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Editorial overview: Current Opinion in Microbiology 2018 Special issue 'Microbial systems biology, vol. 45'.

Hwa T, Sauer U.

Curr Opin Microbiol. 2018 Oct;45:vi-viii. doi: 10.1016/j.mib.2018.09.005. Epub 2018 Oct 17. No abstract available.


Bacterial growth, flow, and mixing shape human gut microbiota density and composition.

Arnoldini M, Cremer J, Hwa T.

Gut Microbes. 2018 Nov 2;9(6):559-566. doi: 10.1080/19490976.2018.1448741. Epub 2018 May 9.


Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress.

Dai X, Zhu M, Warren M, Balakrishnan R, Okano H, Williamson JR, Fredrick K, Hwa T.

MBio. 2018 Feb 13;9(1). pii: e02375-17. doi: 10.1128/mBio.02375-17.


Quantifying the benefit of a proteome reserve in fluctuating environments.

Mori M, Schink S, Erickson DW, Gerland U, Hwa T.

Nat Commun. 2017 Oct 31;8(1):1225. doi: 10.1038/s41467-017-01242-8.


A global resource allocation strategy governs growth transition kinetics of Escherichia coli.

Erickson DW, Schink SJ, Patsalo V, Williamson JR, Gerland U, Hwa T.

Nature. 2017 Nov 2;551(7678):119-123. doi: 10.1038/nature24299. Epub 2017 Oct 25.


Effect of water flow and chemical environment on microbiota growth and composition in the human colon.

Cremer J, Arnoldini M, Hwa T.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6438-6443. doi: 10.1073/pnas.1619598114. Epub 2017 Jun 6.


Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth.

Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T.

Nat Microbiol. 2016 Dec 12;2:16231. doi: 10.1038/nmicrobiol.2016.231.


Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel.

Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT, Zhang Z, Gutierrez E, Groisman A, Hwa T.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11414-11419. Epub 2016 Sep 28.


Constrained Allocation Flux Balance Analysis.

Mori M, Hwa T, Martin OC, De Martino A, Marinari E.

PLoS Comput Biol. 2016 Jun 29;12(6):e1004913. doi: 10.1371/journal.pcbi.1004913. eCollection 2016 Jun.


Overflow metabolism in Escherichia coli results from efficient proteome allocation.

Basan M, Hui S, Okano H, Zhang Z, Shen Y, Williamson JR, Hwa T.

Nature. 2015 Dec 3;528(7580):99-104. doi: 10.1038/nature15765.


Inflating bacterial cells by increased protein synthesis.

Basan M, Zhu M, Dai X, Warren M, Sévin D, Wang YP, Hwa T.

Mol Syst Biol. 2015 Oct 30;11(10):836. doi: 10.15252/msb.20156178.


A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates.

Hermsen R, Okano H, You C, Werner N, Hwa T.

Mol Syst Biol. 2015 Apr 9;11(4):801. doi: 10.15252/msb.20145537.


Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR.

Mol Syst Biol. 2015 Feb 12;11(1):784. doi: 10.15252/msb.20145697.


Emergence of robust growth laws from optimal regulation of ribosome synthesis.

Scott M, Klumpp S, Mateescu EM, Hwa T.

Mol Syst Biol. 2014 Aug 22;10:747. doi: 10.15252/msb.20145379.


Direct coupling analysis for protein contact prediction.

Morcos F, Hwa T, Onuchic JN, Weigt M.

Methods Mol Biol. 2014;1137:55-70. doi: 10.1007/978-1-4939-0366-5_5.


Predicting the spatiotemporal dynamics of hair follicle patterns in the developing mouse.

Cheng CW, Niu B, Warren M, Pevny LH, Lovell-Badge R, Hwa T, Cheah KS.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2596-601. doi: 10.1073/pnas.1313083111. Epub 2014 Feb 3.


Bacterial growth: global effects on gene expression, growth feedback and proteome partition.

Klumpp S, Hwa T.

Curr Opin Biotechnol. 2014 Aug;28:96-102. doi: 10.1016/j.copbio.2014.01.001. Epub 2014 Feb 2. Review.


Coevolutionary signals across protein lineages help capture multiple protein conformations.

Morcos F, Jana B, Hwa T, Onuchic JN.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20533-8. doi: 10.1073/pnas.1315625110. Epub 2013 Dec 2.


The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria.

Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T.

Science. 2013 Nov 29;342(6162):1237435. doi: 10.1126/science.1237435.


Molecular crowding limits translation and cell growth.

Klumpp S, Scott M, Pedersen S, Hwa T.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16754-9. doi: 10.1073/pnas.1310377110. Epub 2013 Sep 30.


Coordination of bacterial proteome with metabolism by cyclic AMP signalling.

You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T.

Nature. 2013 Aug 15;500(7462):301-6. doi: 10.1038/nature12446. Epub 2013 Aug 7.


On ribosome load, codon bias and protein abundance.

Klumpp S, Dong J, Hwa T.

PLoS One. 2012;7(11):e48542. doi: 10.1371/journal.pone.0048542. Epub 2012 Nov 7.


Need-based activation of ammonium uptake in Escherichia coli.

Kim M, Zhang Z, Okano H, Yan D, Groisman A, Hwa T.

Mol Syst Biol. 2012;8:616. doi: 10.1038/msb.2012.46.


Stripe formation in bacterial systems with density-suppressed motility.

Fu X, Tang LH, Liu C, Huang JD, Hwa T, Lenz P.

Phys Rev Lett. 2012 May 11;108(19):198102. Epub 2012 May 8.


On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient.

Hermsen R, Deris JB, Hwa T.

Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10775-80. doi: 10.1073/pnas.1117716109. Epub 2012 Jun 18.


Genomics-aided structure prediction.

Sułkowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10340-5. doi: 10.1073/pnas.1207864109. Epub 2012 Jun 12.


Occurrence of oriental flies associated with indoor and outdoor human remains in the tropical climate of north Malaysia.

Kumara TK, Disney RH, Abu Hassan A, Flores M, Hwa TS, Mohamed Z, CheSalmah MR, Bhupinder S.

J Vector Ecol. 2012 Jun;37(1):62-8. doi: 10.1111/j.1948-7134.2012.00200.x.


Speed, sensitivity, and bistability in auto-activating signaling circuits.

Hermsen R, Erickson DW, Hwa T.

PLoS Comput Biol. 2011 Nov;7(11):e1002265. doi: 10.1371/journal.pcbi.1002265. Epub 2011 Nov 17.


Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1293-301. doi: 10.1073/pnas.1111471108. Epub 2011 Nov 21.


Sequential establishment of stripe patterns in an expanding cell population.

Liu C, Fu X, Liu L, Ren X, Chau CK, Li S, Xiang L, Zeng H, Chen G, Tang LH, Lenz P, Cui X, Huang W, Hwa T, Huang JD.

Science. 2011 Oct 14;334(6053):238-41. doi: 10.1126/science.1209042.


Gene length may contribute to graded transcriptional responses in the Drosophila embryo.

McHale P, Mizutani CM, Kosman D, MacKay DL, Belu M, Hermann A, McGinnis W, Bier E, Hwa T.

Dev Biol. 2011 Dec 1;360(1):230-40. doi: 10.1016/j.ydbio.2011.08.016. Epub 2011 Sep 3.


Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses.

Wang TY, Chen HL, Lu MJ, Chen YC, Sung HM, Mao CT, Cho HY, Ke HM, Hwa TY, Ruan SK, Hung KY, Chen CK, Li JY, Wu YC, Chen YH, Chou SP, Tsai YW, Chu TC, Shih CA, Li WH, Shih MC.

Biotechnol Biofuels. 2011 Aug 17;4:24. doi: 10.1186/1754-6834-4-24.


Overcoming fluctuation and leakage problems in the quantification of intracellular 2-oxoglutarate levels in Escherichia coli.

Yan D, Lenz P, Hwa T.

Appl Environ Microbiol. 2011 Oct;77(19):6763-71. doi: 10.1128/AEM.05257-11. Epub 2011 Aug 5.


Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.

Hao Y, Zhang ZJ, Erickson DW, Huang M, Huang Y, Li J, Hwa T, Shi H.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12473-8. doi: 10.1073/pnas.1100432108. Epub 2011 Jul 8.


Bacterial growth laws and their applications.

Scott M, Hwa T.

Curr Opin Biotechnol. 2011 Aug;22(4):559-65. doi: 10.1016/j.copbio.2011.04.014. Epub 2011 May 16. Review.


Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.

Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M.

PLoS One. 2011 May 9;6(5):e19729. doi: 10.1371/journal.pone.0019729.


Sources and sinks: a stochastic model of evolution in heterogeneous environments.

Hermsen R, Hwa T.

Phys Rev Lett. 2010 Dec 10;105(24):248104. Epub 2010 Dec 8.


Interdependence of cell growth and gene expression: origins and consequences.

Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T.

Science. 2010 Nov 19;330(6007):1099-102. doi: 10.1126/science.1192588.


Computational modeling of phosphotransfer complexes in two-component signaling.

Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H.

Methods Enzymol. 2010;471:43-58. doi: 10.1016/S0076-6879(10)71003-X. Epub 2010 Mar 1.


Inference of direct residue contacts in two-component signaling.

Lunt B, Szurmant H, Procaccini A, Hoch JA, Hwa T, Weigt M.

Methods Enzymol. 2010;471:17-41. doi: 10.1016/S0076-6879(10)71002-8. Epub 2010 Mar 1.


Reversible adenylylation of glutamine synthetase is dynamically counterbalanced during steady-state growth of Escherichia coli.

Okano H, Hwa T, Lenz P, Yan D.

J Mol Biol. 2010 Dec 3;404(3):522-36. doi: 10.1016/j.jmb.2010.09.046. Epub 2010 Sep 29.


Growth rate-dependent global effects on gene expression in bacteria.

Klumpp S, Zhang Z, Hwa T.

Cell. 2009 Dec 24;139(7):1366-75. doi: 10.1016/j.cell.2009.12.001.


High-resolution protein complexes from integrating genomic information with molecular simulation.

Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22124-9. doi: 10.1073/pnas.0912100106. Epub 2009 Dec 17.


Traffic patrol in the transcription of ribosomal RNA.

Klumpp S, Hwa T.

RNA Biol. 2009 Sep-Oct;6(4):392-4. Epub 2009 Sep 7. Review.


Evolutionary selection between alternative modes of gene regulation.

Gerland U, Hwa T.

Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8841-6. doi: 10.1073/pnas.0808500106. Epub 2009 May 22.


Identification of direct residue contacts in protein-protein interaction by message passing.

Weigt M, White RA, Szurmant H, Hoch JA, Hwa T.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):67-72. doi: 10.1073/pnas.0805923106. Epub 2008 Dec 30.


Growth-rate-dependent partitioning of RNA polymerases in bacteria.

Klumpp S, Hwa T.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20245-50. doi: 10.1073/pnas.0804953105. Epub 2008 Dec 10.


Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination.

Klumpp S, Hwa T.

Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18159-64. doi: 10.1073/pnas.0806084105. Epub 2008 Nov 18.


Designing sequential transcription logic: a simple genetic circuit for conditional memory.

Fritz G, Buchler NE, Hwa T, Gerland U.

Syst Synth Biol. 2007 Apr;1(2):89-98. doi: 10.1007/s11693-007-9006-8. Epub 2007 Aug 21.

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