A5038044466- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Viral Infectious Diseases and Gene Expression in Insects
- Legume Nitrogen Fixing Symbiosis
- Plant-Microbe Interactions and Immunity
- DNA Repair Mechanisms
- Congenital Heart Disease Studies
- Protein Structure and Dynamics
- interferon and immune responses
- Estrogen and related hormone effects
- Plant Pathogenic Bacteria Studies
- Glycosylation and Glycoproteins Research
- Congenital heart defects research
- Genetic Mapping and Diversity in Plants and Animals
- Plant Parasitism and Resistance
- Microbial Metabolism and Applications
- Evolution and Genetic Dynamics
- Innovative Microfluidic and Catalytic Techniques Innovation
- Coronary Artery Anomalies
- Single-cell and spatial transcriptomics
- Biosimilars and Bioanalytical Methods
Sri Ramachandra Institute of Higher Education and Research
2025
Case Western Reserve University
2011
University of California, Berkeley
2004-2008
International Rice Research Institute
2007
Sainsbury Laboratory
2005
University of Warwick
2005
Abstract The tomato (Lycopersicon esculentum) Cf-9 resistance gene encodes the first characterized member of plant receptor-like protein (RLP) family. Other RLPs such as CLAVATA2 and TOO MANY MOUTHS are known to regulate development. domain structure consists extracellular leucine-rich repeats, a transmembrane helix, short cytoplasmic region. Here, we identify 90 in rice (Oryza sativa) compare them with functionally from different species 56 Arabidopsis (Arabidopsis thaliana) RLPs, including...
Abstract Deep mutational scanning is a powerful approach to investigate wide variety of research questions including protein function and stability. Here, we perform deep on three essential E. coli proteins (FabZ, LpxC MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, study the effect mutations their original genomic context. We use more than 17,000 variants interrogate importance individual amino acids supporting viability. Additionally, exploit these...
During infection of Arabidopsis thaliana , the bacterium Pseudomonas syringae pv tomato delivers effector protein AvrRpt2 into plant cell cytosol. Within cell, undergoes N-terminal processing and causes elimination RIN4. Previous work established that is a putative cysteine protease, RIN4 require an intact predicted catalytic triad in AvrRpt2. In this work, proteolytic events depend on activity were characterized. The amino acid sequence surrounding site two related sequences from triggered...
Function prediction by homology is widely used to provide preliminary functional annotations for genes which experimental evidence of function unavailable or limited. This approach has been shown be prone systematic error, including percolation annotation errors through sequence databases. Phylogenomic analysis avoids these in but difficult automate high-throughput application. To address this limitation, we present a computationally efficient pipeline phylogenomic classification proteins....
We report an extensive proteome analysis of rice etioplasts, which were highly purified from dark-grown leaves by a novel protocol using Nycodenz density gradient centrifugation. Comparative protein profiling different cell compartments leaf tissue demonstrated the purity etioplast preparation absence diagnostic marker proteins other compartments. Systematic identified 240 unique that provide new insights into heterotrophic plant metabolism and control gene expression. They include several...
Abstract Biomanufacturing could contribute as much ${\$}$30 trillion to the global economy by 2030. However, success of growing bioeconomy depends on our ability manufacture high-performing strains in a time- and cost-effective manner. The Design–Build–Test–Learn (DBTL) framework has proven be an effective strain engineering approach. Significant improvements have been made genome engineering, genotyping, phenotyping throughput over last couple decades that greatly accelerated DBTL cycles....
Abstract Background Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone systematic error. Phylogenomic analysis reduces these errors inferring protein function within evolutionary context entire family. However, accuracy for multi-domain proteins depends on all members having same overall domain structure. By contrast, most common homolog detection methods are optimized retrieving local homologs, and do not address this...
The Agrobacterium T-DNA transporter belongs to a growing class of evolutionarily conserved transporters, called type IV secretion systems (T4SSs). VirB4, 789 aa, is the largest T4SS component, providing rich source possible structural domains. Here, we use variety bioinformatics methods predict that C-terminal domain VirB4 (including Walker A and B nucleotide-binding motifs) related by divergent evolution cytoplasmic TrwB, coupling protein required for conjugative transfer plasmid R388 from...
Abstract The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated function prediction by homology through integration of variety experimental data bioinformatics methods in an framework. Users can submit sequences classification subfamilies. is available...
The Generation Challenge Programme (GCP; www.generationcp.org ) has developed an online resource documenting stress-responsive genes comparatively across plant species. This public is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. central objective this to elucidate orthologous paralogous relationships between that may be involved in response environmental stress, mainly abiotic stresses such as water deficit...
With the explosion in sequence data, accurate prediction of protein function has become a vital task prioritizing experimental investigation. While computationally efficient methods for homology-based have been developed to make this approach feasible high-throughput mode, it is not without its dangers. Biological processes such as gene duplication, domain shuffling, and speciation produce families related genes whose products can vastly different molecular functions. Standard...
Abstract Genome engineering methodologies are transforming biological research and discovery. Approaches based on CRISPR technology have been broadly adopted there is growing interest in the generation of massively parallel edited cell libraries. Comparing libraries generated by these varying approaches challenging researchers lack a common framework for defining assessing characteristics Here we describe evaluating genomes established methods sampling complex populations. We define specific...
Abstract Deep mutational scanning is a powerful approach to investigate wide variety of research questions including protein function and stability. We performed deep on three essential E. coli proteins (FabZ, LpxC MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing. This allowed us study the effect introduced mutations their original genomic context. Using more than 17,000 variants FabZ, MurA from saturation editing libraries constructed here, we have...
Prediction of molecular function proteins has become an important task in the genomics era. A wide variety sequence analysis tools are available to biologists for this task. We have selected one or two primary protocols tasks such as domain detection, subcellular localization, and motif detection. also present a strategy integration results from different protocols. All resources needed these accessible via publicly Web servers databases require little no computational expertise.
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Abstract Prediction of molecular function proteins has become an important task in the genomics era. A wide variety sequence analysis tools are available to biologists for this task. We have selected one or two primary protocols tasks such as domain detection, subcellular localization, and motif detection. also present a strategy integration results from different protocols. All resources needed these accessible via publicly Web servers databases require little no computational expertise.