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Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”https://doi.org/10.1186/s13104-022-06061-9__BMC Research Notes. Springer Nature, 2022.https://doi.org/10.1186/s13104-022-06061-9 .

Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gasper Tkadik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.”https://doi.org/10.7554/eLife.64543__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/eLife.64543 .

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Glover, Georgina, Margaritis Voliotis, Urszula apiska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.”https://doi.org/10.1038/s42003-022-03336-6__Communications Biology. Springer Nature, 2022.https://doi.org/10.1038/s42003-022-03336-6 .

Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to C.”https://doi.org/10.7554/eLife.78995__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/eLife.78995 .

Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber and Point Mutations.”https://doi.org/10.7554/ELIFE.82240__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/ELIFE.82240 .

Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.”https://doi.org/10.5061/dryad.rfj6q57ds__Dryad, 2022.https://doi.org/10.5061/dryad.rfj6q57ds .

Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.”https://doi.org/10.1371/journal.ppat.1009172__PLoS Pathogens. Public Library of Science, 2021.https://doi.org/10.1371/journal.ppat.1009172 .

Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.”https://doi.org/10.1016/j.tcs.2021.05.023__Theoretical Computer Science. Elsevier, 2021.https://doi.org/10.1016/j.tcs.2021.05.023 .

Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.”https://doi.org/10.1021/acsami.1c09850__ACS Applied Materials and Interfaces. American Chemical Society, 2021.https://doi.org/10.1021/acsami.1c09850 .

Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.”https://doi.org/10.7554/elife.68876__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.68876 .

Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.”https://doi.org/10.1093/protein/gzab025__Protein Engineering, Design and Selection. Oxford University Press, 2021.https://doi.org/10.1093/protein/gzab025 .

Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”https://doi.org/10.7554/elife.65993__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.65993 .

Le, Dai, Ekaterina Krasnopeeva, Faris Sinjab, Teuta Pilizota, and Minsu Kim. “Active Efflux Leads to Heterogeneous Dissipation of Proton Motive Force by Protonophores in Bacteria.”https://doi.org/10.1128/mbio.00676-21__MBio. American Society for Microbiology, 2021.https://doi.org/10.1128/mbio.00676-21 .

Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”https://doi.org/10.15479/at:ista:10307__Institute of Science and Technology Austria, 2021.https://doi.org/10.15479/at:ista:10307 .

Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to C.”https://doi.org/10.1101/2021.10.18.464770__BioRxiv. Cold Spring Harbor Laboratory, n.d.https://doi.org/10.1101/2021.10.18.464770 .

Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.”https://doi.org/10.1007/978-1-0716-0755-8_16__In Photoswitching Proteins, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020.https://doi.org/10.1007/978-1-0716-0755-8_16 .

Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.”https://doi.org/10.15479/AT:ISTA:8155__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8155 .

Grah, Rok, Benjamin Zoller, and Gasper Tkadik. “Normative Models of Enhancer Function.”https://doi.org/10.1101/2020.04.08.029405__BioRxiv. Cold Spring Harbor Laboratory, 2020.https://doi.org/10.1101/2020.04.08.029405 .

Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.”https://doi.org/10.1371/journal.pcbi.1007642__PLOS Computational Biology. Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642 .

Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.”https://doi.org/10.15479/AT:ISTA:7680__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:7680 .

Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gasper Tkadik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”https://doi.org/10.1038/s41559-020-1132-7__Nature Ecology &; Evolution. Springer Nature, 2020.https://doi.org/10.1038/s41559-020-1132-7 .

Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.”https://doi.org/10.15479/AT:ISTA:8653__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8653 .

Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.”https://doi.org/10.1038/s41467-019-09974-5__Nature Communications. Springer Nature, 2019.https://doi.org/10.1038/s41467-019-09974-5 .

Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.”https://doi.org/10.3389/fmicb.2019.01171__Frontiers in Microbiology. Frontiers, 2019.https://doi.org/10.3389/fmicb.2019.01171 .

Ruess, Jakob, Maros Pleska, Calin C Guet, and Gasper Tkadik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.”https://doi.org/10.1371/journal.pcbi.1007168__PLoS Computational Biology. Public Library of Science, 2019.https://doi.org/10.1371/journal.pcbi.1007168 .

Ruess, Jakob, Maros Pleska, Calin C Guet, and Gasper Tkadik. “Supporting Text and Results.”https://doi.org/10.1371/journal.pcbi.1007168.s001__Public Library of Science, 2019.https://doi.org/10.1371/journal.pcbi.1007168.s001 .

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Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.”https://doi.org/10.1007/s00294-018-0879-8__Current Genetics. Springer, 2019.https://doi.org/10.1007/s00294-018-0879-8 .

Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.”https://doi.org/10.1073/pnas.1812015116__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019.https://doi.org/10.1073/pnas.1812015116 .

Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.”https://doi.org/10.15479/AT:ISTA:6371__Institute of Science and Technology Austria, 2019.https://doi.org/10.15479/AT:ISTA:6371 .

Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.”https://doi.org/10.1007/978-1-4939-7792-5_15__Methods in Molecular Biology. Springer, 2018.https://doi.org/10.1007/978-1-4939-7792-5_15 .

Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.”https://doi.org/10.1007/s00453-017-0369-2__Algorithmica. Springer, 2018.https://doi.org/10.1007/s00453-017-0369-2 .

Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.”https://doi.org/10.1016/j.jbiotec.2018.01.008__Journal of Biotechnology. Elsevier, 2018.https://doi.org/10.1016/j.jbiotec.2018.01.008 .

Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.”https://doi.org/10.1371/journal.pbio.2005971__PLoS Biology. Public Library of Science, 2018.https://doi.org/10.1371/journal.pbio.2005971 .

Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.”https://doi.org/10.1371/journal.pbio.2005971.s008__Public Library of Science, 2018.https://doi.org/10.1371/journal.pbio.2005971.s008 .

Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.”https://doi.org/10.1038/s41559-017-0424-z__Nature Ecology and Evolution. Springer Nature, 2018.https://doi.org/10.1038/s41559-017-0424-z .

Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.”https://doi.org/10.1038/s41467-018-04342-1__Nature Communications. Springer Nature, 2018.https://doi.org/10.1038/s41467-018-04342-1 .

Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.”https://doi.org/10.1093/molbev/msy163__Molecular Biology and Evolution. Oxford University Press, 2018.https://doi.org/10.1093/molbev/msy163 .

Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.”https://doi.org/10.1093/nar/gky079__Nucleic Acids Research. Oxford University Press, 2018.https://doi.org/10.1093/nar/gky079 .

De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gasper Tkadik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.”https://doi.org/10.1038/s41467-018-05417-9__Nature Communications. Springer Nature, 2018.https://doi.org/10.1038/s41467-018-05417-9 .

Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.”https://doi.org/10.15479/AT:ISTA:th1059__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:th1059 .

Igler, Claudia, Mato Lagator, Gasper Tkadik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”https://doi.org/10.1038/s41559-018-0651-y__Nature Ecology and Evolution. Nature Publishing Group, 2018.https://doi.org/10.1038/s41559-018-0651-y .

Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.”https://doi.org/10.1002/ange.201611998__Angewandte Chemie. Wiley, 2017.https://doi.org/10.1002/ange.201611998 .

Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”https://doi.org/10.7554/eLife.28921__ELife. eLife Sciences Publications, 2017.https://doi.org/10.7554/eLife.28921 .

Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gasper Tkadik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.”https://doi.org/10.1038/s41467-017-01683-1__Nature Communications. Nature Publishing Group, 2017.https://doi.org/10.1038/s41467-017-01683-1 .

Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.”https://doi.org/10.7717/peerj.3830__PeerJ. PeerJ, 2017.https://doi.org/10.7717/peerj.3830 .

Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.”https://doi.org/10.7554/eLife.23136__ELife. eLife Sciences Publications, 2017.https://doi.org/10.7554/eLife.23136 .

Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.”https://doi.org/10.1371/journal.pgen.1007122__PLoS Genetics. Public Library of Science, 2017.https://doi.org/10.1371/journal.pgen.1007122 .

Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.”https://doi.org/10.6084/m9.figshare.5633917.v1__The Royal Society, 2017.https://doi.org/10.6084/m9.figshare.5633917.v1 .

Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.”https://doi.org/10.1371/journal.pgen.1007122.s017__Public Library of Science, 2017.https://doi.org/10.1371/journal.pgen.1007122.s017 .

Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.”https://doi.org/10.1371/journal.pcbi.1005609.s001__Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005609.s001 .

Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.”https://doi.org/10.1371/journal.pcbi.1005609.s002__Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005609.s002 .

Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.”https://doi.org/10.1371/journal.pgen.1007122.s016__Public Library of Science, 2017.https://doi.org/10.1371/journal.pgen.1007122.s016 .

Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.”https://doi.org/10.1371/journal.pcbi.1005609.s003__Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005609.s003 .

Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.”https://doi.org/10.1371/journal.pcbi.1005609.s004__Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005609.s004 .

Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.”https://doi.org/10.1371/journal.pgen.1007122.s018__Public Library of Science, 2017.https://doi.org/10.1371/journal.pgen.1007122.s018 .

Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.”https://doi.org/10.1098/rsbl.2017.0646__Biology Letters. The Royal Society, 2017.https://doi.org/10.1098/rsbl.2017.0646 .

Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.”https://doi.org/10.15479/AT:ISTA:th_916__Institute of Science and Technology Austria, 2017.https://doi.org/10.15479/AT:ISTA:th_916 .

Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”https://doi.org/10.1007/s00236-016-0278-x__Acta Informatica. Springer, 2017.https://doi.org/10.1007/s00236-016-0278-x .

Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.”https://doi.org/10.1007/s00453-016-0212-1__Algorithmica. Springer, 2017.https://doi.org/10.1007/s00453-016-0212-1 .

Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.”https://doi.org/10.1111/mmi.13597__Molecular Microbiology. Wiley-Blackwell, 2017.https://doi.org/10.1111/mmi.13597 .

Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.”https://doi.org/10.7554/eLife.25192__ELife. eLife Sciences Publications, 2017.https://doi.org/10.7554/eLife.25192 .

Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.”https://doi.org/10.1016/j.automatica.2017.03.030__Automatica. International Federation of Automatic Control, 2017.https://doi.org/10.1016/j.automatica.2017.03.030 .

Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkadik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”https://doi.org/10.1126/science.aaf4762__Science. American Association for the Advancement of Science, 2017.https://doi.org/10.1126/science.aaf4762 .

Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.”https://doi.org/10.1002/anie.201611998__Angewandte Chemie - International Edition. Wiley-Blackwell, 2017.https://doi.org/10.1002/anie.201611998 .

Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.”https://doi.org/10.7554/eLife.25100__ELife. eLife Sciences Publications, 2017.https://doi.org/10.7554/eLife.25100 .

Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.”https://doi.org/10.1371/journal.pcbi.1005609__PLoS Computational Biology. Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005609 .

Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.”https://doi.org/10.1016/j.devcel.2017.09.014__Developmental Cell. Cell Press, 2017.https://doi.org/10.1016/j.devcel.2017.09.014 .

Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.”https://doi.org/10.1021/acssynbio.6b00013__ACS Synthetic Biology. American Chemical Society, 2016.https://doi.org/10.1021/acssynbio.6b00013 .

Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.”https://doi.org/10.1137/15M103306X__SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016.https://doi.org/10.1137/15M103306X .

Miki, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,”https://doi.org/10.2514/6.2016-3764__1–19. AIAA, 2016.https://doi.org/10.2514/6.2016-3764 .

Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.”https://doi.org/10.1038/nchembio.2176__Nature Chemical Biology. Nature Publishing Group, 2016.https://doi.org/10.1038/nchembio.2176 .

Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,”https://doi.org/10.1109/ACC.2016.7526722__Vol. 2016–July. IEEE, 2016.https://doi.org/10.1109/ACC.2016.7526722 .

Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.”https://doi.org/10.1038/ncomms10333__Nature Communications. Nature Publishing Group, 2016.https://doi.org/10.1038/ncomms10333 .

Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.”https://doi.org/10.1126/science.aag0822__Science. American Association for the Advancement of Science, 2016.https://doi.org/10.1126/science.aag0822 .

Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.”https://doi.org/10.1145/2908812.2908909__In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016.https://doi.org/10.1145/2908812.2908909 .

Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.”https://doi.org/10.1073/pnas.1518830113__PNAS. National Academy of Sciences, 2016.https://doi.org/10.1073/pnas.1518830113 .

Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.”https://doi.org/10.1093/molbev/msv269__Molecular Biology and Evolution. Oxford University Press, 2016.https://doi.org/10.1093/molbev/msv269 .

Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,”https://doi.org/10.1007/978-3-319-26916-0_10__9271:173–91. Springer, 2016.https://doi.org/10.1007/978-3-319-26916-0_10 .

Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.”https://doi.org/10.1371/journal.pgen.1005974__PLoS Genetics. Public Library of Science, 2016.https://doi.org/10.1371/journal.pgen.1005974 .

Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.”https://doi.org/10.1371/journal.pgen.1005974.s015__Public Library of Science, 2016.https://doi.org/10.1371/journal.pgen.1005974.s015 .

Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.”https://doi.org/10.1093/molbev/msv270__Molecular Biology and Evolution. Oxford University Press, 2016.https://doi.org/10.1093/molbev/msv270 .

Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,”https://doi.org/10.4230/LIPIcs.CONCUR.2016.20__Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.https://doi.org/10.4230/LIPIcs.CONCUR.2016.20 .

Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,”https://doi.org/10.1007/978-3-662-49674-9_7__9636:112–29. Springer, 2016.https://doi.org/10.1007/978-3-662-49674-9_7 .

Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.”https://doi.org/10.1016/j.cub.2015.12.041__Current Biology. Cell Press, 2016.https://doi.org/10.1016/j.cub.2015.12.041 .

Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gasper Tkadik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”https://doi.org/10.1038/ncomms12307__Nature Communications. Nature Publishing Group, 2016.https://doi.org/10.1038/ncomms12307 .

Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.”https://doi.org/10.1145/2739480.2754758__In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015.https://doi.org/10.1145/2739480.2754758 .

Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Dofan Çörüf, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.”https://doi.org/10.1016/j.jtbi.2015.07.011__https://doi.org/10.1016/j.jtbi.2015.07.011__Journal of Theoretical Biology. Elsevier, 2015.https://doi.org/10.1016/j.jtbi.2015.07.011 .

Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.”https://doi.org/10.1109/TAC.2014.2364971__IEEE Transactions on Automatic Control. IEEE, 2015.https://doi.org/10.1109/TAC.2014.2364971 .

Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkadik. “Other Fitness Models for Comparison &; for Interacting TFBSs.”https://doi.org/10.1371/journal.pgen.1005639.s001__Public Library of Science, 2015.https://doi.org/10.1371/journal.pgen.1005639.s001 .

Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.”https://doi.org/10.5061/dryad.cj910__Dryad, 2015.https://doi.org/10.5061/dryad.cj910 .

Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkadik. “Dynamics of Transcription Factor Binding Site Evolution.”https://doi.org/10.1371/journal.pgen.1005639__PLoS Genetics. Public Library of Science, 2015.https://doi.org/10.1371/journal.pgen.1005639 .

Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.”https://doi.org/10.1007/978-3-662-46681-0_47__Lecture Notes in Computer Science. Springer, 2015.https://doi.org/10.1007/978-3-662-46681-0_47 .

Grabowska, Anna, Ewa Wywia, Stanislaw Dunin Horkawicz, Anna asica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.”https://doi.org/10.1371/journal.pone.0106247__PLoS One. Public Library of Science, 2014.https://doi.org/10.1371/journal.pone.0106247 .

Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.”https://doi.org/10.1007/s00285-013-0738-7__Journal of Mathematical Biology. Springer, 2014.https://doi.org/10.1007/s00285-013-0738-7 .

Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.”https://doi.org/10.1111/evo.12440__Evolution. Wiley, 2014.https://doi.org/10.1111/evo.12440 .

Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.”https://doi.org/10.5061/dryad.s42n1__Dryad, 2014.https://doi.org/10.5061/dryad.s42n1 .

Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.”https://doi.org/10.1098/rspb.2014.1679__Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2014.https://doi.org/10.1098/rspb.2014.1679 .

Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.”https://doi.org/10.5061/dryad.85dn7__Dryad, 2014.https://doi.org/10.5061/dryad.85dn7 .

Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.”https://doi.org/10.1111/evo.12373__Evolution. Wiley, 2014.https://doi.org/10.1111/evo.12373 .

Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.”https://doi.org/10.5061/dryad.jc402__Dryad, 2014.https://doi.org/10.5061/dryad.jc402 .

Milenkovi, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.”https://doi.org/10.1159/000365548__Dementia and Geriatric Cognitive Disorders. Karger Publishers, 2014.https://doi.org/10.1159/000365548 .

Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?”https://doi.org/10.1145/2463372.2463568__In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013.https://doi.org/10.1145/2463372.2463568 .

Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.”https://doi.org/10.1534/genetics.113.153536__Genetics. Genetics Society of America, 2013.https://doi.org/10.1534/genetics.113.153536 .

Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.”https://doi.org/10.1145/2463372.2463470__In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013.https://doi.org/10.1145/2463372.2463470 .

Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”https://doi.org/10.1126/science.1229858__Science. American Association for the Advancement of Science, 2013.https://doi.org/10.1126/science.1229858 .

Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.”https://doi.org/10.1098/rspb.2012.3035__Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2013.https://doi.org/10.1098/rspb.2012.3035 .

Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.”https://doi.org/10.5061/dryad.b1q2n__Dryad, 2013.https://doi.org/10.5061/dryad.b1q2n .

Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.”https://doi.org/10.1109/TCBB.2012.91__IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE, 2012.https://doi.org/10.1109/TCBB.2012.91 .

Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.”https://doi.org/10.1111/mmi.12071__Molecular Microbiology. Wiley-Blackwell, 2012.https://doi.org/10.1111/mmi.12071 .

Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.”https://doi.org/10.1371/journal.pgen.1002803__PLoS Genetics. Public Library of Science, 2012.https://doi.org/10.1371/journal.pgen.1002803 .

Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,”https://doi.org/10.1007/978-3-642-31424-7_24__7358:294–309. Springer, 2012.https://doi.org/10.1007/978-3-642-31424-7_24 .

Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.”https://doi.org/10.1016/j.bpj.2011.09.040__Biophysical Journal. Elsevier, 2011.https://doi.org/10.1016/j.bpj.2011.09.040 .

Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.

Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”https://doi.org/10.1109/QEST.2010.33__193–94. IEEE, 2010.https://doi.org/10.1109/QEST.2010.33 .

Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,”https://doi.org/10.1109/HiBi.2009.23__4:118–27. IEEE, 2009.https://doi.org/10.1109/HiBi.2009.23 .