A5076978787- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Protein Structure and Dynamics
- Bacterial Genetics and Biotechnology
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Ubiquitin and proteasome pathways
- Advanced Biosensing Techniques and Applications
- CRISPR and Genetic Engineering
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Biotin and Related Studies
- Blood properties and coagulation
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Monoclonal and Polyclonal Antibodies Research
- Adipose Tissue and Metabolism
Oregon Health & Science University
2023-2025
Center for Systems Biology
2018-2025
Boston University
2018-2025
Cancer Institute (WIA)
2025
OHSU Knight Cancer Institute
2023-2025
University of Toronto
2014-2024
Babcock University
2024
University of Miami
2024
Shandong Academy of Agricultural Sciences
2023
Stanford University
2022
Background Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of expression experiments. This finds coherent gene-sets, pathways, that are statistically over-represented in given list. Ideally, number resulting sets smaller than genes list, thus simplifying interpretation. However, increasing and redundancy gene-sets used by many current software works against this ideal. Principal Findings To overcome gene-set...
Protein and messenger RNA (mRNA) copy numbers vary from cell to in isogenic bacterial populations. However, these molecules often exist low are difficult detect single cells. We carried out quantitative system-wide analyses of protein mRNA expression individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent fusion library for Escherichia coli. found that almost all number distributions can be described by the gamma distribution two fitting parameters...
Delivery and toxicity are critical issues facing nanomedicine research. Currently, there is limited understanding connection between the physicochemical properties of a nanomaterial its interactions with physiological system. As result, it remains unclear how to optimally synthesize chemically modify nanomaterials for in vivo applications. It has been suggested that after synthesis, known as "synthetic identity", not what cell encounters vivo. Adsorption blood components phagocytes can size,...
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...
Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based chromatographic separation cultured cell extracts into more than one thousand biochemical fractions that were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network 13,993...
Using quantitative models to predict the biological interactions of nanoparticles will accelerate translation nanotechnology. Here, we characterized serum protein corona 'fingerprint' formed around a library 105 surface-modified gold nanoparticles. Applying bioinformatics-inspired approach, developed multivariate model that uses fingerprint cell association 50% more accurately than parameters describing nanoparticle size, aggregation state, and surface charge. Our implicates set...
Set2 methylates Lys36 of histone H3. We show here that yeast copurifies with RNA polymerase II (RNAPII). Chromatin immunoprecipitation analyses demonstrated and H3 methylation are associated the coding regions several genes were tested correlate active transcription. Both depend, as well, on Paf1 elongation factor complex. The C terminus Set2, which contains a WW domain, is also required for effective methylation. Deletion CTK1, encoding an RNAPII CTD kinase, prevents recruitment, suggesting...
To physically characterize the web of interactions connecting Saccharomyces cerevisiae proteins suspected to be RNA polymerase II (RNAPII) elongation factors, subunits Spt4/Spt5 and Spt16/Pob3 (corresponding human DSIF FACT), Spt6, TFIIF (Tfg1, -2, -3), TFIIS, Rtf1, Elongator (Elp1, -3, -4, -5, -6) were affinity purified under conditions designed minimize loss associated polypeptides then identified by mass spectrometry. was discovered associate with three distinct complexes: histones;...
One-third of the 4,225 protein-coding genes Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted E. coli, including pathogenic strains. To elucidate orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged strains and generated comprehensive genomic context inferences derive a high-confidence compendium for virtually...
SUMO, or Smt3 in Saccharomyces cerevisiae, is a ubiquitin-like protein that post-translationally attached to multiple proteins vivo. Many of these substrate modifications are cell cycle-regulated, and SUMO conjugation essential for viability most eukaryotes. However, only limited number SUMO-modified have been definitively identified date, this has hampered study the mechanisms by which ligation regulates specific cellular pathways. Here we use combination yeast two-hybrid screening, high...
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses plasmids in prokaryotes. Cas1 is CRISPR-associated protein that common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show purified Escherichia coli (YgbT) exhibits nuclease activity single-stranded branched DNAs including Holliday junctions, replication forks 5'-flaps. The crystal structure YgbT...