نتائج البحث - "de bruijn graphs"

المساهمون: Pennsylvania State University (Penn State), Penn State System, Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur Paris (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, This material is based upon work supported by the National Science Foundation under grant nos. 2138585 and 1931531. Research reported in this publication was also supported by the National Institutes of Health under Grant NIH R01GM146462 (to P.M.). A.R. was supported by the National Institutes of Health Computation, Bioinformatics, and Statistics (CBIOS) training program.

المصدر: EISSN: 1868-8969 ; Leibniz International Proceedings in Informatics ; https://pasteur.hal.science/pasteur-04195997 ; Leibniz International Proceedings in Informatics , 273 (17), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp.1-14, 2023, 978-3-95977-294-5. ⟨10.4230/LIPIcs.WABI.2023.17⟩

مصطلحات موضوعية: colored de Bruijn graphs, disk compression, k-mer sets, simplitigs, spectrum-preserving string sets, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]

الاتاحة: https://pasteur.hal.science/pasteur-04195997
https://pasteur.hal.science/pasteur-04195997v2/document
https://pasteur.hal.science/pasteur-04195997v2/file/LIPIcs-WABI-2023-17.pdf
https://doi.org/10.4230/LIPIcs.WABI.2023.17

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4

Conference

An FPGA-based data pre-processing architecture to accelerate De-novo genome assembly

المؤلفون: Γαλανος Γεωργιος(http://users.isc.tuc.gr/~ggalanos), Galanos Georgios(http://users.isc.tuc.gr/~ggalanos), Μαλακωνακης Παυλος(http://users.isc.tuc.gr/~pmalakonakis), Malakonakis Pavlos(http://users.isc.tuc.gr/~pmalakonakis), Δολλας Αποστολος(http://users.isc.tuc.gr/~adollas), Dollas Apostolos(http://users.isc.tuc.gr/~adollas)

مصطلحات موضوعية: FPGA accelerator, Genome assembly, Dataset filtering, Velvet, de Bruijn graphs

Relation: info:eu-repo/grantAgreement/EC/FP7/246686; http://purl.tuc.gr/dl/dias/AE8A9926-209C-4135-92C6-1B1F113BC998

الاتاحة: http://purl.tuc.gr/dl/dias/AE8A9926-209C-4135-92C6-1B1F113BC998

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5

Academic Journal

ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks

المؤلفون: Freire, Borja, Ladra, Susana, Paramá, José R., Salmela, Leena

مصطلحات موضوعية: 'de novo' viral quasispecies assembly, Genome assembly, De Bruijn graphs

Relation: info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-78011-C4-1-R/ES/DATOS 4.0: RETOS Y SOLUCIONES-UDC/; info:eu-repo/grantAgreement/MECD/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FPU17%2F02742/ES/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-105221RB-C41/ES/VISUALIZACION Y EXPLORACION BASADA EN FLUJOS Y ANALITICA DE BIG DATA ESPACIAL/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114635RB-I00/ES/EXPLOTACION ENRIQUECIDA DE TRAYECTORIAS CON ESTRUCTURAS DE DATOS COMPACTAS Y GIS/; info:eu-repo/grantAgreement/EC/H2020/690941; https://doi.org/10.1109/TCBB.2022.3190282; http://hdl.handle.net/2183/40128

الاتاحة: http://hdl.handle.net/2183/40128
https://doi.org/10.1109/TCBB.2022.3190282

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6

Academic Journal

Improved node and arc multiplicity estimation in de Bruijn graphs using approximate inference in conditional random fields

المؤلفون: Steyaert, Aranka, Audenaert, P., Fostier, Jan

المصدر: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS ; ISSN: 1545-5963 ; ISSN: 1557-9964

مصطلحات موضوعية: Technology and Engineering, Mathematics and Statistics, Applied Mathematics, Genetics, Biotechnology, message passing order, de bruijn graphs, conditional random fields, Belief propagation

وصف الملف: application/pdf

Relation: https://biblio.ugent.be/publication/01GW23A6BSACN17W4QA65W0PSR; http://doi.org/10.1109/tcbb.2022.3229085; https://biblio.ugent.be/publication/01GW23A6BSACN17W4QA65W0PSR/file/01GW2DXX433A2S8H175EFPPNXR

الاتاحة: https://biblio.ugent.be/publication/01GW23A6BSACN17W4QA65W0PSR
http://hdl.handle.net/1854/LU-01GW23A6BSACN17W4QA65W0PSR
https://doi.org/10.1109/tcbb.2022.3229085
https://biblio.ugent.be/publication/01GW23A6BSACN17W4QA65W0PSR/file/01GW2DXX433A2S8H175EFPPNXR

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7

Academic Journal

SAUTE: sequence assembly using target enrichment

المؤلفون: Alexandre Souvorov, Richa Agarwala

المصدر: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-22 (2021)

مصطلحات موضوعية: Illumina reads, De-novo assembly, de Bruijn graphs, Antimicrobial resistance, RNA-seq, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1471-2105

URL الوصول: https://doaj.org/article/d4fc765b390d448e86692a7e07a65688

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8

Academic Journal

Disk compression of k-mer sets

المؤلفون: Amatur Rahman, Rayan Chikhi, Paul Medvedev

المصدر: Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-14 (2021)

مصطلحات موضوعية: De Bruijn graphs, Compression, k-mer sets, Spectrum-preserving string sets, Biology (General), QH301-705.5, Genetics, QH426-470

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1748-7188

URL الوصول: https://doaj.org/article/7126c47cc903415d9ed68f00ae1e8d99

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9

Academic Journal

Simplitigs as an efficient and scalable representation of de Bruijn graphs

المؤلفون: Karel Břinda, Michael Baym, Gregory Kucherov

المصدر: Genome Biology, Vol 22, Iss 1, Pp 1-24 (2021)

مصطلحات موضوعية: Sequence analysis, de Bruijn graphs, Simplitigs, k-mers, de Bruijn graph representation, Scalability, Biology (General), QH301-705.5, Genetics, QH426-470

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1474-760X

URL الوصول: https://doaj.org/article/d577f3a473874b568592374e10d3cd10

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10

Academic Journal

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

المؤلفون: Aranka Steyaert, Pieter Audenaert, Jan Fostier

المصدر: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-18 (2020)

مصطلحات موضوعية: Next-generation sequencing, De Bruijn graphs, Probabilistic graphical models, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03740-x; https://doaj.org/toc/1471-2105

URL الوصول: https://doaj.org/article/e161feb46e364215bd1f977e499798f7

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11

Academic Journal

Alignment- and reference-free phylogenomics with colored de Bruijn graphs

المؤلفون: Roland Wittler

المصدر: Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-12 (2020)

مصطلحات موضوعية: Phylogenomics, Phylogenetics, Phylogenetic splits, Colored de Bruijn graphs, Biology (General), QH301-705.5, Genetics, QH426-470

وصف الملف: electronic resource

Relation: http://link.springer.com/article/10.1186/s13015-020-00164-3; https://doaj.org/toc/1748-7188

URL الوصول: https://doaj.org/article/4a54f2bf46dd42dcae01d3e229a0aba6

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12

Academic Journal

Applications of de Bruijn graphs in microbiome research

المؤلفون: Keith Dufault‐Thompson, Xiaofang Jiang

المصدر: iMeta, Vol 1, Iss 1, Pp n/a-n/a (2022)

مصطلحات موضوعية: de Bruijn graphs, microbiome, Omics, Computer applications to medicine. Medical informatics, R858-859.7

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2770-596X

URL الوصول: https://doaj.org/article/234fadfd99a84f249340bf69d8ca5fcf

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13

Dissertation/ Thesis

Computational Methods for the Analysis of Mitochondrial Genomes: Using Annotated de Bruijn Graphs

المؤلفون: Fiedler, Lisa

Thesis Advisors: Universität Leipzig

مصطلحات موضوعية: de Bruijn graphs, mitochondrial genomes, annotation, breakpoints, info:eu-repo/classification/ddc/000, ddc:000

الاتاحة: https://ul.qucosa.de/id/qucosa%3A91193
https://ul.qucosa.de/api/qucosa%3A91193/attachment/ATT-0/

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14

Streaming Methods for Assembly Graph Analysis

المؤلفون: Welcher, Camille Scott

مصطلحات موضوعية: Bioinformatics, Computer science, annotation, bioinformatics, de Bruijn graphs, genomics, MinHash, sketching

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/75f2c6t2

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15

Book

Compressed weighted de Bruijn graphs

المؤلفون: Italiano G. F., Prezza N., Sinaimeri B., Venturini R.

المساهمون: Gawrychowski and Starikovskaya, Italiano, Giuseppe Francesco, Prezza, Nicola, Sinaimeri, Blerina, Venturini, R.

مصطلحات موضوعية: Compressed data structures, K-mer annotation, Partial sums, Weighted de Bruijn graphs

Relation: info:eu-repo/semantics/altIdentifier/isbn/978-3-95977-186-3; ispartofbook:Leibniz International Proceedings in Informatics, LIPIcs; volume:191; firstpage:1; lastpage:16; numberofpages:16; serie:LEIBNIZ INTERNATIONAL PROCEEDINGS IN INFORMATICS; http://hdl.handle.net/11385/210659; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85115272790; https://drops.dagstuhl.de/opus/volltexte/2021/13967/pdf/LIPIcs-CPM-2021-16.pdf

الاتاحة: http://hdl.handle.net/11385/210659
https://doi.org/10.4230/LIPIcs.CPM.2021.16
https://drops.dagstuhl.de/opus/volltexte/2021/13967/pdf/LIPIcs-CPM-2021-16.pdf

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16

Academic Journal

Constructing Strings Avoiding Forbidden Substrings

المؤلفون: Bernardini, Giulia, Marchetti-Spaccamela, Alberto, Pissis, Solon P., Stougie, Leen, Sweering, Michelle

المساهمون: Giulia Bernardini and Alberto Marchetti-Spaccamela and Solon P. Pissis and Leen Stougie and Michelle Sweering

مصطلحات موضوعية: string algorithms, forbidden strings, de Bruijn graphs, data sanitization

وصف الملف: application/pdf

Relation: Is Part Of LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021); https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.9

الاتاحة: https://doi.org/10.4230/LIPIcs.CPM.2021.9
https://nbn-resolving.org/urn:nbn:de:0030-drops-139604
https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.9

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17

Academic Journal

Finite Automata with Colored Accepting States and Their Unmixedness Problems

المؤلفون: Akira ITO, Yoshiaki TAKAHASHI

المصدر: IEICE Transactions on Information and Systems. 2022, E105.D(3):491

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18

Conference

Latin Hypercubes and Cellular Automata

المؤلفون: Gadouleau, Maximilien, Mariot, Luca

المساهمون: Durham University, Delft University of Technology (TU Delft), Hector Zenil, TC 1, WG 1.5

المصدر: Lecture Notes in Computer Science ; 26th International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA) ; https://inria.hal.science/hal-03659462 ; 26th International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA), Aug 2020, Stockholm, Sweden. pp.139-151, ⟨10.1007/978-3-030-61588-8_11⟩

مصطلحات موضوعية: Latin squares, Latin hypercubes, Cellular automata, Bipermutivity, Toeplitz matrices, De bruijn graphs, [INFO]Computer Science [cs]

جغرافية الموضوع: Stockholm, Sweden

Time: Stockholm, Sweden

Relation: hal-03659462; https://inria.hal.science/hal-03659462; https://inria.hal.science/hal-03659462/document; https://inria.hal.science/hal-03659462/file/496967_1_En_11_Chapter.pdf

الاتاحة: https://inria.hal.science/hal-03659462
https://inria.hal.science/hal-03659462/document
https://inria.hal.science/hal-03659462/file/496967_1_En_11_Chapter.pdf
https://doi.org/10.1007/978-3-030-61588-8_11

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19

Academic Journal

Disk Compression of k-mer Sets

المؤلفون: Rahman, Amatur, Chikhi, Rayan, Medvedev, Paul

المساهمون: Amatur Rahman and Rayan Chikhi and Paul Medvedev

مصطلحات موضوعية: de Bruijn graphs, compression, k-mer sets, spectrum-preserving string sets

وصف الملف: application/pdf

Relation: Is Part Of LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020); https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.16

الاتاحة: https://doi.org/10.4230/LIPIcs.WABI.2020.16
https://nbn-resolving.org/urn:nbn:de:0030-drops-128057
https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.16

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20

Academic Journal

Inference of viral quasispecies with a paired de Bruijn graph

المؤلفون: Freire, Borja, Ladra, Susana, Paramá, José R., Salmela, Leena

مصطلحات موضوعية: Genome assembly, De Bruijn graphs, 'de novo' viral quasispecies assembly

Relation: info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-78011-C4-1-R/ES/DATOS 4.0: RETOS Y SOLUCIONES-UDC/; info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-77158-C4-3-R/ES/VELOCITY: PROCESADO EFICIENTE DE BIG DATA ESPAZO-TEMPORAL PARA FLATCITY; info:eu-repo/grantAgreement/MECD/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FPU17%2F02742/ES/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTC-2017-5908-7/ES/STEPS. Soluciones Tecnológicas para la Evolución en la Prestación de Servicios en campo/; info:eu-repo/grantAgreement/EC/H2020/690941; https://doi.org/10.1093/bioinformatics/btaa782; Borja Freire, Susana Ladra, Jose R Paramá, Leena Salmela, Inference of viral quasispecies with a paired de Bruijn graph, Bioinformatics, Volume 37, Issue 4, February 2021, Pages 473–481, https://doi.org/10.1093/bioinformatics/btaa782; http://hdl.handle.net/2183/40132

الاتاحة: http://hdl.handle.net/2183/40132
https://doi.org/10.1093/bioinformatics/btaa782

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