Division of Health Sciences and Technology,
Department of Physics
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Using orthologous and paralogous proteins to identify specificity determining residues.
Genome biology , 2002 | Pubmed ID: 11897020
Structural analysis of conserved base pairs in protein-DNA complexes.
Nucleic acids research Apr, 2002 | Pubmed ID: 11917033
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.
Journal of molecular biology Aug, 2002 | Pubmed ID: 12139929
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2003 | Pubmed ID: 12679523
Protein complexes and functional modules in molecular networks.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2003 | Pubmed ID: 14517352
Diffusion in correlated random potentials, with applications to DNA.
Physical review. E, Statistical, nonlinear, and soft matter physics Jun, 2004 | Pubmed ID: 15244613
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
Biophysical journal Dec, 2004 | Pubmed ID: 15465864
CoC: a database of universally conserved residues in protein folds.
Bioinformatics (Oxford, England) May, 2005 | Pubmed ID: 15746286
A metabolic network in the evolutionary context: multiscale structure and modularity.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2006 | Pubmed ID: 16731630
Using the topology of metabolic networks to predict viability of mutant strains.
Biophysical journal Sep, 2006 | Pubmed ID: 16782788
Intricate knots in proteins: Function and evolution.
PLoS computational biology Sep, 2006 | Pubmed ID: 16978047
Zfx controls the self-renewal of embryonic and hematopoietic stem cells.
Cell Apr, 2007 | Pubmed ID: 17448993
Protein knot server: detection of knots in protein structures.
Nucleic acids research Jul, 2007 | Pubmed ID: 17517776
How gene order is influenced by the biophysics of transcription regulation.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2007 | Pubmed ID: 17709750
Operating regimes of signaling cycles: statics, dynamics, and noise filtering.
PLoS computational biology Dec, 2007 | Pubmed ID: 18159939
Tumor suppressor p53 slides on DNA with low friction and high stability.
Biophysical journal Jul, 2008 | Pubmed ID: 18424488
Spatial effects on the speed and reliability of protein-DNA search.
Nucleic acids research Jun, 2008 | Pubmed ID: 18453629
Predicting transcription factor specificity with all-atom models.
Nucleic acids research Nov, 2008 | Pubmed ID: 18829719
Using evolutionary information to find specificity-determining and co-evolving residues.
Methods in molecular biology (Clifton, N.J.) , 2009 | Pubmed ID: 19381538
Using genome-wide measurements for computational prediction of SH2-peptide interactions.
Nucleic acids research Aug, 2009 | Pubmed ID: 19502496
Different gene regulation strategies revealed by analysis of binding motifs.
Trends in genetics : TIG Oct, 2009 | Pubmed ID: 19815308
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science (New York, N.Y.) Oct, 2009 | Pubmed ID: 19815776
A Stevedore's protein knot.
PLoS computational biology Apr, 2010 | Pubmed ID: 20369018
Quantitative characterization of filament dynamics by single-molecule lifetime measurements.
Methods in cell biology , 2010 | Pubmed ID: 20466154
Nucleosome-mediated cooperativity between transcription factors.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2010 | Pubmed ID: 21149679
A single-molecule characterization of p53 search on DNA.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2011 | Pubmed ID: 21178072
The fractal globule as a model of chromatin architecture in the cell.
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology Jan, 2011 | Pubmed ID: 21274616
Dancing on DNA: kinetic aspects of search processes on DNA.
Chemphyschem : a European journal of chemical physics and physical chemistry Jun, 2011 | Pubmed ID: 21560221
Bridging the resolution gap in structural modeling of 3D genome organization.
PLoS computational biology Jul, 2011 | Pubmed ID: 21779160
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.
Nature biotechnology Dec, 2011 | Pubmed ID: 22101486
Nynke L. van Berkum*,1,
Erez Lieberman-Aiden*,2,3,4,5,
Louise Williams*,2,
Maxim Imakaev6,
Andreas Gnirke2,
Leonid A. Mirny3,6,
Job Dekker1,
Eric S. Lander2,7,8
1Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,
2, Broad Institute of Harvard and Massachusetts Institute of Technology,
3Division of Health Sciences and Technology, Massachusetts Institute of Technology,
4Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University ,
5Department of Applied Mathematics, Harvard University ,
6Department of Physics, Massachusetts Institute of Technology,
7Department of Systems Biology, Harvard Medical School,
8Department of Biology, Massachusetts Institute of Technology
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