Publications for Thomas Ferenci
2016
Maharjan, R., Ferenci, T. (2016). Metastable coexistence of multiple genotypes in a constant environment with a single resource through fixed settings of a multiplication-survival trade-off.
Research in Microbiology , 167, 240-246.
Ferenci, T. (2016). Trade-off Mechanisms
Shaping the Diversity of Bacteria. Trends in
Microbiology , 24(3), 209-223. <a href="http://dx.doi.org/10.1016/j.tim.2015.11.00
9">[More Information]</a>
2015
Ferenci, T., Phan, K. (2015). How porin heterogeneity and trade-offs affect the antibiotic susceptibility of gram-negative bacteria. Genes ,
6(4), 1113-1124. <a href="http://dx.doi.org/10.3390/genes6041113">
[More Information]</a>
Ferenci, T., Maharjan, R. (2015). Mutational heterogeneity: A key ingredient of bet-hedging and evolutionary divergence?: The broad spectrum of mutations and their flexible frequency in populations provides a source of risk avoidance and alternative evolutionary strategies. BioEssays , 37(2), 123-130. <a href="http://dx.doi.org/10.1002/bies.201400153"
>[More Information]</a>
Maharjan, R., Ferenci, T. (2015). Mutational
Signatures Indicative of Environmental Stress in
Bacteria. Molecular Biology and Evolution ,
32(2), 380-391. <a href="http://dx.doi.org/10.1093/molbev/msu306"
>[More Information]</a>
Maharjan, R., Liu, B., Feng, L., Ferenci, T.,
Wang, L. (2015). Simple Phenotypic Sweeps
Hide Complex Genetic Changes in Populations. Genome Biology and Evolution ,
7(2), 531-544. <a href="http://dx.doi.org/10.1093/gbe/evv004">[M ore Information]</a>
2014
Behrends, V., Maharjan, R., Ryall, B., Feng, L.,
Liu, B., Wang, L., Bundy, J., Ferenci, T. (2014).
A metabolic trade-off between phosphate and glucose utilization in Escherichia coli. Molecular
BioSystems , 10(11), 2820-2822. <a href="http://dx.doi.org/10.1039/c4mb00313f">[
More Information]</a>
Maharjan, R., Ferenci, T. (2014). Stress-Induced
Mutation Rates Show a Sigmoidal and Saturable
Increase Due to the RpoS Sigma Factor in
Escherichia coli. Genetics , 198(3), 1231-1235.
<a href="http://dx.doi.org/10.1534/genetics.114.170
Publications for Thomas Ferenci
258">[More Information]</a>
Ferenci, T. (2014). Survival of the Different.
Australasian Science , , 32-33.
Eydallin, G., Ryall, B., Maharjan, R., Ferenci, T.
(2014). The nature of laboratory domestication changes in freshly isolated Escherichia coli strains. Environmental Microbiology , 16(3),
813-828. <a href="http://dx.doi.org/10.1111/1462-2920.1220
8">[More Information]</a>
2013
Maharjan, R., Gaffé, J., Plucain, J., Schliep, M.,
Wang, L., Feng, L., Tenaillon, O., Ferenci, T.,
Schneider, D. (2013). A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli. BMC Genomics , 14(1), 1-12. <a href="http://dx.doi.org/10.1186/1471-2164-14-4
41">[More Information]</a>
Phan, K., Ferenci, T. (2013). A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli. The
ISME Journal , 7(10), 2034-2043. <a href="http://dx.doi.org/10.1038/ismej.2013.82">
[More Information]</a>
Maharjan, R., Ferenci, T. (2013). Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations. Evolution , 67(9), 2762-2768. <a href="http://dx.doi.org/10.1111/evo.12137">[Mo re Information]</a>
Maharjan, R., Liu, B., Li, Y., Reeves, P., Wang,
L., Ferenci, T. (2013). Mutation accumulation and fitness in mutator subpopulations of Escherichia coli.
Biology Letters , 9(1), 1-5. <a href="http://dx.doi.org/10.1098/rsbl.2012.0961"
>[More Information]</a>
Maharjan, R., McKenzie, C., Yeung, A., Ferenci,
T. (2013). The basis of antagonistic pleiotropy in hfq mutations that have opposite effects on fitness at slow and fast growth rates. Heredity ,
110(1), 10-18. <a href="http://dx.doi.org/10.1038/hdy.2012.46">[
More Information]</a>
Maharjan, R., Nilsson, S., Sung, J., Haynes, K.,
Beardmore, R., Hurst, L., Ferenci, T., Gudelj, I.
(2013). The form of a trade-off determines the response to competition. Ecology Letters , 16(10),
1267-1276. <a href="http://dx.doi.org/10.1111/ele.12159">[Mor e Information]</a>
2012
Ryall, B., Eydallin, G., Ferenci, T. (2012).
Culture history and population heterogeneity as

Publications for Thomas Ferenci determinants of bacterial adaptation: the adaptomics of a single environmental transition.
Microbiology and Molecular Biology Reviews ,
76(3), 597-625. <a href="http://dx.doi.org/10.1128/MMBR.05028-1
1">[More Information]</a>
Schliep, M., Ryall, B., Ferenci, T. (2012). The identification of global patterns and unique signatures of proteins across 14 environments using outer membrane proteomics of bacteria.
Molecular BioSystems , 8(11), 3017-3027. <a href="http://dx.doi.org/10.1039/c2mb25212k">[
More Information]</a>
Maharjan, R., Ferenci, T., Reeves, P., Li, Y., Liu,
B., Wang, L. (2012). The multiplicity of divergence mechanisms in a single evolving population. Genome Biology , 13(6), 1-16. <a href="http://dx.doi.org/10.1186/gb-2012-13-6-r4
1">[More Information]</a>
2011
Gaffe, J., McKenzie, C., Maharjan, R.,
Coursange, E., Ferenci, T., Schneider, D. (2011).
Insertion Sequence-Driven Evolution of
Escherichia coli in Chemostats. Journal of
Molecular Evolution , 72(4), 398-412. <a href="http://dx.doi.org/10.1007/s00239-011-943
9-2">[More Information]</a>
Ferenci, T., Galbiati, H., Betteridge, T., Phan, K.,
Spira, B. (2011). The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in
Escherichia coli. BMC Microbiology , 11, 1-11.
<a href="http://dx.doi.org/10.1186/1471-2180-11-6
2">[More Information]</a>
Spira, B., de Almeida Toledo, R., Maharjan, R.,
Ferenci, T. (2011). The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example.
BMC Microbiology , 11, 1-9. <a href="http://dx.doi.org/10.1186/1471-2180-11-2
48">[More Information]</a>
2010
Gudelj, I., Weitz, J., Ferenci, T., Horner-Devine,
M., Marx, C., Meyer, J., Forde, S. (2010). An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure. Ecology Letters , 13,
1073-1084. <a href="http://dx.doi.org/10.1111/j.1461-0248.201
0.01507.x">[More Information]</a>
Wang, L., Spira, B., Zhou, Z., Feng, L.,
Maharjan, R., Li, X., Li, F., McKenzie, C.,
Reeves, P., Ferenci, T. (2010). Divergence
Involving Global Regulatory Gene Mutations in an Escherichia Coli Population Evolving under
Phosphate Limitation. Genome Biology and
Evolution , 2(1), 478-487. <a href="http://dx.doi.org/10.1093/gbe/evq035">[M ore Information]</a>
Maharjan, R., Zhou, Z., Ren, Y., Li, Y., Gaffé, J.,
Schneider, D., McKenzie, C., Reeves, P.,
Ferenci, T., Wang, L. (2010). Genomic
Identification of a Novel Mutation in hfq That
Provides Multiple Benefits in Evolving
Glucose-Limited Populations of Escherichia coli.
Journal of Bacteriology , 192(17), 4517-4521. <a href="http://dx.doi.org/10.1128/JB.00368-10">[
More Information]</a>
Levert, M., Zamfir, O., Clermont, O., Bouvet,
O., Lespinats, S., Hipeaux, M., Branger, C.,
Picard, B., Saint-Ruf, C., Norel, F., Phan, K.,
Ferenci, T., et al (2010). Molecular and
Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli
Extraintestinal Infections. PLoS Pathogens , 6(9), e1001125-1-e1001125-19. <a href="http://dx.doi.org/10.1371/journal.ppat.100
1125">[More Information]</a>
2009
Ferenci, T., Yee, K., Betteridge, T., Ren, Y., Liu,
Y., Feng, L., Reeves, P., Wang, L. (2009).
Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli
K-12. Journal of Bacteriology , 191(12),
4025-4029. <a href="http://dx.doi.org/10.1128/JB.00118-09">[
More Information]</a>
2008
Spira, B., Ferenci, T. (2008). Alkaline phosphatase as a reporter of sigma(S) levels and rpoS polymorphisms in different E. coli strains.
Archives of Microbiology , 189(1), 43-47. <a href="http://dx.doi.org/10.1007/s00203-007-029
1-0">[More Information]</a>
Spira, B., Hu, X., Ferenci, T. (2008). Strain variation in ppGpp concentration and RpoS levels in laboratory strains of Escherichia coli
K-12. Microbiology , 154(9), 2887-2895. <a href="http://dx.doi.org/10.1099/mic.0.2008/0184
57-0">[More Information]</a>
2007
Ferenci, T. (2007). Bacterial Physiology,
Regulation and Mutational Adaptation in a
Chemostat Environment. Advances in Microbial
Physiology , 53, 169-229, 315. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=17707145">[More Information]</a>
Maharjan, R., Seeto, S., Ferenci, T. (2007).
Divergence and redundancy of transport and metabolic rate-yield strategies in a single

Publications for Thomas Ferenci
Escherichia coli population. Journal of
Bacteriology , 189(6), 2350-2358. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=17158684">[More Information]</a>
Ferenci, T. (2007). Sensing nutrient levels in bacteria. Nature Chemical Biology , 3(10),
607-608. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=17876315">[More Information]</a> van der Werf, M., Takors, R., Smedsgaard, J.,
Nielsen, J., Ferenci, T., Portais, J., Wittmann, C.,
Hooks, M., Tomassini, A., Oldiges, M., et al
(2007). Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments.
Metabolomics , 3(3), 189-194. <a href="http://dx.doi.org/10.1007/s11306-007-008
0-4">[More Information]</a>
Ferenci, T. (2007). The spread of a beneficial mutation in experimental bacterial populations: the influence of the environment and genotype on the fixation of rpoS mutations. Heredity , , 1-7.
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=18073783">[More Information]</a>
Ferenci, T., Spira, B. (2007). Variation in Stress
Responses within a Bacterial Species and the
Indirect Costs of Stress Resistance. Annals of the
New York Academy of Sciences , 1113, 105-113.
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=17483210">[More Information]</a>
2006
Ferenci, T. (2006). A cultural divide on the use of chemostats. Microbiology , 152(5), 1247-1248.
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=16622042">[More Information]</a>
Maharjan, R., Seeto, S., McRobb, L., Ferenci, T.
(2006). Clonal Adaptive Radiation in a Constant
Environment. Science , 313(5786), 514-517. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=16825532">[More Information]</a>
King, T., Seeto, S., Ferenci, T. (2006).
Genotype-by-environment interactions influencing the emergence of rpoS mutations in
Escherichia coli populations. Genetics , 172(4),
2071-2079. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=16489226">[More Information]</a>
2005
Ferenci, T., Maharjan, R. (2005). Comparative metabolome profiling using two dimensional thin layer chromatography (2DTLC). In
Vaidyanathan S; Harrigan G; Goodacre R (Eds.),
Metabolome Analyses - Strategies for Systems
Biology , (pp. 63-81). USA: Springer
Science+Business Media.
King, T., Ferenci, T. (2005). Divergent roles of
RpoS in Escherichia coli under aerobic and anaerobic conditions. FEMS Microbiology
Letters , 244(2), 323-327. <a href="http://dx.doi.org/10.1016/j.femsle.2005.02.
002">[More Information]</a>
Ferenci, T. (2005). Maintaining a healthy
SPANC balance through regulatory and mutational adaptation. Molecular Microbiology ,
57(1), 1-8. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=15948944">[More Information]</a>
Maharjan, R., Ferenci, T. (2005). Metabolomic diversity in the species Escherichia coli and its relationship to genetic population structure.
Metabolomics , 1(3), 235-242.
Maharjan, R., Yu, P., Seeto, S., Ferenci, T.
(2005). The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. Research in
Microbiology , 156(2), 178-183. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract
&list_uids=15748982">[More Information]</a>
2004
King, T., Ishihama, A., Kori, A., Ferenci, T.
(2004). A Regulatory Trade-Off As A Source Of
Strain Variation In The Species Escherichia Coli.
Journal of Bacteriology , 186(17), 5614-5620.
Seeto, S., McRobb, L., Ferenci, T. (2004). The
Multifactorial Influences Of Rpos, Mlc And cAMP On PtsG Expression Under
Glucose-Limited And Anaerobic Conditions.
Research in Microbiology , 155(3), 211-215.
2003
Maharjan, R., Ferenci, T. (2003). Global metabolite analysis: the influence of extraction methodology on metabolome profiles of
Escherichia coli. Analytical Biochemistry ,
313(1), 145-154.
Tsunedomi, R., Izu, H., Kawai, T., Matsushita,
K., Ferenci, T., Yamada, M. (2003). The activator of GntII genes for gluconate metabolism, GntH exerts negative control of
GntR-Regulated GntI genes in Escherichia coli.
Journal of Bacteriology , 185(6), 1783-1795.

Publications for Thomas Ferenci
King, T., Ferenci, T., Szabo, E. (2003). The effect of growth atmosphere on the ability of
Listeria monocytogenes to survive exposure to acid, proteolytic enzymes and bile salts.
International Journal Of Food Microbiology ,
84(2), 133-143.
McRobb, L., Seeto, S., Ferenci, T. (2003). The
Influence of Cellular Physiology on the Initiation of Mutational Pathways in Escherichia coli Populations. Proceedings of the Royal
Society B: Biological Sciences , 270(1517),
843-848.
Ferenci, T. (2003). What is driving the acquisition of mutS and rpoS polymorphisms in
Escherichia coli? Trends in Microbiology ,
11(10), 457-461.
2002
McRobb, L., Seeto, S., Ferenci, T. (2002).
Enrichment and elimination of mutY mutators in
Escherichia coli populations. Genetics , 162(3),
1055-1062.
McRobb, L., Pinto (Pinto-Nadanachandran), R.,
Seeto, S., Ferenci, T. (2002). Regulation of mutY and nature of mutator mutations in Escherichia coli populations under nutrient limitation.
Journal of Bacteriology , 184(3), 739-745.
McRobb, L., King, T., Ferenci, T. (2002). RpoS mutations and loss of general stress resistance in
Escherichia coli populations as a consequence of conflict between competing stress responses.
Journal of Bacteriology , 184(3), 806-811.
Schlegel, A., Danot, O., Richet, E., Ferenci, T.,
Boos, W. (2002). The N terminus of the
Escherichia coli transcription activator MalT is the domain of interaction with MalY. Journal of
Bacteriology , 184(11), 3069-3077.
2001
Liu, X., Ferenci, T. (2001). An analysis of multifactorial influcences on the transcriptional control of ompF and ompC porin expression under nutrient limitation. Microbiology , 147,
2981-2989.
Ferenci, T. (2001). Hungry bacteria - definition and properties of a nutritional state.
Environmental Microbiology , 3, 605-611.