Ferrari, Margherita Maria; Pasotti, Anita; Traetta, Tommaso On non-isomorphic biminimal pots realizing the cube. (English) Zbl 1518.05062 Bull. Inst. Comb. Appl. 98, 122-139 (2023). MSC: 05C15 05C20 05C90 92E10 92D20 PDFBibTeX XMLCite \textit{M. M. Ferrari} et al., Bull. Inst. Comb. Appl. 98, 122--139 (2023; Zbl 1518.05062) Full Text: arXiv Link
Dias, Fernando H. C.; Williams, Lucia; Mumey, Brendan; Tomescu, Alexandru I. Fast, flexible, and exact minimum flow decompositions via ILP. (English) Zbl 1496.92066 Pe’er, Itsik (ed.), Research in computational molecular biology. 26th annual international conference, RECOMB 2022, San Diego, CA, USA, May 22–25, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13278, 230-245 (2022). MSC: 92D20 90C10 PDFBibTeX XMLCite \textit{F. H. C. Dias} et al., Lect. Notes Comput. Sci. 13278, 230--245 (2022; Zbl 1496.92066) Full Text: DOI arXiv
Khan, Shahbaz; Kortelainen, Milla; Cáceres, Manuel; Williams, Lucia; Tomescu, Alexandru I. Safety and completeness in flow decompositions for RNA assembly. (English) Zbl 1494.92088 Pe’er, Itsik (ed.), Research in computational molecular biology. 26th annual international conference, RECOMB 2022, San Diego, CA, USA, May 22–25, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13278, 177-192 (2022). MSC: 92D20 PDFBibTeX XMLCite \textit{S. Khan} et al., Lect. Notes Comput. Sci. 13278, 177--192 (2022; Zbl 1494.92088) Full Text: DOI arXiv
Mallawaarachchi, Vijini; Lin, Yu MetaCoAG: binning metagenomic contigs via composition, coverage and assembly graphs. (English) Zbl 1496.92071 Pe’er, Itsik (ed.), Research in computational molecular biology. 26th annual international conference, RECOMB 2022, San Diego, CA, USA, May 22–25, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13278, 70-85 (2022). MSC: 92D20 92-08 PDFBibTeX XMLCite \textit{V. Mallawaarachchi} and \textit{Y. Lin}, Lect. Notes Comput. Sci. 13278, 70--85 (2022; Zbl 1496.92071) Full Text: DOI
Guterman, A. E.; Kreines, E. M.; Ostroukhova, N. V. Transformations of assembly number for 4-regular graphs. (English. Russian original) Zbl 1491.05118 J. Math. Sci., New York 262, No. 1, 11-26 (2022); translation from Zap. Nauchn. Semin. POMI 504, 21-46 (2021). MSC: 05C45 05C30 05C90 92D20 PDFBibTeX XMLCite \textit{A. E. Guterman} et al., J. Math. Sci., New York 262, No. 1, 11--26 (2022; Zbl 1491.05118); translation from Zap. Nauchn. Semin. POMI 504, 21--46 (2021) Full Text: DOI
Khadiev, Kamil; Remidovskii, Vladislav Classical and quantum algorithms for constructing text from dictionary problem. (English) Zbl 07735513 Nat. Comput. 20, No. 4, 713-724 (2021). MSC: 68W32 68Q12 68W40 92D20 PDFBibTeX XMLCite \textit{K. Khadiev} and \textit{V. Remidovskii}, Nat. Comput. 20, No. 4, 713--724 (2021; Zbl 07735513) Full Text: DOI arXiv
Maruyama, Kohei; Seki, Shinnosuke Counting infinitely by oritatami co-transcriptional folding. (English) Zbl 07735493 Nat. Comput. 20, No. 2, 329-340 (2021). MSC: 68Q07 92D20 PDFBibTeX XMLCite \textit{K. Maruyama} and \textit{S. Seki}, Nat. Comput. 20, No. 2, 329--340 (2021; Zbl 07735493) Full Text: DOI
Khadiev, Kamil; Remidovskii, Vladislav Classical and quantum algorithms for assembling a text from a dictionary. (English) Zbl 07728699 Nonlinear Phenom. Complex Syst., Minsk 24, No. 3, 207-221 (2021). MSC: 81P68 68Q12 14F08 81T30 68Q07 92D20 81-10 PDFBibTeX XMLCite \textit{K. Khadiev} and \textit{V. Remidovskii}, Nonlinear Phenom. Complex Syst., Minsk 24, No. 3, 207--221 (2021; Zbl 07728699) Full Text: DOI
Fazekas, Szilárd Zsolt; Kim, Hwee; Matsuoka, Ryuichi; Morita, Reoto; Seki, Shinnosuke Linear bounds on the size of conformations in greedy deterministic oritatami. (English) Zbl 1517.68120 Int. J. Found. Comput. Sci. 32, No. 5, 575-596 (2021). MSC: 68Q07 92D20 PDFBibTeX XMLCite \textit{S. Z. Fazekas} et al., Int. J. Found. Comput. Sci. 32, No. 5, 575--596 (2021; Zbl 1517.68120) Full Text: DOI
Gatter, Thomas; von Löhneysen, Sarah; Drozdova, Polina; Hartmann, Tom; Stadler, Peter F. Economic genome assembly from low coverage illumina and nanopore data. (English) Zbl 1518.92109 Kingsford, Carl (ed.) et al., 20th international workshop on algorithms in bioinformatics. WABI 2020, September 7–9, 2020, Pisa, Italy, virtual conference. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 172, Article 10, 22 p. (2020). MSC: 92D20 92D10 92-08 PDFBibTeX XMLCite \textit{T. Gatter} et al., LIPIcs -- Leibniz Int. Proc. Inform. 172, Article 10, 22 p. (2020; Zbl 1518.92109) Full Text: DOI
Mukherjee, Kingshuk; Rossi, Massimiliano; Salmela, Leena; Boucher, Christina Fast and efficient Rmap assembly using the bi-labelled de Bruijn graph. (English) Zbl 1518.92112 Kingsford, Carl (ed.) et al., 20th international workshop on algorithms in bioinformatics. WABI 2020, September 7–9, 2020, Pisa, Italy, virtual conference. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 172, Article 9, 16 p. (2020). MSC: 92D20 92D10 92-08 PDFBibTeX XMLCite \textit{K. Mukherjee} et al., LIPIcs -- Leibniz Int. Proc. Inform. 172, Article 9, 16 p. (2020; Zbl 1518.92112) Full Text: DOI
Mallawaarachchi, Vijini G.; Wickramarachchi, Anuradha S.; Lin, Yu Graphbin2: refined and overlapped binning of metagenomic contigs using assembly graphs. (English) Zbl 1518.92110 Kingsford, Carl (ed.) et al., 20th international workshop on algorithms in bioinformatics. WABI 2020, September 7–9, 2020, Pisa, Italy, virtual conference. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 172, Article 8, 21 p. (2020). MSC: 92D20 92D10 05C90 92-08 PDFBibTeX XMLCite \textit{V. G. Mallawaarachchi} et al., LIPIcs -- Leibniz Int. Proc. Inform. 172, Article 8, 21 p. (2020; Zbl 1518.92110) Full Text: DOI
Schrinner, Sven; Goel, Manish; Wulfert, Michael; Spohr, Philipp; Schneeberger, Korbinian; Klau, Gunnar W. The longest run subsequence problem. (English) Zbl 1518.92115 Kingsford, Carl (ed.) et al., 20th international workshop on algorithms in bioinformatics. WABI 2020, September 7–9, 2020, Pisa, Italy, virtual conference. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 172, Article 6, 13 p. (2020). MSC: 92D20 92D10 92-08 68W32 PDFBibTeX XMLCite \textit{S. Schrinner} et al., LIPIcs -- Leibniz Int. Proc. Inform. 172, Article 6, 13 p. (2020; Zbl 1518.92115) Full Text: DOI
Brzozowski, Janusz A.; Kari, Lila; Li, Bai; Szykuła, Marek State complexity of overlap assembly. (English) Zbl 1458.68091 Int. J. Found. Comput. Sci. 31, No. 8, 1113-1132 (2020). MSC: 68Q45 92D20 PDFBibTeX XMLCite \textit{J. A. Brzozowski} et al., Int. J. Found. Comput. Sci. 31, No. 8, 1113--1132 (2020; Zbl 1458.68091) Full Text: DOI
Mattamira, Chiara DNA self-assembly design for gear graphs. (English) Zbl 1465.92081 Undergrad. Math J. 21, No. 1, Paper No. 11, 16 p. (2020). MSC: 92D20 05C92 PDFBibTeX XMLCite \textit{C. Mattamira}, Undergrad. Math J. 21, No. 1, Paper No. 11, 16 p. (2020; Zbl 1465.92081) Full Text: Link
Bonvicini, Simona; Ferrari, Margherita Maria On the minimum number of bond-edge types and tile types: an approach by edge-colorings of graphs. (English) Zbl 1435.05053 Discrete Appl. Math. 277, 1-13 (2020). MSC: 05C09 05C90 05C15 92D20 PDFBibTeX XMLCite \textit{S. Bonvicini} and \textit{M. M. Ferrari}, Discrete Appl. Math. 277, 1--13 (2020; Zbl 1435.05053) Full Text: DOI
Lv, Youlong; Zhang, Jie A genetic regulatory network based method for multi-objective sequencing problem in mixed-model assembly lines. (English) Zbl 1497.92100 Math. Biosci. Eng. 16, No. 3, 1228-1243 (2019). MSC: 92C42 92D20 PDFBibTeX XMLCite \textit{Y. Lv} and \textit{J. Zhang}, Math. Biosci. Eng. 16, No. 3, 1228--1243 (2019; Zbl 1497.92100) Full Text: DOI
Salas, Gicela G. Saucedo; Hernandez, Alan E. Lopez; He, Jiadi; Karki, Chitra; Xie, Yixin; Sun, Shengjie; Xian, Yuejiao; Li, Lin Using computational approaches to study dengue virus capsid assembly. (English) Zbl 1439.92145 Comput. Math. Biophys. 7, No. 1, 64-72 (2019). MSC: 92D20 92C40 92-08 PDFBibTeX XMLCite \textit{G. G. S. Salas} et al., Comput. Math. Biophys. 7, No. 1, 64--72 (2019; Zbl 1439.92145) Full Text: DOI
Han, Yo-Sub; Kim, Hwee Ruleset optimization on isomorphic oritatami systems. (English) Zbl 1423.68169 Theor. Comput. Sci. 785, 128-139 (2019). MSC: 68Q05 92D20 PDFBibTeX XMLCite \textit{Y.-S. Han} and \textit{H. Kim}, Theor. Comput. Sci. 785, 128--139 (2019; Zbl 1423.68169) Full Text: DOI Link
Guerrini, Veronica; Rosone, Giovanna Lightweight metagenomic classification via eBWT. (English) Zbl 1416.92130 Holmes, Ian (ed.) et al., Algorithms for computational biology. 6th international conference, AlCoB 2019, Berkeley, CA, USA, May 28–30, 2019. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 11488, 112-124 (2019). MSC: 92D20 62P10 PDFBibTeX XMLCite \textit{V. Guerrini} and \textit{G. Rosone}, Lect. Notes Comput. Sci. 11488, 112--124 (2019; Zbl 1416.92130) Full Text: DOI Link
Cazaux, Bastien; Lecroq, Thierry; Rivals, Eric Linking indexing data structures to de Bruijn graphs: construction and update. (English) Zbl 1423.68121 J. Comput. Syst. Sci. 104, 165-183 (2019). MSC: 68P05 68W40 92D20 PDFBibTeX XMLCite \textit{B. Cazaux} et al., J. Comput. Syst. Sci. 104, 165--183 (2019; Zbl 1423.68121) Full Text: DOI
Deng, Tao Configuration of DNA polyhedra of truncated tetrahedron, cuboctahedron, truncated octahedron. (English) Zbl 1412.92239 J. Theor. Biol. 472, 4-10 (2019). MSC: 92D20 PDFBibTeX XMLCite \textit{T. Deng}, J. Theor. Biol. 472, 4--10 (2019; Zbl 1412.92239) Full Text: DOI
Ellis-Monaghan, Joanna; Jonoska, Nataša; Pangborn, Greta Tile-based DNA nanostructures. Mathematical design and problem encoding. (English) Zbl 1409.92182 Robeva, Raina (ed.) et al., Algebraic and combinatorial computational biology. Amsterdam: Elsevier/Academic Press. Math. Sci. Eng., 35-60 (2019). MSC: 92D20 05C90 PDFBibTeX XMLCite \textit{J. Ellis-Monaghan} et al., in: Algebraic and combinatorial computational biology. Amsterdam: Elsevier/Academic Press. 35--60 (2019; Zbl 1409.92182) Full Text: DOI
Orponen, Pekka Design methods for 3D wireframe DNA nanostructures. (English) Zbl 1528.68122 Nat. Comput. 17, No. 1, 147-160 (2018). MSC: 68Q07 68U05 92D20 PDFBibTeX XMLCite \textit{P. Orponen}, Nat. Comput. 17, No. 1, 147--160 (2018; Zbl 1528.68122) Full Text: DOI
Han, Yo-Sub; Kim, Hwee; Ota, Makoto; Seki, Shinnosuke Nondeterministic seedless oritatami systems and hardness of testing their equivalence. (English) Zbl 1528.68119 Nat. Comput. 17, No. 1, 67-79 (2018). MSC: 68Q07 68U05 92D20 PDFBibTeX XMLCite \textit{Y.-S. Han} et al., Nat. Comput. 17, No. 1, 67--79 (2018; Zbl 1528.68119) Full Text: DOI
Amărioarei, Alexandru; Barad, Gefry; Czeizler, Eugen; Dobre, Ana-Maria; Iţcuş, Corina; Mitrana, Victor; Păun, Andrei; Păun, Mihaela; Spencer, Frankie; Trandafir, Romică; Tuşa, Iris DNA-guided assembly of nanocellulose meshes. (English) Zbl 1522.68203 Fagan, David (ed.) et al., Theory and practice of natural computing. 7th international conference, TPNC 2018, Dublin, Ireland, December 12–14, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 11324, 253-265 (2018). MSC: 68Q07 92D20 PDFBibTeX XMLCite \textit{A. Amărioarei} et al., Lect. Notes Comput. Sci. 11324, 253--265 (2018; Zbl 1522.68203) Full Text: DOI
Boroojeny, Ali Ebrahimpour; Shrestha, Akash; Sharifi-Zarchi, Ali; Renick Gallagher, Suzanne; Sahinalp, S. Cenk; Chitsaz, Hamidreza GTED: graph traversal edit distance. (English) Zbl 1510.92087 Raphael, Benjamin J. (ed.), Research in computational molecular biology. 22nd annual international conference, RECOMB 2018, Paris, France, April 21–24, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10812, 37-53 (2018). MSC: 92C42 92D20 05C90 90C05 92-04 PDFBibTeX XMLCite \textit{A. E. Boroojeny} et al., Lect. Notes Comput. Sci. 10812, 37--53 (2018; Zbl 1510.92087) Full Text: DOI
Walve, Riku; Rastas, Pasi; Salmela, Leena Kermit: guided long read assembly using coloured overlap graphs. (English) Zbl 1494.92091 Parida, Laxmi (ed.) et al., 18th international workshop on algorithms in bioinformatics, WABI 2018, Helsinki, Finland, August 20–22, 2018. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 113, Article 11, 11 p. (2018). MSC: 92D20 92-08 PDFBibTeX XMLCite \textit{R. Walve} et al., LIPIcs -- Leibniz Int. Proc. Inform. 113, Article 11, 11 p. (2018; Zbl 1494.92091) Full Text: DOI
Prezza, Nicola; Pisanti, Nadia; Sciortino, Marinella; Rosone, Giovanna Detecting mutations by eBWT. (English) Zbl 1494.92089 Parida, Laxmi (ed.) et al., 18th international workshop on algorithms in bioinformatics, WABI 2018, Helsinki, Finland, August 20–22, 2018. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 113, Article 3, 15 p. (2018). MSC: 92D20 92-08 PDFBibTeX XMLCite \textit{N. Prezza} et al., LIPIcs -- Leibniz Int. Proc. Inform. 113, Article 3, 15 p. (2018; Zbl 1494.92089) Full Text: DOI arXiv
Brzozowski, Janusz A.; Kari, Lila; Li, Bai; Szykuła, Marek State complexity of overlap assembly. (English) Zbl 1458.68090 Câmpeanu, Cezar (ed.), Implementation and application of automata. 23rd international conference, CIAA 2018, Charlottetown, PE, Canada, July 30 – August 2, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10977, 109-120 (2018). MSC: 68Q45 92D20 PDFBibTeX XMLCite \textit{J. A. Brzozowski} et al., Lect. Notes Comput. Sci. 10977, 109--120 (2018; Zbl 1458.68090) Full Text: DOI arXiv
Ferrari, Margherita Maria; Cook, Anna; Houlihan, Alana; Rouleau, Rebecca; Seeman, Nadrian C.; Pangborn, Greta; Ellis-Monaghan, Joanna Design formalism for DNA self-assembly of polyhedral skeletons using rigid tiles. (English) Zbl 1390.92161 J. Math. Chem. 56, No. 5, 1365-1392 (2018). MSC: 92E10 92D20 PDFBibTeX XMLCite \textit{M. M. Ferrari} et al., J. Math. Chem. 56, No. 5, 1365--1392 (2018; Zbl 1390.92161) Full Text: DOI
Kasprzak, Marta Classification of de Bruijn-based labeled digraphs. (English) Zbl 1376.05134 Discrete Appl. Math. 234, 86-92 (2018). MSC: 05C78 05C20 05C76 05C45 05C90 92D20 PDFBibTeX XMLCite \textit{M. Kasprzak}, Discrete Appl. Math. 234, 86--92 (2018; Zbl 1376.05134) Full Text: DOI
Blazewicz, Jacek; Kasprzak, Marta; Kierzynka, Michal; Frohmberg, Wojciech; Swiercz, Aleksandra; Wojciechowski, Pawel; Zurkowski, Piotr Graph algorithms for DNA sequencing – origins, current models and the future. (English) Zbl 1375.92041 Eur. J. Oper. Res. 264, No. 3, 799-812 (2018). MSC: 92D20 92C40 05C85 68R10 PDFBibTeX XMLCite \textit{J. Blazewicz} et al., Eur. J. Oper. Res. 264, No. 3, 799--812 (2018; Zbl 1375.92041) Full Text: DOI
Enaganti, Srujan Kumar; Ibarra, Oscar H.; Kari, Lila; Kopecki, Steffen On the overlap assembly of strings and languages. (English) Zbl 1415.68127 Nat. Comput. 16, No. 1, 175-185 (2017). MSC: 68Q45 68Q05 68Q10 92D20 PDFBibTeX XMLCite \textit{S. K. Enaganti} et al., Nat. Comput. 16, No. 1, 175--185 (2017; Zbl 1415.68127) Full Text: DOI
Quiroz-Ibarra, J. Emilio; Mallén-Fullerton, Guillermo M.; Fernández-Anaya, Guillermo DNA paired fragment assembly using graph theory. (English) Zbl 1461.92076 Algorithms (Basel) 10, No. 2, Paper No. 36, 14 p. (2017). MSC: 92D20 05C85 05C90 68P05 PDFBibTeX XMLCite \textit{J. E. Quiroz-Ibarra} et al., Algorithms (Basel) 10, No. 2, Paper No. 36, 14 p. (2017; Zbl 1461.92076) Full Text: DOI
Lim, Jihyuk; Park, Kunsoo Algorithm engineering for all-pairs suffix-prefix matching. (English) Zbl 1432.68608 Iliopoulos, Costas S. (ed.) et al., 16th international symposium on experimental algorithms, SEA 2017, London, UK, June 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 75, Article 14, 12 p. (2017). MSC: 68W32 92-08 92D20 PDFBibTeX XMLCite \textit{J. Lim} and \textit{K. Park}, LIPIcs -- Leibniz Int. Proc. Inform. 75, Article 14, 12 p. (2017; Zbl 1432.68608) Full Text: DOI
Rogers, Trent A.; Seki, Shinnosuke Oritatami system; a survey and the impossibility of simple simulation at small delays. (English) Zbl 1382.92211 Fundam. Inform. 154, No. 1-4, 359-372 (2017). MSC: 92D20 68Q05 PDFBibTeX XMLCite \textit{T. A. Rogers} and \textit{S. Seki}, Fundam. Inform. 154, No. 1--4, 359--372 (2017; Zbl 1382.92211) Full Text: DOI
Brenner, Michael P. Ideas about self assembly. (English) Zbl 1380.82010 Bowick, Mark J. (ed.) et al., Mathematics and materials. Lectures presented at the IAS/Park City Mathematics Institute (PCMI) Graduate Summer School, Park City, UT, USA, July 2014. Providence, RI: American Mathematical Society (AMS); Princeton, NJ: Institute for Advanced Study (IAS); Philadelphia, PA: Society for Industrial and Applied Mathematics (SIAM) (ISBN 978-1-4704-2919-5/hbk; 978-1-4704-3749-7/ebook). IAS/Park City Mathematics Series 23, 169-199 (2017). MSC: 82B03 82D60 92D20 82C31 97M50 PDFBibTeX XMLCite \textit{M. P. Brenner}, IAS/Park City Math. Ser. 23, 169--199 (2017; Zbl 1380.82010)
Mohammed, Abdulmelik; Czeizler, Elena; Czeizler, Eugen Computational modelling of the kinetic tile assembly model using a rule-based approach. (English) Zbl 1383.68032 Theor. Comput. Sci. 701, 203-215 (2017). MSC: 68Q05 92D20 PDFBibTeX XMLCite \textit{A. Mohammed} et al., Theor. Comput. Sci. 701, 203--215 (2017; Zbl 1383.68032) Full Text: DOI Link
Lim, Jihyuk; Park, Kunsoo A fast algorithm for the all-pairs suffix-prefix problem. (English) Zbl 1380.68479 Theor. Comput. Sci. 698, 14-24 (2017). MSC: 68W32 92D20 PDFBibTeX XMLCite \textit{J. Lim} and \textit{K. Park}, Theor. Comput. Sci. 698, 14--24 (2017; Zbl 1380.68479) Full Text: DOI
Liu, Yuewu; Zou, Xiufen Mathematical modeling of HIV-like particle assembly in vitro. (English) Zbl 1377.92032 Math. Biosci. 288, 46-51 (2017). MSC: 92C40 92D20 PDFBibTeX XMLCite \textit{Y. Liu} and \textit{X. Zou}, Math. Biosci. 288, 46--51 (2017; Zbl 1377.92032) Full Text: DOI
Ellis-Monaghan, Joanna A.; Pangborn, Greta; Seeman, Nadrian C.; Blakeley, Sam; Disher, Conor; Falcigno, Mary; Healy, Brianna; Morse, Ada; Singh, Bharti; Westland, Melissa Design tools for reporter strands and DNA origami scaffold strands. (English) Zbl 1370.68091 Theor. Comput. Sci. 671, 69-78 (2017). MSC: 68Q05 05C45 68Q10 68R10 68U05 92D20 PDFBibTeX XMLCite \textit{J. A. Ellis-Monaghan} et al., Theor. Comput. Sci. 671, 69--78 (2017; Zbl 1370.68091) Full Text: DOI
Ota, Makoto; Seki, Shinnosuke Rule set design problems for oritatami systems. (English) Zbl 1370.68096 Theor. Comput. Sci. 671, 26-35 (2017). MSC: 68Q05 68Q10 68Q25 68U05 92D20 PDFBibTeX XMLCite \textit{M. Ota} and \textit{S. Seki}, Theor. Comput. Sci. 671, 26--35 (2017; Zbl 1370.68096) Full Text: DOI
Mäkinen, Veli; Staneva, Valeria; Tomescu, Alexandru I.; Valenzuela, Daniel; Wilzbach, Sebastian Interval scheduling maximizing minimum coverage. (English) Zbl 1370.68040 Discrete Appl. Math. 225, 130-135 (2017). MSC: 68M20 68W25 90B35 92D20 PDFBibTeX XMLCite \textit{V. Mäkinen} et al., Discrete Appl. Math. 225, 130--135 (2017; Zbl 1370.68040) Full Text: DOI arXiv Link
Keith, Jonathan M. (ed.) Bioinformatics. Volume I. Data, sequence analysis, and evolution. 2nd edition. (English) Zbl 1378.92002 Methods in Molecular Biology 1525. New York, NY: Humana Press/Springer (ISBN 978-1-4939-6620-2/hbk; 978-1-4939-6622-6/ebook). x, 491 p. (2017). Reviewer: Irina Ioana Mohorianu (Norwich) MSC: 92-02 92-08 92C40 92D15 92D10 00B15 PDFBibTeX XMLCite \textit{J. M. Keith} (ed.), Bioinformatics. Volume I. Data, sequence analysis, and evolution. 2nd edition. New York, NY: Humana Press/Springer (2017; Zbl 1378.92002) Full Text: DOI
Majumder, Urmi; Garg, Sudhanshu; LaBean, Thomas H.; Reif, John H. Activatable tiles for compact robust programmable molecular assembly and other applications. (English) Zbl 1415.68093 Nat. Comput. 15, No. 4, 611-634 (2016). MSC: 68Q05 92D20 PDFBibTeX XMLCite \textit{U. Majumder} et al., Nat. Comput. 15, No. 4, 611--634 (2016; Zbl 1415.68093) Full Text: DOI
Fu, Lili; Jiang, Binhui; Hu, Xiaomin DNA sequence assembly of Paenibacillus Shenyangensis. (Chinese. English summary) Zbl 1374.92112 J. Northeast. Univ., Nat. Sci. 37, No. 10, 1465-1468 (2016). MSC: 92D20 92C40 PDFBibTeX XMLCite \textit{L. Fu} et al., J. Northeast. Univ., Nat. Sci. 37, No. 10, 1465--1468 (2016; Zbl 1374.92112) Full Text: DOI
Doumic, Marie; Eugène, Sarah; Robert, Philippe Asymptotics of stochastic protein assembly models. (English) Zbl 1353.92069 SIAM J. Appl. Math. 76, No. 6, 2333-2352 (2016). MSC: 92D20 60J75 60K40 92C40 PDFBibTeX XMLCite \textit{M. Doumic} et al., SIAM J. Appl. Math. 76, No. 6, 2333--2352 (2016; Zbl 1353.92069) Full Text: DOI arXiv
Osipov, V. Al. Wavelet analysis on symbolic sequences and two-fold de Bruijn sequences. (English) Zbl 1348.65185 J. Stat. Phys. 164, No. 1, 142-165 (2016). MSC: 65T60 37N25 92D20 PDFBibTeX XMLCite \textit{V. Al. Osipov}, J. Stat. Phys. 164, No. 1, 142--165 (2016; Zbl 1348.65185) Full Text: DOI arXiv
Farkaš, Tomáš; Kubán, Peter; Lucká, Mária Effective parallel multicore-optimized \(k\)-mers counting algorithm. (English) Zbl 1442.68279 Freivalds, Rūsiņš Mārtiņš (ed.) et al., SOFSEM 2016: theory and practice of computer science. 42nd international conference on current trends in theory and practice of computer science, Harrachov, Czech Republic, January 23–28, 2016. Proceedings. Berlin: Springer. Lect. Notes Comput. Sci. 9587, 469-477 (2016). MSC: 68W32 68P10 68W10 92D20 PDFBibTeX XMLCite \textit{T. Farkaš} et al., Lect. Notes Comput. Sci. 9587, 469--477 (2016; Zbl 1442.68279) Full Text: DOI
Ellis-Monaghan, Joanna A.; McDowell, Andrew; Moffatt, Iain; Pangborn, Greta DNA origami and the complexity of Eulerian circuits with turning costs. (English) Zbl 1415.68081 Nat. Comput. 14, No. 3, 491-503 (2015). MSC: 68Q05 05C45 05C85 68Q25 90C27 92D20 PDFBibTeX XMLCite \textit{J. A. Ellis-Monaghan} et al., Nat. Comput. 14, No. 3, 491--503 (2015; Zbl 1415.68081) Full Text: DOI arXiv
Mallén-Fullerton, Guillermo M.; Quiroz-Ibarra, J. Emilio; Miranda, Antonio; Fernández-Anaya, Guillermo Modified classical graph algorithms for the DNA fragment assembly problem. (English) Zbl 1461.68159 Algorithms (Basel) 8, No. 3, 754-773 (2015). MSC: 68R10 05C85 68W05 92D20 PDFBibTeX XMLCite \textit{G. M. Mallén-Fullerton} et al., Algorithms (Basel) 8, No. 3, 754--773 (2015; Zbl 1461.68159) Full Text: DOI
Kurochkina, Natalya A.; Iadarola, Michael J. Helical assemblies: structure determinants. (English) Zbl 1406.92462 J. Theor. Biol. 369, 80-84 (2015). MSC: 92D20 92C40 PDFBibTeX XMLCite \textit{N. A. Kurochkina} and \textit{M. J. Iadarola}, J. Theor. Biol. 369, 80--84 (2015; Zbl 1406.92462) Full Text: DOI
Zhou, Xu; Zhou, Yantao; Li, Kenli; Pan, Guo An efficient tile assembly model for maximum matching problem. (Chinese. English summary) Zbl 1340.68039 J. Hunan Univ., Nat. Sci. 42, No. 2, 114-120 (2015). MSC: 68Q10 68T20 92D20 68W10 68W40 PDFBibTeX XMLCite \textit{X. Zhou} et al., J. Hunan Univ., Nat. Sci. 42, No. 2, 114--120 (2015; Zbl 1340.68039)
Picardi, Ernesto (ed.) RNA bioinformatics. (English) Zbl 1318.92003 Methods in Molecular Biology 1269. New York, NY: Humana Press/Springer (ISBN 978-1-4939-2290-1/hbk; 978-1-4939-2291-8/ebook). xii, 415 p. (2015). Reviewer: Irina Ioana Mohorianu (Norwich) MSC: 92-06 92B05 92D10 92D20 92E10 00B15 PDFBibTeX XMLCite \textit{E. Picardi} (ed.), RNA bioinformatics. New York, NY: Humana Press/Springer (2015; Zbl 1318.92003) Full Text: DOI Link
Ezzeddine, Anna Bou; Kasala, Stefan; Navrat, Pavol Applying the firefly approach to the dna fragments assembly problem. (English) Zbl 1313.92041 Ann. Univ. Sci. Budap. Rolando Eötvös, Sect. Comput. 42, 69-81 (2014). MSC: 92D20 68T20 PDFBibTeX XMLCite \textit{A. B. Ezzeddine} et al., Ann. Univ. Sci. Budap. Rolando Eötvös, Sect. Comput. 42, 69--81 (2014; Zbl 1313.92041)
Cameron, Maria; Vanden-Eijnden, Eric Flows in complex networks: theory, algorithms, and application to lennard-Jones cluster rearrangement. (English) Zbl 1301.82031 J. Stat. Phys. 156, No. 3, 427-454 (2014). MSC: 82C05 60J75 82C20 60J27 65C40 PDFBibTeX XMLCite \textit{M. Cameron} and \textit{E. Vanden-Eijnden}, J. Stat. Phys. 156, No. 3, 427--454 (2014; Zbl 1301.82031) Full Text: DOI arXiv
Demaine, Erik D.; Demaine, Martin L.; Fekete, Sándor P.; Patitz, Matthew J.; Schweller, Robert T.; Winslow, Andrew; Woods, Damien One tile to rule them all: simulating any tile assembly system with a single universal tile. (English) Zbl 1410.68123 Esparza, Javier (ed.) et al., Automata, languages, and programming. 41st international colloquium, ICALP 2014, Copenhagen, Denmark, July 8–11, 2014. Proceedings, Part I. Berlin: Springer. Lect. Notes Comput. Sci. 8572, 368-379 (2014). MSC: 68Q05 92D20 PDFBibTeX XMLCite \textit{E. D. Demaine} et al., Lect. Notes Comput. Sci. 8572, 368--379 (2014; Zbl 1410.68123) Full Text: DOI Link
Göös, Mika; Lempiäinen, Tuomo; Czeizler, Eugen; Orponen, Pekka Search methods for tile sets in patterned DNA self-assembly. (English) Zbl 1311.68150 J. Comput. Syst. Sci. 80, No. 1, 297-319 (2014). MSC: 68T20 52C20 68Q17 92D20 PDFBibTeX XMLCite \textit{M. Göös} et al., J. Comput. Syst. Sci. 80, No. 1, 297--319 (2014; Zbl 1311.68150) Full Text: DOI arXiv
Blazewicz, Jacek; Frohmberg, Wojciech; Gawron, Piotr; Kasprzak, Marta; Kierzynka, Michal; Swiercz, Aleksandra; Wojciechowski, Pawel DNA sequence assembly involving an acyclic graph model. (English) Zbl 1328.92052 Found. Comput. Decis. Sci. 38, No. 1, 25-34 (2013). MSC: 92D20 92E10 05C90 PDFBibTeX XMLCite \textit{J. Blazewicz} et al., Found. Comput. Decis. Sci. 38, No. 1, 25--34 (2013; Zbl 1328.92052) Full Text: DOI
Burns, Jonathan; Dolzhenko, Egor; Jonoska, Nataša; Muche, Tilahun; Saito, Masahico Four-regular graphs with rigid vertices associated to DNA recombination. (English) Zbl 1287.05063 Discrete Appl. Math. 161, No. 10-11, 1378-1394 (2013). MSC: 05C30 05C90 92D20 92D10 PDFBibTeX XMLCite \textit{J. Burns} et al., Discrete Appl. Math. 161, No. 10--11, 1378--1394 (2013; Zbl 1287.05063) Full Text: DOI
Czeizler, Eugen; Popa, Alexandru Synthesizing minimal tile sets for complex patterns in the framework of patterned DNA self-assembly. (English) Zbl 1296.68065 Theor. Comput. Sci. 499, 23-37 (2013). MSC: 68Q17 05B45 92D20 PDFBibTeX XMLCite \textit{E. Czeizler} and \textit{A. Popa}, Theor. Comput. Sci. 499, 23--37 (2013; Zbl 1296.68065) Full Text: DOI
Chandran, Harish; Gopalkrishnan, Nikhil; Reif, John Tile complexity of approximate squares. (English) Zbl 1262.68185 Algorithmica 66, No. 1, 1-17 (2013). MSC: 68W25 68Q25 92D20 PDFBibTeX XMLCite \textit{H. Chandran} et al., Algorithmica 66, No. 1, 1--17 (2013; Zbl 1262.68185) Full Text: DOI
Maňuch, Ján; Stacho, Ladislav; Stoll, Christine Step-wise tile assembly with a constant number of tile types. (English) Zbl 1251.68103 Nat. Comput. 11, No. 3, 535-550 (2012). MSC: 68Q05 92D20 52C45 90C27 PDFBibTeX XMLCite \textit{J. Maňuch} et al., Nat. Comput. 11, No. 3, 535--550 (2012; Zbl 1251.68103) Full Text: DOI
Angeleska, Angela; Jonoska, Nataša; Saito, Masahico Rewriting rule chains modeling DNA rearrangement pathways. (English) Zbl 1284.68314 Theor. Comput. Sci. 454, 5-22 (2012). MSC: 68Q42 92D20 PDFBibTeX XMLCite \textit{A. Angeleska} et al., Theor. Comput. Sci. 454, 5--22 (2012; Zbl 1284.68314) Full Text: DOI
Brijder, Robert; Gillis, Joris J. M.; Van den Bussche, Jan A comparison of graph-theoretic DNA hybridization models. (English) Zbl 1242.68082 Theor. Comput. Sci. 429, 46-53 (2012). MSC: 68P05 68P15 68R10 68Q10 05C78 92D20 PDFBibTeX XMLCite \textit{R. Brijder} et al., Theor. Comput. Sci. 429, 46--53 (2012; Zbl 1242.68082) Full Text: DOI
Majumder, Urmi; Reif, John H. Design of a biomolecular device that executes process algebra. (English) Zbl 1214.68250 Nat. Comput. 10, No. 1, 447-466 (2011). MSC: 68Q85 68Q05 92C40 92D20 PDFBibTeX XMLCite \textit{U. Majumder} and \textit{J. H. Reif}, Nat. Comput. 10, No. 1, 447--466 (2011; Zbl 1214.68250) Full Text: DOI
Kurochkina, Natalya Helix-helix interactions and their impact on protein motifs and assemblies. (English) Zbl 1406.92461 J. Theor. Biol. 264, No. 2, 585-592 (2010). MSC: 92D20 PDFBibTeX XMLCite \textit{N. Kurochkina}, J. Theor. Biol. 264, No. 2, 585--592 (2010; Zbl 1406.92461) Full Text: DOI
Keener, J. P. A molecular ruler mechanism for length control of extended protein structures in bacteria. (English) Zbl 1406.92459 J. Theor. Biol. 263, No. 4, 481-489 (2010). MSC: 92D20 35Q92 PDFBibTeX XMLCite \textit{J. P. Keener}, J. Theor. Biol. 263, No. 4, 481--489 (2010; Zbl 1406.92459) Full Text: DOI
Rogojin, Vladimir On computational properties of gene assembly in ciliates. (English) Zbl 1232.92061 Comput. Sci. J. Mold. 18, No. 2(53), 171-209 (2010). MSC: 92D20 68Q99 68Q10 PDFBibTeX XMLCite \textit{V. Rogojin}, Comput. Sci. J. Mold. 18, No. 2(53), 171--209 (2010; Zbl 1232.92061)
Dal Palù, Alessandro; Dovier, Agostino; Fogolari, Federico; Pontelli, Enrico CLP-based protein fragment assembly. (English) Zbl 1209.68089 Theory Pract. Log. Program. 10, No. 4-6, 709-724 (2010). MSC: 68N17 PDFBibTeX XMLCite \textit{A. Dal Palù} et al., Theory Pract. Log. Program. 10, No. 4--6, 709--724 (2010; Zbl 1209.68089) Full Text: DOI arXiv
Jonoska, Nataša; McColm, Gregory L. Complexity classes for self-assembling flexible tiles. (English) Zbl 1169.68019 Theor. Comput. Sci. 410, No. 4-5, 332-346 (2009). MSC: 68Q15 68Q10 92D20 PDFBibTeX XMLCite \textit{N. Jonoska} and \textit{G. L. McColm}, Theor. Comput. Sci. 410, No. 4--5, 332--346 (2009; Zbl 1169.68019) Full Text: DOI
Harju, Tero; Li, Chang; Petre, Ion Graph theoretic approach to parallel gene assembly. (English) Zbl 1200.05238 Discrete Appl. Math. 156, No. 18, 3416-3429 (2008). MSC: 05C90 05C22 05C70 92D20 PDFBibTeX XMLCite \textit{T. Harju} et al., Discrete Appl. Math. 156, No. 18, 3416--3429 (2008; Zbl 1200.05238) Full Text: DOI
Rolfsson, Ottar; Toropova, Katerina; Morton, Victoria; Francese, Simona; Basnak, Gabriella; Thompson, Gary S.; Homans, Stephen W.; Ashcroft, Alison E.; Stonehouse, Nicola J.; Ranson, Neil A.; Stockley, Peter G. RNA packing specificity and folding during assembly of the bacteriophage MS2. (English) Zbl 1154.92019 Comput. Math. Methods Med. 9, No. 3-4, 339-349 (2008). MSC: 92C40 PDFBibTeX XMLCite \textit{O. Rolfsson} et al., Comput. Math. Methods Med. 9, No. 3--4, 339--349 (2008; Zbl 1154.92019) Full Text: DOI EuDML
Tolley, Arron C.; Stonehouse, Nicola J. Conformational changes in the connector protein complex of the bacteriophage \(\varphi 29\) DNA packaging motor. (English) Zbl 1154.92313 Comput. Math. Methods Med. 9, No. 3-4, 327-337 (2008). MSC: 92C40 PDFBibTeX XMLCite \textit{A. C. Tolley} and \textit{N. J. Stonehouse}, Comput. Math. Methods Med. 9, No. 3--4, 327--337 (2008; Zbl 1154.92313) Full Text: DOI EuDML
Bennett, Antonette; McKenna, Robert; Agbandje-McKenna, Mavis A comparative analysis of the structural architecture of ssDNA viruses. (English) Zbl 1155.92309 Comput. Math. Methods Med. 9, No. 3-4, 183-196 (2008). MSC: 92C40 92C05 PDFBibTeX XMLCite \textit{A. Bennett} et al., Comput. Math. Methods Med. 9, No. 3--4, 183--196 (2008; Zbl 1155.92309) Full Text: DOI EuDML
Majumder, Urmi; LaBean, Thomas H.; Reif, John H. Activatable tiles: Compact, robust programmable assembly and other applications. (English) Zbl 1137.68398 Garzon, Max H. (ed.) et al., DNA computing. 13th international meeting on DNA computing, DNA13, Memphis, TN, USA, June 4–8, 2007. Revised selected papers. Berlin: Springer (ISBN 978-3-540-77961-2/pbk). Lecture Notes in Computer Science 4848, 15-25 (2008). MSC: 68Q10 68Q05 52C20 92C40 92D20 PDFBibTeX XMLCite \textit{U. Majumder} et al., Lect. Notes Comput. Sci. 4848, 15--25 (2008; Zbl 1137.68398) Full Text: DOI
Kesseler, Kevin J.; Kaufmann, William K.; Reardon, Joyce T.; Elston, Timothy C.; Sancar, Aziz A mathematical model for human nucleotide excision repair: damage recognition by random order assembly and kinetic proofreading. (English) Zbl 1453.92210 J. Theor. Biol. 249, No. 2, 361-375 (2007). MSC: 92D10 92D20 PDFBibTeX XMLCite \textit{K. J. Kesseler} et al., J. Theor. Biol. 249, No. 2, 361--375 (2007; Zbl 1453.92210) Full Text: DOI Link
Keef, T.; Micheletti, C.; Twarock, R. Master equation approach to the assembly of viral capsids. (English) Zbl 1447.92305 J. Theor. Biol. 242, No. 3, 713-721 (2006). MSC: 92D20 92C40 PDFBibTeX XMLCite \textit{T. Keef} et al., J. Theor. Biol. 242, No. 3, 713--721 (2006; Zbl 1447.92305) Full Text: DOI arXiv
Bouchard, Ann M.; Osbourn, Gordon C. Dynamic self-assembly in living systems as computation. (English) Zbl 1113.68050 Nat. Comput. 5, No. 4, 321-362 (2006). MSC: 68Q05 PDFBibTeX XMLCite \textit{A. M. Bouchard} and \textit{G. C. Osbourn}, Nat. Comput. 5, No. 4, 321--362 (2006; Zbl 1113.68050) Full Text: DOI
Franco, Giuditta; Jonoska, Nataša Forbidding-enforcing graphs for self-assembly. (English) Zbl 1089.68041 Congr. Numerantium 177, 51-63 (2005). MSC: 68Q10 68R10 92D20 PDFBibTeX XMLCite \textit{G. Franco} and \textit{N. Jonoska}, Congr. Numerantium 177, 51--63 (2005; Zbl 1089.68041)
Carbone, Alessandra; Mao, Chengde; Constantinou, Pamela E.; Ding, Baoquan; Kopatsch, Jens; Sherman, William B.; Seeman, Nadrian C. 3D fractal DNA assembly from coding, geometry and protection. (English) Zbl 1061.68163 Nat. Comput. 3, No. 3, 235-252 (2004). MSC: 68U05 92D20 28A80 PDFBibTeX XMLCite \textit{A. Carbone} et al., Nat. Comput. 3, No. 3, 235--252 (2004; Zbl 1061.68163)
Carbone, Alessandra; Seeman, Nadrian C. Coding and geometrical shapes in nanostructures: a fractal DNA-assembly. (English) Zbl 1058.68094 Nat. Comput. 2, No. 2, 133-151 (2003). MSC: 68T05 92D20 28A80 PDFBibTeX XMLCite \textit{A. Carbone} and \textit{N. C. Seeman}, Nat. Comput. 2, No. 2, 133--151 (2003; Zbl 1058.68094) Full Text: DOI
Sa-Ardyen, Phiset; Jonoska, Nataša; Seeman, Nadrian C. Self-assembling DNA graphs. (English) Zbl 1059.68604 Nat. Comput. 2, No. 4, 427-438 (2003). MSC: 68R10 68Q05 92D20 PDFBibTeX XMLCite \textit{P. Sa-Ardyen} et al., Nat. Comput. 2, No. 4, 427--438 (2003; Zbl 1059.68604) Full Text: DOI
Blayo, Philippe; Rouzé, Pierre; Sagot, Marie-France Orphan gene finding – an exon assembly approach. (English) Zbl 1038.68147 Theor. Comput. Sci. 290, No. 3, 1407-1431 (2003). MSC: 68W05 PDFBibTeX XMLCite \textit{P. Blayo} et al., Theor. Comput. Sci. 290, No. 3, 1407--1431 (2003; Zbl 1038.68147) Full Text: DOI
Parsons, Rebecca J. Evolutionary approaches to computational biology. (English) Zbl 0918.92022 Salzberg, Steven L. (ed.) et al., Computational methods in molecular biology. Amsterdam: Elsevier. New Comprehensive Biochemistry. 32, 165-186 (1998). MSC: 92D15 92-08 92D20 PDFBibTeX XMLCite \textit{R. J. Parsons}, in: Computational methods in molecular biology. Amsterdam: Elsevier. 165--186 (1998; Zbl 0918.92022)
Huang, Xiaoqiu Assembly of shotgun sequencing data. (English) Zbl 0860.92018 Speed, Terry (ed.) et al., Genetic mapping and DNA sequencing. Proceedings of the 1994 IMA summer program on molecular biology. New York, NY: Springer. IMA Vol. Math. Appl. 81, 207-215 (1996). MSC: 92C40 92D20 92-08 PDFBibTeX XMLCite \textit{X. Huang}, IMA Vol. Math. Appl. 81, 207--215 (1996; Zbl 0860.92018)
Kececioglu, J. D.; Myers, E. W. Combinatorial algorithms for DNA sequence assembly. (English) Zbl 0831.92013 Algorithmica 13, No. 1-2, 7-51 (1995). MSC: 92C40 92-08 68R10 68Q25 92D20 PDFBibTeX XMLCite \textit{J. D. Kececioglu} and \textit{E. W. Myers}, Algorithmica 13, No. 1--2, 7--51 (1995; Zbl 0831.92013) Full Text: DOI
Berger, Bonnie; Shor, Peter W.; Tucker-Kellogg, Lisa; King, Jonathan Local rule-based theory of virus shell assembly. (English) Zbl 0799.92004 Proc. Natl. Acad. Sci. USA 91, No. 16, 7732-7736 (1994). MSC: 92C40 PDFBibTeX XMLCite \textit{B. Berger} et al., Proc. Natl. Acad. Sci. USA 91, No. 16, 7732--7736 (1994; Zbl 0799.92004) Full Text: DOI Link