List of works - Boris Shakhnovich

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

scientific article

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

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

List of works by Boris Shakhnovich

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

Assessing transcription factor motif drift from noisy decoy sequences.

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

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

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

Defining functional distance using manifold embeddings of gene ontology annotations

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

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

Expanding protein universe and its origin from the biological Big Bang

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

Imprint of evolution on protein structures.

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

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

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

Origins and impact of constraints in evolution of gene families

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

Protein structure and evolutionary history determine sequence space topology

Proteomic traces of speciation

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