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Systems & Evolutionary
Biology
S. Klumpp and T. Hwa
"Growth-rate dependent partitioning of RNA polymerases in
bacteria",
[supplemental information]
(in submission).
S. Klumpp and T. Hwa
"Stochasticity and traffic jams in the transcription of ribosomal
RNA: Novel role of termination and antitermination",
[supplemental information]
(in submission).
E. Levine, M. Huang, Y.W. Huang, T. Kuhlman, H. Shi, Z. Zhang, and T.
Hwa
"On Noise and Silence in small RNA regulation",
(in submission).
U. Gerland and T. Hwa
"Evolutionary Selection Between Deifferent Modes of Gene Regulation",
(in submission).
J. Liu, A. Desai, J. N. Onuchic, T. Hwa
"A Mechano-biochemical mechanism for Mono-oriented Chromosome Oscillation
in Mitosis",
PNAS 104: 16104-9 (2007).
G. Fritz, N.E. Buchler, T. Hwa, and U. Gerland
"A Genetic
Circuit for Epigenetic Memory"
Syst Synth Biol 1: 89-98 (2007).
E. Levine, Z. Zhang, T. Kuhlman, and T. Hwa
"Quantitative
Characteristics of Gene Regulation Mediated by small RNA" , [supplementary
information]
PLoS Biol 5: e229.
E. Levine and T. Hwa
"Stochastic Fluctuations in Metabolic Pathways"
PNAS 104: 9244-9249 (2007).
M. Scott, T. Hwa, B. Ingalls
"Deterministic Characterization of Stochastic Genetic Circuits"
PNAS 104: 7402-7407 (2007).
T. Kuhlman, Z. Zhang, M. Saier, Jr, and T. Hwa
"Quantitative
Characterization of Combinatorial Transcriptional Control of the
lactose operon of E. coli"
PNAS 104: 6043-6048 (2007).
N.E. Buchler, U. Gerland, and T. Hwa
"Nonlinear protein degradation
on the funtions of genetic circuits"
PNAS 102 : 9559-9564 (2005).
L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev,
T. Kuhlman, R. Philips
"Transcriptional Regulation by the Numbers: Applications"
Curr. Op. Genet. Dev. 15 : 125-135 (2005).
L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev, R.
Philips
"Transcriptional Regulation by the Numbers: Models"
Curr. Op. Genet. Dev. 15 : 116-124 (2005).
T. Hwa
"A genetic switch: New lessons from a classic system"
Science 305: 345 (2004).
W. Peng, H. Levine, T. Hwa, and David A. Kessler
"Analytical
study of the effect of recombination on evolution via DNA shuffling"
Phys. Rev. E 69: 051911 (2004).
N. Buchler, U. Gerland and T. Hwa
"On Schemes of
Combinatorial Transcription Control"
PNAS 100: 5136-5141 (2003).
W. Peng, U. Gerland, T. Hwa and H. Levine,
"Dynamics of
Competitive Evolution on a Smooth Landscape"
Phys. Rev. Lett. 90: 088103 (2003).
U. Gerland and T. Hwa
"On the
Selection and Evolution of Regulatory DNA Motifs"
J. Mol. Evol 55: 386-400 (2002).
U. Gerland, J.D. Moroz and T. Hwa,
"Physical
Constraints and Functional Characteristics of Transcription Factor-DNA
Interaction"
PNAS 99: 12015-12020 (2002).
R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
"Spatial details of transient protein interactions in bacterial
two-component signaling pathways deduced from genomic libraries",
"[Supplementary
Figures]"
(submitted, 2007).
R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
"Features
of Protein-protein Interactions in Two-component Signaling deduced from
Genomic Libraraies "
M. Lipatov, P.F. Arndt, T. Hwa, and D.A. Petrov
"A
Novel Method Distinguishes Between Mutation Rates and Fixation
Biases
in Patterns of Single-Nucleotide Substitution"
J. Mol. Evol. 62:
168-175 (2006).
P.F. Arndt, T. Hwa, and D.A. Petrov
"Substantial regional variation in substitution rates in the human
genome:
importance of GC content, gene density and telomere-specfic effects"
J. Mol. Evol. 60:
748-763 (2005).
P.F. Arndt and T. Hwa
"Identification and Measurement of Neighbor Dependent Nucleotide
Substitution Processes"
Bioinformatics 21: 2322-2328 (2005).
P.F. Arndt and T. Hwa
"Regional and time-resolved mutation patterns of the human genome"
Bioinformatics 20: 1482-1485 (2004).
P.F. Arndt, D.A. Petrov and T. Hwa
"Distinct
changes of genomic biases in nucleotide substitution at the time of
mammalian radiation"
Mol. Biol. Evol. 20: 1887-1896 (2003).
P.F. Arndt, C.B. Burge and T. Hwa,
"DNA Sequence
Evolution with Neighbor-Dependent Mutation"
J Comput Biol. 10: 313-22 (2003).
Y.-k. Yu, R. Bundschuh, and T. Hwa,
"Hybrid
Alignment: High Performance with Universal Statistics"
Bioinformatics 18: 865-872 (2002).
R. Sasik, N. Iranfar, T. Hwa, W.F. Loomis,
"Extracting
Transcriptional Events from the Temporal Gene Expression Patterns
during
Dictyostelium Development"
Bioinformatics 18: 61-66 (2002).
Y.-k. Yu, R. Bundschuh, and T. Hwa,
"Statistical
Significance and Extreme Ensemble of Gapped Local Hybrid Alignment"
in Biological Evolution and Statistical Physics (Lecture Notes in
Physics, vol 585)
M. Lassig and A. Valleriani eds., 3-21 (Springer-Verlag, Berlin,
2002).
N. Iranfar, D. Fuller, R. Sasik, T. Hwa, M. Laub, W.F. Loomis,
"Expression
Patterns of Cell-type Specific Genes in Dictyostelium"
Mol. Biol. Cell 12: 2590-2600 (2001).
R. Sasik, T. Hwa, N. Iranfar, and W. F. Loomis,
"Percolation
Clustering: A Novel Approach Applied to the Clustering
of Gene Expression Patterns in Dictyostelium Development"
Proceedings of the Pacific Symposium on Biocomputing,
R. B. Altman et al. eds, 335-347 (World Scientific, Singapore,
2001).
Y.-k. Yu and T. Hwa,
"Statistical
Significance of Probabilistic Sequence Alignment and Related Local
Hidden Markov Models"
J. Comp. Biol. 8, 249-282 (2001).
S. Altschul, R. Bundschuh, R. Olsen and T. Hwa,
"The
Estimation of Statistical Parameters for Local Alignment Score
Distributions"
Nucleic Acids Research 29, 351--361 (2001).
D. Drasdo, T. Hwa and M. Lassig,
"Scaling Laws and
Similarity Detection in Sequence Alignment with Gaps"
J. Comp. Biol. 7 , 115-141 (2001).
R. Bundschuh and T. Hwa,
"An
Analytical Study of the Phase Transition Line in Local Sequence
Alignment with Gaps"
Discrete Applied Math. 104, 113-142, (2000).
T. Hwa,
"From
Mesoscopic Vortex Physics to Genomics"
Nature 399, 17-19 (1999).
R. Olsen, R. Bundschuh and T. Hwa,
"Rapid
Assessment of Extremal Statistics for Gapped Local Alignment"
in Proceedings of The Seventh International Conference on
Intelligent Systems for Molecular Biology (ISMB99),
T. Lengauer et al. eds., 211--222 (AAAI Press, Menlo Park,
1999).
R. Olsen, T. Hwa and M. Lassig,
"Optimizing
Smith-Waterman Alignments"
in Pacific Symposium on Biocomputing 4, 302-313 (1999).
D. Drasdo, T. Hwa and M. Lassig,
"A
Statistical Theory of Sequence Alignment with Gaps"
in Proceedings of The Sixth International Conference on Intelligent
Systems for Molecular Biology (ISMB98),
J. Glasnow et al. eds, 52-58 (AAAI Press, Menlo Park, 1998).
T. Hwa and M. Lassig,
"Optimal
Detection of Sequence Similarity by Local Alignment"
in Proceedings of the Second Annual International Conference on
Computational Molecular Biology (RECOMB98),
S. Istrail, P. Pevzner, and M.S. Waterman eds, 109-116 (ACM Press,
1998).
T. Hwa,
"From Flux Pinning to DNA Sequence Alignment",
Quantum Coherence and Decoherence, K. Fujikawa and Y. A. Ono
eds,
109-114 (Elsevier, Amsterdam, 1996).
[Abstract in
HTML format] [Document
in Postscript format]
T. Hwa and M. Lassig,
"Similarity-Detection and Localization,"
Phys. Rev. Lett. 76, 2591-2594 (1996).
[Abstract in
HTML format] [Document
in Postscript format]
U. Gerland, R. Bundschuh, T. Hwa
"Using nanopores
to learn RNA structures"
Phys. Biol. 1: 19-27, (2004).
U. Gerland, R. Bundschuh and T. Hwa,
"Mechanically
probing the folding pathway of single RNA molecules"
Biophys. J. 84: 2831-2840 (2003).
T. Hwa, E. Marinari, K. Sneppen and L.-H. Tang,
"Localization
of denaturation bubbles in heterogeneous DNA sequences"
PNAS 100: 4411-4416 (2003).
R. Bundschuh and T. Hwa,
"Statistical
Mechanics of secondary structures formed by random RNA sequences"
Phys. Rev. E 65: 031903 (2002).
R. Bundschuh and T. Hwa,
"Phases
of the Secondary Structures of RNA Sequences"
Europhys. Lett. 59: 903-909 (2002).
U. Gerland, R. Bundschuh, and T. Hwa,
"Force-induced
Denaturation of RNA"
Biophys. J. 81, 1324-1332 (2001).
R. Bundschuh and T. Hwa,
"RNA
Structure Formation: A Solvable Model of Heteropolymer Folding"
Phys. Rev. Lett. 83, 1479-1482 (1999).
D. Cule and T. Hwa,
"Polymer
Reptation in Disordered Media",
Phys. Rev. Lett. 80,
3145-3148 (1998).
D. Cule and T. Hwa,
"Denaturation
of Heterogeneous DNA",
Phys. Rev. Lett. 79,
2375-2378 (1997).
C. Zeng, P. Leath and T. Hwa,
"Universal
Susceptibility Variations in 1+1 Dimensional Vortex Glass"
Physica C 332, 232-236 (2000).
B. Boghosian, C.C. Chow and T. Hwa,
"Hydrodynamics of
the Kuramoto-Sivashinsky Equation in Two Dimensions"
Phys. Rev. Lett. 83, 5262-5265 (1999).
C. Zeng, P. Leath and T. Hwa,
"Thermodynamics
of Mesoscopic Vortex Systems in 1+1 Dimensions"
Phys. Rev. Lett. 83, 4860-4863 (1999).
D. Cule and T. Hwa,
"Static and
Dynamic Properties of Inhomogeneous Elastic Media on Disordered
Substrate",
Phys. Rev. B 57,
8235-8253 (1998).
M.A. Munoz and T. Hwa,
"On Nonlinear
Diffusion with Multiplicative Noise",
Europhys. Lett. 41, 147-152 (1998).
T. Hwa and D. Cule,
"Polymer
Adsorption on Disordered Substrates"
Phys. Rev. Lett. 79,
4930 (1997).
J. Kierfeld, T. Natterman and T. Hwa,
"Topological Order in Vortex Glass Phases of Type-II Superconductors,"
Phys. Rev. B 55,
626-629 (1997).
[Abstract in
HTML format] [Document
in Postscript format]
J. Kierfeld and T. Hwa,
"Interacting Arrays of Steps and Lines in Random Media,"
Phys. Rev. Lett. 77,
4233-4236 (1996).
[Abstract in
HTML format] [Document
in Postscript format]
D. Cule and T. Hwa,
"Tribology of Sliding Elastic Media,"
Phys. Rev. Lett. 77,
278-281 (1996).
[Abstract in
HTML format] [Document
in Postscript format]
E. Frey, U. C. Tauber and T. Hwa,
"Mode-Coupling and Renormalization Group Results for the noisy-Burgers'
Equations,"
Phys. Rev. E 53,
4424-4438 (1996).
[Abstract in
HTML format] [Document
in Postscript format]
C. C. Chow and T. Hwa,
"Defect-Mediated Stability: An Effective Hydrodynamic Theory of
Spatio-Temporal Chaos,"
Physica D 84, 494-512
(1995).
[Abstract in HTML
format] [Document
in Postscript format]
T. Hwa,
"Flux Pinning in High-Temperature Superconductors,"
McGraw-Hill 1995 Yearbook on Science & Technology .
[Abstract in
HTML format] [Document
in Postscript format]
T. Hwa and T. Nattermann,
"Disorder-Induced Depinning Transition,"
Phys. Rev. B 51,
455-469 (1995).
[Abstract in
HTML format] [Document
in Postscript format]
G. G. Batrouni and T. Hwa,
"Dynamic and Static Properties of Randomly Pinned Planar Flux Array,"
Phys. Rev. Lett. 72,
4133-4136 (1994).
[Abstract in
HTML format] [Document
in Postscript format]
T. Hwa and D. S. Fisher,
"Vortex Glass Phase and Universal Susceptibility Variations in Planar
Arrays of Flux Lines,"
Phys. Rev. Lett. 72,
2466-2469 (1994).
[Abstract in HTML
format] [Document
in Postscript format]
T. Hwa and D. S. Fisher,
"Anomalous Fluctuations of Directed Polymers in Random Media,"
Phys. Rev. B 49,
3136-3154 (1994).
[Abstract in HTML
format] [Document
in Postscript format]
T. Hwa, P. le Doussal, D. R. Nelson and V. M. Vinokur,
"Enhanced Flux Pinning and Forced Entanglement in High Temperature
Superconductors with Randomly Splayed Columnar Defects,"
Phys. Rev. Lett. 71,
3545-3548 (1993).
[Abstract in
HTML format] [Document
in Postscript format]
T. Hwa, D. R. Nelson and V. M. Vinokur,
"Flux Line Pinning by Competing Disorders,"
Phys. Rev. B 67, 1167-1174 (1993).
M. Paczuski, M. Barma, S. N. Majumdar and T. Hwa,
"Fluctuations of a Stationary Nonequilibrium Interface,"
Phys. Rev. Lett. 69,
2735 (1992).
T. Hwa,
"Nonequilibrium Dynamics of Driven Line Liquids,"
Phys. Rev. Lett. 69,
1552-1555 (1992).
G. Grinstein, T.Hwa and H.J. Jensen,
"1/f-Noise in Dissipative Transport,"
Phys. Rev. A 45,
R559-562 (1992).
X. Wen, C. W. Garland, T. Hwa, M. Kardar, E. Kokufuta, Y. Li, M.
Orkisz and T. Tanaka,
"Crumpled and Collapsed Conformations in Solid Membranes,"
Nature 355, 426
(1992).
T. Hwa and M. Kardar,
"Avalanches, Hydrodynamics, and Great Events in Models of Sandpiles,"
Phys. Rev. A 45, 7002
(1992).
T. Hwa, M. Kardar and M. Paczuski,
"Growth-Induced Roughening of Crystalline Facets,"
Phys. Rev. Lett. 66,
441-444 (1991).
T. Hwa, E. Kokufuta and T. Tanaka,
"Conformation of Graphite-Oxide Membranes in Solution,"
Phys. Rev. A 44,
R2235-2238 (1991).
B. Duplantier, T. Hwa and M. Kardar,
"Renormalizability of the Self-Avoiding Tethered Manifolds,"
Phys. Rev. Lett. 64,
2022-2025 (1990).
T. Hwa,
"Exploring the Generalized epsilon-expansion for Self-Avoiding Tethered
Manifolds,"
Phys. Rev. A 41,
1751-1755 (1990).
T. Hwa and M. Kardar,
"Dissipative Transport in Open Systems: An Investigation of
Self-Organized Criticality,"
Phys. Rev. Lett. 62,
1813-1816 (1989).
E. Medina, T. Hwa, M. Kardar and Y.-C. Zhang,
"Renormalization-Group Studies of the Burgers' Equation with Correlated
Noise,"
Phys. Rev. A 39 ,
3053 (1989).
T. Hwa and M. Kardar,
"Evolution of Surface Patterns on Swelling Gels,"
Phys. Rev. Lett. 61,
106-109 (1988).