Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Boris E. Shakhnovich"'
Publikováno v:
PLoS Computational Biology, Vol 3, Iss 7, p e139 (2007)
In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the mod
Externí odkaz:
https://doaj.org/article/dfa9b5f3e1ac4fa087478d7a02aba0f2
Publikováno v:
PLoS Computational Biology, Vol 3, Iss 5, p e90 (2007)
Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for research in gene regulation, a major mechanism controlli
Externí odkaz:
https://doaj.org/article/d71a33e2ae1f456b919e547c0a4c4058
Autor:
Boris E Shakhnovich
Publikováno v:
PLoS Computational Biology, Vol 1, Iss 3 (2005)
Externí odkaz:
https://doaj.org/article/edd3b98955fa4ef5b9ae7ec14e1495dd
Autor:
Boris E Shakhnovich
Publikováno v:
PLoS Computational Biology, Vol 1, Iss 1, p e9 (2005)
Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current limitations of annotation. Howe
Externí odkaz:
https://doaj.org/article/fdddaf496cb44bc8a34bb3bc88e119ce
Publikováno v:
Current Opinion in Structural Biology. 18:375-381
Significant progress has been made in recent years in a variety of seemingly unrelated fields such as sequencing, protein structure prediction, and high-throughput transcriptomics and metabolomics. At the same time, new microscopic models have been d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::925084c9f318bc487bef5b62ce1eeda8
https://doi.org/10.1016/j.sbi.2008.02.007
https://doi.org/10.1016/j.sbi.2008.02.007
Autor:
Gilad Lerman, Boris E. Shakhnovich
Publikováno v:
Proceedings of the National Academy of Sciences. 104:11334-11339
Although rigorous measures of similarity for sequence and structure are now well established, the problem of defining functional relationships has been particularly daunting. Here, we present several manifold embedding techniques to compute distances
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f37eed84b9b4da35bd32de7d1dd7b99
https://doi.org/10.1073/pnas.0702965104
https://doi.org/10.1073/pnas.0702965104
Autor:
Boris E. Shakhnovich, Eugene V. Koonin
Publikováno v:
Genome Research. 16:1529-1536
Recent investigations of high-throughput genomic and phenomic data have uncovered a variety of significant but relatively weak correlations between a gene’s functional and evolutionary characteristics. In particular, essential genes and genes with
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce6f978bd58f5976e44469a7b793e3db
https://doi.org/10.1101/gr.5346206
https://doi.org/10.1101/gr.5346206
Autor:
Boris E. Shakhnovich
Publikováno v:
ISMB (Supplement of Bioinformatics)
Analysis of increasingly saturated sequence databases have shown that gene family sizes are highly skewed with many families being small and few containing many, far-diverged homologs. Additionally, recently published results have identified a struct
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e4582974ff4b90b2f09b41442b1a7497
https://doi.org/10.1093/bioinformatics/btl211
https://doi.org/10.1093/bioinformatics/btl211
Publikováno v:
Genome Research. 15:385-392
Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function, gene duplication, pseudogene formation, and possibly
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c3ac8440f57dffa6f74778ac5b4ebf2
https://doi.org/10.1101/gr.3133605
https://doi.org/10.1101/gr.3133605
Publikováno v:
Proceedings of the National Academy of Sciences. 101:2846-2851
We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence dupl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d78c31dcbd0acf71c1fe629655fb5d7b
https://doi.org/10.1073/pnas.0306638101
https://doi.org/10.1073/pnas.0306638101