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List of works by Boris Shakhnovich

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

scientific article published in July 2007

Assessing transcription factor motif drift from noisy decoy sequences.

scientific article published on January 2005

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

scientific article published on 10 April 2007

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

scientific article published in January 2004

Correction: Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context

scientific article

Defining functional distance using manifold embeddings of gene ontology annotations

scholarly article

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

scientific article

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

scientific article

Expanding protein universe and its origin from the biological Big Bang

scientific article

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

scientific article published on February 2003

Imprint of evolution on protein structures.

scientific article

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

scientific article

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

scientific article

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

scientific article

Origins and impact of constraints in evolution of gene families

scientific article

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

scientific article published on 3 January 2007

Protein structure and evolutionary history determine sequence space topology

scientific article

Proteomic traces of speciation

scientific article published in February 2004

Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation

scientific article published in April 2004

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