Russell Schwartz

..The results further validate the proposed computational methods by showing consistency with several previous findings on these cancers and provide novel insights into the mechanisms of tumor progression in these patients...

..We close with a consideration of mechanisms by which these obstacles may be overcome in actual viral systems...

..We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome...

..An alternative approach uses tissue-wide measures of whole tumors to provide a detailed picture of averaged tumor state but at the cost of losing information about intra-tumor heterogeneity...

..The author's recent work in this area has been compiled into a set of computational tools available at http://www-2.cs.cmu.edu/~russells/software/hapmotif.html...

....

..It further presents results on simulated data, in order to validate the method, and on two real datasets from the literature, in order to illustrate its practical application...

..Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes...

....

..We demonstrate the full pipeline on simulated and real comparative genomic hybridization (CGH) data, validating its effectiveness and making novel predictions of major progression pathways and ancestral cell states in breast cancers...

..Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined...

..Our results suggest that a network correction approach improves estimates of tumor similarity, but sophisticated network models are needed to control for the large hypothesis space and sparse data currently available...

..The consensus tree approach thus provides a promising new model for the robust inference of substructure and ancestry from large-scale genetic variation data...

....

..Making phylogenetic predictions on the scale needed for whole-genome analysis is, however, extremely computationally demanding...

..Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters...

..The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved...

..Experimental analysis validates a prediction of the models that altering guanine nucleotide exchange factor expression levels will modulate Golgi size...

....

....

..These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions...

..The results demonstrate the ability of such data fitting to learn very different pathway types and show some of the versatility of pathways that may exist across real viruses...

..In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models...

..These techniques are also likely to have broader use in accelerating SSA models so as to apply them to systems and parameter ranges that are currently computationally intractable...

..The method and results have potential applications in cell and molecular biology as well as self-assembly for organic and inorganic systems...

..The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment...

..This prediction was supported by a demonstration that exogenous expression of the Golgi target SNARE syntaxin-5 alters Golgi size in living cells...

..The results suggest the importance of identifying the actual binding pattern if one is to build reliable models of capsid assembly or other complex self-assembly processes...

..Because molecular reactions are intrinsically stochastic and asynchronous, these findings may have broad implications in modelling and understanding complex biological systems...

..The gene targets of these two transcription factors are of considerable interest, since they may help develop hypotheses about how neural activity is coupled to changes in neural function...

..These conclusions have direct implications for cell shape and structure, as well as tumor cell migration...

..The third class of methods uses sequence profiles obtained by clustering known epitopes to score candidate peptides. By integrating these methods, using a simple voting heuristic, we achieve improved accuracy over the state of the art...

..These may prove to underlie differences in the ecology and behaviour of these diverse species...

....

..For purposes of SNP selection, it seems likely that methods that do not arbitrarily impose block boundaries among correlated SNPs might perform better than block-based methods...

..The primary conclusion is that some important simplified variants of the problem yield tractable problems while more general variants tend to be intractable in the worst case...

..The methods to be developed are likely to have broader applicability to solid tumor progression in general and to related problems of analyzing cell differentiation in mixed samples. ..

..The work will also have broader relevance to understanding virus assembly in general and to developing computer models useful in a broad range of biomedical modeling applications. ..