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Book

    R.G. Endres, Physical principles in sensing and signaling, Oxford University Press, January 2013

    ISBNs: 9780199600632 (hardback) and 9780199600649 (paperback)

Submissions

• J. Tica, M. Oliver Huidobro, T. Zhu, G.K.A. Wachter, R.H. Pazuki, E. Tonello, H. Siebert, M.P.H. Stumpf, R.G. Endres, M. Isalan. A three-

  node Turing gene circuit forms periodic spatial patterns in bacteria, submitted. 

• A. Matas-Gil, R.G. Endres. Unraveling biochemical spatial patterns: machine learning approaches to the inverse problem of Turing patterns,

  arxiv.org/abs/2309.06339, submitted

• R.H. Pazuki, R.G. Endres. Upper limits on the robustness of Turing models and other multiparametric dynamical systems,

   arxiv.org/abs/2309.04741, submitted

Journal publications

• M. Rudzite, S. Subramoni, R.G. Endres, A. Filloux. Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin  

   potency and type IV pili-dependent interaction. PLoS Pathog 19: e1011428 (2023).

• R. Illukkumbura, N. Hirani, J. Borrego-Pinto, T. Bland, K. Ng, L. Hubatsch, J. McQuade, R.G. Endres, N. Goehring. Design principles for  

  selective polarization of PAR proteins by cortical flows accepted at Journal of Cell Biology. J Cell Biol 222: e202209111 (2023).

• H. Cavanagh, D. Kempe, JK Mazalo, M. Biro, R.G. Endres. T cell morphodynamics reveal periodic shape oscillations in three-dimensional    migration. J. R. Soc. Interface 19: 20220081 (2022).

• J. Cook, S. Pawar, R.G. Endres. Thermodynamic constraints on the diversity of microbial ecosystems. PLoS Comp. Biol. 17: e1009643 

  (2022).

• H. Cavanagh, A. Mosbach, G. Scalliet, R. Lind, R.G. Endres. Physics-informed deep learning characterizes morphodynamics of Asian

  Soybean Rust disease. Nature Comm. 12: 6424 (2021).

• D.L. Bodor, W. Pönisch, R.G. Endres, E.K. Paluch. Of cell shapes and motion: the physical basis of animal cell migration. Dev. Cell. 52:  

  550 (2020).

• L.S. Muhle, L.J. Schumacher, S.S. Ding, A.E.X. Brown, R.G. Endres. Benefits of collective feeding in patchy food environments tested  

  with C. elegans worms. Phil. Trans. B 375: 20190382 (2020).

• J.  Cook, R.G. Endres. Thermodynamics of switching in multistable non-equilibrium systems. J. Chem. Phys. 152: 054108 (2020).

• B. Ni, R. Colin, H. Link, R.G. Endres, V. Sourjik. Growth-rate dependent resource investment in bacterial motile behavior quantitatively

  follows potential benefit of chemotaxis. Proc. Natl. Acad. Sci. USA 117: 595 (2020).
• G. Micali, R.G. Endres. Maximal information transmission is compatible with ultrasensitive biological pathways. Sci. Rep. 9: 16898 (2019).

• L. Yolland, M. Burki, S. Marcotti, A. Luchici, F. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M. Sixt, A. Davidson, W. Wood, L.

  Schumacher, R.G. Endres, M. Miodownik, B. Stramer. Persistent and polarized global actin flow is essential for directionality during cell

  migration. Nature Cell Biol 21: 1370 (2019).

• L. Tweedy, P. Witzel, D. Heinrich, R. H. Insall, R.G. Endres. Screening by changes in stereotypical behavior during cell motility. Sci. Rep.

  9: 8784 (2019).

• S.S. Ding, L.J. Schumacher, A.E. Javer, R.G. Endres, A.E.X. Brown. Shared behavioral mechanisms underlie C. elegans aggregation

   and swarming. eLife 8: e43318 (2019).

• J. Lopez-Garrido, N. Ojkic, K. Khanna, F.R. Wagner, E. Villa, R.G. Endres, K. Pogliano, Chromosome translocation inflates Bacillus   

   subtilis forespores and impacts cellular morphology. Cell 172: 758 (2018).

• L.W. Yap, R.G. Endres, Model of cell-wall dynamics during sporulation in Bacillus subtilis. Soft Matter 13: 8089 (2017).

• R.G. Endres, Entropy production selects nonequilibrium states in multistable systems. Sci. Rep. 7: 14437 (2017) [among Top 100 Scientific

   Reports Physics papers in 2017]

• G. Micali, R. Colin, V. Sourjik, R.G. Endres, Drift and behavior of E. coli cells, Biophys. J. (lett.) 113: 2321 (2017).

• D.M. Richards, R.G. Endres, How cells engulf: theoretical approaches to phagocytosis. Rep. Prog. Phys. 80: 126601 (2017).

• R. Rotrattanadumrong, R.G. Endres, Emergence of cooperativity in a model biofilm. J. Phys. D 50: 234006 (2017).

• G. De Palo, D. Yi, R.G. Endres, A critical-like collective state leads to long-range cell communication in Dictyostelium discoideum

    aggregation, PLoS Biol 15(4): e1002602 (2017).

• N. Ojkic, J. Lopez-Garrido, K. Pogliano, R.G. Endres, Cell wall remodeling drives engulfment during Bacillus subtilis sporulation,

    eLife  5: e18657 (2016).

• D.M. Richards, R.G. Endres, Target-shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis,

    Proc. Natl. Acad. Sci. USA 113: 6113 (2016).

• G. Micali, R.G. Endres, Bacterial chemotaxis: information processing, thermodynamics, and behavior. Current Opin. Microbiol. 30: 8   

    (2016).

• G. Aquino, N.S. Wingreen, R.G. Endres, Know the single-receptor sensing limit? Think again. J. Stat. Phys. 162:1353 (2016).

• S. Eismann, R.G. Endres, Protein-connectivity in chemotaxis receptor complexes. PLoS Comp. Biol. 11: e1004650 (2015).

• G. Micali, G. Aquino, D. Richards, R.G. Endres, Accurate encoding and decoding by single cells: amplitude versus frequency modulation.

    PLoS Comp. Biol. 11: e1004222 (2015).

 • R.G. Endres, Bistability: requirements on cell-volume, protein diffusion, and thermodynamics. PLoS ONE 10: e0121681 (2015).

  • N. Ojkic, J. Lopez-Garrido, K. Pogliano, R.G. Endres. Bistable forespore engulfment in Bacillus subtilis by a zipper mechanism in absence

     of the cell wall. PLoS Comp. Biol, 10: e1003912 (2014).

  • D. Clausznitzer, G. Micali, S. Neumann, V. Sourjik, R.G. Endres. Predicting chemical environments of bacteria from receptor signaling.

     PLoS Comp. Biol. 10: e1003870 (2014).

  • S. Fan, R.G. Endres. Minimal model for metabolism-dependent chemotaxis in R. sphaeroides. J. Roy. Soc. Interface 4: 20140002 (2014).

  • D. Richards, R.G. Endres. The mechanism of phagocytosis: two stages of engulfment. Biophys. J. 107: 1542 (2014).

  • G. Aquino, L. Tweedy, D. Heinrich, R.G. Endres. Memory improves precision of cell sensing in fluctuating environments. Sci. Rep. 4: 

     5688 (2014).

  • S.V. Pageon, G. Aquino, K. Lagrue, K. Köhler, R.G. Endres, D.M. Davis. Dynamics of Natural Killer cell receptor revealed by quantitative

      analysis of photoswitchable protein. Biophys. J. 105: 1987 (2013)

  • G. De Palo, R.G. Endres, Unraveling eukaryotic adaptation pathways: lessons from protocells. PLoS Comp. Biol. 9: e1003300 (2013).

  • L. Tweedy, B. Meier, J. Stephan, D. Heinrich, R.G. Endres. Distinct cell shapes determine accurate chemotaxis. Sci. Rep. 3: 2606 (2013).

  • B. Raymond, J. Young, M. Pallett, R.G. Endres, A. Clements, G. Frankel. Subversion of trafficking, apoptosis and innate immunity by

     type III secretion system effectors. Trends Microbiol 21: 430-41 (2013).

  • R.G. Endres. Signaling cross-talk: new insights require new vocabulary. Biophys. J. 103: 2241 (2012) [invited commentary].

  • A. Dart, S. Tollis, M. D. Bright, G. Frankel, R.G. Endres. The motor protein Myosin 1G functions in Fcg-mediated phagocytosis, J. Cell

     Sci. 125: 6020 (2012).

  • R.G. Endres. Intracellular chemical gradients: morphing principle in bacteria. BMC Biophys.  5: 18 (2012). [invited commentary]

  • R. Kalaji, A.P. Wheeler, J.C. Erasmus, S.Y. Lee, R.G. Endres, L. Cramer, V. M.M. Braga. ROCK1 and ROCK2 regulate epithelial

     polarization and geometric cell shape. Biol. Cell. 104: 435 (2012).

  • D. Clausznitzer, R.G. Endres. Noise characteristics of the Escherichia coli rotary motor. BMC Systems Biology 5: 151 (2011).

  • G. Aquino, D. Clausznitzer, S. Tollis, R.G. Endres. Optimal receptor-cluster size determined by intrinsic and extrinsic noise. Phys. Rev. E

    83: 021914 (2011).

  • R.G. Endres. Making an impact in biology, Phys. World 23, 16 (2010). [invited opinion piece]

  • S. Tollis, A. Dart, G. Tzircotis, R.G. Endres. The zipper mechanism in phagocytosis: energetic requirements and variability in phagocytic

     cup shape, BMC Syst. Biol. 4:149 (2010).

  • G. Aquino, R.G. Endres. Increased accuracy of ligand sensing by receptor diffusion on cell surface, Phys. Rev. E 82, 041902 (2010).

  • D. Clausznitzer, O. Oleksiuk, L. Løvdok, V. Sourjik, R.G. Endres. Chemotactic response and adaptation dynamics in Escherichia coli,

     PLoS Comp. Biol. 6: e1000784 (2010).

  • G. Aquino, R.G. Endres. Increased accuracy of ligand sensing by receptor internalization, Phys. Rev. E 81: 021909 (2010).

  • T. Gurry, O. Kahramanogullari, R.G. Endres. Assembly and signaling of Ras nanoclusters in plasma membrane. PLoS One 4: e6148

      (2009).

  • R.G. Endres. Polar chemoreceptor clustering by coupled trimers of dimers, Biophys. J. 96, 453 (2009).

   • R.G. Endres, N.S. Wingreen. Maximum likelihood and the single receptor, Phys. Rev. Lett. 103, 158101 (2009).

   • R.G. Endres, N.S Wingreen, Accuracy of direct gradient sensing by cell-surface receptors. Prog. Biophys. Mol. Biol. 100, 33 (2009).

  • R.G. Endres, N.S. Wingreen. Accuracy of direct gradient sensing by single cells, Proc. Natl. Acad. Sci. USA 105, 15749 (2008).

  • R.G. Endres, O. Oleksiuk, C.H. Hansen, Y. Meir, V. Sourjik, N.S. Wingreen. Variable sizes of E. coli chemoreceptor signaling teams, Mol. Sys. Biol. 4, 211 (2008).

  • C. H. Hansen, R.G. Endres, N.S. Wingreen, PLoS Comput. Biol. 4, e1 (2008).

  • R.G. Endres, J. Falke, N.S. Wingreen. Chemotaxis receptor complexes: from signaling to assembly, PLoS Comput. Biol. 3, e150 (2007).

  • M.S. Xu, R.G. Endres, Y. Arakawa. , Small , 1539 (2007).

  • A.R. Ureta, R.G. Endres, N.S. Wingreen, T.J. Silhavy, J. Bacteriol. , 446(2007).

  • R.G. Endres, N.S. Wingreen. Precise adaptation in bacterial chemotaxis through assistance neighborhoods, Proc. Natl. Acad. Sci. USA 103, 13040 (2006).

  • R.G. Endres, N.S. Wingreen. Weight matrices for protein-DNA binding sites from a single co-crystal structure, Phys. Rev. E 73, 061921 (2006).

  • M. Skoge, R.G. Endres, N.S. Wingreen. Biophys. J. , 4317 (2006).

  • J.E. Keymer*, R.G. Endres*, M. Skoge, Y. Meir, N.S. Wingreen. , Proc. Natl. Acad. Sci. USA , 1786 (2006). (* both contributed equally)

  • M.S. Xu, R.G. Endres, S. Tsukamoto, M. Kitamura, S. Ishida, Y. Arakawa, Small , 1168 (2005).

  • M.S. Xu, S. Tsukamoto, S. Ishida, M. Kitamura, Y. Arakawa, R.G. Endres, M. Shimoda, Appl. Phys. Lett. , 083902 (2005).

  • R.G. Endres. Accelerating all-atom protein folding simulations through reduced dihedral barriers, Mol. Sim. 31, 773 (2005).

  • A. Hübsch, R.G. Endres, D.L. Cox, R.R.P. Singh. , Phys. Rev. Lett. , 178102 (2005).

  • M.X. LaBute, R.G. Endres, D.L. Cox. , J. Chem. Phys. , 8221 (2004).

  • R.G. Endres, T.C. Schulthess, N.S. Wingreen. Toward an atomistic model for predicting transcription-factor binding sites, Proteins 57, 262 (2004).

  • R.G. Endres, D.L. Cox, R.R.P. Singh. Colloquium: the quest for high-conductance DNA, Rev. Mod. Phys. 76, 195 (2004).

  • R.G. Endres, C.Y. Fong, L.H. Yang, G. Witte, Ch. Wöll. Structural and electronic properties of pentacene molecule and molecular pentacene solid, Comp. Mat. Sci. 29, 362 (2004). (cited 57 times)

  • R.G. Endres, M.X. LaBute, D.L. Cox. Theory of adiabatic hexaamminecobalt self-exchange, J. Chem. Phys. 118, 8706 (2003).

  • R.G. Endres, D.L. Cox, R.R.P. Singh, S.K. Pati. Mediation of long range charge transfer by magnetic bound states, Phys. Rev. Lett. 88, 166601 (2002).

  • M.X. LaBute, R.V. Kulkarni, R.G. Endres, D.L. Cox. , J. Chem. Phys. , 3681 (2002).

Book chapters

ʉۢ D. Clausznitzer, J. P. Armitage, R.G. Endres, Bacterial chemotaxis: rising complexity in Systems Biology

    of Microorganisms, Horizon Scientific Press, Eds.: Brian Robertson and Brendan Wren (2012).

 

  • S. Tollis, N. Gopaldass, T. Soldati, R.G. Endres, How one cell eats another: principles of phagocytosis,

    in Systems Biology of Microorganisms, Horizon Scientific Press, Eds.: Brian Robertson

    and Brendan Wren (2012).

 

  • M.S. Xu, R.G. Endres, Y. Arakawa, Transverse electronic signature of DNA for electronic

    sequencing, in Nano Science and Technology, Springer-Verlag, Heidelberg, Ed.: K. von Klitzing

    (2007). ISSN 1434-4904.

 

  • R.G. Endres, A. Hübsch, D.L. Cox, R.R.P. Singh, Electronic properties of DNA: from elementary  

    Slater-Koster-Hückel theory of the Ï€-stack to ab initio calculations of the optical conductivity, in 

    Modern methods for theoretical physical chemistry of biopolymers, Elsevier, Amsterdam, Eds.:

    E.B. Starikov, S. Tanaka, J.P. Lewis (2006). ISBN: 0-444-52220-4.


  • R.G. Endres, Inner-sphere reorganization energies of outer-sphere self-exchange reactions    

    utilizing density functional theory, in Trends in chemical physics research, Nova Science 

    Publishers, New York, Ed.: A.N. Linke (2005). ISBN: 1-59454-483-2.


  • R.G. Endres, T.C. Schulthess, N.S. Wingreen, Preferred binding sites of gene-regulatory proteins  

    based on the deterministic dead-end elimination algorithm in Computer Simulation Studies in  

    Condensed-Matter Physics XVII, Springer Proceedings in Physics, Eds.: D.P.Landau, S.P.Lewis,

    H.-B.Schuttler (2005). ISBN: 3-540-26564-3.

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