A5040624110- Plant Molecular Biology Research
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- Plant nutrient uptake and metabolism
- Light effects on plants
- Plant Gene Expression Analysis
- Plant Stress Responses and Tolerance
- Genomics and Phylogenetic Studies
- Plant tissue culture and regeneration
- Ubiquitin and proteasome pathways
- Microbial Metabolic Engineering and Bioproduction
- Adipose Tissue and Metabolism
- Medical Imaging Techniques and Applications
- Gene Regulatory Network Analysis
- Cancer, Hypoxia, and Metabolism
- Genetic Mapping and Diversity in Plants and Animals
- Cellular Mechanics and Interactions
- Insect-Plant Interactions and Control
- Advanced Proteomics Techniques and Applications
- RNA modifications and cancer
- Protein Tyrosine Phosphatases
- Autophagy in Disease and Therapy
- Elasticity and Material Modeling
- Viral Infectious Diseases and Gene Expression in Insects
- Gene expression and cancer classification
Broad Institute
2022-2025
Iowa State University
2019-2024
North Carolina State University
2014-2024
Massachusetts Institute of Technology
2023
Zero to Three
2019
Rust College
2018
University of Strathclyde
2009
Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood
Abstract The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity throughput. However, reproducible quantification thousands proteins within a single cell remains challenging. To address some those limitations, we present dedicated sample preparation chip, proteoCHIP EVO 96 that directly interfaces with Evosep One. This, combination Bruker timsTOF demonstrates double identifications without manual handling...
Significance We developed a computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance. showed the capacity of our to integrate spatial temporal transcriptional improves performance inference algorithms. The combination this with Arabidopsis stem cell-specific data resulted in networks capture regulations cell-enriched cells throughout root development. Our combined approach molecular biology, mathematical led successful...
To understand complex regulatory processes in multicellular organisms, it is critical to be able quantitatively analyze protein movement and protein-protein interactions time space. During Arabidopsis development, the intercellular of SHORTROOT (SHR) subsequent interaction with its downstream target SCARECROW (SCR) control root patterning cell fate specification. However, quantitative information about spatio-temporal dynamics SHR SHR-SCR currently unavailable. Here, we quantify parameters...
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets unravel the molecular signaling events of BR response in Arabidopsis. We profile levels 26,669 transcripts, 9,533 protein groups, 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths time. then construct network inference pipeline called Spatiotemporal Clustering...
Abstract Mass spectrometry (MS)-based single-cell proteomics (SCP) has gained massive attention as a viable complement to other single cell approaches. The rapid technological and computational advances in the field have pushed boundaries of sensitivity throughput. However, reproducible quantification thousands proteins within at reasonable proteome depth characterize biological phenomena remains challenge. To address some those limitations we present combination fully automated sample...
Although genomic anomalies in glioblastoma (GBM) have been well studied for over a decade, its 5-year survival rate remains lower than 5%. We seek to expand the molecular landscape of high-grade glioma, composed IDH-wildtype GBM and IDH-mutant grade 4 astrocytoma, by integrating proteomic, metabolomic, lipidomic, post-translational modifications (PTMs) with transcriptomic measurements uncover multi-scale regulatory interactions governing tumor development evolution. Applying 14 proteogenomic...
ABSTRACT How plants determine the final size of growing cells is an important, yet unresolved, issue. Root hairs provide excellent model system with which to study this as their cell remarkably constant under environmental conditions. Previous studies have demonstrated that a basic helix-loop helix transcription factor ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) promotes root hair growth, but how growth terminated not known. In study, we demonstrate trihelix GT-2-LIKE1 (GTL1) and its homolog DF1...
Both plants and animals must contend with changes in their environment. The ability to respond appropriately these often underlies the of individual survive. In plants, an early response environmental stress is alteration plasmodesmatal permeability accompanying cell signaling. However, ways which plasmodesmata are modified, molecular players involved this regulation, biological significance responses not well understood. Here, we examine effects nutrient scarcity excess on...
Abstract Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play crucial role cell renewal, regeneration, organization. A number stem type-specific genes have known maintenance, identity, and/or division. Yet, how expressed across different types, referred to here as stem-cell-ubiquitous genes, contribute regulation is less understood. Here, we find that, Arabidopsis root, gene, TESMIN-LIKE CXC2 (TCX2),...
Recent advances in single-cell proteomics for animal systems could be adapted plants to increase our understanding of plant development, response stimuli, and cell-to-cell signaling.
The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic abiotic stress responses, reproduction. To gain new insights into the molecular interplay these processes to identify FER functions, we carried out quantitative transcriptome, proteome, phosphoproteome profiling Arabidopsis (Arabidopsis thaliana) wild-type fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, stress, were significantly enriched among...
Significance Proper elaboration of the plant body plan requires that cell division patterns are coordinated during development in complex tissues. Activation cycle machinery is critical for this process, but it not clear how or if links to cell-to-cell communication networks important development. Here we show key divisions generate root controlled by signaling peptides which act through plant-specific receptor kinases control expression a specific cyclinD regulatory gene. We gene depends on...
Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In Arabidopsis root, stem are maintained an undifferentiated state by less mitotically active population called quiescent center (QC). Determining how QC regulates surrounding initials, or what makes fundamentally different from actively dividing is important for understanding divisions maintained. Here we gained insight into differences between cortex endodermis initials (CEI) studying...
Abstract Brassinosteroids (BRs) regulate plant growth, development, and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1), whose degradation occurs through proteasome autophagy pathways. The E3 ubiquitin ligase(s) that modify BES1 for autophagy-mediated remain to be fully defined. Here, we identified an F-box family ligase named BES1-ASSOCIATED F-BOX1 (BAF1) in Arabidopsis thaliana. BAF1 interacts with mediates its ubiquitination degradation. Our...
Brassinosteroids (BRs) and Target of Rapamycin Complex (TORC) are two major actors coordinating plant growth stress responses. function through a signaling pathway to extensively regulate gene expression TORC is known translation autophagy. Recent studies have revealed connections between these pathways, but system-wide view their interplay still missing. We quantified the level 23 975 transcripts, 11 183 proteins, 27 887 phosphorylation sites in wild-type Arabidopsis thaliana mutants with...
The acquisition of quantitative information on plant development across a range temporal and spatial scales is essential to understand the mechanisms growth. Recent years have shown emergence imaging methodologies that enable capture analysis growth, from dynamics molecules within cells measurement morphometricand physiological traits in field-grown plants. In some instances, these methods can be parallelized multiple samples increase throughput. When high throughput combined with...
Abstract Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how signals are integrated from in etiolated Arabidopsis ( thaliana ) seedlings. To do so comprehensively characterized transcription factor during responses reconstructed dynamic transcriptional regulatory models...
Lung cancer leads cancer-related deaths worldwide, with 2024 estimates of 234,580 new cases in the United States. This study explores roles tumor driver aberrations, epithelial transcriptional states, and microenvironment composition lung outcomes using proteogenomic data from 965 patients across Clinical Proteomic Tumor Analysis Consortium (CPTAC) International Cancer Proteogenome (ICPC). We examined oncogenic alterations, stromal cell type enrichment distributions, modules activities, drug...
A-Kinase Anchoring Protein 11 (AKAP11) is a shared genetic risk factor for schizophrenia and bipolar disorder, yet its role in the brain remains poorly understood. Through multi-omic analysis of Akap11 mutant mouse brains cultured astrocytes, we identified significant transcriptomic, proteomic, metabolomic alterations. Key findings include upregulation cholesterol fatty acid metabolic pathways, accumulation lipid species such as cholesteryl esters, triacylglycerols, ceramides,...
Stem cells give rise to the entirety of within an organ. Maintaining stem cell identity and coordinately regulating divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) SHORTROOT (SHR), regulate in root niche. However, how these proteins function establish systemic behaviour not well understood. We propose a non-cell autonomous role WOX5 cortex endodermis initial (CEI) identify regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR...
Summary Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA‐sequencing data analysis, are automated or restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet , user‐friendly platform that can process raw any organism an reference genome using modified...