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Items: 20

1.

Improvisation in evolution of genes and genomes: whose structure is it anyway?

Shakhnovich BE, Shakhnovich EI.

Curr Opin Struct Biol. 2008 Jun;18(3):375-81. doi: 10.1016/j.sbi.2008.02.007. Epub 2008 May 17. Review.

2.

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI.

PLoS Comput Biol. 2007 Jul;3(7):e139.

3.

Defining functional distance using manifold embeddings of gene ontology annotations.

Lerman G, Shakhnovich BE.

Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11334-9. Epub 2007 Jun 26.

4.

Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

Reddy TE, DeLisi C, Shakhnovich BE.

PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10.

5.

Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.

Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi C.

Nucleic Acids Res. 2007;35(3):e20. Epub 2007 Jan 3.

6.

Structural similarity enhances interaction propensity of proteins.

Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI.

J Mol Biol. 2007 Feb 2;365(5):1596-606. Epub 2006 Nov 10.

7.

Origins and impact of constraints in evolution of gene families.

Shakhnovich BE, Koonin EV.

Genome Res. 2006 Dec;16(12):1529-36. Epub 2006 Oct 19.

8.
9.

Assessing transcription factor motif drift from noisy decoy sequences.

Reddy TE, DeLisi C, Shakhnovich BE.

Genome Inform. 2005;16(1):59-67.

PMID:
16362907
10.

Improving the precision of the structure-function relationship by considering phylogenetic context.

Shakhnovich BE.

PLoS Comput Biol. 2005 Jun;1(1):e9. Epub 2005 Jun 24. Erratum in: PLoS Comput Biol. 2005 Aug;1(3):244.

11.

Protein structure and evolutionary history determine sequence space topology.

Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E.

Genome Res. 2005 Mar;15(3):385-92.

12.

Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow.

Shakhnovich BE, Reddy TE, Galinsky K, Mellor J, Delisi C.

Genome Inform. 2004;15(1):221-8.

PMID:
15712124
13.

ELISA: a unified, multidimensional view of the protein domain universe.

Shakhnovich BE, Harvey JM, Delisi C.

Genome Inform. 2004;15(1):213-20.

PMID:
15712123
14.

Proteomic traces of speciation.

Deeds EJ, Shakhnovich B, Shakhnovich EI.

J Mol Biol. 2004 Feb 20;336(3):695-706.

PMID:
15095981
15.
16.

Imprint of evolution on protein structures.

Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2846-51. Epub 2004 Feb 17.

17.

ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.

Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E.

BMC Bioinformatics. 2003 Sep 2;4:34. Epub 2003 Sep 2.

18.

Natural selection of more designable folds: a mechanism for thermophilic adaptation.

England JL, Shakhnovich BE, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8727-31. Epub 2003 Jul 3.

19.

Functional fingerprints of folds: evidence for correlated structure-function evolution.

Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI.

J Mol Biol. 2003 Feb 7;326(1):1-9.

PMID:
12547186
20.

Expanding protein universe and its origin from the biological Big Bang.

Dokholyan NV, Shakhnovich B, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14132-6. Epub 2002 Oct 16.

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