Khatamov, N. M.; Malikov, N. N. 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). MSC: 82B20 92D20 92C40 92E10 PDFBibTeX XMLCite \textit{N. M. Khatamov} and \textit{N. N. Malikov}, Theor. Math. Phys. 218, No. 2, 346--356 (2024; Zbl 07825106); translation from Teor. Mat. Fiz. 218, No. 2, 400--411 (2024) Full Text: DOI
Cifuentes, Diego; Draisma, Jan; Henriksson, Oskar; Korchmaros, Annachiara; Kubjas, Kaie 3D genome reconstruction from partially phased Hi-C data. (English) Zbl 07815434 Bull. Math. Biol. 86, No. 4, Paper No. 33, 30 p. (2024). MSC: 92D10 92D20 14P05 65H14 PDFBibTeX XMLCite \textit{D. Cifuentes} et al., Bull. Math. Biol. 86, No. 4, Paper No. 33, 30 p. (2024; Zbl 07815434) Full Text: DOI arXiv OA License
Cheng, Lei; Yu, Tong; Khalitov, Ruslan; Yang, Zhirong Self-supervised learning for DNA sequences with circular dilated convolutional networks. (English) Zbl 07804145 Neural Netw. 171, 466-473 (2024). MSC: 92D20 68T07 PDFBibTeX XMLCite \textit{L. Cheng} et al., Neural Netw. 171, 466--473 (2024; Zbl 07804145) Full Text: DOI
Gao, Ziyao; He, Jianfeng; Li, Jing; Leung, Kingsley Unraveling the complexity of Exendin-4 folding through two distinct pathways. (English) Zbl 07796560 J. Math. Chem. 62, No. 2, 356-366 (2024). MSC: 92C40 92D20 82M37 PDFBibTeX XMLCite \textit{Z. Gao} et al., J. Math. Chem. 62, No. 2, 356--366 (2024; Zbl 07796560) Full Text: DOI
Strahov, Eugene Multiple partition structures and harmonic functions on branching graphs. (English) Zbl 07796438 Adv. Appl. Math. 153, Article ID 102617, 49 p. (2024). MSC: 92D20 92D10 05E05 65P10 31C20 28A99 PDFBibTeX XMLCite \textit{E. Strahov}, Adv. Appl. Math. 153, Article ID 102617, 49 p. (2024; Zbl 07796438) Full Text: DOI arXiv
Zhang, Shengli; Zhao, Ya; Liang, Yunyun AMP-EF: an ensemble framework of extreme gradient boosting and bidirectional long short-term memory network for identifying antimicrobial peptides. (English) Zbl 07794804 MATCH Commun. Math. Comput. Chem. 91, No. 1, 109-131 (2024). MSC: 92D20 PDFBibTeX XMLCite \textit{S. Zhang} et al., MATCH Commun. Math. Comput. Chem. 91, No. 1, 109--131 (2024; Zbl 07794804) Full Text: DOI
Bailey, Lora; Blake, Heather Smith; Cochran, Garner; Fox, Nathan; Levet, Michael; Mahmoud, Reem; Singgih, Inne; Stadnyk, Grace; Wiedemann, Alexander Pairwise Rearrangement is Fixed-Parameter Tractable in the Single Cut-and-Join Model. arXiv:2402.01942 Preprint, arXiv:2402.01942 [q-bio.GN] (2024). MSC: 92-08 92D10 92D20 68Q17 BibTeX Cite \textit{L. Bailey} et al., ``Pairwise Rearrangement is Fixed-Parameter Tractable in the Single Cut-and-Join Model'', Preprint, arXiv:2402.01942 [q-bio.GN] (2024) Full Text: arXiv OA License
Yau, Stephen S.-T.; Zhao, Xin; Tian, Kun; Yu, Hongyu Mathematical principles in bioinformatics. (English) Zbl 07819836 Interdisciplinary Applied Mathematics 58. Cham: Springer (ISBN 978-3-031-48294-6/hbk; 978-3-031-48297-7/pbk; 978-3-031-48295-3/ebook). (2023). MSC: 92-02 92D20 PDFBibTeX XML Full Text: DOI
Silalahi, Agustinus; Sukwadi, Ronald; Vanessa; Le, Minh-Tai; Nguyen, Thi Bich Thu A hybrid model of analytical network process and mixed-integer programming for selecting restaurant food supplier. (English) Zbl 07811074 Math. Appl. (Warsaw) 51, No. 1, 13-31 (2023). MSC: 62J05 92D20 PDFBibTeX XMLCite \textit{A. Silalahi} et al., Math. Appl. (Warsaw) 51, No. 1, 13--31 (2023; Zbl 07811074) Full Text: DOI
Gundogdu, Pelin; Payá-Milans, Miriam; Alamo-Alvarez, Inmaculada; Nepomuceno-Chamorro, Isabel A.; Dopazo, Joaquin; Loucera, Carlos 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 PDFBibTeX XMLCite \textit{P. Gundogdu} et al., Lect. Notes Comput. Sci. 14137, 62--77 (2023; Zbl 07810884) Full Text: DOI
Manca, Vincenzo; Bonnici, Vincenzo Infogenomics. The informational analysis of genomes. (English) Zbl 07799403 Emergence, Complexity and Computation 48. Cham: Springer (ISBN 978-3-031-44500-2/hbk; 978-3-031-44503-3/pbk; 978-3-031-44501-9/ebook). xiii, 287 p. (2023). MSC: 92-01 92-08 92D20 PDFBibTeX XMLCite \textit{V. Manca} and \textit{V. Bonnici}, Infogenomics. The informational analysis of genomes. Cham: Springer (2023; Zbl 07799403) Full Text: DOI
Zhang, Shengli; Li, Xinjie; Shi, Hongyan; Jing, Yuanyuan; Liang, Yunyun; Zhang, Yusen Fer-COCL: a novel method based on multiple deep learning algorithms for identifying fertility-related proteins. (English) Zbl 07794787 MATCH Commun. Math. Comput. Chem. 90, No. 3, 537-559 (2023). MSC: 92C40 92D20 68T07 PDFBibTeX XMLCite \textit{S. Zhang} et al., MATCH Commun. Math. Comput. Chem. 90, No. 3, 537--559 (2023; Zbl 07794787) Full Text: DOI
Huang, Shu-Yu; Chang, Chi-Fon; Lin, Jung-Hsin; Malliavin, Thérèse E. 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 PDFBibTeX XMLCite \textit{S.-Y. Huang} et al., Lect. Notes Comput. Sci. 14072, 531--540 (2023; Zbl 07789332) Full Text: DOI
Hengeveld, Simon B.; Merabti, Mathieu; Pascale, Fabien; Malliavin, Thérèse E. 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 PDFBibTeX XMLCite \textit{S. B. Hengeveld} et al., Lect. Notes Comput. Sci. 14072, 520--530 (2023; Zbl 07789331) Full Text: DOI
Da Rocha, Wagner; Lavor, Carlile; Liberti, Leo; Malliavin, Thérèse E. 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 PDFBibTeX XMLCite \textit{W. Da Rocha} et al., Lect. Notes Comput. Sci. 14072, 511--519 (2023; Zbl 07789330) Full Text: DOI
Sharma, Lavkush; Deepak, Akshay; Ranjan, Ashish; Krishnasamy, Gopalakrishnan A novel hybrid CNN and BiGRU-attention based deep learning model for protein function prediction. (English) Zbl 07784219 Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20220057, 18 p. (2023). MSC: 92C40 92D20 68T07 PDFBibTeX XMLCite \textit{L. Sharma} et al., Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20220057, 18 p. (2023; Zbl 07784219) Full Text: DOI
Shi, Yang; Shi, Weiping; Wang, Mengqiao; Lee, Ji-Hyun; Kang, Huining; Jiang, Hui Accurate and fast small \(p\)-value estimation for permutation tests in high-throughput genomic data analysis with the cross-entropy method. (English) Zbl 07784216 Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20210067, 22 p. (2023). MSC: 92D20 62P10 PDFBibTeX XMLCite \textit{Y. Shi} et al., Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20210067, 22 p. (2023; Zbl 07784216) Full Text: DOI
Knodel, Markus M.; Nägel, Arne; Herrmann, Eva; Wittum, Gabriel 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). MSC: 65M08 65M06 65N08 92C37 92D20 92D25 35Q92 35R01 PDFBibTeX XMLCite \textit{M. M. Knodel} et al., Springer Proc. Math. Stat. 432, 315--323 (2023; Zbl 07781712) Full Text: DOI
Missarov, M. D.; Khajrullin, D. A. 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). MSC: 81T30 81Q65 11F33 83F05 92D20 PDFBibTeX XMLCite \textit{M. D. Missarov} and \textit{D. A. Khajrullin}, Izv. Math. 87, No. 5, 1011--1023 (2023; Zbl 07771715); translation from Izv. Ross. Akad. Nauk, Ser. Mat. 87, No. 5, 164--176 (2023) Full Text: DOI MNR
Chandra, Ghanshyam; Jain, Chirag 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 PDFBibTeX XMLCite \textit{G. Chandra} and \textit{C. Jain}, Lect. Notes Comput. Sci. 13976, 58--73 (2023; Zbl 1528.92026) Full Text: DOI
Fan, Jason; Khan, Jamshed; Pibiri, Giulio Ermanno; Patro, Rob 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 PDFBibTeX XMLCite \textit{J. Fan} et al., Lect. Notes Comput. Sci. 13976, 21--40 (2023; Zbl 07770168) Full Text: DOI
Loffredo, E.; Vesconi, E.; Razban, R.; Peleg, O.; Shakhnovich, E.; Cocco, S.; Monasson, R. Evolutionary dynamics of a lattice dimer: a toy model for stability vs. affinity trade-offs in proteins. (English) Zbl 1526.92040 J. Phys. A, Math. Theor. 56, No. 45, Article ID 455002, 26 p. (2023). MSC: 92D15 92C40 92D20 PDFBibTeX XMLCite \textit{E. Loffredo} et al., J. Phys. A, Math. Theor. 56, No. 45, Article ID 455002, 26 p. (2023; Zbl 1526.92040) Full Text: DOI arXiv
Gorin, Gennady; Yoshida, Shawn; Pachter, Lior Assessing Markovian and delay models for single-nucleus RNA sequencing. (English) Zbl 1526.92046 Bull. Math. Biol. 85, No. 11, Paper No. 114, 27 p. (2023). MSC: 92D20 92C40 PDFBibTeX XMLCite \textit{G. Gorin} et al., Bull. Math. Biol. 85, No. 11, Paper No. 114, 27 p. (2023; Zbl 1526.92046) Full Text: DOI
Shegay, M. V.; Popova, N. N. Genetic algorithm for guide tree optimization. (English. Russian original) Zbl 1526.92047 Mosc. Univ. Comput. Math. Cybern. 47, No. 1, 45-52 (2023); translation from Vestn. Mosk. Univ., Ser. XV 2023, No. 1, 54-61 (2023). MSC: 92D20 68W50 PDFBibTeX XMLCite \textit{M. V. Shegay} and \textit{N. N. Popova}, Mosc. Univ. Comput. Math. Cybern. 47, No. 1, 45--52 (2023; Zbl 1526.92047); translation from Vestn. Mosk. Univ., Ser. XV 2023, No. 1, 54--61 (2023) Full Text: DOI
Colijn, Caroline (ed.); Halloran, M. Elizabeth (ed.); O’Neill, Philip D. (ed.); Trapman, Pieter (ed.) Design and analysis of infectious disease studies. Abstracts from the workshop held February 19–25, 2023. (English) Zbl 1525.00015 Oberwolfach Rep. 20, No. 1, 487-535 (2023). MSC: 00B05 00B25 92-06 62-06 05C05 05C12 05C82 37E25 37N25 62F15 62H30 62M05 62M09 62N01 62N02 62P10 92-04 92-08 92C60 92D20 92D30 PDFBibTeX XMLCite \textit{C. Colijn} (ed.) et al., Oberwolfach Rep. 20, No. 1, 487--535 (2023; Zbl 1525.00015) Full Text: DOI
Petoukhov, Sergey; He, Matthew Algebraic biology, matrix genetics, and genetic intelligence. (English) Zbl 07745811 Singapore: World Scientific (ISBN 978-981-12-7825-9/hbk; 978-981-12-7827-3/ebook). (2023). MSC: 92-02 92D10 92D20 92C10 15-XX PDFBibTeX XML Full Text: DOI
Siqueira, Gabriel; Alexandrino, Alexsandro Oliveira; Dias, Zanoni Signed rearrangement distances considering repeated genes, intergenic regions, and indels. (English) Zbl 07742793 J. Comb. Optim. 46, No. 2, Paper No. 16, 36 p. (2023). MSC: 92D10 92D20 PDFBibTeX XMLCite \textit{G. Siqueira} et al., J. Comb. Optim. 46, No. 2, Paper No. 16, 36 p. (2023; Zbl 07742793) Full Text: DOI
Ashraf, Mohammad; Rehman, Washiqur; Mohammad, Ghulam; Asim, Mohd On reversible codes over a non-chain ring. (English) Zbl 07735385 Comput. Appl. Math. 42, No. 6, Paper No. 269, 26 p. (2023). MSC: 94B05 94B15 92D20 PDFBibTeX XMLCite \textit{M. Ashraf} et al., Comput. Appl. Math. 42, No. 6, Paper No. 269, 26 p. (2023; Zbl 07735385) Full Text: DOI
Bian, Yuanyuan; He, Chong; Qiu, Jing A Bayesian model to identify multiple expression patterns with simultaneous FDR control for a multi-factor RNA-seq experiment. (English) Zbl 1520.92046 Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20220025, 18 p. (2023). MSC: 92D20 93C40 PDFBibTeX XMLCite \textit{Y. Bian} et al., Stat. Appl. Genet. Mol. Biol. 22, No. 1, Article ID 20220025, 18 p. (2023; Zbl 1520.92046) Full Text: DOI
Mäkinen, Veli; Belazzougui, Djamal; Cunial, Fabio; Tomescu, Alexandru I. 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). MSC: 92-02 92D20 92C40 92-08 PDFBibTeX XMLCite \textit{V. Mäkinen} et al., Genome-scale algorithm design. Bioinformatics in the era of high-throughput sequencing. 2nd edition. Cambridge: Cambridge University Press (2023; Zbl 1523.92002) Full Text: DOI
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
Muthu, Poosan; Modak, Bikash Within-host models of dengue virus transmission with immune response. (English) Zbl 1518.92113 Comput. Math. Biophys. 11, No. 1, Article ID 20220150, 31 p. (2023). MSC: 92D20 34D23 49J15 PDFBibTeX XMLCite \textit{P. Muthu} and \textit{B. Modak}, Comput. Math. Biophys. 11, No. 1, Article ID 20220150, 31 p. (2023; Zbl 1518.92113) Full Text: DOI
Idhaya, T.; Suruliandi, A.; Calitoiu, Dragos; Raja, S. P. Calibrating the classifier for protein family prediction with protein sequence using machine learning techniques: an empirical investigation. (English) Zbl 1519.92162 Int. J. Wavelets Multiresolut. Inf. Process. 21, No. 3, Article ID 2250045, 34 p. (2023). MSC: 92D20 68T05 PDFBibTeX XMLCite \textit{T. Idhaya} et al., Int. J. Wavelets Multiresolut. Inf. Process. 21, No. 3, Article ID 2250045, 34 p. (2023; Zbl 1519.92162) Full Text: DOI
Ai, Liang; Feng, Jie; Yao, Yu Hua A novel fast approach for protein classification and evolutionary analysis. (English) Zbl 1519.92154 MATCH Commun. Math. Comput. Chem. 90, No. 2, 381-398 (2023). MSC: 92D20 92D15 PDFBibTeX XMLCite \textit{L. Ai} et al., MATCH Commun. Math. Comput. Chem. 90, No. 2, 381--398 (2023; Zbl 1519.92154) Full Text: DOI
Qi, Zhaohui; Ning, Yingqiang; Huang, Yinmei Protein sequence comparison method based on 3-ary Huffman coding. (English) Zbl 1519.92170 MATCH Commun. Math. Comput. Chem. 90, No. 2, 357-380 (2023). MSC: 92D20 PDFBibTeX XMLCite \textit{Z. Qi} et al., MATCH Commun. Math. Comput. Chem. 90, No. 2, 357--380 (2023; Zbl 1519.92170) Full Text: DOI
Gadgil, Siddhartha; Krishnapur, Manjunath Random words in free groups, non-crossing matchings and RNA secondary structures. (English) Zbl 1519.92159 Indian J. Pure Appl. Math. 54, No. 1, 146-158 (2023). MSC: 92D20 20E05 PDFBibTeX XMLCite \textit{S. Gadgil} and \textit{M. Krishnapur}, Indian J. Pure Appl. Math. 54, No. 1, 146--158 (2023; Zbl 1519.92159) Full Text: DOI arXiv
Sapundzhi, Fatima; Popstoilov, Metodi; Lazarova, Meglena 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 PDFBibTeX XMLCite \textit{F. Sapundzhi} et al., Lect. Notes Comput. Sci. 13858, 279--288 (2023; Zbl 1521.92009) Full Text: DOI
Seo, Seunghyun; Shin, Heesung On Delannoy paths without peaks and valleys. (English) Zbl 1514.05015 Discrete Math. 346, No. 7, Article ID 113399, 12 p. (2023). MSC: 05A15 05A05 92D20 PDFBibTeX XMLCite \textit{S. Seo} and \textit{H. Shin}, Discrete Math. 346, No. 7, Article ID 113399, 12 p. (2023; Zbl 1514.05015) Full Text: DOI arXiv
Cheng, Xiao-Sheng; Deng, Qingying; Diao, Yuanan Constructions of DNA and polypeptide cages based on plane graphs and odd crossing \(\pi \)-junctions. (English) Zbl 1511.92048 Appl. Math. Comput. 443, Article ID 127773, 15 p. (2023). MSC: 92D20 92E10 05C10 PDFBibTeX XMLCite \textit{X.-S. Cheng} et al., Appl. Math. Comput. 443, Article ID 127773, 15 p. (2023; Zbl 1511.92048) Full Text: DOI
Heitsch, Christine; Huynh, Chi N. Y.; Johnston, Greg On a barrier height problem for RNA branching. (English) Zbl 1512.92059 J. Comb. 14, No. 4, 485-506 (2023). MSC: 92D20 05A18 05C05 PDFBibTeX XMLCite \textit{C. Heitsch} et al., J. Comb. 14, No. 4, 485--506 (2023; Zbl 1512.92059) Full Text: DOI arXiv
Cheek, David; Johnston, Samuel G. G. Ancestral reproductive bias in branching processes. (English) Zbl 1511.60121 J. Math. Biol. 86, No. 5, Paper No. 70, 24 p. (2023). MSC: 60J80 60G51 60K05 92D10 92D20 PDFBibTeX XMLCite \textit{D. Cheek} and \textit{S. G. G. Johnston}, J. Math. Biol. 86, No. 5, Paper No. 70, 24 p. (2023; Zbl 1511.60121) Full Text: DOI arXiv
Redmon, Eric; Mena, Miles; Vesta, Megan; Cortes, Alvi Renzyl; Gernes, Lauren; Merheb, Simon; Soto, Nick; Stimpert, Chandler; Harsy, Amanda Optimal tilings of bipartite graphs using self-assembling DNA. (English) Zbl 1508.05140 PUMP J. Undergrad. Res. 6, 124-150 (2023). MSC: 05C70 05C90 92D20 PDFBibTeX XMLCite \textit{E. Redmon} et al., PUMP J. Undergrad. Res. 6, 124--150 (2023; Zbl 1508.05140) Full Text: Link
Ceniceros, Jose; Elhamdadi, Mohamed; Magill, Brendan; Rosario, Gabriana RNA foldings, oriented stuck knots, and state sum invariants. (English) Zbl 1511.57012 J. Math. Phys. 64, No. 3, Article ID 031702, 17 p. (2023). MSC: 57K12 57K14 92D20 PDFBibTeX XMLCite \textit{J. Ceniceros} et al., J. Math. Phys. 64, No. 3, Article ID 031702, 17 p. (2023; Zbl 1511.57012) Full Text: DOI arXiv
Guo, Qianghui; Jin, Yinglie; Sun, Lisa H.; Weng, Mingxing A semi-bijective algorithm for saturated extended 2-regular simple stacks. (English) Zbl 1510.05009 Adv. Appl. Math. 146, Article ID 102491, 27 p. (2023). MSC: 05A15 05A19 92D20 PDFBibTeX XMLCite \textit{Q. Guo} et al., Adv. Appl. Math. 146, Article ID 102491, 27 p. (2023; Zbl 1510.05009) Full Text: DOI arXiv
Michel, Christian J.; Sereni, Jean-Sébastien Reading frame retrieval of genes: a new parameter of codon usage based on the circular code theory. (English) Zbl 1508.92187 Bull. Math. Biol. 85, No. 4, Paper No. 24, 21 p. (2023). MSC: 92D20 05C90 PDFBibTeX XMLCite \textit{C. J. Michel} and \textit{J.-S. Sereni}, Bull. Math. Biol. 85, No. 4, Paper No. 24, 21 p. (2023; Zbl 1508.92187) Full Text: DOI
Chen, Ricky X. F.; Reidys, Christian M.; Waterman, Michael S. RNA secondary structures with given motif specification: combinatorics and algorithms. (English) Zbl 1508.92181 Bull. Math. Biol. 85, No. 3, Paper No. 21, 24 p. (2023). MSC: 92D20 05C92 PDFBibTeX XMLCite \textit{R. X. F. Chen} et al., Bull. Math. Biol. 85, No. 3, Paper No. 21, 24 p. (2023; Zbl 1508.92181) Full Text: DOI
Sagitov, Serik; Ståhlberg, Anders Counting unique molecular identifiers in sequencing using a multi-type branching process with immigration. (English) Zbl 1504.92092 J. Theor. Biol. 558, Article ID 111365, 8 p. (2023). MSC: 92D20 PDFBibTeX XMLCite \textit{S. Sagitov} and \textit{A. Ståhlberg}, J. Theor. Biol. 558, Article ID 111365, 8 p. (2023; Zbl 1504.92092) Full Text: DOI arXiv
Rozikov, Utkir A. Gibbs measures in biology and physics. The Potts model. (English) Zbl 1526.82002 Singapore: World Scientific (ISBN 978-981-12-5123-8/hbk; 978-981-12-5125-2/ebook). xix, 346 p. (2023). Reviewer: Nasir N. Ganikhodjaev (Tashkent) MSC: 82-01 82B26 82B20 05C05 82D10 92D20 00A06 PDFBibTeX XMLCite \textit{U. A. Rozikov}, Gibbs measures in biology and physics. The Potts model. Singapore: World Scientific (2023; Zbl 1526.82002) Full Text: DOI
Wang, Xianyong; Wang, Zhenghua Bioinformatics. Volume 1. Sequence analysis and parallel computing (to appear). (English) Zbl 07377452 Berlin: De Gruyter (ISBN 978-3-11-046208-1/hbk; 978-3-11-046274-6/ebook). 320 p. (2023). MSC: 92-02 92D20 92C40 92C42 PDFBibTeX XMLCite \textit{X. Wang} and \textit{Z. Wang}, Bioinformatics. Volume 1. Sequence analysis and parallel computing (to appear). Berlin: De Gruyter (2023; Zbl 07377452)
Bailey, Lora; Blake, Heather Smith; Cochran, Garner; Fox, Nathan; Levet, Michael; Mahmoud, Reem; Matson, Elizabeth; Singgih, Inne; Stadnyk, Grace; Wang, Xinyi; Wiedemann, Alexander Complexity and Enumeration in Models of Genome Rearrangement. arXiv:2305.01851 Preprint, arXiv:2305.01851 [q-bio.GN] (2023). MSC: 92-08 92D10 92D20 68Q17 BibTeX Cite \textit{L. Bailey} et al., ``Complexity and Enumeration in Models of Genome Rearrangement'', Preprint, arXiv:2305.01851 [q-bio.GN] (2023) Full Text: arXiv OA License
Castro, Richard; Chang, Zhibin; Ha, Ethan; Hall, Evan; Maharaj, Hiren On a Subset Metric. arXiv:2302.13433 Preprint, arXiv:2302.13433 [math.MG] (2023). MSC: 54E35 05C12 92D20 51K99 68P20 68U10 BibTeX Cite \textit{R. Castro} et al., ``On a Subset Metric'', Preprint, arXiv:2302.13433 [math.MG] (2023) Full Text: arXiv OA License
Rozikov, U. A. Kittel’s molecular zipper model on Cayley trees. arXiv:2301.07337 Preprint, arXiv:2301.07337 [math-ph] (2023). MSC: 92D20 82B20 60J10 BibTeX Cite \textit{U. A. Rozikov}, ``Kittel's molecular zipper model on Cayley trees'', Preprint, arXiv:2301.07337 [math-ph] (2023) Full Text: arXiv OA License
Kolias, Pavlos; Papadopoulou, Alexandra 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 PDFBibTeX XMLCite \textit{P. Kolias} and \textit{A. Papadopoulou}, Springer Proc. Math. Stat. 408, 179--196 (2022; Zbl 07819614) Full Text: DOI arXiv
Bonizzoni, P.; Costantini, M.; De Felice, C.; Petescia, A.; Pirola, Y.; Previtali, M.; Rizzi, R.; Stoye, J.; Zaccagnino, R.; Zizza, R. Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. (English) Zbl 07816919 Inf. Sci. 607, 458-476 (2022). MSC: 92D20 68T05 PDFBibTeX XMLCite \textit{P. Bonizzoni} et al., Inf. Sci. 607, 458--476 (2022; Zbl 07816919) Full Text: DOI arXiv
Melese, Abdisa Shiferaw Modelling of pathogens impact on the human disease transmission with optimal control strategies. (English) Zbl 07798309 J. Math. Sci., New York 266, No. 5, Series A, 675-695 (2022). MSC: 92D20 34D20 34D23 34C23 49J15 PDFBibTeX XMLCite \textit{A. S. Melese}, J. Math. Sci., New York 266, No. 5, 675--695 (2022; Zbl 07798309) Full Text: DOI
Ding, Yijie; Tiwari, Prayag; Guo, Fei; Zou, Quan Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization. (English) Zbl 1526.92045 Neural Netw. 156, 170-178 (2022). MSC: 92D20 68T07 PDFBibTeX XMLCite \textit{Y. Ding} et al., Neural Netw. 156, 170--178 (2022; Zbl 1526.92045) Full Text: DOI
Varela, Daniel; Santos, José Protein structure prediction in an atomic model with differential evolution integrated with the crowding niching method. (English) Zbl 07732604 Nat. Comput. 21, No. 4, 537-551 (2022). MSC: 92D20 68W50 PDFBibTeX XMLCite \textit{D. Varela} and \textit{J. Santos}, Nat. Comput. 21, No. 4, 537--551 (2022; Zbl 07732604) Full Text: DOI
Díaz-Domínguez, Diego; Puglisi, Simon J.; Salmela, Leena 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). MSC: 92D10 92D20 68P05 68W32 PDFBibTeX XMLCite \textit{D. Díaz-Domínguez} et al., Lect. Notes Comput. Sci. 13617, 198--213 (2022; Zbl 07722484) Full Text: DOI arXiv
Kovačević, M. On the maximum number of non-confusable strings evolving under short tandem duplications. (English. Russian original) Zbl 1528.68333 Probl. Inf. Transm. 58, No. 2, 111-121 (2022); translation from Probl. Peredachi Inf. 58, No. 2, 12-23 (2022). MSC: 68R15 92D20 94A40 94B25 94B50 PDFBibTeX XMLCite \textit{M. Kovačević}, Probl. Inf. Transm. 58, No. 2, 111--121 (2022; Zbl 1528.68333); translation from Probl. Peredachi Inf. 58, No. 2, 12--23 (2022) Full Text: DOI arXiv
Balamanikandan, P.; Bharathi, S. Jeya A mathematical modelling to detect sickle cell anemia using quantum graph theory and aquila optimization classifier. (English) Zbl 1508.92047 Math. Biosci. Eng. 19, No. 10, 10060-10077 (2022). MSC: 92C32 92D20 81Q35 05C90 PDFBibTeX XMLCite \textit{P. Balamanikandan} and \textit{S. J. Bharathi}, Math. Biosci. Eng. 19, No. 10, 10060--10077 (2022; Zbl 1508.92047) Full Text: DOI
Soemartojo, Saskya Mary; Siswantining, Titin; Fernando, Yoel; Sarwinda, Devvi; Al-Ash, Herley Shaori; Syarofina, Sarah; Saputra, Noval Iterative bicluster-based Bayesian principal component analysis and least squares for missing-value imputation in microarray and RNA-sequencing data. (English) Zbl 1508.92189 Math. Biosci. Eng. 19, No. 9, 8741-8759 (2022). MSC: 92D20 62P10 62H25 PDFBibTeX XMLCite \textit{S. M. Soemartojo} et al., Math. Biosci. Eng. 19, No. 9, 8741--8759 (2022; Zbl 1508.92189) Full Text: DOI
Cho, Heyrim; Kuo, Ya-Huei; Rockne, Russell C. Comparison of cell state models derived from single-cell RNA sequencing data: graph versus multi-dimensional space. (English) Zbl 1508.92076 Math. Biosci. Eng. 19, No. 8, 8505-8536 (2022). MSC: 92C37 92D20 35Q92 PDFBibTeX XMLCite \textit{H. Cho} et al., Math. Biosci. Eng. 19, No. 8, 8505--8536 (2022; Zbl 1508.92076) Full Text: DOI
Yan, Jun; Jiang, Tengsheng; Liu, Junkai; Lu, Yaoyao; Guan, Shixuan; Li, Haiou; Wu, Hongjie; Ding, Yijie DNA-binding protein prediction based on deep transfer learning. (English) Zbl 1508.92191 Math. Biosci. Eng. 19, No. 8, 7719-7736 (2022). MSC: 92D20 68T07 PDFBibTeX XMLCite \textit{J. Yan} et al., Math. Biosci. Eng. 19, No. 8, 7719--7736 (2022; Zbl 1508.92191) Full Text: DOI
Kim, Hyoungjun; Lee, Hwa Jeong; No, Sungjong; Oh, Seungsang; Yoo, Hyungkee Lattice conformation of theta-curves accompanied with Brunnian property. (English) Zbl 1511.92049 J. Phys. A, Math. Theor. 55, No. 43, Article ID 435207, 11 p. (2022). MSC: 92D20 57K10 PDFBibTeX XMLCite \textit{H. Kim} et al., J. Phys. A, Math. Theor. 55, No. 43, Article ID 435207, 11 p. (2022; Zbl 1511.92049) Full Text: DOI
Liu, Jian; Xia, Ke-Lin; Wu, Jie; Yau, Stephen Shing-Toung; Wei, Guo-Wei Biomolecular topology: modelling and analysis. (English) Zbl 1501.55006 Acta Math. Sin., Engl. Ser. 38, No. 10, 1901-1938 (2022). MSC: 55N31 92E10 92D20 62R40 92C40 57Z10 55-02 57-02 92-02 PDFBibTeX XMLCite \textit{J. Liu} et al., Acta Math. Sin., Engl. Ser. 38, No. 10, 1901--1938 (2022; Zbl 1501.55006) Full Text: DOI
Nieto, J.; Vásquez, M. O. Wellposedness of a DNA replication model based on a nucleation-growth process. (English) Zbl 1501.35416 Commun. Pure Appl. Anal. 21, No. 8, 2643-2660 (2022). MSC: 35Q92 92D20 74N05 74E15 35A01 35A02 35R09 45K05 82D60 80A22 00A71 PDFBibTeX XMLCite \textit{J. Nieto} and \textit{M. O. Vásquez}, Commun. Pure Appl. Anal. 21, No. 8, 2643--2660 (2022; Zbl 1501.35416) Full Text: DOI
Chen, Duan; Li, Shaoyu; Wang, Xue Geometric structure guided model and algorithms for complete deconvolution of gene expression data. (English) Zbl 1496.92064 Found. Data Sci. 4, No. 3, 441-466 (2022). MSC: 92D20 15A23 PDFBibTeX XMLCite \textit{D. Chen} et al., Found. Data Sci. 4, No. 3, 441--466 (2022; Zbl 1496.92064) Full Text: DOI arXiv
Sheng, Ke-Ning; Naus, Joseph I. Exact probability of fixed patterns occurring in a random sequence. (English) Zbl 07603791 Commun. Stat., Simulation Comput. 51, No. 9, 4867-4882 (2022). MSC: 39A10 62P10 65C50 92D20 PDFBibTeX XMLCite \textit{K.-N. Sheng} and \textit{J. I. Naus}, Commun. Stat., Simulation Comput. 51, No. 9, 4867--4882 (2022; Zbl 07603791) Full Text: DOI
Weinberger, Nir; Merhav, Neri The DNA storage channel: capacity and error probability bounds. (English) Zbl 1515.94048 IEEE Trans. Inf. Theory 68, No. 9, 5657-5700 (2022). MSC: 94A40 92D20 PDFBibTeX XMLCite \textit{N. Weinberger} and \textit{N. Merhav}, IEEE Trans. Inf. Theory 68, No. 9, 5657--5700 (2022; Zbl 1515.94048) Full Text: DOI
Hamilton, W.; Borgert, J. E.; Hamelryck, T.; Marron, J. S. 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 PDFBibTeX XMLCite \textit{W. Hamilton} et al., Assoc. Women Math. Ser. 30, 223--244 (2022; Zbl 1500.92075) Full Text: DOI arXiv
Bura, Andrei C.; He, Qijun; Reidys, Christian M. Loop homology of bi-secondary structures. II. (English) Zbl 1500.92072 J. Algebr. Comb. 56, No. 3, 785-798 (2022). MSC: 92D20 55U10 PDFBibTeX XMLCite \textit{A. C. Bura} et al., J. Algebr. Comb. 56, No. 3, 785--798 (2022; Zbl 1500.92072) Full Text: DOI arXiv
Folifack Signing, V. R.; Gakam Tegue, G. A.; Kountchou, M.; Njitacke, Z. T.; Tsafack, N.; Nkapkop, J. D. D.; Lessouga Etoundi, C. M.; Kengne, J. A cryptosystem based on a chameleon chaotic system and dynamic DNA coding. (English) Zbl 1498.94061 Chaos Solitons Fractals 155, Article ID 111777, 15 p. (2022). MSC: 94A60 92D20 PDFBibTeX XMLCite \textit{V. R. Folifack Signing} et al., Chaos Solitons Fractals 155, Article ID 111777, 15 p. (2022; Zbl 1498.94061) Full Text: DOI
Georgiev, Danko D.; Glazebrook, James F. Thermal stability of solitons in protein \(\alpha\)-helices. (English) Zbl 1498.92139 Chaos Solitons Fractals 155, Article ID 111644, 19 p. (2022). MSC: 92D20 82C22 82C31 60J70 PDFBibTeX XMLCite \textit{D. D. Georgiev} and \textit{J. F. Glazebrook}, Chaos Solitons Fractals 155, Article ID 111644, 19 p. (2022; Zbl 1498.92139) Full Text: DOI arXiv
Georgiev, Danko D.; Glazebrook, James F. Quantum tunneling of three-spine solitons through excentric barriers. (English) Zbl 1507.81179 Phys. Lett., A 448, Article ID 128319, 14 p. (2022). MSC: 81U26 35C08 92D20 82C70 PDFBibTeX XMLCite \textit{D. D. Georgiev} and \textit{J. F. Glazebrook}, Phys. Lett., A 448, Article ID 128319, 14 p. (2022; Zbl 1507.81179) Full Text: DOI arXiv
Deng, Tao; Huang, Mengge; Zhang, Jingyi An assembling procedure for DNA bipyramids with minimum component strands. (English) Zbl 1498.92137 MATCH Commun. Math. Comput. Chem. 87, No. 1, 179-192 (2022). MSC: 92D20 92-04 PDFBibTeX XMLCite \textit{T. Deng} et al., MATCH Commun. Math. Comput. Chem. 87, No. 1, 179--192 (2022; Zbl 1498.92137) Full Text: DOI
Zhang, Yuping; Mao, Disheng; Ouyang, Zhengqing Model-based distance embedding with applications to chromosomal conformation biology. (English) Zbl 1498.62276 Ann. Appl. Stat. 16, No. 3, 1253-1267 (2022). MSC: 62P10 49M15 65K05 92D20 PDFBibTeX XMLCite \textit{Y. Zhang} et al., Ann. Appl. Stat. 16, No. 3, 1253--1267 (2022; Zbl 1498.62276) Full Text: DOI
Zhang, Chuanyi; Sashittal, Palash; El-Kebir, Mohammed 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 PDFBibTeX XMLCite \textit{C. Zhang} et al., Lect. Notes Comput. Sci. 13278, 360--362 (2022; Zbl 1496.92077) Full Text: DOI
Zhang, Pengfei; Jiang, Zhengyuan; Wang, Yixuan; Li, Yu 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 PDFBibTeX XMLCite \textit{P. Zhang} et al., Lect. Notes Comput. Sci. 13278, 326--348 (2022; Zbl 1496.92078) Full Text: DOI arXiv
Ivanov, Pesho; Bichsel, Benjamin; Vechev, Martin 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 PDFBibTeX XMLCite \textit{P. Ivanov} et al., Lect. Notes Comput. Sci. 13278, 306--325 (2022; Zbl 1496.92069) Full Text: DOI
Luo, Xiang Ge; Kuipers, Jack; Beerenwinkel, Niko 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 PDFBibTeX XMLCite \textit{X. G. Luo} et al., Lect. Notes Comput. Sci. 13278, 304--305 (2022; Zbl 1496.92070) Full Text: DOI
Hua, Dunming; Gu, Ming; Du, Yanyi; Qi, Li; Du, Xiangjun; Bai, Zhidong; Zhu, Xiaopeng; Tian, Dechao 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 PDFBibTeX XMLCite \textit{D. Hua} et al., Lect. Notes Comput. Sci. 13278, 302--303 (2022; Zbl 1496.92068) Full Text: DOI
Gibney, Daniel; Thankachan, Sharma V.; Aluru, Srinivas 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 PDFBibTeX XMLCite \textit{D. Gibney} et al., Lect. Notes Comput. Sci. 13278, 263--278 (2022; Zbl 1494.92086) Full Text: DOI arXiv
Jain, Chirag; Gibney, Daniel; Thankachan, Sharma V. Co-linear chaining with overlaps and gap costs. (English) Zbl 1497.92185 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, 246-262 (2022). MSC: 92D20 PDFBibTeX XMLCite \textit{C. Jain} et al., Lect. Notes Comput. Sci. 13278, 246--262 (2022; Zbl 1497.92185) Full Text: DOI
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
Mahbub, Sazan; Sawmya, Shashata; Saha, Arpita; Reaz, Rezwana; Rahman, M. Sohel; Bayzid, Md. Shamsuzzoha 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 PDFBibTeX XMLCite \textit{S. Mahbub} et al., Lect. Notes Comput. Sci. 13278, 159--176 (2022; Zbl 1496.92060) Full Text: DOI
Saeedi, Seyran; Serrano, Myrna; Yang, Dennis G.; Brooks, J. Paul; Buck, Gregory A.; Arodz, Tomasz 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 PDFBibTeX XMLCite \textit{S. Saeedi} et al., Lect. Notes Comput. Sci. 13278, 126--142 (2022; Zbl 1496.92076) Full Text: DOI
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
Hoang, Minh; Zheng, Hongyu; Kingsford, Carl 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 PDFBibTeX XMLCite \textit{M. Hoang} et al., Lect. Notes Comput. Sci. 13278, 52--69 (2022; Zbl 1496.92067) Full Text: DOI
Demetçi, Pınar; Santorella, Rebecca; Sandstede, Björn; Singh, Ritambhara 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 PDFBibTeX XMLCite \textit{P. Demetçi} et al., Lect. Notes Comput. Sci. 13278, 3--19 (2022; Zbl 1496.92065) Full Text: DOI
Duarte-González, Mario E.; Bastos, Gustavo Terra; Palazzo, Reginaldo jun. Identification of proteins by the use of Chinese remainder theorem codes over finite commutative rings. (English) Zbl 1513.92050 Comput. Appl. Math. 41, No. 6, Paper No. 231, 18 p. (2022). MSC: 92D20 13A99 PDFBibTeX XMLCite \textit{M. E. Duarte-González} et al., Comput. Appl. Math. 41, No. 6, Paper No. 231, 18 p. (2022; Zbl 1513.92050) Full Text: DOI
Amihere, Sylvia; Geng, Weihua; Zhao, Shan Benchmarking electrostatic free energy of the nonlinear Poisson-Boltzmann model for the Kirkwood sphere. (English) Zbl 1511.81141 Commun. Inf. Syst. 22, No. 3, 305-315 (2022). MSC: 81V55 92D20 35Q20 57R67 81V10 78A30 82B30 65N12 PDFBibTeX XMLCite \textit{S. Amihere} et al., Commun. Inf. Syst. 22, No. 3, 305--315 (2022; Zbl 1511.81141) Full Text: DOI
Puliparambil, Bhavithry Sen; Tomal, Jabed; Yan, Yan 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 PDFBibTeX XMLCite \textit{B. S. Puliparambil} et al., Lect. Notes Comput. Sci. 13234, 295--310 (2022; Zbl 1496.92075) Full Text: DOI
Mane, Aniket; Faizrahnemoon, Mahsa; Chauve, Cedric A mixed integer linear programming algorithm for plasmid binning. (English) Zbl 1496.92072 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, 279-292 (2022). MSC: 92D20 90C11 PDFBibTeX XMLCite \textit{A. Mane} et al., Lect. Notes Comput. Sci. 13234, 279--292 (2022; Zbl 1496.92072) Full Text: DOI
Swenson, Krister M.; Elghraoui, Afif; Valafar, Faramarz; Mirarab, Siavash; Weller, Mathias 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 PDFBibTeX XMLCite \textit{K. M. Swenson} et al., Lect. Notes Comput. Sci. 13234, 146--167 (2022; Zbl 1496.92054) Full Text: DOI
Liyanage, Janaka S. S.; Estepp, Jeremie H.; Srivastava, Kumar; Li, Yun; Mori, Motomi; Kang, Guolian GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing. (English) Zbl 1494.92068 Stat. Appl. Genet. Mol. Biol. 21, No. 1, Article ID 20210071, 22 p. (2022). MSC: 92D10 92D20 62P10 PDFBibTeX XMLCite \textit{J. S. S. Liyanage} et al., Stat. Appl. Genet. Mol. Biol. 21, No. 1, Article ID 20210071, 22 p. (2022; Zbl 1494.92068) Full Text: DOI
Błażej, Paweł; Kowalski, Dariusz R.; Mackiewicz, Dorota; Wnetrzak, Małgorzata; Aloqalaa, Daniyah A.; Mackiewicz, Paweł The structure of the genetic code as an optimal graph clustering problem. (English) Zbl 1497.92171 J. Math. Biol. 85, No. 1, Paper No. 9, 22 p. (2022). MSC: 92D10 92D20 05C90 PDFBibTeX XMLCite \textit{P. Błażej} et al., J. Math. Biol. 85, No. 1, Paper No. 9, 22 p. (2022; Zbl 1497.92171) Full Text: DOI
Choudhary, Kapil Kumar; Kumar, Rajiv; Kumar, Rajesh Weak solution and qualitative behavior of a prion proliferation model in the presence of chaperone. (English) Zbl 1493.92040 Acta Appl. Math. 180, Paper No. 9, 23 p. (2022). MSC: 92D20 45K05 92C50 PDFBibTeX XMLCite \textit{K. K. Choudhary} et al., Acta Appl. Math. 180, Paper No. 9, 23 p. (2022; Zbl 1493.92040) Full Text: DOI
Rahman, Tanbin; Huang, Hsin-En; Li, Yujia; Tai, An-Shun; Hseih, Wen-Ping; McClung, Colleen A.; Tseng, George A sparse negative binomial classifier with covariate adjustment for RNA-seq data. (English) Zbl 1498.62248 Ann. Appl. Stat. 16, No. 2, 1071-1089 (2022). MSC: 62P10 62H30 92D20 PDFBibTeX XMLCite \textit{T. Rahman} et al., Ann. Appl. Stat. 16, No. 2, 1071--1089 (2022; Zbl 1498.62248) Full Text: DOI
Wang, Jianqiao; Wang, Wanjie; Li, Hongzhe Sparse block signal detection and identification for shared cross-trait association analysis. (English) Zbl 1498.62263 Ann. Appl. Stat. 16, No. 2, 866-886 (2022). MSC: 62P10 62G10 62H25 92D20 PDFBibTeX XMLCite \textit{J. Wang} et al., Ann. Appl. Stat. 16, No. 2, 866--886 (2022; Zbl 1498.62263) Full Text: DOI