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Found 3,844 Documents (Results 1–100)

Holliday junctions in the set of DNA molecules for new translation-invariant Gibbs measures of the Potts model. (English. Russian original) Zbl 07825106

Theor. Math. Phys. 218, No. 2, 346-356 (2024); translation from Teor. Mat. Fiz. 218, No. 2, 400-411 (2024).
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Pairwise Rearrangement is Fixed-Parameter Tractable in the Single Cut-and-Join Model. arXiv:2402.01942

Preprint, arXiv:2402.01942 [q-bio.GN] (2024).
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Cell-level pathway scoring comparison with a biologically constrained variational autoencoder. (English) Zbl 07810884

Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 62-77 (2023).
MSC:  92D20
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Exploration of conformations for an intrinsically disordered protein. (English) Zbl 07789332

Nielsen, Frank (ed.) et al., Geometric science of information. 6th international conference, GSI 2023, St. Malo, France, August 30 – September 1, 2023. Proceedings. Part II. Cham: Springer. Lect. Notes Comput. Sci. 14072, 531-540 (2023).
MSC:  92D20
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A study on the covalent geometry of proteins and its impact on distance geometry. (English) Zbl 07789331

Nielsen, Frank (ed.) et al., Geometric science of information. 6th international conference, GSI 2023, St. Malo, France, August 30 – September 1, 2023. Proceedings. Part II. Cham: Springer. Lect. Notes Comput. Sci. 14072, 520-530 (2023).
MSC:  92D20
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Pseudo-dihedral angles in proteins providing a new description of the Ramachandran map. (English) Zbl 07789330

Nielsen, Frank (ed.) et al., Geometric science of information. 6th international conference, GSI 2023, St. Malo, France, August 30 – September 1, 2023. Proceedings. Part II. Cham: Springer. Lect. Notes Comput. Sci. 14072, 511-519 (2023).
MSC:  92D20
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PDE models of virus replication coupling 2D manifold and 3D volume effects evaluated at realistic reconstructed cell geometries. (English) Zbl 07781712

Franck, Emmanuel (ed.) et al., Finite volumes for complex applications X – Volume 1. Elliptic and parabolic problems. FVCA 10, Strasbourg, France, October 30 – November 3, 2023. Invited contributions. Cham: Springer. Springer Proc. Math. Stat. 432, 315-323 (2023).
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The renormalization group transformation in the generalized fermionic hierarchical model. (English. Russian original) Zbl 07771715

Izv. Math. 87, No. 5, 1011-1023 (2023); translation from Izv. Ross. Akad. Nauk, Ser. Mat. 87, No. 5, 164-176 (2023).
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Sequence to graph alignment using gap-sensitive co-linear chaining. (English) Zbl 1528.92026

Tang, Haixu (ed.), Research in computational molecular biology. 27th annual international conference, RECOMB 2023, Istanbul, Turkey, April 16–19, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13976, 58-73 (2023).
MSC:  92D20
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Spectrum preserving tilings enable sparse and modular reference indexing. (English) Zbl 07770168

Tang, Haixu (ed.), Research in computational molecular biology. 27th annual international conference, RECOMB 2023, Istanbul, Turkey, April 16–19, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13976, 21-40 (2023).
MSC:  92D20 92D10 92-04
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Genome-scale algorithm design. Bioinformatics in the era of high-throughput sequencing. 2nd edition. (English) Zbl 1523.92002

Cambridge: Cambridge University Press (ISBN 978-1-00-934123-3/hbk; 978-1-00-934125-7/ebook). xxiv, 444 p. (2023).
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RMSD calculations for comparing protein three-dimensional structures. (English) Zbl 1521.92009

Georgiev, Ivan (ed.) et al., Numerical methods and applications. 10th international conference, NMA 2022, Borovets, Bulgaria, August 22–26, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13858, 279-288 (2023).
MSC:  92-08 92D20
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Complexity and Enumeration in Models of Genome Rearrangement. arXiv:2305.01851

Preprint, arXiv:2305.01851 [q-bio.GN] (2023).
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Investigating some attributes of periodicity in DNA sequences via semi-Markov modelling. (English) Zbl 07819614

Malyarenko, Anatoliy (ed.) et al., Stochastic processes, statistical methods, and engineering mathematics. SPAS 2019, Västerås, Sweden, September 30 – October 2, 2019. Cham: Springer. Springer Proc. Math. Stat. 408, 179-196 (2022).
MSC:  60K15 92D20
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Computing all-vs-all MEMs in run-length-encoded collections of HiFi reads. (English) Zbl 07722484

Arroyuelo, Diego (ed.) et al., String processing and information retrieval. 29th international symposium, SPIRE 2022, Concepción, Chile, November 8–10, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13617, 198-213 (2022).
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Persistent topology of protein space. (English) Zbl 1500.92075

Gasparovic, Ellen (ed.) et al., Research in computational topology 2. Proceedings of the second women in computational topology, WinCompTop, research collaboration workshop, Mathematical Sciences Institute, MSI, Australian National University, ANU, Canberra, Australia, July 1–5, 2019. Cham: Springer. Assoc. Women Math. Ser. 30, 223-244 (2022).
MSC:  92D20 55N31
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CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses. (English) Zbl 1496.92077

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, 360-362 (2022).
MSC:  92D20
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CLMB: deep contrastive learning for robust metagenomic binning. (English) Zbl 1496.92078

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, 326-348 (2022).
MSC:  92D20 68T07
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Fast and optimal sequence-to-graph alignment guided by seeds. (English) Zbl 1496.92069

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, 306-325 (2022).
MSC:  92D20 05C90
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Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from tumor mutation trees. (English) Zbl 1496.92070

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, 304-305 (2022).
MSC:  92D20 92D15 92C32
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Diffdomain enables identification of structurally reorganized topologically associating domains. (English) Zbl 1496.92068

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, 302-303 (2022).
MSC:  92D20
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The complexity of approximate pattern matching on de Bruijn graphs. (English) Zbl 1494.92086

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, 263-278 (2022).
MSC:  92D20 92C15 68Q17
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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
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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
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QT-GILD: Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data. (English) Zbl 1496.92060

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, 159-176 (2022).
MSC:  92D15 92D20 92-08
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Real-valued group testing for quantitative molecular assays. (English) Zbl 1496.92076

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, 126-142 (2022).
MSC:  92D20
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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
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DeepMinimizer: a differentiable framework for optimizing sequence-specific minimizer schemes. (English) Zbl 1496.92067

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, 52-69 (2022).
MSC:  92D20 68T07
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Unsupervised integration of single-cell multi-omics datasets with disproportionate cell-type representation. (English) Zbl 1496.92065

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, 3-19 (2022).
MSC:  92D20 92C37
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Benchmarking penalized regression methods in machine learning for single cell RNA sequencing data. (English) Zbl 1496.92075

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, 295-310 (2022).
MSC:  92D20 68T05 62P10
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Quantifying hierarchical conflicts in homology statements. (English) Zbl 1496.92054

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, 146-167 (2022).
MSC:  92D10 92D20
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