Systems & Evolutionary Biology

M. Kim, Z. Zhang, H. Okano, D. Yan, A. Groisman, and T. Hwa.
"Need-based activation of ammonium uptake in Escherichia coli"
Mol. Syst. Biol. 8: 616 (2012). .

R. Hermsen, J. B. Deris, and T. Hwa
"On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient"
PNAS 109: 10775-10780 (2012). [Highlight from PNAS] [UC Health] [Physics Today Update]

J.I. Sulkowska, F. Morcos, M. Weigt, T. Hwa, and J.N. Onuchic.
"Genomics-aided structure prediction"
PNAS 109: 10340-10345 (2012).

X. Fu, L.H. Tang, C. Liu, J.D. Huang, T. Hwa, and P. Lenz
"Stripe formation in bacterial systems with density-suppresed motility",
Phys. Rev. Lett. 108 198102 (2012).

F. Morcos, A. Pagnini, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, and M. Weigt
"Direct-coupling analysis of residue co-evolution captures native contacts across many protein families",
PNAS 108: E1293-1301 (2011).

C. Liu, X. Fu, L. Liu, X. Ren, C.K.L. Chau, S. Li, L. Xiang, H. Zeng, G. Chen, L.H. Tang, P. Lenz, X. Cui, W. Huang, T. Hwa, and J.D. Huang
"Sequential establishment of stripe patterns in an expanding cell population"
Science 334: 238-241 (2011). [Science Daily], [Physics Today]

P. McHale, C. M. Mizutani, D. Kosman, D. L. MacKay, M. Belu, W. McGinnis, E. Bier, and T. Hwa.
"Differential response to a morphogen gradient mediated by gene-length associated transcriptional delay", [cover page]
Develop. Biol. 360: 230-40 (2011).

R. Hermsen, D.W. Erickson, and T. Hwa.
"Speed, sensitivity, and bistability in auto-activating signaling circuits"
PLoS Comp. Biol. 7: e1002265 (2011).

D. Yan, P. Lenz, and T. Hwa.
"Quantification of intracellular 2-oxoglutarate levels in E. coli: Overcoming fluctuation and leakage problems"
Appl. Environ. Microbiol. 77: 6763-6771 (2011).

Y. Hao, Z.J. Zhang, D.W. Erickson, M. Huang, Y. Huang, J. Li, T. Hwa, and H. Shi.
"Quantifying the sequence-function relation in gene silencing by bacterial small RNAs",
PNAS 108: 12473-8 (2011).

M. Scott and T. Hwa
"Bacterial growth laws and their applications",
Curr Opin Biotechnol. 22: 559-565 (2011).

A. Procaccini, B. Lunt, H. Szurmant, T. Hwa, and M. Weigt.
“Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and Crosstalks”,
PLoS One: e19729 (2011).

M. Scott, C. W. Gunderson, E. Mateescu, Z. Zhang and T. Hwa
"Interdependence of cell growth and gene expression: origins and consequences",
Science 330: 1099-1102 (2010). [Supporting Onilne Material]
[Perspective in Science], [Physics Today], [Chem & Engr News]

R. Hermsen and T. Hwa
"Sources and sinks: a stochastic model of evolution in heterogeneous environments",
Phys. Rev. Lett. 105: 248104 (2010). [highlight in Physics]

H. Okano, T. Hwa, P. Lenz, D. Yan
"Reversible Adenylylation of Glutamine Synthetase is Dynamically Counterbalanced during Steady-State Growth of Escherichia coli",
J. Mol. Biol. 404: 522-536 (2010).

A. Schug, M. Weigt, J.N. Onuchic, T. Hwa, and H. Szurmant
"High resolution protein complexes from integrating genomic information with molecular simulation",
PNAS 106: 22124-22129 (2009).

S. Klumpp, Z. Zhang and T. Hwa
"Growth-rate dependent global effects on gene expression in bacteria" ,
Cell 139: 1366-1375 (2009).

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).

S. Klumpp and T. Hwa
"Traffic patrol in the transcription of ribosomal RNA",
RNA Biology 6: 392-394 (2009).

U. Gerland and T. Hwa
"Evolutionary Selection Between Deifferent Modes of Gene Regulation",
PNAS 106 : 8841-6 (2009).

M. Weigt, R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
"Identification of direct residue contacts in protein-protein interaction by message passing"
PNAS 106 : 67-72 (2009).

S. Klumpp and T. Hwa
"Growth-rate dependent partitioning of RNA polymerases in bacteria",
PNAS 105: 20245-20250 (2008).

E. Levine and T. Hwa
"Small RNAs establish gene expression thresholds"
Current Opinion in Microbiology 11: 574-579 (2008).

S. Klumpp and T. Hwa
"Stochasticity and traffic jams in the transcription of ribosomal RNA: Novel role of termination and antitermination",
PNAS 105: 18159-18164 (2008).

J. Liu, A. Desai, J. N. Onuchic, T. Hwa
"An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis",
PNAS 105: 13752-7 (2008).

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" ,
PLoS Biol 5: e229 (2007).

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).

Bioinformatics & Genomics

A. Schug, M. Weigt, J. Hoch, J. Onuchic, T. Hwa and H. Szurmant
"Computational Modeling of Phosphotransfer Complexes in Two-Component Signaling"
Methods in Enzymology, 471: 43-58 (2010).

B. Lunt, H. Szurmant, A. Procaccini, J. Hoch, T. Hwa, and M. Weigt,
"Inference of Direct Residue Contacts in Two-Component Signaling"
Methods in Enzymology, 471: 17-41 (2010).

M. Weigt, R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
"Identification of direct residue contacts in protein-protein interaction by message passing"
PNAS 106 : 67-72 (2009).

R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
"Features of Protein-protein Interactions in Two-component Signaling deduced from Genomic Libraraies "
Methods in Enzymology 422: 75-101 (2007).

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]

Molecular Biophysics

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).

Statistical Physics

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).
 
 

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