Research Topics
Genomes and GenesSpecies | Jay ShendureSummaryAffiliation: Princeton University Country: USA Publications
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Detail Information
Publications
Accurate multiplex polony sequencing of an evolved bacterial genomeJay Shendure
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Science 309:1728-32. 2005..Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents...- Multiplex amplification of large sets of human exonsGregory J Porreca
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Nat Methods 4:931-6. 2007..We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing... - Long-range polony haplotyping of individual human chromosome moleculesKun Zhang
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Genet 38:382-7. 2006..This haplotyping method is well suited for candidate gene-based association studies as well as for investigating the pattern of recombination in mammalian cells... 
Discovering functional transcription-factor combinations in the human cell cycleZhou Zhu
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Res 15:848-55. 2005..We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes...- Single molecule profiling of alternative pre-mRNA splicingJun Zhu
Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Science 301:836-8. 2003..Digital polony exon profiling can be used to investigate the physiological and pathological roles of alternately spliced messenger RNAs, as well as the mechanisms by which these messenger RNAs are produced... - Advanced sequencing technologies: methods and goalsJay Shendure
Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Nat Rev Genet 5:335-44. 2004 - Fluorescent in situ sequencing on polymerase coloniesRobi D Mitra
Lipper Center for Computational Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
Anal Biochem 320:55-65. 2003..Finally, we have developed software for automated image alignment and sequence calling... - Computational discovery of sense-antisense transcription in the human and mouse genomesJay Shendure
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Genome Biol 3:RESEARCH0044. 2002..Several of these cases support the hypothesis that a subset of the instances of substantial mouse-human conservation in the 5' and 3' UTRs of transcripts might be explained in part by functionality of an overlapping transcriptional unit... - Polony DNA sequencingGregory J Porreca
Harvard Medical School, Boston, Massachusetts, USA
Curr Protoc Mol Biol . 2006..Each sequencing run results in millions of 26-bp reads that can be aligned to the reference genome, allowing the identification of differences between sequences... - Digital genotyping and haplotyping with polymerase coloniesRobi D Mitra
Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 100:5926-31. 2003..The results indicate that polony genotyping and haplotyping may play an important role in understanding the structure of genetic variation... - Identification of foreign gene sequences by transcript filtering against the human genomeGriffin Weber
Department of Adult Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
Nat Genet 30:141-2. 2002..We demonstrate the potential of this method by identifying sequences from known pathogens in established expressed-sequence tag libraries... - Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy projectAnne W Higgins
Department of Pathology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
Am J Hum Genet 82:712-22. 2008..Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation... - A molecular pathway including Id2, Tbx5, and Nkx2-5 required for cardiac conduction system developmentIvan P G Moskowitz
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Cell 129:1365-76. 2007..We conclude that a molecular pathway including Tbx5, Nkx2-5, and Id2 coordinates specification of ventricular myocytes into the ventricular conduction system lineage... - Assaying chromosomal inversions by single-molecule haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Nat Methods 3:439-45. 2006..The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer... - Sequencing thoroughbredsGeorge Church
Nat Biotechnol 24:139. 2006 - The beginning of the end for microarrays?Jay Shendure
Nat Methods 5:585-7. 2008