Leonid A. Mirny

Using orthologous and paralogous proteins to identify specificity determining residues.

Structural analysis of conserved base pairs in protein-DNA complexes.

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases.

Protein complexes and functional modules in molecular networks.

Diffusion in correlated random potentials, with applications to DNA.

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.

CoC: a database of universally conserved residues in protein folds.

A metabolic network in the evolutionary context: multiscale structure and modularity.

Using the topology of metabolic networks to predict viability of mutant strains.

Intricate knots in proteins: Function and evolution.

Zfx controls the self-renewal of embryonic and hematopoietic stem cells.

Protein knot server: detection of knots in protein structures.

How gene order is influenced by the biophysics of transcription regulation.

Operating regimes of signaling cycles: statics, dynamics, and noise filtering.

Tumor suppressor p53 slides on DNA with low friction and high stability.

Spatial effects on the speed and reliability of protein-DNA search.

Predicting transcription factor specificity with all-atom models.

Using evolutionary information to find specificity-determining and co-evolving residues.

Using genome-wide measurements for computational prediction of SH2-peptide interactions.

Different gene regulation strategies revealed by analysis of binding motifs.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

A Stevedore's protein knot.

Quantitative characterization of filament dynamics by single-molecule lifetime measurements.

Nucleosome-mediated cooperativity between transcription factors.

A single-molecule characterization of p53 search on DNA.

The fractal globule as a model of chromatin architecture in the cell.

Dancing on DNA: kinetic aspects of search processes on DNA.

Bridging the resolution gap in structural modeling of 3D genome organization.

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.