A5034710937- Polynomial and algebraic computation
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Artificial Intelligence in Games
- RNA Interference and Gene Delivery
- Bioinformatics and Genomic Networks
- Mathematical Dynamics and Fractals
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Advanced Topology and Set Theory
- Gene expression and cancer classification
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Differential Equations and Dynamical Systems
- Numerical Methods and Algorithms
- Advanced Optimization Algorithms Research
- Evolutionary Algorithms and Applications
- Biomedical Text Mining and Ontologies
- RNA modifications and cancer
- Computational Physics and Python Applications
- Parallel Computing and Optimization Techniques
- Game Theory and Voting Systems
- Glycosylation and Glycoproteins Research
- Formal Methods in Verification
- Microbial Metabolic Engineering and Bioproduction
American Chemical Society
2022
University of California, San Francisco
2010-2012
University of California, Berkeley
2003-2011
QB3
2006-2010
Biocom
2010
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and assessment (http://salilab.org/modeller/). currently contains 10,355,444 reliable domains in 2,421,920 unique sequences. allows users to update demand, request additional sequences through interface the ModWeb server...
Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction protein–protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm identify orthologs based on analysis. Results benchmark dataset from TreeFam-A manually curated orthology database show that provides combination high recall precision competitive both InParanoid OrthoMCL, allows users target different...
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and assessment (http://salilab.org/modeller/). currently contains 10,355,444 reliable domains in 2,421,920 unique sequences. allows users to update demand, request additional sequences through interface the ModWeb server...
The set of Nash equilibria a finite game is the nonnegative solutions to system polynomial equations. In this survey article, we describe how construct certain special games and explain find all complex roots corresponding systems, including equilibria. We then systems for arbitrary generic games, by polyhedral homotopy continuation starting from specially constructed games. use Gröbner bases solve these learn geometric information about solution varies with payoff functions. Finally, review...
Abstract The role of genetic instability in driving carcinogenesis remains controversial. Genetic should accelerate by increasing the rate advantageous driver mutations; however, can also potentially retard tumour growth deleterious mutation. As such, it is unclear whether genetically unstable clones would tend to be more selectively than their stable counterparts within a growing tumour. Here, we show circumstances where evolves during progression towards cancer. We employ Wright–Fisher...
Every real algebraic variety is isomorphic to the set of totally mixed Nash equilibria some three-person game, and also an N-person game in which each player has two pure strategies. From Nash-Tognoli Theorem it follows that every compact differentiable manifold can be encoded as game. Moreover, there exist isolated arbitrary topological degree.
We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for estimation of protein multiple sequence alignments (MSAs) phylogenetic trees. The takes as input a set sequences in FASTA format, outputs MSA; these can be viewed online or downloaded from website. SATCHMO-JS is an extension SATCHMO algorithm, employs divide-and-conquer strategy to at higher point tree, reducing computational complexity progressive all-versus-all...
A central concern of game theory is the computation Nash equilibria. These are characterized by systems polynomial equations and inequalities. We survey use currently available software to solve these systems, conclude that polyhedral homotopy continuation appears scale best with increasing problem size.
UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established collaboration to improve data sharing. One of major steps in this effort was 'Dicty annotation marathon', week-long exercise with 30 annotators aimed at achieving increase number D. discoideum proteins represented UniProtKB/Swiss-Prot. The marathon led over 1000 Concomitantly, there were large updates dictyBase concerning gene symbols, names models. This...
A number of platforms are potentially suitable for live coverage conferences.The most common ones compared in Supplementary Table S1, and include dedicated services such as CoverItLive (http://www.coveritlive.com/)or ScribbleLive (http://www.scribblelive.com) well other more general wikis, blogs, Twitter (http://www.twitter.com),FriendFeed (http://www.friendfeed.com)or the upcoming Google Wave (http://wave.google.com).Blogs have been used a long time to report reflect on conference...
In last year's report on microblogging ISMB 2008 [1], the authors anticipated that new methods of using Web and reporting conference would make live blogging even easier (http://www.bork.embl.de/~jensen/ismb2008/keynotes.php.html). This year, ISMB/ECCB 2009 site contained all features mock-up, far more bloggers participated than there was increased coverage talks special sessions. We, in turn, look forward to technologies appearing horizon (such as Google Wave), how both tools will next an...
We were pleased to see PLoS Conference Postcards return the Pacific Symposium on Biocomputing (PSB), held January 4–11, 2011. This year we received a Postcard from A. Murat Eren, PhD student at University of New Orleans, in which he discusses software package designed for use microbial ecology research. hope ISMB 2011, and if you would like contribute can find out more at: http://www.ploscompbiol.org/doi/pcbi.1000746.
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit many roles of RNA physiology for use medicine. With rapid success development lipid-RNA nanoparticles mRNA vaccines against COVID-19 with several approved RNA-based drugs, catapulted forefront drug research. diverse functions beyond role producing antigens or therapeutic proteins, classes serve regulatory cells tissues. These RNAs have potential as new therapeutics, itself serving...
We prove a theorem computing the number of solutions to system equations which is generic subject sparsity conditions embodied in graph. apply this games obeying graphical models and extensive-form games. define emergent-node tree structures as additional normal form may have. our having such structures. briefly discuss how emergent node relate cooperative
The set of Nash equilibria a finite game is the nonnegative solutions to system polynomial equations. In this survey article we describe how construct certain special games and explain find all complex roots corresponding systems, including equilibria. We then systems for arbitrary generic games, by polyhedral homotopy continuation starting from specially constructed games. use Groebner bases solve these learn geometric information about solution varies with payoff functions. Finally, review...
Every real algebraic variety is isomorphic to the set of totally mixed Nash equilibria some three-person game, and also an $N$-person game in which each player has two pure strategies. From Nash-Tognoli Theorem it follows that every compact differentiable manifold can be encoded as game. Moreover, there exist isolated arbitrary topological degree.