A5011670317- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer Cells and Metastasis
- Cancer Research and Treatments
- Tissue Engineering and Regenerative Medicine
- Immune cells in cancer
- Cancer-related gene regulation
- Cancer Immunotherapy and Biomarkers
- Helicobacter pylori-related gastroenterology studies
- Immune Cell Function and Interaction
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Algal biology and biofuel production
- Peptidase Inhibition and Analysis
- Photosynthetic Processes and Mechanisms
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Legume Nitrogen Fixing Symbiosis
- Congenital heart defects research
- Birth, Development, and Health
- Bladder and Urothelial Cancer Treatments
University of California, Los Angeles
2016-2025
Broad Center
2014-2024
QB3
2019-2024
APLA Health
2011-2024
University of Lincoln
2023
University of Trento
2020-2023
Institute of Molecular and Cell Biology
2008-2023
Quantitative BioSciences
2019-2023
University of California System
2023
Digital Proteomics (United States)
2013-2022
A computational method is proposed for inferring protein interactions from genome sequences on the basis of observation that some pairs interacting proteins have homologs in another organism fused into a single chain. Searching many genomes revealed 6809 such putative protein-protein Escherichia coli and 45,502 yeast. Many members these were confirmed as functionally related; filtering further enriches interactions. Some links to several other proteins; coupled appear represent functional...
Determining protein functions from genomic sequences is a central goal of bioinformatics. We present method based on the assumption that proteins function together in pathway or structural complex are likely to evolve correlated fashion. During evolution, all such functionally linked tend be either preserved eliminated new species. describe this property evolution by characterizing each its phylogenetic profile, string encodes presence absence every known genome. show having matching similar...
Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although likely has conserved role gene silencing, the levels and patterns of appear to vary drastically among different Here we used shotgun genomic bisulfite sequencing (BS-Seq) compare eight diverse plant animal genomes. We found that are very similar flowering plants with methylated cytosines detected all sequence contexts, whereas CG predominates animals. Vertebrates have throughout genome...
Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and several cases, H3K27me3 is also required for the proper expression developmentally important genes plants. However, extent to which regulates plant on a genome-wide scale remains unknown. In addition, it not clear whether establishment spreading occur through same mechanisms plants animals. We identified regions containing genome flowering Arabidopsis thaliana using high-density...
Abstract Background Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties chromatin. In plants, methylation histone H3 lysine 4 (H3K4me) is associated with genes and required for plant development. Results We have characterized genome-wide distribution mono-, di- trimethylation H3K4 (H3K4me1, H3K4me2 H3K4me3, respectively) Arabidopsis thaliana seedlings using chromatin...
Alterations in the composition of intestinal microbiota have been correlated with aging and measures frailty elderly. However, relationships between microbial dynamics, age-related changes physiology, organismal health remain poorly understood. Here, we show that dysbiosis microbiota, characterized by an expansion Gammaproteobacteria, is tightly linked to age-onset barrier dysfunction Drosophila. Indeed, alterations precede predict onset aged flies. Changes occurring prior contribute...
Abstract To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 cancer primary tumor samples, including 179 classified as microsatellite instability–high (MSI-high). This set includes The Cancer Genome Atlas cohort 592 completed here. MSI-high, a hypermutated, immunogenic subtype had high rate significantly mutated genes important immune-modulating pathways antigen presentation machinery, biallelic losses B2M HLA due to copy-number...
Abstract Background DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides effective approach for studying genome-wide at base resolution. Libraries such as whole genome bisulfite (WGBS) and reduced represented (RRBS) are widely used generating methylomes, demanding efficient versatile tools aligning data. Results We have developed BS-Seeker2, updated version of BS Seeker, a full...
Nitrogen (N) is a key nutrient that limits global primary productivity; hence, N-use efficiency of compelling interest in agriculture and aquaculture. We used Chlamydomonas reinhardtii as reference organism for multicomponent analysis the N starvation response. In presence acetate, respiratory metabolism prioritized over photosynthesis; consequently, N-sparing response targets proteins, pigments, RNAs involved photosynthesis chloroplast function those respiration. Transcripts proteins...
Methylation of histone H3 lysine 9 (H3K9) is a hallmark transcriptional silencing in many organisms. In Arabidopsis thaliana, dimethylation H3K9 (H3K9m2) important the transposons and control DNA methylation. We constructed high-resolution genome-wide map H3K9m2 methylation by using chromatin immunoprecipitation coupled with whole genome Roche Nimblegen microarrays (ChIP-chip). observed very high coincidence between CHG (where H either A,T or C) throughout genome. The coding regions genes...
In honey bees ( Apis mellifera ), the development of a larva into either queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand role methylation in this process we sequenced larval methylomes both queens workers. We show that number differentially methylated genes (DMGs) head is significantly increased relative to adult brain (2,399 vs. 560) more than 80% DMGs up-methylated larvae. Several highly...
Interest in exploiting algae as a biofuel source and the role of inorganic nutrient deficiency inducing triacylglyceride (TAG) accumulation cells necessitates strategy to efficiently formulate species-specific culture media that can easily be manipulated. Using reference organism Chlamydomonas reinhardtii, we tested hypothesis modeling trace element supplements after cellular ionome would result optimized cell growth. We determined metal content several commonly used strains various...
The transition metal copper (Cu) is essential for all living organisms but toxic when present in excess. To identify Cu deficiency responses comprehensively, we conducted genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and a mutant defective the gene encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7), which acts as transcriptional regulator responses. In response to deficiency, FERRIC REDUCTASE OXIDASE5 (FRO5) FRO4 levels increased strongly, an...