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Found 245 Documents (Results 1–100)

Compression of multiple \(k\)-mer sets by iterative SPSS decomposition. (English) Zbl 1519.92165

Carbone, Alessandra (ed.) et al., 21st international workshop on algorithms in bioinformatics, WABI 2021, August 2–4, 2021, virtual conference. Proceedings. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 201, Article 12, 17 p. (2021).
MSC:  92D20 92-08
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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
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Lower density selection schemes via small universal hitting sets with short remaining path length. (English) Zbl 1500.92082

Schwartz, Russell (ed.), Research in computational molecular biology. 24th annual international conference, RECOMB 2020, Padua, Italy, May 10–13, 2020. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12074, 202-217 (2020).
MSC:  92D20
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Alignment- and reference-free phylogenomics with colored de Bruijn graphs. (English) Zbl 1495.92049

Huber, Katharina T. (ed.) et al., 19th international workshop on algorithms in bioinformatics, WABI 2019, Niagara Falls, NY, USA, September 8–10, 2019. Proceedings. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 143, Article 2, 14 p. (2019).
MSC:  92D15 05C90 92-08
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Simulating the DNA overlap graph in succinct space. (English) Zbl 07559194

Pisanti, Nadia (ed.) et al., 30th annual symposium on combinatorial pattern matching, CPM 2019, Pisa, Italy, June 18–20, 2019. Proceedings. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 128, Article 26, 20 p. (2019).
MSC:  68W32
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Fully-functional bidirectional Burrows-Wheeler indexes and infinite-order de Bruijn graphs. (English) Zbl 07559178

Pisanti, Nadia (ed.) et al., 30th annual symposium on combinatorial pattern matching, CPM 2019, Pisa, Italy, June 18–20, 2019. Proceedings. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 128, Article 10, 15 p. (2019).
MSC:  68W32
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MULKSG: MULtiple K Simultaneous Graph assembly. (English) Zbl 1416.92120

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, 125-136 (2019).
MSC:  92D10 68W10 05C90
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Inversion of mutually orthogonal cellular automata. (English) Zbl 1515.68196

Mauri, Giancarlo (ed.) et al., Cellular automata. 13th international conference on cellular automata for research and industry, ACRI 2018, Como, Italy, September 17–21, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 11115, 364-376 (2018).
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Reverse de Bruijn: utilizing reverse peptide synthesis to cover all amino acid \(k\)-mers. (English) Zbl 1510.92147

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, 154-166 (2018).
MSC:  92D20 05C20 92-08
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External memory BWT and LCP computation for sequence collections with applications. (English) Zbl 1494.92085

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 10, 14 p. (2018).
MSC:  92D20 92-08
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On leaf node edge switchings in spanning trees of de Bruijn graphs. (English) Zbl 1459.05152

Ghosh, Debdas (ed.) et al., Mathematics and computing. 4th international conference, ICMC 2018, Varanasi, India, January 9–11, 2018. Revised selected papers. Singapore: Springer. Commun. Comput. Inf. Sci. 834, 110-117 (2018).
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Circular slider graphs: de Bruijn, Kautz, Rauzy, lamplighters and spiders. (English) Zbl 1425.05065

Sobieczky, Florian (ed.), Unimodularity in randomly generated graphs. AMS special session on unimodularity in randomly generated graphs, Denver, CO, USA, October 8–9, 2016. Proceedings. Providence, RI: American Mathematical Society (AMS). Contemp. Math. 719, 129-154 (2018).
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A self-stabilizing general de Bruijn graph. (English) Zbl 1498.68029

Spirakis, Paul (ed.) et al., Stabilization, safety, and security of distributed systems. 19th international symposium, SSS 2017, Boston, MA, USA, November 5–8, 2017. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10616, 250-264 (2017).
MSC:  68M14 68M12 68R10
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Rainbowfish: a succinct colored de Bruijn graph representation. (English) Zbl 1436.92008

Schwartz, Russell (ed.) et al., 17th international workshop on algorithms in bioinformatics, WABI 2017, Boston, MA, USA, August 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 88, Article 18, 15 p. (2017).
MSC:  92C40 92-08 05C90
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Disentangled long-read de Bruijn graphs via optical maps. (English) Zbl 1443.92132

Schwartz, Russell (ed.) et al., 17th international workshop on algorithms in bioinformatics, WABI 2017, Boston, MA, USA, August 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 88, Article 1, 14 p. (2017).
MSC:  92D20 92-08
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On universal partial words. (English) Zbl 1378.05112

Drmota, Michael (ed.) et al., Extended abstracts of the ninth European conference on combinatorics, graph theory and applications, EuroComb 2017, Vienna, Austria, August 28 – September 1, 2017. Amsterdam: Elsevier. Electronic Notes in Discrete Mathematics 61, 231-237 (2017).
MSC:  05C45 05C38 68R15
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Layer structure of De Bruijn and Kautz digraphs. An application to deflection routing. (English) Zbl 1356.05057

de Mier, Anna (ed.) et al., Discrete mathematical days. Extended abstracts of the 10th “Jornadas de matemática discreta y algorítmica” (JMDA), Barcelona, Spain, July 6–8, 2016. Amsterdam: Elsevier. Electronic Notes in Discrete Mathematics 54, 157-162 (2016).
MSC:  05C20 05C76
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Efficient design of compact unstructured RNA libraries covering all \(k\)-mers. (English) Zbl 1367.92089

Pop, Mihai (ed.) et al., Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10–12, 2015. Proceedings. Berlin: Springer (ISBN 978-3-662-48220-9/pbk; 978-3-662-48221-6/ebook). Lecture Notes in Computer Science 9289. Lecture Notes in Bioinformatics, 308-325 (2015).
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Bloom filter trie – a data structure for pan-genome storage. (English) Zbl 1367.92034

Pop, Mihai (ed.) et al., Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10–12, 2015. Proceedings. Berlin: Springer (ISBN 978-3-662-48220-9/pbk; 978-3-662-48221-6/ebook). Lecture Notes in Computer Science 9289. Lecture Notes in Bioinformatics, 217-230 (2015).
MSC:  92C40 92-08 68P05
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Construction of a de Bruijn graph for assembly from a truncated suffix tree. (English) Zbl 1423.68120

Dediu, Adrian-Horia (ed.) et al., Language and automata theory and applications. 9th international conference, LATA 2015, Nice, France, March 2–6, 2015. Proceedings. Berlin: Springer. Lect. Notes Comput. Sci. 8977, 109-120 (2015).
MSC:  68P05 68W32 68W40
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Shifted de Bruijn graphs. (English) Zbl 1327.05154

Pinto, Raquel (ed.) et al., Coding theory and applications. 4th international Castle Meeting, ICMCTA, Palmela Castle, Portugal, September 15–18, 2014. Cham: Springer (ISBN 978-3-319-17295-8/hbk; 978-3-319-17296-5/ebook). CIM Series in Mathematical Sciences 3, 195-202 (2015).
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Reconstruction of a word from a finite set of its subwords under the unit shift hypothesis. I. Reconstruction without forbidden words. (English. Russian original) Zbl 1298.68208

Cybern. Syst. Anal. 50, No. 1, 148-156 (2014); translation from Kibern. Sist. Anal. 2014, No. 1, 168-177 (2014).
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On perfect absorbants in de Bruijn digraphs. (English) Zbl 1303.05076

Fellows, Michael (ed.) et al., Frontiers in algorithmics and algorithmic aspects in information and management. Third joint international conference, FAW-AAIM 2013, Dalian, China, June 26–28, 2013. Proceedings. Berlin: Springer (ISBN 978-3-642-38755-5/pbk). Lecture Notes in Computer Science 7924, 303-314 (2013).
MSC:  05C20 68R10
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Stationary distribution and eigenvalues for a de Bruijn process. (English) Zbl 1271.05038

Kotsireas, Ilias S. (ed.) et al., Advances in combinatorics. In part based on the 3rd Waterloo workshop on computer algebra (WWCA, W80) 2011, Waterloo, Canada, May 26–29, 2011. Dedicated to Herbert Saul Wilf on the occasion of his 80th birthday. Berlin: Springer (ISBN 978-3-642-30978-6/hbk; 978-3-642-30979-3/ebook). 101-120 (2013).
MSC:  60J27 60C05 05C80
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Designing q-unique DNA sequences with integer linear programs and Euler tours in de Bruijn graphs. (English) Zbl 1472.92162

Böcker, Sebastian (ed.) et al., German conference on bioinformatics 2012, GCB’12, September 19–22, 2012, Jena, Germany. Selected papers based on the presentations at the conference. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. OASIcs – OpenAccess Ser. Inform. 26, 82-92, electronic only (2012).
MSC:  92D20 90C10 05C92
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Constructing orthogonal de Bruijn sequences. (English) Zbl 1342.68249

Dehne, Frank (ed.) et al., Algorithms and data structures. 12th international symposium, WADS 2011, New York, NY, USA, August 15–17, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-22299-3/pbk). Lecture Notes in Computer Science 6844, 595-606 (2011).
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An algebraic analogue of a formula of Knuth. (English. French summary) Zbl 1374.05115

Proceedings of the 22nd annual international conference on formal power series and algebraic combinatorics, FPSAC 2010, San Francisco, USA, August 2–6, 2010. Nancy: The Association. Discrete Mathematics & Theoretical Computer Science (DMTCS). Discrete Mathematics and Theoretical Computer Science. Proceedings, 379-390 (2010).
MSC:  05C25 05C50
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Improving the generalized Feistel. (English) Zbl 1279.94117

Hong, Seokhie (ed.) et al., Fast software encryption. 17th international workshop, FSE 2010, Seoul, Korea, February 7–10, 2010. Revised selected papers. Berlin: Springer (ISBN 978-3-642-13857-7/pbk). Lecture Notes in Computer Science 6147, 19-39 (2010).
MSC:  94A60
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