Publications

2023

  1. Attiya, H., Castañeda, A., and Nowak, T. 2023. Topological Characterization of Task Solvability in General Models of Computation. In: Proceedings of the 37th International Symposium on Distributed Computing (DISC 2023). Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, 5:1–5:21.
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  2. Bund, J., Függer, M., and Medina, M. 2023. PALS: Distributed Gradient Clocking on Chip. IEEE Transactions on Very Large Scale Integration (VLSI) Systems.
  3. Cravo, F., Függer, M., and Nowak, T. 2023. An Allee-based Distributed Algorithm for Microbial Whole-Cell Sensors. bioRxiv.
  4. Ferdowsi, A., Függer, M., Nowak, T., and Schmid, U. 2023. Continuity of Thresholded Mode-Switched ODEs and Digital Circuit Delay Models. Proceedings of the 26th ACM International Conference on Hybrid Systems: Computation and Control (HSCC).
  5. Pandi, A., Adam, D., Zare, A., et al. 2023. Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. Nature Communications 14, 1, 7197.

2022

  1. Azad, M.S., Batista, A.C., Faulon, J.-L., Beisel, C.L., Bonnet, J., and Kushwaha, M. 2022. Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates. Journal of visualized experiments: JoVE 186.
  2. Batista, A.C., Levrier, A., Soudier, P., et al. 2022. Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts. ACS synthetic biology 11, 2, 732–746.
  3. Bérard, B., Bollig, B., Bouyer, P., Függer, M., and Sznajder, N. 2022. Synthesis in Presence of Dynamic Links. Information and Computation 289.
  4. Cravo, F., Függer, M., Nowak, T., and Prakash, G. 2022. MobsPy: A Meta-Species Language for Chemical Reaction Networks. Computational Methods in Systems Biology, Springer International Publishing, 277–285.
  5. Cravo, F. and Nowak, T. 2022. Stochastic Multi-Distribution Modeling of Inter-Contact Times. In: Proceedings of the 2022 International Conference on Information Networking (ICOIN 2022). IEEE, New York, 220–225.
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  6. Függer, M., Kinali, A., Lenzen, C., and Wiederhake, B. 2022. Fast All-Digital Clock Frequency Adaptation Circuit for Voltage Droop Tolerance. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 41, 8, 2518–2531.
  7. Függer, M., Lenzen, C., and Schmid, U. 2022. On Specifications and Proofs of Timed Circuits. In: J.-F. Raskin, K. Chatterjee, L. Doyen and R. Majumdar, eds., Principles of Systems Design: Essays Dedicated to Thomas A. Henzinger on the Occasion of His 60th Birthday. Springer Nature Switzerland, Cham, 107–130.
  8. Hérisson, J., Duigou, T., Lac, M. du, et al. 2022. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nature Communications 13.
  9. Pathania, A., Hopper, C., Pandi, A., Függer, M., Nowak, T., and Kushwaha, M. 2022. A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission. bioRxiv.
  10. Soudier, P., Faure, L., Kushwaha, M., and Faulon, J.-L. 2022. Cell-Free Biosensors and AI Integration. Methods in molecular biology (Clifton, NJ) 2433, 303–323.
  11. Soudier, P., Pinzon, D.R., Reif-Trauttmansdorff, T., et al. 2022. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima. Synthetic and systems biotechnology 7, 2, 791–801.
  12. Soudier, P., Zúñiga, A., Duigou, T., et al. 2022. PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H 2 O 2 as Signal Integrator. ACS synthetic biology 11, 8, 2578–2588.

2021

  1. Batista, A.C., Soudier, P., Kushwaha, M., and Faulon, J.-L. 2021. Optimising protein synthesis in cell-free systems, a review. Engineering Biology 5, 1, 10–19.
  2. Beal, J., Baldwin, G.S., Farny, N.G., et al. 2021. Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs. PloS one 16, 6, e0252263.
  3. Burman, J., Chen, H.-L., Chen, H.-P., et al. 2021. Time-Optimal Self-Stabilizing Leader Election in Population Protocols. In: Proceedings of the 41st ACM Symposium on Distributed Computing (PODC 2021). ACM, New York, 33–44.
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  4. Cho, D.-J., Függer, M., Hopper, C., Kushwaha, M., Nowak, T., and Soubeyran, Q. 2021. Distributed computation with continual population growth. Distributed Computing 35, 6, 547–569.
  5. Dür, W., Függer, M., and Steininger, A. 2021. Generation of a fault-tolerant clock through redundant crystal oscillators. Microelectronics Reliability 120, 114088.
  6. Függer, M., Nowak, T., and Schwarz, M. 2021. Tight Bounds for Asymptotic and Approximate Consensus. Journal of the ACM (JACM).
  7. Kennedy-Cochran-Patrick, A., Merlet, G., Nowak, T., and Sergeev, S. 2021. New bounds on the periodicity transient of the powers of a tropical matrix: Using cyclicity and factor rank. Linear Algebra and Its Applications 811, 279–309.
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  8. Maier, J., Öhlinger, D., Schmid, U., Függer, M., and Nowak, T. 2021. A Composable Glitch-Aware Delay Model. Proceedings of the 2021 on Great Lakes Symposium on VLSI, Association for Computing Machinery, 147–154.
  9. Merlet, G., Nowak, T., and Sergeev, S. 2021. On the tightness of bounds for transients of weak CSR expansions and periodicity transients of critical rows and columns of tropical matrix powers. Linear and Multilinear Algebra 70, 19, 4320–4350.
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  10. Öhlinger, D., Maier, J., Függer, M., and Schmid, U. 2021. The Involution Tool for Accurate Digital Timing and Power Analysis. Integration 76, 87–98.

2020

  1. Bakura, S.A., Lambert, A., and Nowak, T. 2020. Clock Synchronization with Exponential Smoothing for Dynamic Networks, In: Proceedings of the 54th Annual Conference on Information Sciences and Systems (CISS 2020). IEEE, New York.
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  2. Bund, J., Függer, M., Lenzen, C., and Medina, M. 2020. Synchronizer-Free Digital Link Controller. IEEE Transactions on Circuits and Systems I 67, 10, 3562–3573.
  3. Bund, J., Függer, M., Lenzen, C., Medina, M., and Rosenbaum, W. 2020. PALS: Plesiochronous and Locally Synchronous Systems. 26th IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC), IEEE Computer Society, 36–43.
  4. Bérard, B., Bollig, B., Bouyer, P., Függer, M., and Sznajder, N. 2020. Synthesis in Presence of Dynamic Links. Proceedings of the 11th International Symposium on Games, Automata, Logics, and Formal Verification (GandALF’20).
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  5. Cho, D.-J., Függer, M., Hopper, C., Kushwaha, M., Nowak, T., and Soubeyran, Q. 2020. Distributed Computation with Continual Population Growth. 34th International Symposium on Distributed Computing (DISC), Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 7:1–7:17.
  6. Függer, M., Kushwaha, M., and Nowak, T. 2020. Digital Circuit Design for Biological and Silicon Computers. In: V. Singh, ed., Advances in Synthetic Biology. Springer, Heidelberg, 153–171.
  7. Függer, M., Najvirt, R., Nowak, T., and Schmid, U. 2020. A Faithful Binary Circuit Model. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39, 10, 2784–2797.
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  8. Függer, M., Nowak, T., and Winkler, K. 2020. On the radius of nonsplit graphs and information dissemination in dynamic networks. Discrete Applied Mathematics 282, 257–264.
  9. Galizi, R., Duncan, J.N., Rostain, W., et al. 2020. Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics. The CRISPR journal 3, 5, 398–408.
  10. Xu, C., Beauquier, J., Burman, J., Kutten, S., and Nowak, T. 2020. Data collection in population protocols with non-uniformly random scheduler. Theoretical Computer Science 806, 516–530.
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2019

  1. Maier, J., Függer, M., Nowak, T., and Schmid, U. 2019. Transistor-Level Analysis of Dynamic Delay Models. 25th IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC), 76–85.
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  2. Nowak, T. and Rybicki, J. 2019. Byzantine Approximate Agreement on Graphs. In: Proceedings of the 33rd International Symposium on Distributed Computing (DISC 2019). Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, 29:1–29:17.
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  3. Nowak, T., Schmid, U., and Winkler, K. 2019. Topological Characterization of Consensus under General Message Adversaries. In: Proceedings of the 39th ACM Symposium on Distributed Computing (PODC 2019). ACM, New York, 218–227.
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  4. Pandi, A., Koch, M., Voyvodic, P.L., et al. 2019. Metabolic perceptrons for neural computing in biological systems. Nature communications 10, 1, 3880.
  5. Öhlinger, D., Maier, J., Függer, M., and Schmid, U. 2019. The Involution Tool for Accurate Digital Timing and Power Analysis. 29th International Symposium on Power and Timing Modeling, Optimization and Simulation (PATMOS), 1–8.
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2018

  1. Beal, J., Haddock-Angelli, T., Baldwin, G., et al. 2018. Quantification of bacterial fluorescence using independent calibrants. PloS one 13, 6, e0199432.
  2. Függer, M., Kinali, A., Lenzen, C., and Wiederhake, B. 2018. Fast All-Digital Clock Frequency Adaptation Circuit for Voltage Droop Tolerance. IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC), 68–77.
  3. Függer, M. and Nowak, T. 2018. Fast Multidimensional Asymptotic and Approximate Consensus. 32nd International Symposium on Distributed Computing (DISC), 27:1–27:15.
  4. Függer, M., Nowak, T., and Schwarz, M. 2018. Tight Bounds for Asymptotic and Approximate Consensus. ACM Symposium on Principles of Distributed Computing (PODC), ACM, 325–334.
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  5. Friedrichs, S., Függer, M., and Lenzen, C. 2018. Metastability-Containing Circuits. IEEE Transactions on Computers 67, 8.
  6. Függer, M., Maier, J., Najvirt, R., Nowak, T., and Schmid, U. 2018. A Faithful Binary Circuit Model with Adversarial Noise. Design, Automation & Test in Europe (DATE), IEEE, 1327–1332.
  7. Han, C.-Y., Nowak, T., and Lambert, A. 2018. Pulse Synchronization for Vehicular Networks. In: Proceedings of the 2018 IEEE Intelligent Vehicle Symposium (IV 2018). IEEE, New York, 1125–1130.
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2017

  1. Beauquier, J., Burman, J., Kutten, S., Nowak, T., and Xu, C. 2017. Data Collection in Population Protocols with Non-uniformly Random Scheduler. In: Proceedings of the 13th International Symposium on Algorithms and Experiments for Wireless Sensor Networks (ALGOSENSORS 2017). Springer, Heidelberg, 13–25.
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  2. Charron-Bost, B., Függer, M., and Nowak, T. 2017. New transience bounds for max-plus linear systems. Discrete Applied Mathematics 219, 83–99.
  3. Függer, M., Kinali, A., Lenzen, C., and Polzer, T. 2017. Metastability-Aware Memory-Efficient Time-to-Digital Converter. IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC), 49–56.
  4. Függer, M., Nowak, T., and Schwarz, M. 2017. Brief Announcement: Lower Bounds for Asymptotic Consensus in Dynamic Networks. 31st International Symposium on Distributed Computing (DISC), 51:1–51:3.
  5. Tarawneh, G., Függer, M., and Lenzen, C. 2017. Metastability Tolerant Computing. IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC), 25–32.

2016

  1. Charron-Bost, B., Függer, M., and Nowak, T. 2016. Fast, Robust, Quantizable Approximate Consensus. 43rd International Colloquium on Automata, Languages, and Programming (ICALP), 137:1–137:14.
  2. Charron-Bost, B., Függer, M., and Nowak, T. 2016. Multidimensional Asymptotic Consensus in Dynamic Networks. CoRR abs/1611.02496.
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  3. Dolev, D., Függer, M., Lenzen, C., Perner, M., and Schmid, U. 2016. HEX: Scaling honeycombs is easier than scaling clock trees. Journal of Computer and System Sciences 82, 5, 929–956.
  4. Függer, M., Nowak, T., and Schmid, U. 2016. Unfaithful Glitch Propagation in Existing Binary Circuit Models. IEEE Transactions on Computers 65, 3, 964–978.
  5. Kushwaha, M., Rostain, W., Prakash, S., Duncan, J.N., and Jaramillo, A. 2016. Using RNA as Molecular Code for Programming Cellular Function. ACS synthetic biology 5, 8, 795–809.
  6. Rodrigo, G., Prakash, S., Cordero, T., Kushwaha, M., and Jaramillo, A. 2016. Functionalization of an Antisense Small RNA. Journal of molecular biology 428, 5 Pt B, 889–892.

2015

  1. Bouillard, A. and Nowak, T. 2015. Fast Symbolic Computation of the Worst-Case Delay in Tandem Networks and Applications. Performance Evaluation 91, 270–285.
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  2. Charron-Bost, B., Függer, M., L. Welch, J., and Widder, J. 2015. Time Complexity of Link Reversal Routing. ACM Transactions on Algorithms 11, 3, 18:1–18:39.
  3. Charron-Bost, B., Függer, M., and Nowak, T. 2015. Approximate Consensus in Highly Dynamic Networks: The Role of Averaging Algorithms. 42nd International Colloquium on Automata, Languages, and Programming (ICALP), 528–539.
  4. Dolev, D., Függer, M., Lenzen, C., Schmid, U., and Steininger, A. 2015. Fault-tolerant Distributed Systems in Hardware. Bulletin of EATCS 2, 116.
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  5. Függer, M., Najvirt, R., Nowak, T., and Schmid, U. 2015. Towards Binary Circuit Models That Faithfully Capture Physical Solvability. Design, Automation & Test in Europe (DATE), 1455–1460.
  6. Függer, M., Kößler, A., Nowak, T., Schmid, U., and Zeiner, M. 2015. The effect of forgetting on the performance of a synchronizer. Performance Evaluation 93, 1–16.
  7. Függer, M., Nowak, T., and Charron-Bost, B. 2015. Diffusive clock synchronization in highly dynamic networks. 2015 49th Annual Conference on Information Sciences and Systems (CISS), 1–6.
  8. Kushwaha, M. and Salis, H.M. 2015. A portable expression resource for engineering cross-species genetic circuits and pathways. Nature communications 6, 7832.
  9. Najvirt, R., Függer, M., Nowak, T., Schmid, U., Hofbauer, M., and Schweiger, K. 2015. Experimental Validation of a Faithful Binary Circuit Model. Proceedings of the 25th Edition on Great Lakes Symposium on VLSI (GLSVLSI), ACM, 355–360.
  10. Nowak, T. 2015. Asymptotic Consensus Without Self-Confidence. In: Proceedings of the 54th IEEE Conference on Decision and Control (CDC 2015). IEEE, New York, 4133–4138.
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2014

  1. Dolev, D., Függer, M., Schmid, U., and Lenzen, C. 2014. Fault-tolerant Algorithms for Tick-generation in Asynchronous Logic: Robust Pulse Generation. Journal of the ACM (JACM) 61, 5, 30:1–30:74.
  2. Dolev, D., Függer, M., Posch, M., Schmid, U., Steininger, A., and Lenzen, C. 2014. Rigorously modeling self-stabilizing fault-tolerant circuits: An ultra-robust clocking scheme for systems-on-chip. Journal of Computer and System Sciences 80, 4, 860–900.
  3. Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., and Salis, H.M. 2014. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular systems biology 10, 6, 731.
  4. Függer, M., Kößler, A., Nowak, T., Schmid, U., and Zeiner, M. 2014. The Effect of Forgetting on the Performance of a Synchronizer. Algorithms for Sensor Systems, Springer Berlin Heidelberg, 185–200.
  5. Merlet, G., Nowak, T., Schneider, H., and Sergeev, S. 2014. Generalizations of bounds on the index of convergence to weighted digraphs. Discrete Applied Mathematics 178, 121–134.
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  6. Merlet, G., Nowak, T., Schneider, H., and Sergeev, S. 2014. Generalizations of Bounds on the Index of Convergence to Weighted Digraphs. In: Proceedings of the 53rd IEEE Conference on Decision and Control (CDC 2014). IEEE, New York, 1594–1599.
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  7. Merlet, G., Nowak, T., and Sergeev, S. 2014. Weak CSR expansions and transience bounds in max-plus algebra. Linear Algebra and Its Applications 461, 163–199.
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  8. Nowak, T. and Charron-Bost, B. 2014. General Transience Bounds in Tropical Linear Algebra via Nachtigall Decomposition. In: G.K. Litvinov and S.N. Sergeev, eds., Tropical and Idempotent Mathematics. American Mathematical Society, Providence, 277–289.
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  9. Reinbacher, T., Függer, M., and Brauer, J. 2014. Runtime verification of embedded real-time systems. Formal Methods in System Design 44, 3, 203–239.