A5017236112- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Enzyme Structure and Function
- S100 Proteins and Annexins
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Enzyme Catalysis and Immobilization
- Plant tissue culture and regeneration
- Animal and Plant Science Education
- Misinformation and Its Impacts
- Health and Medical Research Impacts
- Biomedical and Engineering Education
- Doctoral Education Challenges and Solutions
- Microbial Natural Products and Biosynthesis
- Diverse Educational Innovations Studies
- Media Influence and Health
- Diversity and Career in Medicine
- Algorithms and Data Compression
- Climate Change Communication and Perception
- Genetics, Bioinformatics, and Biomedical Research
- Mentoring and Academic Development
- Career Development and Diversity
- Advances in Oncology and Radiotherapy
Communications Technology Laboratory
2021-2024
Ibis Reproductive Health
2018-2020
University of California, San Francisco
2009-2018
QB3
2009-2013
Boston University
2013
Universität Hamburg
2013
Massachusetts Institute of Technology
2013
Albert Einstein College of Medicine
2009
Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...
Due to the rapid release of new data from genome sequencing projects, majority protein sequences in public databases have not been experimentally characterized; rather, are annotated using computational analysis. The level misannotation and types large currently unknown analyzed depth. We investigated levels for molecular function four sequence (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, KEGG) a model set 37 enzyme families which extensive experimental information is available....
The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies.Members of such superfamilies are in their overall reactions yet share common ancestor and some conserved active site features associated with functional attributes as partial reaction.Thus, despite different functions, members these 'look alike', making them easy to misannotate.To...
The ongoing functional annotation of proteins relies upon the work curators to capture experimental findings from scientific literature and apply them protein sequence structure data. However, with increasing use high-throughput assays, a small number studies dominate annotations collected in databases. Here we investigate just how prevalent is "few articles -- many proteins" phenomenon. We examine experimentally validated provided by several groups GO Consortium, show that distribution per...
The Graduate Student Internships for Career Exploration (GSICE) program at the University of California, San Francisco (UCSF), offers structured training and hands-on experience through internships a broad range PhD-level careers. GSICE model was successfully replicated Davis (UC Davis). Here, we present outcome data total 217 PhD students participating in UCSF UC programs from 2010 to 2015 2014 2015, respectively. internship two sites demonstrated comparable participation, completion rates,...
Behavioral medicine scientists, practitioners, and educators can engage in evidence-based science communication strategies to amplify the combat misinformation. Such efforts are critical protect public health during crises such as COVID-19 pandemic promote overall well-being.
Abstract Population growth and climate change will impact food security potentially exacerbate the environmental toll that agriculture has taken on our planet. These existential concerns demand a passionate, interdisciplinary, diverse community of plant science professionals is trained during 21st century. Furthermore, societal trends question importance expert knowledge highlight need to better communicate value rigorous fundamental scientific exploration. Engaging students general public...
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies divergent evolution of enzyme function. Each the different reactions catalyzed by members initiated abstraction α-proton carboxylate substrate that coordinated to an essential Mg2+. muconate lactonizing (MLE) from Pseudomonas putida, member family catalyzes syn-cycloisomerization cis,cis-muconate (4S)-muconolactone in β-ketoadipate pathway, has provided critical insights into structural bases...
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ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTEvolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms Two Families cis,cis-Muconate Lactonizing EnzymesAyano Sakai, Alexander A. Fedorov, Elena V. Alexandra M. Schnoes, Margaret E. Glasner, Shoshana Brown, Marc Rutter, Kevin Bain, Shawn Chang, Tarun Gheyi, J. Michael Sauder, Stephen K. Burley, Patricia C. Babbitt, Steven Almo, and John Gerlt*Cite this: Biochemistry 2009, 48, 11,...
The large number of uncharacterized sequences in commonly used sequence databases cannot be experimentally characterized and therefore must annotated using computational methods. In this work we computationally evaluate the predicted functions proteins several mechanistically diverse enzyme superfamilies. Our approach is based upon principles chemistry-constrained evolution—the theory that some step or characteristic chemical activity conserved element evolution. This principle has allowed...
Abstract Importance Despite the importance of clinician-scientists in propelling biomedical advances, proportion physicians engaged both hypothesis-driven research and clinical care continues to decline. Recently, multiple institutions have developed programs that promote MD-only pursuing careers science, but few reports on impact these are available. Objective To assess if a cohort-based training program for physician-scientists includes didactic experiential curricula favorably informs...