to sites of polarized cell growth and participates in cytoskeletal functions in Saccharomyces cerevisiae. Mol Biol Cell. 1997; (10): 1829-44
- Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein. Genes Dev. 1996; (7): 777-93
- Selection of polarized growth sites in yeast. Trends Cell Biol. 1996; (11): 434-41
- Target gene identification: target specific transcriptional activation by three murine homeodomain/VP16 hybrid proteins in Saccharomyces cerevisiae. J Exp Zool. 1996; (3): 145-56
- A highly divergent gamma-tubulin gene is essential for cell growth and proper microtubule organization in Saccharomyces cerevisiae. J Cell Biol. 1995; (6 Pt 2): 1775-88
- Two short autoepitopes on the nuclear dot antigen are similar to epitopes encoded by the Epstein-Barr virus. Proc Natl Acad Sci U S A. 1995; (5): 1639-43
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