Research Topics
| JEF BOEKESummaryAffiliation: Johns Hopkins University Country: USA Publications
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Detail Information
Publications
Identifying related L1 retrotransposons by analyzing 3' transduced sequencesSuzanne T Szak
National Center for Biotechnology Information (NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Genome Biol 4:R30. 2003..The occurrence of L1-mediated transduction in the human genome may be less frequent than previously thought, and an accurate estimate is confounded by the frequent occurrence of segmental genomic duplications...- Transposon technology and vertebrate functional genomicsWenfeng An
Department of Molecular Biology and Genetics and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Genome Biol 6:361. 2005..A report on the Third Annual International Conference on Transposition and Animal Biotechnology, Minneapolis, USA, 23-24 June 2005, and the FASEB Summer Research Conference 'Mammalian Mobile Elements', Tuscon, USA, 4-9 June, 2005... - Molecular archeology of L1 insertions in the human genomeSuzanne T Szak
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Genome Biol 3:research0052. 2002..In addition, the formation of 5' truncated and 5' inverted L1s are probably not due to the action of the L1 endonuclease... - Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotranspositionLixin Dai
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
BMC Biochem 12:18. 2011..Full-length L1 encodes two open reading frames (ORF1, ORF2) and ORF2 has reverse transcriptase activity... - Great exaptationsKathleen H Burns
Department of Pathology, The Johns Hopkins Hospital, 600 North Wolfe Street, Baltimore, MD 21287, USA
J Biol 7:5. 2008..Recent work has discovered many instances of LINE incorporation into exons, reminding us of the hazards they pose to genes in their vicinity as well as their potential to be co-opted for the host's purposes... - Domesticated DNA transposon proteins mediate retrotransposon controlJef D Boeke
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
Cell Res 18:331-3. 2008 
The unusual phylogenetic distribution of retrotransposons: a hypothesisJef D Boeke
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 13:1975-83. 2003....- Characterization of a synthetic human LINE-1 retrotransposon ORFeus-HsWenfeng An
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Mob DNA 2:2. 2011..Owing to the elevated expression of the L1 RNA/protein and its high retrotransposition ability, ORFeus-Hs and its chimeric derivatives will be useful tools for mechanistic L1 studies and mammalian genome manipulation... - Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genesNurjana Bachman
The Johns Hopkins University School of Medicine, Department of Molecular Biology and Genetics, Baltimore, Maryland 21205, USA
Genome Res 14:1232-47. 2004..We showed that the presence and relative position of additional tDNAs and LTRs surrounding the target tDNA dramatically influenced the frequency of insertion events upstream of that target... - Retrotransposon overdose and genome integrityLisa Z Scheifele
Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 106:13927-32. 2009..Abrogation of normal DNA replication leads to rampant genome instability primarily in the form of chromosomal aberrations and confirms the central role of DNA replication accuracy in the stabilization of repetitive DNA... - Improved microarray methods for profiling the Yeast Knockout strain collectionDaniel S Yuan
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Nucleic Acids Res 33:e103. 2005..The materials, protocols, data and associated software described here comprise a suite of experimental resources that should facilitate the use of TAG microarrays for a wide variety of genetic screens... - GeneDesign 3.0 is an updated synthetic biology toolkitSarah M Richardson
McKusick Nathans Institute of Genetic Medicine, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
Nucleic Acids Res 38:2603-6. 2010.... - A robust toolkit for functional profiling of the yeast genomeXuewen Pan
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Mol Cell 16:487-96. 2004..Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network... - Transposon insertion site profiling chip (TIP-chip)Sarah J Wheelan
High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 103:17632-7. 2006..In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern... - LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?Jeffrey S Han
Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Bioessays 27:775-84. 2005..Here we provide a review of L1 replication and its potential functional consequences... - Global synthetic-lethality analysis and yeast functional profilingSiew Loon Ooi
High Throughput Biology Center, Institute of Genetic Medicine, Department of Biostatistics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
Trends Genet 22:56-63. 2006.... - TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAsNurjana Bachman
The Johns Hopkins University School of Medicine, Department of Molecular Biology and Genetics, Baltimore, Maryland 21205, USA
Genes Dev 19:955-64. 2005..This study provides the first example for recruitment of an ATP-dependent chromatin-remodeling factor by a general transcription factor in vivo... - A DNA integrity network in the yeast Saccharomyces cerevisiaeXuewen Pan
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
Cell 124:1069-81. 2006..This network will guide more detailed characterization of mechanisms governing DNA integrity in yeast and other organisms... - Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in poolsBrian D Peyser
McKusick-Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
Nucleic Acids Res 33:e140. 2005.... - Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome courseJessica S Dymond
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
Genetics 181:13-21. 2009..Regular "lab meeting" sessions help prepare them for future roles in laboratory science... - Human l1 retrotransposition is associated with genetic instability in vivoDavid E Symer
Department of Molecular Biology and Genetics, John Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Cell 110:327-38. 2002..In a striking number of integrants, short identical sequences were shared between the donor and the target site's 3' end, suggesting a mechanistic model that helps explain the structure of L1 insertions... 
Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarrayPamela B Meluh
Department of Molecular Biology and Genetics, The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
Methods Mol Biol 416:221-47. 2008..Analysis of double-mutant strains is of growing importance in defining the spectrum of essential cellular functionalities and in understanding how these functionalities interrelate...- Ty1 defect in proteolysis at high temperatureJoseph F Lawler
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
J Virol 76:4233-40. 2002..Taken together, these results suggest that alterations in Ty1 proteins that occur at high temperature affect both protease activity and RT activity, such that Ty1 transposition is abolished... - Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomesJeffrey S Han
Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Nature 429:268-74. 2004..Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome... - Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitroNurjana Bachman
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Methods Enzymol 350:230-47. 2002 - GeneDesign: rapid, automated design of multikilobase synthetic genesSarah M Richardson
High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 16:550-6. 2006..GeneDesign has been implemented as a publicly accessible Web-based resource and can be found at http://slam.bs.jhmi.edu/gd... - Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domainsRobert M Yarrington
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore MD 21205, USA
J Virol 81:9004-12. 2007..These intriguing results reveal that the effect of these suppressor mutations is transmitted to the polymerase domain and suggest biochemical communication between these two domains during reverse transcription... - Inhibition of reverse transcription in vivo by elevated manganese ion concentrationEric C Bolton
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
Mol Cell 9:879-89. 2002..We propose that occupancy of the B site is the major determinant of catalytic activity and that Mn(2+) at this site greatly reduces catalytic activity... - Stacking the deck: double-tiled DNA microarraysSarah J Wheelan
The High Throughput Biology Center and Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, BRB Suite 331 Baltimore, Maryland 21205, USA
Nat Methods 3:903-7. 2006.... - The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylationIvana Celic
High Throughput Biology Center, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Curr Biol 16:1280-9. 2006..Acetylation of histone H3 lysine 56 (K56Ac) occurs transiently in newly synthesized H3 during passage through S phase and is removed in G2. However, the physiologic roles and effectors of K56Ac turnover are unknown... - Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiaeEdel M Hyland
High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Mol Cell Biol 25:10060-70. 2005..Finally, we allude to the possible molecular mechanisms underlying the effects of these modifications... - Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolutionSarah J Wheelan
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 15:1073-8. 2005..Gene-breaking represents a new mechanism through which L1 elements remodel mammalian genomes... - Mobile interspersed repeats are major structural variants in the human genomeCheng Ran Lisa Huang
Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Cell 141:1171-82. 2010..We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further... - dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiaeXuewen Pan
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
Methods 41:206-21. 2007..This technology has been effectively adapted to study other types of genome-wide genetic interactions including gene-compound synthetic lethality, secondary mutation suppression, dosage-dependent synthetic lethality and suppression... - Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of viewEric C Bolton
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 13:254-63. 2003..Direct analysis of PTR3 transcription, promoted by sequences very close to a tRNA gene, shows that this tRNA position effect can operate on a native chromosomal gene... - Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposonEric C Bolton
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
RNA 11:308-22. 2005..Our results suggest that the intramolecular interaction between the 5'-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription... - DNA helicase gene interaction network defined using synthetic lethality analyzed by microarraySiew Loon Ooi
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 617 Hunterian Building, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
Nat Genet 35:277-86. 2003..SLAM detects synthetic lethality efficiently and ranks candidate genetic interactions, making it an especially useful method... - Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesisYu yi Lin
High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Cell 136:1073-84. 2009..Our findings demonstrate a regulatory function for the NuA4 complex in glucose metabolism and life span by acetylating a critical metabolic enzyme... - Silent information regulator 3: the Goldilocks of the silencing complexAnne Norris
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genes Dev 24:115-22. 2010..Finally, we synthesize these ideas to revise the model for how Sir3p mediates silent chromatin formation in yeast, in part through its affinity for the LRS region of the nucleosome, which must be "just right.".. - The incredible shrinking world of DNA microarraysSarah J Wheelan
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Mol Biosyst 4:726-32. 2008.... - Conditional activation of a single-copy L1 transgene in mice by CreWenfeng An
The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genesis 46:373-83. 2008..This conditional transgenic ORFeus mouse model should allow further exploration of posttranscriptional cellular requirements for L1 retrotransposition and facilitate the development of ORFeus mouse lines suitable for in vivo mutagenesis... - CLONEQC: lightweight sequence verification for synthetic biologyPablo A Lee
Department of Computer Science, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21215, USA
Nucleic Acids Res 38:2617-23. 2010..This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source... - HistoneHits: a database for histone mutations and their phenotypesHailiang Huang
Department of Biomedical Engineering, Johns Hopkins University and School of Medicine, Baltimore, Maryland 21218, USA
Genome Res 19:674-81. 2009..All data sets are freely available for download... - A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylationYu yi Lin
High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genes Dev 22:2062-74. 2008..These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes... - From the shards of a shattered genome, diversityLisa Z Scheifele
Department of Molecular Biology and Genetics, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 105:11593-4. 2008 - Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutantsJunbiao Dai
High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Cell 134:1066-78. 2008.... - Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interactionAnne Norris
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
PLoS Genet 4:e1000301. 2008..Based on these findings, we propose an electrostatic model for how an extensive surface on the Sir3p BAH domain may regulate docking onto the LRS surface... - Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactionsYan Qi
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
Genome Res 18:1991-2004. 2008..The kernels show significant improvement over previous best methods for predicting genetic interactions and protein co-complex membership from genetic interaction data... - An evaluation of detection methods for large lariat RNAsCandice E Coombes
Department of Oncology, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
RNA 11:323-31. 2005..Thus, the role of the Dbr1 protein in Ty1 retrotransposition remains elusive... - A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activityJoseph F Lawler
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
J Virol 76:346-54. 2002..Remarkably, these mutants have distinct defects in reverse transcription... - Gene function prediction from congruent synthetic lethal interactions in yeastPing Ye
Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
Mol Syst Biol 1:2005.0026. 2005..These in silico methods can predict phenotypes and gene functions and are applicable to genomic synthetic lethality screens in yeast and analogous RNA interference screens in metazoans... - A highly active synthetic mammalian retrotransposonJeffrey S Han
Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Nature 429:314-8. 2004..These synthetic retrotransposons are also the most highly active L1 elements known so far and have potential as practical tools for manipulating mammalian genomes... - Active retrotransposition by a synthetic L1 element in miceWenfeng An
High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 103:18662-7. 2006..The results suggest that ORFeus may be developed into useful tools for in vivo mutagenesis... - A core nucleosome surface crucial for transcriptional silencingJeong-Hyun Park
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, USA
Nat Genet 32:273-9. 2002..These two clusters relieve distinct forms of transcriptional repression (silencing versus repression resulting from lack of Swi/Snf chromatin remodeling activity)... - Mighty Piwis defend the germline against genome intrudersKathryn A O'Donnell
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Cell 129:37-44. 2007..2007; Houwing et al., 2007). This function may be conserved in mice as loss of Miwi2, a mouse Piwi homolog, leads to germline stem cell and meiotic defects correlated with increased transposon activity (Carmell et al., 2007)... - Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiaeJames P Kastenmayer
Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20889, USA
Genome Res 16:365-73. 2006..Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions... - Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivorsPatrick H Maxwell
Laboratory of Developmental Genetics, Wadsworth Center, and Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201-2002, USA
Mol Cell Biol 24:9887-98. 2004..We propose that Y'-oligo(A)-Ty1 cDNA recombines with Y' elements at eroding telomeres in survivors and may play a role in telomere maintenance in the absence of telomerase... - Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutantMarnie E Gelbart
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Genes Dev 19:942-54. 2005.... - Molecular biology. Ring around the retroelementPhilip S Perlman
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Science 303:182-4. 2004 - Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiaeVincent J Starai
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53726 4087, USA
Genetics 163:545-55. 2003..The data suggest that the Hst3 and Hst4 proteins are the most important for allowing growth on these short-chain fatty acids... - Functional profiling of the Saccharomyces cerevisiae genomeGuri Giaever
Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
Nature 418:387-91. 2002..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics... - FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulationMiguel Arevalo-Rodriguez
Department of Molecular Genetics and Microbiology, Box 3546, 322 CARL Building, Research Dr, Duke University Medical Center, Durham, NC 27710, USA
Eukaryot Cell 3:1287-96. 2004..Because this pathway is conserved in fungi but not in mammals, our findings suggest a facile route to synergistic antifungal drug development via concomitant inhibition of FKBP12 and Hom6... - Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain proteinAngela R Brannon
Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0455, USA
Proc Natl Acad Sci U S A 102:2998-3003. 2005..The S. cerevisiae-based plasmid maintenance assays described here are invaluable tools for dissecting mechanisms of episomal viral genome replication and screening for additional host protein factors involved in plasmid maintenance... - Plasmid-chromosome shuffling for non-deletion alleles in yeastZhiwei Huang
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nat Methods 5:167-9. 2008..This simple method will facilitate characterization of essential gene functions and genome-wide investigation of protein structure-function relationships... - The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencingChristopher J Fry
Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, Suite 210, Worcester, MA 01605, USA
Mol Cell Biol 26:9045-59. 2006..Our study shows that structurally similar nucleosomal surfaces provide distinct functionalities in vivo and in vitro... - Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasetsT K B Gandhi
Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
Nat Genet 38:285-93. 2006..The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states... - Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediatesFuyang Li
Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA
Mol Cell 30:325-35. 2008..Deletion of SAW1 abolished association of Rad1 at SSA intermediates in vivo. We propose that Saw1 targets Rad1/Rad10 to Rad52-coated recombination intermediates... - Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiaeShay Ben-Aroya
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
Mol Cell 30:248-58. 2008..The importance of this collection is demonstrated by biochemical and genetic screens that reveal essential genes involved in RNA processing and maintenance of chromosomal stability... - Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiaeSara A Zurita-Martinez
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
Genetics 176:2139-50. 2007.... - Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathwayJoseph J Sandmeier
Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908, USA
Genetics 160:877-89. 2002..We propose a model in which two components of the NAD(+) salvage pathway, Pnc1p and Npt1p, function together in recycling the nuclear nicotinamide generated by Sir2p deacetylase activity back into NAD(+)...
Research Grants
- TRANSPOSITION MECHANISMSJEF BOEKE; Fiscal Year: 2006..Based on the results of these experiments, we will pursue the isolation of compounds that raise intracellular Mn+2 in human cells by interfering with the human Pmr1p protein. ..
- TRANSCRIPTIONAL SILENCING MECHANISMSJEF BOEKE; Fiscal Year: 2005..We will use the tools of molecular genetics, biochemistry and structural biology to carry out a comprehensive analysis of the molecular mechanisms involved in silencing. ..
- YEAST GENETIC INTERACTION MAPJEF BOEKE; Fiscal Year: 2006..Because yeast and human genes are often conserved in structure and function, many parts of this wiring diagram will be directly applicable to studies of human gene function and dysfunction. ..
- YEAST GENETIC INTERACTION MAPJEF BOEKE; Fiscal Year: 2007..The method we developed during the initial funding period is in production and can be applied genome scale. Thus, to our knowledge, we are the only group that can complete the remaining 98% of the yeast synthetic lethal interaction map. ..
- TRANSPOSITION MECHANISMSJEF BOEKE; Fiscal Year: 2007..Based on the results of these experiments, we will pursue the isolation of compounds that raise intracellular Mn+2 in human cells by interfering with the human Pmrlp protein. ..
- TRANSPOSITION MECHANISMSJEF BOEKE; Fiscal Year: 2002..We will examine the transcriptional interactions between Ty1 elements and the pol III genes that often lie adjacent to them. ..
- TRANSPOSITION MECHANISMSJEF BOEKE; Fiscal Year: 1990..4) To identify and characterize DNA intermediates in Ty element transposition. 5) To examine the factors influencing target specificity of Ty insertion...
- TRANSPOSITION MECHANISMSJEF BOEKE; Fiscal Year: 1993....
- TRANSPOSITION MECHANISMSJef D Boeke; Fiscal Year: 2010..Additionally, we study how the jumping genes interact with the machinery that protects our DNA from damage, a process that can lead to cancer. ..