A5024120181- Genomics and Chromatin Dynamics
- Fungal and yeast genetics research
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Monoclonal and Polyclonal Antibodies Research
- Metabolomics and Mass Spectrometry Studies
- Advanced Proteomics Techniques and Applications
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- Advanced Biosensing Techniques and Applications
- Advanced Radiotherapy Techniques
- Chromosomal and Genetic Variations
- Gut microbiota and health
- Genomic variations and chromosomal abnormalities
- Immunotherapy and Immune Responses
- Health, Environment, Cognitive Aging
- Cancer-related molecular mechanisms research
Stanford University
2016-2025
Stanford Medicine
2016-2025
Palo Alto University
2015-2025
Menlo School
2013-2025
Mayo Clinic in Florida
2016-2025
University Hospitals of Cleveland
2025
University School
2025
Case Western Reserve University
2025
Cardiovascular Institute of the South
2015-2024
MIT Lincoln Laboratory
2020-2024
The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches required to systematically determine their function. A total 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with precise deletion one 2026 ORFs (more than one-third the genome). Of deleted ORFs, 17 percent essential for viability rich medium. phenotypes more 500 assayed parallel. strains, 40 showed quantitative growth...
As the sequencing of healthy and disease genomes becomes more commonplace, detailed annotation provides interpretation for individual variation responsible normal phenotypes. Current approaches focus on direct changes in protein coding genes, particularly nonsynonymous mutations that directly affect gene product. However, most occurs outside genes and, indeed, markers generated from genome-wide association studies (GWAS) identify variants segments. Identification potential regulatory perturb...
The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed in which complementary DNA fragments are subjected to high-throughput sequencing mapped the genome. applied generate high-resolution transcriptome map yeast genome demonstrated that most (74.5%) nonrepetitive sequence is transcribed. confirmed many known predicted introns others not actively...
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding histone modifications in living cells. Despite its widespread use, there are considerable differences how these experiments conducted, results scored evaluated quality, data metadata archived public use. These practices affect quality utility any global ChIP experiment. Through our experience...
To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a proteome microarray screened for ability interact with phospholipids. We identified many new calmodulin- phospholipid-interacting proteins; common potential binding motif was calmodulin-binding Thus, microarrays an entire eukaryotic can be prepared diverse biochemical activities. also...
Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed method, CNVnator, for CNV discovery genotyping from read-depth (RD) analysis of personal sequencing. Our method based on combining established mean-shift approach with additional refinements (multiple-bandwidth partitioning GC correction) to broaden range discovered CNVs. calibrated CNVnator using extensive validation performed by 1000 Genomes Project. Because this, we could...
Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; ensemble these binding events forms regulatory network, constituting wiring diagram for cell. To examine principles human transcriptional we determined genomic information 119 transcription-related over 450 distinct experiments. We found combinatorial, co-association transcription be highly context specific: combinations at specific locations. In particular, there are significant differences...
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment current data sets, demonstrating that high-throughput two-hybrid (Y2H) screening provides high-quality interaction information. Because large fraction the remains to be mapped, we developed an empirically controlled mapping framework produce “second-generation” high-quality, Y2H...
We have developed an approach using Bayesian networks to predict protein-protein interactions genome-wide in yeast. Our method naturally weights and combines into reliable predictions genomic features only weakly associated with interaction (e.g., messenger RNAcoexpression, coessentiality, colocalization). In addition de novo predictions, it can integrate often noisy, experimental data sets. observe that at given levels of sensitivity, our are more accurate than the existing high-throughput...
Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations rearrangements. We introduce high-throughput massive paired-end mapping (PEM), a large-scale genome-sequencing method identify structural variants (SVs) approximately 3 kilobases (kb) or larger that combines rescue capture paired ends 3-kb fragments, 454 sequencing, computational approach map DNA reads onto reference genome. PEM was used SVs in an...
Elucidating the transcribed regions of genome constitutes a fundamental aspect human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed series high-density oligonucleotide tiling arrays representing sense and antisense strands entire nonrepetitive sequence genome. Transcribed sequences were located across via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained liver tissue. In addition...