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Found 644 Documents (Results 1–100)

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Tong, Xin; Yu, Yixiao; Fang, Ziyi; Jiang, Haitao; Wang, Lusheng; Zhu, Binhai; Zhu, Daming

Cabbage can’t always be transformed into turnip: decision algorithms for sorting by symmetric reversals. (English) Zbl 07900448

Wu, Weili (ed.) et al., Computing and combinatorics. 29th international conference, COCOON 2023, Hawaii, HI, USA, December 15–17, 2023. Proceedings. Part II. Cham: Springer. Lect. Notes Comput. Sci. 14423, 279-294 (2024).
MSC:  68Rxx
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Bailey, Lora; Blake, Heather Smith; Cochran, Garner; Fox, Nathan; Levet, Michael; Mahmoud, Reem; Matson, Elizabeth Bailey; Singgih, Inne; Stadnyk, Grace; Wang, Xinyi; Wiedemann, Alexander

Complexity and enumeration in models of genome rearrangement. (English) Zbl 07900281

Wu, Weili (ed.) et al., Computing and combinatorics. 29th international conference, COCOON 2023, Hawaii, HI, USA, December 15–17, 2023. Proceedings. Part I. Cham: Springer. Lect. Notes Comput. Sci. 14422, 3-14 (2024).
MSC:  68Rxx
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Tubiana, Luca; Alexander, Gareth P.; Barbensi, Agnese; Buck, Dorothy; Cartwright, Julyan H. E.; Chwastyk, Mateusz; Cieplak, Marek; Coluzza, Ivan; Čopar, Simon; Craik, David J.; Di Stefano, Marco; Everaers, Ralf; Faísca, Patrícia F. N.; Ferrari, Franco; Giacometti, Achille; Goundaroulis, Dimos; Haglund, Ellinor; Hou, Ya-Ming; Ilieva, Nevena; Jackson, Sophie E.; Japaridze, Aleksandre; Kaplan, Noam; Klotz, Alexander R.; Li, Hongbin; Likos, Christos N.; Locatelli, Emanuele; López-León, Teresa; Machon, Thomas; Micheletti, Cristian; Michieletto, Davide; Niemi, Antti; Niemyska, Wanda; Niewieczerzal, Szymon; Nitti, Francesco; Orlandini, Enzo; Pasquali, Samuela; Perlinska, Agata P.; Podgornik, Rudolf; Potestio, Raffaello; Pugno, Nicola M.; Ravnik, Miha; Ricca, Renzo; Rohwer, Christian M.; Rosa, Angelo; Smrek, Jan; Souslov, Anton; Stasiak, Andrzej; Steer, Danièle; Sułkowska, Joanna; Sułkowski, Piotr; Sumners, De Witt L.; Svaneborg, Carsten; Szymczak, Piotr; Tarenzi, Thomas; Travasso, Rui; Virnau, Peter; Vlassopoulos, Dimitris; Ziherl, Primož; Žumer, Slobodan

Topology in soft and biological matter. (English) Zbl 07886110

Phys. Rep. 1075, 1-137 (2024).
MSC:  81-XX 82-XX
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Cairo, Massimo; Khan, Shahbaz; Rizzi, Romeo; Schmidt, Sebastian; Tomescu, Alexandru I.; Zirondelli, Elia C.

Cut paths and their remainder structure, with applications. (English) Zbl 07922886

Berenbrink, Petra (ed.) et al., 40th international symposium on theoretical aspects of computer science, STACS 2023, Hamburg, Germany, March 7–9, 2023. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 254, Article 17, 17 p. (2023).
MSC:  68Qxx
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Simonaitis, Pijus; Raphael, Benjamin J.

A maximum parsimony principle for multichromosomal complex genome rearrangements. (English) Zbl 07896517

Boucher, Christina (ed.) et al., 22nd international workshop on algorithms in bioinformatics, WABI 2022, Potsdam, Germany, September 5–7, 2022. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 242, Article 21, 22 p. (2022).
MSC:  92D10 92D20 92C32 92-08
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Wei, Wei; Koslicki, David

WGSUniFrac: applying UniFrac metric to whole genome shotgun data. (English) Zbl 07896511

Boucher, Christina (ed.) et al., 22nd international workshop on algorithms in bioinformatics, WABI 2022, Potsdam, Germany, September 5–7, 2022. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 242, Article 15, 22 p. (2022).
MSC:  92D10 92B10 92D15 92-08
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Braga, Marília D. V.; Brockmann, Leonie R.; Klerx, Katharina; Stoye, Jens

A linear time algorithm for an extended version of the breakpoint double distance. (English) Zbl 07896509

Boucher, Christina (ed.) et al., 22nd international workshop on algorithms in bioinformatics, WABI 2022, Potsdam, Germany, September 5–7, 2022. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 242, Article 13, 16 p. (2022).
MSC:  92D10 92-08 05C12
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Gascon, Mathieu; El-Mabrouk, Nadia

Non-binary tree reconciliation with endosymbiotic gene transfer. (English) Zbl 1542.92087

Boucher, Christina (ed.) et al., 22nd international workshop on algorithms in bioinformatics, WABI 2022, Potsdam, Germany, September 5–7, 2022. Wadern: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 242, Article 5, 20 p. (2022).
Reviewer: Irina Ioana Mohorianu (Oxford)
MSC:  92D10 92-08
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Lima Brito, Klairton; Rodrigues Oliveira, Andre; Oliveira Alexandrino, Alexsandro; Dias, Ulisses; Dias, Zanoni

A new approach for the reversal distance with indels and moves in intergenic regions. (English) Zbl 1496.92051

Jin, Lingling (ed.) et al., Comparative genomics. 19th international conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20–21, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13234, 205-220 (2022).
MSC:  92D10
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Rodrigues Oliveira, Andre; Oliveira Alexandrino, Alexsandro; Jean, Géraldine; Fertin, Guillaume; Dias, Ulisses; Dias, Zanoni

Sorting by \(k\)-cuts on signed permutations. (English) Zbl 1496.92053

Jin, Lingling (ed.) et al., Comparative genomics. 19th international conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20–21, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13234, 189-204 (2022).
MSC:  92D10 68W25 68R10 92-08
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Zeira, Ron; Mon, Geoffrey; Raphael, Benjamin J.

Genome halving and aliquoting under the copy number distance. (English) Zbl 1519.92177

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 18, 25 p. (2021).
MSC:  92D20 92-08
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Išerić, Hamza; Alkan, Can; Hach, Faraz; Numanagić, Ibrahim

BISER: fast characterization of segmental duplication structure in multiple genome assemblies. (English) Zbl 1519.92163

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 15, 18 p. (2021).
MSC:  92D20 92-08
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Nakagawa, Yoshiki; Ohata, Satsuya; Shimizu, Kana

Efficient privacy-preserving variable-length substring match for genome sequence. (English) Zbl 1519.92168

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 2, 23 p. (2021).
MSC:  92D20 92D10 92-08 94A62
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Eizenga, Jordan M.; Lorig-Roach, Ryan; Meredith, Melissa M.; Paten, Benedict

Walk-preserving transformation of overlapped sequence graphs into blunt sequence graphs with GetBlunted. (English) Zbl 07495165

De Mol, Liesbeth (ed.) et al., Connecting with computability. 17th conference on computability in Europe, CiE 2021, virtual event, Ghent, Belgium, July 5–9, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12813, 169-177 (2021).
MSC:  68Qxx
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Brito, Klairton Lima; Alexandrino, Alexsandro Oliveira; Oliveira, Andre Rodrigues; Dias, Ulisses; Dias, Zanoni

Reversals distance considering flexible intergenic regions sizes. (English) Zbl 1480.92134

Martín-Vide, Carlos (ed.) et al., Algorithms for computational biology. 8th international conference, AlCoB 2021, Missoula, MT, USA, June 7–11, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12715, 134-145 (2021).
MSC:  92D10 05C90
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Alexandrino, Alexsandro Oliveira; Brito, Klairton Lima; Oliveira, Andre Rodrigues; Dias, Ulisses; Dias, Zanoni

Reversal distance on genomes with different gene content and intergenic regions information. (English) Zbl 1480.92133

Martín-Vide, Carlos (ed.) et al., Algorithms for computational biology. 8th international conference, AlCoB 2021, Missoula, MT, USA, June 7–11, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12715, 121-133 (2021).
MSC:  92D10 05C90
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Akalin, Altuna
[Franke, Verdan; Uyar, Bora; Ronen, Jonathan]

Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen. (English) Zbl 1482.92002

Chapman & Hall/CRC Computational Biology Series. Boca Raton, FL: CRC Press (ISBN 978-1-4987-8185-5/hbk; 978-0-367-63460-5/pbk; 978-0-429-08431-7/ebook). xxii, 440 p. (2021).
Reviewer: Irina Ioana Mohorianu (Oxford)
MSC:  92-02 92D10 62P10
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Labarre, Anthony

Sorting by prefix block-interchanges. (English) Zbl 07765413

Cao, Yixin (ed.) et al., 31st international symposium on algorithms and computation, ISAAC 2020, Hong Kong, China, virtual conference, December 14–18, 2020. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 181, Article 55, 15 p. (2020).
MSC:  68Wxx
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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
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Rubert, Diego P.; Martinez, Fábio V.; Braga, Marília D. V.

Natural family-free genomic distance. (English) Zbl 1518.92092

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 3, 23 p. (2020).
MSC:  92D10 92C10 92-08
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Zabeti, Hooman; Dexter, Nick; Safari, Amir Hosein; Sedaghat, Nafiseh; Libbrecht, Maxwell; Chindelevitch, Leonid

An interpretable classification method for predicting drug resistance in \(M. tuberculosis\). (English) Zbl 1518.92080

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 2, 18 p. (2020).
MSC:  92C50 90C10 68T05 92-08
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Ivanov, Pesho; Bichsel, Benjamin; Mustafa, Harun; Kahles, André; Rätsch, Gunnar; Vechev, Martin

AStarix: fast and optimal sequence-to-graph alignment. (English) Zbl 1500.92076

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, 104-119 (2020).
MSC:  92D20 05C90
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Katebi, Mohsen; Feijao, Pedro; Booth, Julius; Mansouri, Mehrdad; La, Sean; Sweeten, Alex; Miraskarshahi, Reza; Nguyen, Matthew; Wong, Johnathan; Hsiao, William; Chauve, Cedric; Chindelevitch, Leonid

PathOGiST: a novel method for clustering pathogen isolates by combining multiple genotyping signals. (English) Zbl 1500.92077

Martín-Vide, Carlos (ed.) et al., Algorithms for computational biology. 7th international conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12099, 108-124 (2020).
MSC:  92D20 92C70 62P10
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Oliveira, Andre Rodrigues; Jean, Géraldine; Fertin, Guillaume; Brito, Klairton Lima; Dias, Ulisses; Dias, Zanoni

A 3.5-approximation algorithm for sorting by intergenic transpositions. (English) Zbl 1500.92057

Martín-Vide, Carlos (ed.) et al., Algorithms for computational biology. 7th international conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12099, 16-28 (2020).
MSC:  92D10 68W25 92-08
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de Almeida, Rita M. C.; se Souza, Lars L. S.; Morais, Diego; Dalmolin, Rodrigo J. S.

Transcriptograms: a genome-wide gene expression analysis method. (English) Zbl 1478.92060

Da Silva, Fabrício Alves Barbosa (ed.) et al., Networks in systems biology. Applications for disease modeling. Translated contributions of the 3rd international course on theoretical and applied aspects of systems biology, Rio de Janeiro, Brazil 2019. Cham: Springer. Comput. Biol. 32, 69-91 (2020).
MSC:  92C40
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