Publications

Book: Physical Biology of the Cell
By Rob Phillips, Jane Kondev, Julie Theriot, Hernan Garcia

2016

Bacterial RNA polymerase can retain σ70 throughout transcription.
Harden, T.T. et al.
PNAS 113, 602-607 (2016).

2015

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules
Sandeep Choubey, Jane Kondev, Alvaro Sanchez
PLoS Comput Biol. 2015 November; 11(11): e1004345.

Antenna Mechanism of Length Control of Actin Cables
Lishibanya Mohapatra, Bruce L. Goode, Jane Kondev
PLoS Comput Biol. 2015 June;11(6): e1004160.

2014

A general mechanism for competitor-induced dissociation of molecular complexes
Thayaparan Paramanathan, Daniel Reeves, Larry J. Friedman, Jane Kondev, Jeff Gelles
Nat Commun. 2014; 5: 5207.

Effect of Chromosome Tethering on Nuclear Organization in Yeast
Barış Avşaroğlu, Gabriel Bronk, Susannah Gordon-Messer, Jungoh Ham, Debra A. Bressan, James E. Haber, Jane Kondev
PLoS One. 2014; 9(7): e102474.

2013

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria
Hernan G. Garcia, Alvaro Sanchez, James Q. Boedicker, Melisa Osborne, Jeff Gelles, Jane Kondev, Rob Phillips
Cell Rep. 2012 July 26; 2(1): 150–161.

2011

Dynamics of Homology Searching During Gene Conversion in Saccharomyces cerevisiae Revealed by Donor Competition
Eric Coïc, Joshua Martin, Taehyun Ryu, Sue Yen Tay, Jané Kondev, James E. Haber
Genetics. 2011 December; 189(4): 1225–1233.

Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules
Alvaro Sanchez, Melisa L Osborne, Larry J Friedman, Jane Kondev, Jeff Gelles
EMBO J. 2011 October 5; 30(19): 3940–3946.

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression
Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, Rob Phillips, Jané Kondev
PLoS Comput Biol. 2011 March; 7(3): e1001100.

Thermodynamics of Biological Processes
Hernan G. Garcia, Jane Kondev, Nigel Orme, Julie A. Theriot, Rob Phillips
Methods Enzymol. 2011; 492: 27–59.

2010

Transcription by the Numbers Redux: Experiments and Calculations that Surprise
Hernan G. Garcia, Alvaro Sanchez, Thomas Kuhlman, Jane Kondev, Rob Phillips
Trends Cell Biol. 2010 December; 20(12): 723–733.

Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
Paul A. Wiggins, Keith C. Cheveralls, Joshua S. Martin, Robert Lintner, Jané Kondev
Proc Natl Acad Sci U S A. 2010 March 16; 107(11): 4991–4995.

2009

Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Eric L. Peterson, Jané Kondev, Julie A. Theriot, Rob Phillips
Bioinformatics. 2009 June 1; 25(11): 1356–1362.

2008

Membrane mechanics as a probe of ion-channel gating mechanisms
Daniel Reeves, Tristan Ursell, Pierre Sens, Jane Kondev, Rob Phillips
Phys Rev E Stat Nonlin Soft Matter Phys. 2008 October; 78(4 Pt 1): 041901

Transcriptional control of noise in gene expression
Álvaro Sánchez, Jané Kondev
Proc Natl Acad Sci U S A. 2008 April 1; 105(13): 5081–5086.

2007

Biological Consequences of Tightly Bent DNA: The Other Life Biological of a Macromolecular Celebrity
Hernan G. Garcia, Paul Grayson, Lin Han, Mandar Inamdar, Jané Kondev, Philip C. Nelson, Rob Phillips, Jonathan Widom, Paul A. Wiggins
Biopolymers. 2007 February 5; 85(2): 115–130.

2005

Transcriptional regulation by the numbers: models
Lacramioara Bintu, Nicolas E Buchler, Hernan G Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Rob Phillips
Curr Opin Genet Dev. 2005 April; 15(2): 116–124.

Transcriptional regulation by the numbers: applications
Lacramioara Bintu, Nicolas E Buchler, Hernan G Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Thomas Kuhlman, Rob Phillips
Curr Opin Genet Dev. 2005 April; 15(2): 125–135.

Forces during Bacteriophage DNA Packaging and Ejection
Prashant K. Purohit, Mandar M. Inamdar, Paul D. Grayson, Todd M. Squires, Jané Kondev, Rob Phillips
Biophys J. 2005 February; 88(2): 851–866.

2003

Mechanics of DNA packaging in viruses
Prashant K. Purohit, Jané Kondev, Rob Phillips
Proc Natl Acad Sci U S A. 2003 March 18; 100(6): 3173–3178.