Publications

2024

1. NACO

   Reactamole: functional reactive molecular programming

   Klinge, Titus H., Lathrop, James I., Osera, Peter-Michael,  and Rogers, Allison

   Natural Computing (Apr 2024)

   Bib HTML Code

   @article{10.1007/s11047-024-09982-5,
     author = {Klinge, Titus H. and Lathrop, James I. and Osera, Peter-Michael and Rogers, Allison},
     title = {Reactamole: functional reactive molecular programming},
     journal = {Natural Computing},
     year = {2024},
     month = apr,
     day = {19},
     issn = {1572-9796},
     doi = {10.1007/s11047-024-09982-5},
     url = {https://doi.org/10.1007/s11047-024-09982-5},
   }

2022

1. NACO

   ALCH: An imperative language for chemical reaction network-controlled tile assembly

   Klinge, Titus H., Lathrop, James I., Moreno, Sonia, Potter, Hugh D., Raman, Narun K.,  and Riley, Matthew R.

   Natural Computing (Jan 2022)

   Bib HTML

   @article{10.1007/s11047-021-09878-8,
     author = {Klinge, Titus H. and Lathrop, James I. and Moreno, Sonia and Potter, Hugh D. and Raman, Narun K. and Riley, Matthew R.},
     title = {ALCH: An imperative language for chemical reaction network-controlled tile assembly},
     journal = {Natural Computing},
     year = {2022},
     month = jan,
     day = {21},
     issn = {1572-9796},
     doi = {10.1007/s11047-021-09878-8},
     url = {https://doi.org/10.1007/s11047-021-09878-8},
   }

2020

1. TCS

   Robust biomolecular finite automata

   Klinge, Titus H., Lathrop, James I.,  and Lutz, Jack H.

   Theoretical Computer Science (Jan 2020)

   arXiv Bib HTML

   @article{10.1016/j.tcs.2020.01.008,
     title = {Robust biomolecular finite automata},
     journal = {Theoretical Computer Science},
     volume = {816},
     pages = {114-143},
     year = {2020},
     issn = {0304-3975},
     doi = {10.1016/j.tcs.2020.01.008},
     url = {https://doi.org/10.1016/j.tcs.2020.01.008},
     author = {Klinge, Titus H. and Lathrop, James I. and Lutz, Jack H.},
     keywords = {Biomolecular automata, Input/output chemical reaction networks, Concentration signals, Molecular programming, Robustness}
   }

2019

1. BIOSYS

   Robust chemical circuits

   Ellis, Samuel J.,  Klinge, Titus H.,  and Lathrop, James I.

   Biosystems (Jan 2019)

   arXiv Bib HTML

   @article{10.1016/j.biosystems.2019.103983,
     title = {Robust chemical circuits},
     journal = {Biosystems},
     volume = {186},
     pages = {103983},
     year = {2019},
     note = {Selected papers from the International Conference on the Theory and Practice of Natural Computing 2017},
     issn = {0303-2647},
     doi = {10.1016/j.biosystems.2019.103983},
     url = {https://doi.org/10.1016/j.biosystems.2019.103983},
     author = {Ellis, Samuel J. and Klinge, Titus H. and Lathrop, James I.},
     keywords = {Nanocomputing, Molecular programming, Circuits, Robustness, Chemical reaction networks}
   }

2. NACO

   Real-time computability of real numbers by chemical reaction networks

   Huang, Xiang,  Klinge, Titus H., Lathrop, James I., Li, Xiaoyuan,  and Lutz, Jack H.

   Natural Computing (Mar 2019)

   arXiv Bib HTML

   @article{10.1007/s11047-018-9706-x,
     author = {Huang, Xiang and Klinge, Titus H. and Lathrop, James I. and Li, Xiaoyuan and Lutz, Jack H.},
     title = {Real-time computability of real numbers by chemical reaction networks},
     journal = {Natural Computing},
     year = {2019},
     month = mar,
     day = {01},
     volume = {18},
     number = {1},
     pages = {63-73},
     issn = {1572-9796},
     doi = {10.1007/s11047-018-9706-x},
     url = {https://doi.org/10.1007/s11047-018-9706-x}
   }

3. TOSEM

   Runtime Fault Detection in Programmed Molecular Systems

   Ellis, Samuel J.,  Klinge, Titus H., Lathrop, James I., Lutz, Jack H., Lutz, Robyn R., Miner, Andrew S.,  and Potter, Hugh D.

   ACM Transactions on Software Engineering and Methodology (Mar 2019)

   arXiv Bib HTML

   @article{10.1145/3295740,
     author = {Ellis, Samuel J. and Klinge, Titus H. and Lathrop, James I. and Lutz, Jack H. and Lutz, Robyn R. and Miner, Andrew S. and Potter, Hugh D.},
     title = {Runtime Fault Detection in Programmed Molecular Systems},
     year = {2019},
     issue_date = {April 2019},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     volume = {28},
     number = {2},
     issn = {1049-331X},
     url = {https://doi.org/10.1145/3295740},
     doi = {10.1145/3295740},
     journal = {ACM Transactions on Software Engineering and Methodology},
     month = mar,
     articleno = {6},
     numpages = {20},
     keywords = {chemical reaction networks, molecular system safety, probabilistic model checking, requirements engineering, Molecular programming}
   }

2022

1. ICSE

   Inference and Test Generation Using Program Invariants in Chemical Reaction Networks

   Gerten, Michael C., Marsh, Alexis L., Lathrop, James I., Cohen, Myra B., Miner, Andrew S.,  and Klinge, Titus H.

   In 44th International Conference on Software Engineering (2022)

   Bib HTML PDF

   @inproceedings{10.1145/3510003.3510176,
     author = {Gerten, Michael C. and Marsh, Alexis L. and Lathrop, James I. and Cohen, Myra B. and Miner, Andrew S. and Klinge, Titus H.},
     title = {Inference and Test Generation Using Program Invariants in Chemical Reaction Networks},
     year = {2022},
     isbn = {9781450392211},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     url = {https://doi.org/10.1145/3510003.3510176},
     doi = {10.1145/3510003.3510176},
     booktitle = {44th International Conference on Software Engineering},
     pages = {1193–1205},
     numpages = {13},
     keywords = {test generation, petri nets, invariants, chemical reaction networks},
     location = {Pittsburgh, Pennsylvania},
     series = {ICSE '22}
   }

2021

1. UCNC

   Robust Real-Time Computing with Chemical Reaction Networks

   Fletcher, Willem,  Klinge, Titus H., Lathrop, James I., Nye, Dawn A.,  and Rayman, Matthew

   In 19th International Conference on Unconventional Computation and Natural Computation (2021)

   Bib HTML

   @inproceedings{10.1007/978-3-030-87993-8_3,
     author = {Fletcher, Willem and Klinge, Titus H. and Lathrop, James I. and Nye, Dawn A. and Rayman, Matthew},
     editor = {Kostitsyna, Irina and Orponen, Pekka},
     title = {Robust Real-Time Computing with Chemical Reaction Networks},
     booktitle = {19th International Conference on Unconventional Computation and Natural Computation},
     year = {2021},
     publisher = {Springer International Publishing},
     address = {Cham},
     pages = {35--50},
     isbn = {978-3-030-87993-8},
     url = {https://doi.org/10.1007/978-3-030-87993-8_3},
     doi = {10.1007/978-3-030-87993-8_3}
   }

2. DNA

   Reactamole: Functional Reactive Molecular Programming

   Klinge, Titus H., Lathrop, James I., Osera, Peter-Michael,  and Rogers, Allison

   In 27th International Conference on DNA Computing and Molecular Programming (2021)

   Bib HTML PDF Code

   @inproceedings{10.4230/LIPIcs.DNA.27.10,
     author = {Klinge, Titus H. and Lathrop, James I. and Osera, Peter-Michael and Rogers, Allison},
     title = {{Reactamole: Functional Reactive Molecular Programming}},
     booktitle = {27th International Conference on DNA Computing and Molecular Programming},
     pages = {10:1--10:20},
     series = {Leibniz International Proceedings in Informatics (LIPIcs)},
     isbn = {978-3-95977-205-1},
     issn = {1868-8969},
     year = {2021},
     volume = {205},
     editor = {Lakin, Matthew R. and \v{S}ulc, Petr},
     publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
     address = {Dagstuhl, Germany},
     url = {https://doi.org/10.4230/LIPIcs.DNA.27.10},
     urn = {urn:nbn:de:0030-drops-146775},
     doi = {10.4230/LIPIcs.DNA.27.10},
     annote = {Keywords: Chemical Reaction Network, Functional Reactive Programming, Domain Specific Language}
   }

3. ASE

   ChemTest: An Automated Software Testing Framework for an Emerging Paradigm

   Gerten, Michael C., Lathrop, James I., Cohen, Myra B.,  and Klinge, Titus H.

   In 35th IEEE/ACM International Conference on Automated Software Engineering (2021)

   Bib HTML PDF

   @inproceedings{10.1145/3324884.3416638,
     author = {Gerten, Michael C. and Lathrop, James I. and Cohen, Myra B. and Klinge, Titus H.},
     title = {ChemTest: An Automated Software Testing Framework for an Emerging Paradigm},
     year = {2021},
     isbn = {9781450367684},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     url = {https://doi.org/10.1145/3324884.3416638},
     doi = {10.1145/3324884.3416638},
     booktitle = {35th IEEE/ACM International Conference on Automated Software Engineering},
     pages = {548–560},
     numpages = {13},
     keywords = {flakiness, metamorphic testing, chemical reaction networks, software testing},
     location = {Virtual Event, Australia},
     series = {ASE '20}
   }

2020

1. DNA

   ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly

   Klinge, Titus H., Lathrop, James I., Moreno, Sonia, Potter, Hugh D., Raman, Narun K.,  and Riley, Matthew R.

   In 26th International Conference on DNA Computing and Molecular Programming (2020)

   Bib HTML PDF

   @inproceedings{10.4230/LIPIcs.DNA.2020.6,
     author = {Klinge, Titus H. and Lathrop, James I. and Moreno, Sonia and Potter, Hugh D. and Raman, Narun K. and Riley, Matthew R.},
     title = {{ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly}},
     booktitle = {26th International Conference on DNA Computing and Molecular Programming},
     pages = {6:1--6:22},
     series = {Leibniz International Proceedings in Informatics (LIPIcs)},
     isbn = {978-3-95977-163-4},
     issn = {1868-8969},
     year = {2020},
     volume = {174},
     editor = {Geary, Cody and Patitz, Matthew J.},
     publisher = {Schloss Dagstuhl--Leibniz-Zentrum f{\"u}r Informatik},
     address = {Dagstuhl, Germany},
     url = {https://doi.org/10.4230/LIPIcs.DNA.2020.6},
     urn = {urn:nbn:de:0030-drops-129592},
     doi = {10.4230/LIPIcs.DNA.2020.6}
   }

2019

1. DNA

   Real-Time Equivalence of Chemical Reaction Networks and Analog Computers

   Huang, Xiang,  Klinge, Titus H.,  and Lathrop, James I.

   In 25th International Conference on DNA Computing and Molecular Programming (2019)

   Bib HTML

   @inproceedings{10.1007/978-3-030-26807-7_3,
     author = {Huang, Xiang and Klinge, Titus H. and Lathrop, James I.},
     editor = {Thachuk, Chris and Liu, Yan},
     title = {Real-Time Equivalence of Chemical Reaction Networks and Analog Computers},
     booktitle = {25th International Conference on DNA Computing and Molecular Programming},
     year = {2019},
     publisher = {Springer International Publishing},
     address = {Cham},
     pages = {37--53},
     isbn = {978-3-030-26807-},
     url = {https://doi.org/10.1007/978-3-030-26807-7_3},
     doi = {10.1007/978-3-030-26807-7_3}
   }

2018

1. SIGCSE

   A Functional Approach to Data Science in CS1

   Dahlby Albright, Sarah,  Klinge, Titus H.,  and Rebelsky, Samuel A.

   In 49th ACM Technical Symposium on Computer Science Education (2018)

   Bib HTML

   @inproceedings{10.1145/3159450.3159550,
     author = {Dahlby Albright, Sarah and Klinge, Titus H. and Rebelsky, Samuel A.},
     title = {A Functional Approach to Data Science in CS1},
     year = {2018},
     isbn = {9781450351034},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     url = {https://doi.org/10.1145/3159450.3159550},
     doi = {10.1145/3159450.3159550},
     booktitle = {49th ACM Technical Symposium on Computer Science Education},
     pages = {1035–1040},
     numpages = {6},
     keywords = {map-reduce, cross-disciplinary courses, data science, CS1, racket, functional programming, scheme},
     location = {Baltimore, Maryland, USA},
     series = {SIGCSE '18}
   }

2017

1. TPNC

   Robust Combinatorial Circuits in Chemical Reaction Networks

   Ellis, Samuel J.,  Klinge, Titus H.,  and Lathrop, James I.

   In 6th International Conference on Theory and Practice of Natural Computing (2017)

   Bib HTML

   @inproceedings{10.1007/978-3-319-71069-3_14,
     author = {Ellis, Samuel J. and Klinge, Titus H. and Lathrop, James I.},
     editor = {Mart{\'i}n-Vide, Carlos and Neruda, Roman and Vega-Rodr{\'i}guez, Miguel A.},
     title = {Robust Combinatorial Circuits in Chemical Reaction Networks},
     booktitle = {6th International Conference on Theory and Practice of Natural Computing},
     year = {2017},
     publisher = {Springer International Publishing},
     address = {Cham},
     pages = {178--189},
     url = {https://doi.org/10.1007/978-3-319-71069-3_14},
     doi = {10.1007/978-3-319-71069-3_14},
     isbn = {978-3-319-71069-3}
   }

2. UCNC

   Real-Time Computability of Real Numbers by Chemical Reaction Networks

   Huang, Xiang,  Klinge, Titus H., Lathrop, James I., Li, Xiaoyuan,  and Lutz, Jack H.

   In 14th International Conference on Unconventional Computation and Natural Computation (2017)

   Bib HTML

   @inproceedings{10.1007/978-3-319-58187-3_3,
     author = {Huang, Xiang and Klinge, Titus H. and Lathrop, James I. and Li, Xiaoyuan and Lutz, Jack H.},
     editor = {Patitz, Matthew J. and Stannett, Mike},
     title = {Real-Time Computability of Real Numbers by Chemical Reaction Networks},
     booktitle = {14th International Conference on Unconventional Computation and Natural Computation},
     year = {2017},
     publisher = {Springer International Publishing},
     address = {Cham},
     pages = {29--40},
     url = {https://doi.org/10.1007/978-3-319-58187-3_3},
     doi = {10.1007/978-3-319-58187-3_3},
     isbn = {978-3-319-58187-3}
   }

2016

1. NANOCOM

   Robust Signal Restoration in Chemical Reaction Networks

   Klinge, Titus H.

   In 3rd ACM International Conference on Nanoscale Computing and Communication (2016)

   Bib HTML

   @inproceedings{10.1145/2967446.2967465,
     author = {Klinge, Titus H.},
     title = {Robust Signal Restoration in Chemical Reaction Networks},
     year = {2016},
     isbn = {9781450340618},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     url = {https://doi.org/10.1145/2967446.2967465},
     doi = {10.1145/2967446.2967465},
     booktitle = {3rd ACM International Conference on Nanoscale Computing and Communication},
     articleno = {6},
     numpages = {6},
     keywords = {chemical reaction networks, Molecular programming, signal restoration, robustness},
     location = {New York, NY, USA},
     series = {NANOCOM'16}
   }

2014

1. ASE

   Automated Requirements Analysis for a Molecular Watchdog Timer

   Ellis, Samuel J., Henderson, Eric R.,  Klinge, Titus H., Lathrop, James I., Lutz, Jack H., Lutz, Robyn R., Mathur, Divita,  and Miner, Andrew S.

   In 29th ACM/IEEE International Conference on Automated Software Engineering (2014)

   Bib HTML

   @inproceedings{10.1145/2642937.2643007,
     author = {Ellis, Samuel J. and Henderson, Eric R. and Klinge, Titus H. and Lathrop, James I. and Lutz, Jack H. and Lutz, Robyn R. and Mathur, Divita and Miner, Andrew S.},
     title = {Automated Requirements Analysis for a Molecular Watchdog Timer},
     year = {2014},
     isbn = {9781450330138},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     url = {https://doi.org/10.1145/2642937.2643007},
     doi = {10.1145/2642937.2643007},
     booktitle = {29th ACM/IEEE International Conference on Automated Software Engineering},
     pages = {767–778},
     numpages = {12},
     keywords = {molecular programming, chemical reaction networks, probabilistic model checking, requirements engineering},
     location = {Vasteras, Sweden},
     series = {ASE '14}
   }

2012

1. ICSE

   Engineering and Verifying Requirements for Programmable Self-Assembling Nanomachines

   Lutz, Robyn, Lutz, Jack, Lathrop, James,  Klinge, Titus, Henderson, Eric, Mathur, Divita,  and Sheasha, Dalia Abo

   In 34th International Conference on Software Engineering (2012)

   Bib HTML

   @inproceedings{10.5555/2337223.2337418,
     author = {Lutz, Robyn and Lutz, Jack and Lathrop, James and Klinge, Titus and Henderson, Eric and Mathur, Divita and Sheasha, Dalia Abo},
     title = {Engineering and Verifying Requirements for Programmable Self-Assembling Nanomachines},
     year = {2012},
     isbn = {9781467310673},
     publisher = {IEEE Press},
     booktitle = {34th International Conference on Software Engineering},
     pages = {1361–1364},
     numpages = {4},
     location = {Zurich, Switzerland},
     series = {ICSE '12},
   }