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Terence Tai-Li 'Terry' Hwa, PhD - Publications

Affiliations: 
Physics University of California, San Diego, La Jolla, CA 
Area:
quantitative biology, biological physics, statistical mechanics
Website:
https://matisse.ucsd.edu/principal-investigator-terry-hwa/
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80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Basan M, Honda T, Christodoulou D, Hörl M, Chang YF, Leoncini E, Mukherjee A, Okano H, Taylor BR, Silverman JM, Sanchez C, Williamson JR, Paulsson J, Hwa T, Sauer U. A universal trade-off between growth and lag in fluctuating environments. Nature. PMID 32669712 DOI: 10.1038/S41586-020-2505-4  0.356
2020 Zheng H, Bai Y, Jiang M, Tokuyasu TA, Huang X, Zhong F, Wu Y, Fu X, Kleckner N, Hwa T, Liu C. General quantitative relations linking cell growth and the cell cycle in Escherichia coli. Nature Microbiology. PMID 32424336 DOI: 10.1038/S41564-020-0717-X  0.332
2019 Cremer J, Honda T, Tang Y, Wong-Ng J, Vergassola M, Hwa T. Chemotaxis as a navigation strategy to boost range expansion. Nature. PMID 31695195 DOI: 10.1038/S41586-019-1733-Y  0.318
2019 Zhu M, Mori M, Hwa T, Dai X. Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination. Nature Microbiology. PMID 31451774 DOI: 10.1038/S41564-019-0543-1  0.353
2019 Warren MR, Sun H, Yan Y, Cremer J, Li B, Hwa T. Spatiotemporal establishment of dense bacterial colonies growing on hard agar. Elife. 8. PMID 30855227 DOI: 10.7554/Elife.41093  0.356
2018 Dai X, Zhu M, Warren M, Balakrishnan R, Okano H, Williamson JR, Fredrick K, Hwa T. Slowdown of Translational Elongation inunder Hyperosmotic Stress. Mbio. 9. PMID 29440576 DOI: 10.1128/Mbio.02375-17  0.308
2017 Mori M, Schink S, Erickson DW, Gerland U, Hwa T. Quantifying the benefit of a proteome reserve in fluctuating environments. Nature Communications. 8: 1225. PMID 29089487 DOI: 10.1038/S41467-017-01242-8  0.329
2017 Erickson DW, Schink SJ, Patsalo V, Williamson JR, Gerland U, Hwa T. A global resource allocation strategy governs growth transition kinetics of Escherichia coli. Nature. PMID 29072300 DOI: 10.1038/Nature24299  0.364
2017 Cremer J, Arnoldini M, Hwa T. Effect of water flow and chemical environment on microbiota growth and composition in the human colon. Proceedings of the National Academy of Sciences of the United States of America. PMID 28588144 DOI: 10.1073/Pnas.1619598114  0.304
2016 Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Nature Microbiology. 2: 16231. PMID 27941827 DOI: 10.1038/Nmicrobiol.2016.231  0.351
2016 Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT, Zhang Z, Gutierrez E, Groisman A, Hwa T. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 27681630 DOI: 10.1073/Pnas.1601306113  0.302
2016 Mori M, Hwa T, Martin OC, De Martino A, Marinari E. Constrained Allocation Flux Balance Analysis. Plos Computational Biology. 12: e1004913. PMID 27355325 DOI: 10.1371/Journal.Pcbi.1004913  0.336
2015 Basan M, Zhu M, Dai X, Warren M, Sévin D, Wang YP, Hwa T. Inflating bacterial cells by increased protein synthesis. Molecular Systems Biology. 11: 836. PMID 26519362 DOI: 10.15252/Msb.20156178  0.316
2015 Hermsen R, Okano H, You C, Werner N, Hwa T. A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Molecular Systems Biology. 11: 801. PMID 25862745 DOI: 10.15252/Msb.20145537  0.303
2015 Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Molecular Systems Biology. 11: 784. PMID 25678603 DOI: 10.15252/Msb.20145697  0.348
2014 Scott M, Klumpp S, Mateescu EM, Hwa T. Emergence of robust growth laws from optimal regulation of ribosome synthesis. Molecular Systems Biology. 10: 747. PMID 25149558 DOI: 10.15252/Msb.20145379  0.375
2014 Klumpp S, Hwa T. Bacterial growth: Global effects on gene expression, growth feedback and proteome partition Current Opinion in Biotechnology. 28: 96-102. PMID 24495512 DOI: 10.1016/J.Copbio.2014.01.001  0.362
2013 Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T. The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science (New York, N.Y.). 342: 1237435. PMID 24288338 DOI: 10.1126/Science.1237435  0.75
2013 Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T. The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science (New York, N.Y.). 342: 1237435. PMID 24288338 DOI: 10.1126/Science.1237435  0.75
2013 Klumpp S, Scott M, Pedersen S, Hwa T. Molecular crowding limits translation and cell growth Proceedings of the National Academy of Sciences of the United States of America. 110: 16754-16759. PMID 24082144 DOI: 10.1073/Pnas.1310377110  0.352
2013 You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T. Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature. 500: 301-6. PMID 23925119 DOI: 10.1038/Nature12446  0.422
2013 You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T. Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature. 500: 301-6. PMID 23925119 DOI: 10.1038/Nature12446  0.422
2012 Klumpp S, Dong J, Hwa T. On Ribosome Load, Codon Bias and Protein Abundance Plos One. 7. PMID 23144899 DOI: 10.1371/Journal.Pone.0048542  0.313
2012 Kim M, Zhang Z, Okano H, Yan D, Groisman A, Hwa T. Need-based activation of ammonium uptake in Escherichia coli. Molecular Systems Biology. 8: 616. PMID 23010999 DOI: 10.1038/Msb.2012.46  0.444
2012 Hermsen R, Deris JB, Hwa T. On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient Proceedings of the National Academy of Sciences of the United States of America. 109: 10775-10780. PMID 22711808 DOI: 10.1073/Pnas.1117716109  0.74
2012 Warren M, Hwa T. The Growth of Bacterial Colonies Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.831  0.35
2011 Hermsen R, Erickson DW, Hwa T. Speed, sensitivity, and bistability in Auto-Activating signaling circuits Plos Computational Biology. 7. PMID 22125482 DOI: 10.1371/Journal.Pcbi.1002265  0.302
2011 McHale P, Mizutani CM, Kosman D, MacKay DL, Belu M, Hermann A, McGinnis W, Bier E, Hwa T. Gene length may contribute to graded transcriptional responses in the Drosophila embryo. Developmental Biology. 360: 230-40. PMID 21920356 DOI: 10.1016/J.Ydbio.2011.08.016  0.314
2011 Hao Y, Zhang ZJ, Erickson DW, Huang M, Huang Y, Li J, Hwa T, Shi H. Quantifying the sequence-function relation in gene silencing by bacterial small RNAs Proceedings of the National Academy of Sciences of the United States of America. 108: 12473-12478. PMID 21742981 DOI: 10.1073/Pnas.1100432108  0.312
2010 Hermsen R, Hwa T. Sources and sinks: a stochastic model of evolution in heterogeneous environments. Physical Review Letters. 105: 248104. PMID 21231560 DOI: 10.1103/Physrevlett.105.248104  0.312
2010 Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: Origins and consequences Science. 330: 1099-1102. PMID 21097934 DOI: 10.1126/Science.1192588  0.364
2010 Lunt B, Szurmant H, Procaccini A, Hoch JA, Hwa T, Weigt M. Inference of direct residue contacts in two-component signaling. Methods in Enzymology. 471: 17-41. PMID 20946840 DOI: 10.1016/S0076-6879(10)71002-8  0.302
2010 Okano H, Hwa T, Lenz P, Yan D. Reversible adenylylation of glutamine synthetase is dynamically counterbalanced during steady-state growth of Escherichia coli. Journal of Molecular Biology. 404: 522-36. PMID 20887734 DOI: 10.1016/J.Jmb.2010.09.046  0.314
2009 Klumpp S, Zhang Z, Hwa T. Growth Rate-Dependent Global Effects on Gene Expression in Bacteria Cell. 139: 1366-1375. PMID 20064380 DOI: 10.1016/J.Cell.2009.12.001  0.41
2009 Klumpp S, Hwa T. Traffic patrol in the transcription of ribosomal RNA Rna Biology. 6. PMID 19502817 DOI: 10.4161/Rna.6.4.8952  0.314
2009 Gerland U, Hwa T. Evolutionary selection between alternative modes of gene regulation Proceedings of the National Academy of Sciences of the United States of America. 106: 8841-8846. PMID 19470486 DOI: 10.1073/Pnas.0808500106  0.323
2008 Klumpp S, Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria Proceedings of the National Academy of Sciences of the United States of America. 105: 20245-20250. PMID 19073937 DOI: 10.1073/Pnas.0804953105  0.392
2008 Klumpp S, Hwa T. Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination Proceedings of the National Academy of Sciences of the United States of America. 105: 18159-18164. PMID 19017803 DOI: 10.1073/Pnas.0806084105  0.339
2008 Levine E, Hwa T. Small RNAs establish gene expression thresholds. Current Opinion in Microbiology. 11: 574-9. PMID 18935980 DOI: 10.1016/J.Mib.2008.09.016  0.312
2008 Levine E, Zhang Z, Kuhlman T, Hwa T. Correction: Quantitative characteristics of gene regulation by small RNA (PLoS Biology (2007) 5, 9, (e229) DOI: 10.1371/journal.pbio.0050229) Plos Biology. 6: 0191. DOI: 10.1371/Journal.Pbio.0060005  0.698
2007 Fritz G, Buchler NE, Hwa T, Gerland U. Designing sequential transcription logic: a simple genetic circuit for conditional memory. Systems and Synthetic Biology. 1: 89-98. PMID 19003438 DOI: 10.1007/S11693-007-9006-8  0.667
2007 Fritz G, Buchler NE, Hwa T, Gerland U. Designing sequential transcription logic: a simple genetic circuit for conditional memory. Systems and Synthetic Biology. 1: 89-98. PMID 19003438 DOI: 10.1007/S11693-007-9006-8  0.667
2007 Levine E, Zhang Z, Kuhlman T, Hwa T. Quantitative characteristics of gene regulation by small RNA. Plos Biology. 5: e229. PMID 17713988 DOI: 10.1371/Journal.Pbio.0050229  0.726
2007 White RA, Szurmant H, Hoch JA, Hwa T. Features of Protein-Protein Interactions in Two-Component Signaling Deduced from Genomic Libraries Methods in Enzymology. 422: 75-101. PMID 17628135 DOI: 10.1016/S0076-6879(06)22004-4  0.306
2007 Scott M, Hwa T, Ingalls B. Deterministic characterization of stochastic genetic circuits. Proceedings of the National Academy of Sciences of the United States of America. 104: 7402-7. PMID 17446275 DOI: 10.1073/Pnas.0610468104  0.307
2007 Kuhlman T, Zhang Z, Saier MH, Hwa T. Combinatorial transcriptional control of the lactose operon of Escherichia coli Proceedings of the National Academy of Sciences of the United States of America. 104: 6043-6048. PMID 17376875 DOI: 10.1073/Pnas.0606717104  0.717
2005 Buchler NE, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits. Proceedings of the National Academy of Sciences of the United States of America. 102: 9559-64. PMID 15972813 DOI: 10.1073/Pnas.0409553102  0.666
2005 Buchler NE, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits. Proceedings of the National Academy of Sciences of the United States of America. 102: 9559-64. PMID 15972813 DOI: 10.1073/Pnas.0409553102  0.666
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Transcriptional regulation by the numbers: applications. Current Opinion in Genetics & Development. 15: 125-35. PMID 15797195 DOI: 10.1016/J.Gde.2005.02.006  0.767
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R. Transcriptional regulation by the numbers: models. Current Opinion in Genetics & Development. 15: 116-24. PMID 15797194 DOI: 10.1016/J.Gde.2005.02.007  0.698
2004 Gerland U, Bundschuh R, Hwa T. Translocation of structured polynucleotides through nanopores. Physical Biology. 1: 19-26. PMID 16204818 DOI: 10.1088/1478-3967/1/1/002  0.535
2004 Peng W, Levine H, Hwa T, Kessler DA. Analytical study of the effect of recombination on evolution via DNA shuffling. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 051911. PMID 15244851 DOI: 10.1103/Physreve.69.051911  0.613
2004 Gerland U, Bundschuh R, Hwa T. Translocation of structured polynucleotides through nanopores Physical Biology. 1: 19-26. DOI: 10.1088/1478-3967/1/1/002  0.429
2003 Gerland U, Bundschuh R, Hwa T. Mechanically probing the folding pathway of single RNA molecules Biophysical Journal. 84: 2831-2840. PMID 12719217 DOI: 10.1016/S0006-3495(03)70012-5  0.548
2003 Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. Proceedings of the National Academy of Sciences of the United States of America. 100: 5136-41. PMID 12702751 DOI: 10.1073/Pnas.0930314100  0.698
2003 Peng W, Gerland U, Hwa T, Levine H. Dynamics of competitive evolution on a smooth landscape. Physical Review Letters. 90: 088103. PMID 12633464 DOI: 10.1103/Physrevlett.90.088103  0.616
2002 Gerland U, Hwa T. On the selection and evolution of regulatory DNA motifs Journal of Molecular Evolution. 55: 386-400. PMID 12355260 DOI: 10.1007/S00239-002-2335-Z  0.305
2002 Yu YK, Bundschuh R, Hwa T. Hybrid alignment: High-performance with universal statistics Bioinformatics. 18: 864-872. PMID 12075022 DOI: 10.1093/Bioinformatics/18.6.864  0.523
2002 Bundschuh R, Hwa T. Statistical mechanics of secondary structures formed by random RNA sequences. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 031903. PMID 11909105 DOI: 10.1103/Physreve.65.031903  0.541
2002 Bundschuh R, Hwa T. Phrases of the secondary structures of RNA sequences Europhysics Letters. 59: 903-909. DOI: 10.1209/Epl/I2002-00128-3  0.534
2001 Gerland U, Bundschuh R, Hwa T. Force-induced denaturation of RNA. Biophysical Journal. 81: 1324-32. PMID 11509348 DOI: 10.1016/S0006-3495(01)75789-X  0.539
2001 Altschul SF, Bundschuh R, Olsen R, Hwa T. The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Research. 29: 351-61. PMID 11139604 DOI: 10.1093/Nar/29.2.351  0.511
2000 Bundschuh R, Hwa T. An analytic study of the phase transition line in local sequence alignment with gaps Discrete Applied Mathematics. 104: 113-142. DOI: 10.1016/S0166-218X(00)00188-8  0.517
1999 Olsen R, Bundschuh R, Hwa T. Rapid assessment of extremal statistics for gapped local alignment. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 211-22. PMID 10786304  0.466
1999 Bundschuh R, Hwa T. RNA secondary structure formation: A solvable model of heteropolymer folding Physical Review Letters. 83: 1479-1482. DOI: 10.1103/Physrevlett.83.1479  0.492
1999 Bundschuh R, Hwa T. Analytic study of the phase transition line in local sequence alignment with gaps Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 70-76.  0.446
1994 Hwa T, Kardar M, Paczuski M. Hwa, Kardar, and Paczuski reply. Physical Review Letters. 72: 785. PMID 10056526 DOI: 10.1103/Physrevlett.72.785  0.608
1994 Hwa T, Kardar M, Paczuski M. Hwa, Kardar, and Paczuski reply [3] Physical Review Letters. 72: 785. DOI: 10.1103/PhysRevLett.72.785  0.578
1992 Paczuski M, Barma M, Majumdar SN, Hwa T. Fluctuations of a nonequililbrium interface. Physical Review Letters. 69: 2735. PMID 10046572 DOI: 10.1103/Physrevlett.69.2735  0.509
1992 Hwa T, Kardar M. Avalanches, hydrodynamics, and discharge events in models of sandpiles. Physical Review. A. 45: 7002-7023. PMID 9906772 DOI: 10.1103/Physreva.45.7002  0.479
1992 Paczuski M, Barma M, Majumdar SN, Hwa T. Fluctuations of a nonequililbrium interface [2] Physical Review Letters. 69: 2735. DOI: 10.1103/PhysRevLett.69.2735  0.466
1992 Wen X, Garland CW, Hwa T, Kardar M, Kokufuta E, Li Y, Orkisz M, Tanaka T. Crumpled and collapsed conformations in graphite oxide membranes Nature. 355: 426-428. DOI: 10.1038/355426A0  0.588
1991 Hwa T, Kardar M, Paczuski M. Growth-induced roughening of crystalline facets. Physical Review Letters. 66: 441-444. PMID 10043808 DOI: 10.1103/Physrevlett.66.441  0.645
1991 Hwa T, Kokufuta E, Tanaka T. Conformation of graphite oxide membranes in solution. Physical Review. A. 44: R2235-R2238. PMID 9906266 DOI: 10.1103/Physreva.44.R2235  0.461
1991 Hwa T, Kardar M, Paczuski M. Growth-induced roughening of crystalline facets Physical Review Letters. 66: 441-444. DOI: 10.1103/PhysRevLett.66.441  0.618
1990 Duplantier B, Hwa T, Kardar M. Self-avoiding crumpled manifolds: Perturbative analysis and renormalizability. Physical Review Letters. 64: 2022-2025. PMID 10041557 DOI: 10.1103/Physrevlett.64.2022  0.462
1989 Hwa T, Kardar M. Dissipative transport in open systems: An investigation of self-organized criticality. Physical Review Letters. 62: 1813-1816. PMID 10039777 DOI: 10.1103/Physrevlett.62.1813  0.484
1989 Medina E, Hwa T, Kardar M, Zhang YC. Burgers equation with correlated noise: Renormalization-group analysis and applications to directed polymers and interface growth. Physical Review. A. 39: 3053-3075. PMID 9901600 DOI: 10.1103/Physreva.39.3053  0.604
1989 Hwa T, Kardar M. Fractals and self-organized criticality in dissipative dynamics Physica D: Nonlinear Phenomena. 38: 198-202. DOI: 10.1016/0167-2789(89)90191-7  0.493
1988 Hwa T, Kardar M. Evolution of surface patterns on swelling gels. Physical Review Letters. 61: 106-109. PMID 10038705 DOI: 10.1103/Physrevlett.61.106  0.445
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