G. Tkadik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.

M. Berry, G. Tkadik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.

S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated ion channels,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435, 2013.

D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1. Elsevier, pp. 166–180, 2013.

S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers reveals cell type specific paternal growth dominance,” Cell Reports, vol. 3, no. 3. Cell Press, pp. 960–967, 2013.

J. Levitz et al., “Optical control of metabotropic glutamate receptors,” Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013.

P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” Homology, Homotopy and Applications, vol. 15, no. 1. International Press, pp. 51–72, 2013.

E. Granot Atedgi, G. Tkadik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013.

H. Tay et al., “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013.

V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing Ltd., 2013.

B. Wang et al., “Arabidopsis TWISTED DWAR functionally interacts with auxin exporter ABC on the root plasma membrane,” Plant Cell, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.

P. Marhavý et al., “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013.

C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” PNAS, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013.

A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp. 1–228.

J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,” Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013.

M. Chmelik and V. ehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.

S. Fang et al., “Genotypic recognition and spatial responses by rice roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013.

C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” presented at the  AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.

M. Kerber and H. Edelsbrunner, “D kinetic alpha complexes and their implementation,” in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2013, pp. 70–77.

J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.

N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013.

N. H. Barton, “Does hybridisation influence speciation?  ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.

N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.

G. Tkadik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5. American Physical Society, 2013.

I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” Nature Cell Biology, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013.

P. Baster et al., “SCF^TI AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.

J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013.

S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39.

T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.

K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” Formal Methods in System Design, vol. 42, no. 2. Springer, pp. 142–174, 2013.

H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” Discrete &; Computational Geometry, vol. 49, no. 4. Springer, pp. 797–822, 2013.

C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” Computational Geometry: Theory and Applications, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.

J. Dubuis, G. Tkadik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.

N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069.

K. Chatterjee, M. H. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” Formal Methods in System Design, vol. 42, no. 3. Springer, pp. 301–327, 2013.

M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013.

D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research Foundation, 2013.

Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013.

M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.

M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.

K. Greimel et al., “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.

O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.

E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NC, and NC: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.

S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIV in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013.

S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.

A. Pbndík et al., “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013.

B. Bargmann et al., “A map of cell typespecific auxin responses,” Molecular Systems Biology, vol. 9, no. 1. Nature Publishing Group, 2013.

E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” Immunology Letters, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013.

K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” vol. 8172. Springer, pp. 118–132, 2013.

H. Robert et al., “Local auxin sources orient the apical basal axis in arabidopsis embryos,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013.

K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.

J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, TTP: Tool for Tumor Progression. IST Austria, 2013.

K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with omega-regular objectives,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 165–180, 2013.

K. Chatterjee and R. Ibsen-Jensen, Qualitative analysis of concurrent mean-payoff games. IST Austria, 2013.

T. A. Henzinger and A. Sezgin, How free is your linearizable concurrent data structure? IST Austria, 2013.

K. Chatterjee, M. Chmelik, and M. Tracol, What is decidable about partially observable Markov decision processes with <9-regular objectives. IST Austria, 2013.

K. Chatterjee and R. Ibsen-Jensen, The complexity of ergodic games. IST Austria, 2013.

K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, Perfect-information stochastic mean-payoff parity games. IST Austria, 2013.

K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, Edit distance for timed automata. IST Austria, 2013.

K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in 13th International Conference on Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25.

K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, Distributed synthesis for LTL Fragments. IST Austria, 2013.

K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria, 2013.

U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative starting positions for traditional board games. IST Austria, 2013.

T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013.

T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria, 2013.

K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013.

J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.

C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.

B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.

S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.

A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access -containing heterochromatin,” Cell, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.

J. A. Rodrigues et al., “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.

S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.

K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013.

J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.

X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.

G. Stephens, T. Mora, G. Tkadik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013.

M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.

C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification, vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.

K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in 7th International Conference on Language and Automata Theory and Applications, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.

H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877, pp. 182–183.

D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.

K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,” vol. 7795. Springer, pp. 62–77, 2013.

P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.

B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” PLoS One, vol. 8, no. 12. Public Library of Science, 2013.

J. Reiter, I. Boei, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” Evolutionary Applications, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.

I. Boei et al., “Evolutionary dynamics of cancer in response to targeted combination therapy,” eLife, vol. 2. eLife Sciences Publications, 2013.

J. Reiter, I. Boei, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in Proceedings of 25th Int. Conf. on Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.

P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.

S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” Current Biology, vol. 23, no. 1. Cell Press, pp. 76–82, 2013.

T. Brázdil, K. Chatterjee, V. Forejt, and A. Kudera, “Trading performance for stability in Markov decision processes,” in 28th Annual ACM/IEEE Symposium, New Orleans, LA, United States, 2013, pp. 331–340.

K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in Proceedings of the 16th International conference on Hybrid systems: Computation and control, Philadelphia, PA, United States, 2013, pp. 163–172.

R. Takhanov and V. Kolmogorov, “Inference algorithms for pattern-based CRFs on sequence data,” in ICML’13 Proceedings of the 30th International Conference on International, Atlanta, GA, USA, 2013, vol. 28, no. 3, pp. 145–153.

E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” Plant Signaling &; Behavior, vol. 8, no. 10. Taylor &; Francis, 2013.

D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1759. The Royal Society, 2013.

D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.

S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, Proofs of Space. IST Austria, 2013.

S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in Adenosine, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.

D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model checking: A technique to pass information between verifiers,” in Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, Cary, NC, USA, 2012.

S. Faust, K. Z. Pietrzak, and J. Schipper, “Practical leakage-resilient symmetric cryptography,” in  Conference proceedings CHES 2012, Leuven, Belgium, 2012, vol. 7428, pp. 213–232.