基本信息
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职业迁徙
个人简介
Honors & Awards
George Beadle Award, GSA (2019)
Elected Member, American Academy of Science (2015)
Stanford B. Ascherman Professor, Stanford (2011)
Pioneer Award, Human Proteome Organization (2009)
CT Medal of Science, Connection Academy of Science (2007)
Pew Scholar Award, Pew Foundation (1987-1991)
We are presently in an omics revolution in which genomes and other omes can be readily characterized. Our laboratory uses a variety of approaches to analyze genomes and regulatory networks. Our research focuses on yeast, an ideal model organism ideally suited to genetic analysis, and humans.
1) Transcriptomes
To annotate genomes, we developed RNA sequencing for annotation the yeast and human transcriptomes. We discovered that the eukaryotic transcriptome is much more complex than previously appreciated and that embryonic stem cells have more transcript isoforms than differentiated cells.
2) Transcription Factor Binding Networks
We have also developed methods for mapping transcription factor binding sites through the genome. We used this to develop regulatory maps and have been using this to help decipher the combinatorial regulatory code which factors work together to regulate which genes. Using this approach we have mapped out pathways crucial for metabolism and inflammation.
3) Integrated Regulatory Networks
In addition to transcriptional factor binding networks we have also been mapping phosphorylation and metabolite-protein interaction networks. These studies have revealed novel global regulators and key points in integrated regulatory networks.
4) Variation
We have been analyzing differences between individuals and species at two levels: DNA sequence variation and regulatory information variations. We developed paired end sequencing for humans and found that humans have extensive structural variation (SV), i.e. deletions, insertions and inversions. This is likely to be a major cause of phenotypic variation and human disease. In addition, by mapping binding sites difference among different yeast strains and humans, we have found that individuals differ much more in their regulatory information than in coding sequence differences. We can correlate these differences with those in SNPS and SVs, thereby associating noncoding DNA differences with regulatory information.
5) Human Disease
Finally, we are applying omics approaches of genome sequencing, transcriptomics proteomics metabolomics, DNA methylation and microbiome assays to the analysis of human disease. These integrative omics approaches are being applied to help understand the molecular basis of disease and the development of diagnostics and therapeutics.
George Beadle Award, GSA (2019)
Elected Member, American Academy of Science (2015)
Stanford B. Ascherman Professor, Stanford (2011)
Pioneer Award, Human Proteome Organization (2009)
CT Medal of Science, Connection Academy of Science (2007)
Pew Scholar Award, Pew Foundation (1987-1991)
We are presently in an omics revolution in which genomes and other omes can be readily characterized. Our laboratory uses a variety of approaches to analyze genomes and regulatory networks. Our research focuses on yeast, an ideal model organism ideally suited to genetic analysis, and humans.
1) Transcriptomes
To annotate genomes, we developed RNA sequencing for annotation the yeast and human transcriptomes. We discovered that the eukaryotic transcriptome is much more complex than previously appreciated and that embryonic stem cells have more transcript isoforms than differentiated cells.
2) Transcription Factor Binding Networks
We have also developed methods for mapping transcription factor binding sites through the genome. We used this to develop regulatory maps and have been using this to help decipher the combinatorial regulatory code which factors work together to regulate which genes. Using this approach we have mapped out pathways crucial for metabolism and inflammation.
3) Integrated Regulatory Networks
In addition to transcriptional factor binding networks we have also been mapping phosphorylation and metabolite-protein interaction networks. These studies have revealed novel global regulators and key points in integrated regulatory networks.
4) Variation
We have been analyzing differences between individuals and species at two levels: DNA sequence variation and regulatory information variations. We developed paired end sequencing for humans and found that humans have extensive structural variation (SV), i.e. deletions, insertions and inversions. This is likely to be a major cause of phenotypic variation and human disease. In addition, by mapping binding sites difference among different yeast strains and humans, we have found that individuals differ much more in their regulatory information than in coding sequence differences. We can correlate these differences with those in SNPS and SVs, thereby associating noncoding DNA differences with regulatory information.
5) Human Disease
Finally, we are applying omics approaches of genome sequencing, transcriptomics proteomics metabolomics, DNA methylation and microbiome assays to the analysis of human disease. These integrative omics approaches are being applied to help understand the molecular basis of disease and the development of diagnostics and therapeutics.
研究兴趣
论文共 1217 篇作者统计合作学者相似作者
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Journal of Biological Chemistryno. 3 (2024)
Mahdi Moqri, Chiara Herzog, Jesse R. Poganik,Kejun Ying,Jamie N. Justice,Daniel W. Belsky,Albert T. Higgins-Chen,Brian H. Chen,Alan A. Cohen,Georg Fuellen,Sara Hägg,Riccardo E. Marioni,
Mona Aminbeidokhti, Jia-Hua Qu, Shweta Belur,Hakan Cakmak, Eleni Jaswa,Ruth B. Lathi,Marina Sirota,Michael P. Snyder,Svetlana A. Yatsenko,Aleksandar Rajkovic
Human Geneticsno. 2 (2024): 185-195
Frontiers in pharmacology (2024): 1348112-1348112
MACHINE LEARNING FOR MULTIMODAL HEALTHCARE DATA, ML4MHD 2023 (2024): 54-63
Jessica Pham,Jane Isquith,Larisa Balaian,Luisa Ladel, Shuvro P. Nandi, Karla Mack,Inge van der Werf, Emma Klacking, Antonio Ruiz, David Mays, Paul Gamble, Shelby Giza,
biorxiv(2024)
Calum Harvey, Marcel Weinreich, James A. K. Lee,Allan C. Shaw,Laura Ferraiuolo,Heather Mortiboys,Sai Zhang,Paul J. Hop,Ramona A. J. Zwamborn,Kristel van Eijk,Thomas H. Julian,Tobias Moll,
HELIYONno. 3 (2024): e24975-e24975
Molecular & Cellular Proteomicsno. 3 (2024): 100731-100731
Aushia Tanzih Al Haq, Pao-Pao Yang, Christopher Jin,Jou-Ho Shih,Li-Mei Chen,Hong-Yu Tseng,Yen-An Chen,Yueh-Shan Weng,Lu-Hai Wang,Michael P Snyder,Hsin-Ling Hsu
Research Square (Research Square)no. 5 (2024): 2167-2189
Sai Zhang,Tobias Moll,Jasper Rubin-Sigler, Sharon Tu,Shuya Li,Enming Yuan, Menghui Liu, Afreen Butt,Calum Harvey, Sarah Gornall, Elham Alhalthli,Allan Shaw,
medRxiv : the preprint server for health sciences (2024)
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