Works matching DE "DE Bruijn graph"

Results: 156

Sama: a contig assembler with correctness guarantee.

Published in:

Algorithms for Molecular Biology, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s13015-025-00280-y

By:

Salmela, Leena

Publication type:

Article

A scalable distributed pipeline for reference-free variants calling.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11722-7

By:

Di Rocco, Lorenzo;
Ferraro Petrillo, Umberto

Publication type:

Article

Succinct colored de Bruijn graphs.

Published in:

Bioinformatics, 2017, v. 33, n. 20, p. 3181, doi. 10.1093/bioinformatics/btx067

By:

Muggli, Martin D.;
Bowe, Alexander;
Noyes, Noelle R.;
Morley, Paul S.;
Belk, Keith E.;
Raymond, Robert;
Gagie, Travis;
Puglisi, Simon J.;
Boucher, Christina

Publication type:

Article

Accurate self-correction of errors in long reads using de Bruijn graphs.

Published in:

Bioinformatics, 2017, v. 33, n. 6, p. 799, doi. 10.1093/bioinformatics/btw321

By:

Salmela, Leena;
Walve, Riku;
Rivals, Eric;
Ukkonen, Esko

Publication type:

Article

deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding.

Published in:

Bioinformatics, 2016, v. 32, n. 12, p. i174, doi. 10.1093/bioinformatics/btw266

By:

Bo Liu;
Dixian Zhu;
Yadong Wang

Publication type:

Article

Integration of string and de Bruijn graphs for genome assembly.

Published in:

Bioinformatics, 2016, v. 32, n. 9, p. 1301, doi. 10.1093/bioinformatics/btw011

By:

Yao-Ting Huang;
Chen-Fu Liao

Publication type:

Article

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1001, doi. 10.1093/bioinformatics/btv510

By:

Yuzhen Ye;
Haixu Tang

Publication type:

Article

Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 642, doi. 10.1093/bioinformatics/btu706

By:

Younsi, Reda;
MacLean, Dan

Publication type:

Article

VAGUE: a graphical user interface for the Velvet assembler.

Published in:

Bioinformatics, 2013, v. 29, n. 2, p. 264, doi. 10.1093/bioinformatics/bts664

By:

Powell, David R.;
Seemann, Torsten

Publication type:

Article

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.

Published in:

Bioinformatics, 2012, v. 28, n. 11, p. 1420, doi. 10.1093/bioinformatics/bts174

By:

Peng, Yu;
Leung, Henry C. M.;
Yiu, S. M.;
Chin, Francis Y. L.

Publication type:

Article

HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly.

Published in:

International Journal of Genomics, 2017, p. 1, doi. 10.1155/2017/6120980

By:

Limon, Mahfuzer Rahman;
Sharker, Ratul;
Biswas, Sajib;
Rahman, M. Sohel

Publication type:

Article

Spaced Seed Data Structures for De Novo Assembly.

Published in:

International Journal of Genomics, 2015, v. 2015, p. 1, doi. 10.1155/2015/196591

By:

Birol, Inanç;
Chu, Justin;
Mohamadi, Hamid;
Jackman, Shaun D.;
Raghavan, Karthika;
Vandervalk, Benjamin P.;
Raymond, Anthony;
Warren, René L.

Publication type:

Article

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era.

Published in:

Quantitative Biology, 2019, v. 7, n. 4, p. 278, doi. 10.1007/s40484-019-0181-x

By:

Rizzi, Raffaella;
Beretta, Stefano;
Patterson, Murray;
Pirola, Yuri;
Previtali, Marco;
Della Vedova, Gianluca;
Bonizzoni, Paola

Publication type:

Article

Comparative genomics with succinct colored de Bruijn graphs.

Published in:

Acta Informatica, 2025, v. 62, n. 1, p. 1, doi. 10.1007/s00236-024-00467-7

By:

Ramos, Lucas P.;
Louza, Felipe A.;
Telles, Guilherme P.

Publication type:

Article

NOTE ON OCCURRENCES OF FACTORS IN CIRCULAR WORDS.

Published in:

RAIRO - Theoretical Informatics & Applications, 2016, v. 50, n. 2, p. 167, doi. 10.1051/ita/2016019

By:

ARNOUX, PIERRE

Publication type:

Article

GRASShopPER—An algorithm for de novo assembly based on GPU alignments.

Published in:

PLoS ONE, 2018, v. 13, n. 8, p. 1, doi. 10.1371/journal.pone.0202355

By:

Swiercz, Aleksandra;
Frohmberg, Wojciech;
Kierzynka, Michal;
Wojciechowski, Pawel;
Zurkowski, Piotr;
Badura, Jan;
Laskowski, Artur;
Kasprzak, Marta;
Blazewicz, Jacek

Publication type:

Article

Hybrid de novo tandem repeat detection using short and long reads.

Published in:

BMC Medical Genomics, 2015, v. 8, p. 1, doi. 10.1186/1755-8794-8-S3-S5

By:

Fertin, Guillaume;
Jean, Géraldine;
Radulescu, Andreea;
Rusu, Irena

Publication type:

Article

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05613-5

By:

Faltejsková, Kateřina;
Vondrášek, Jiří

Publication type:

Article

Pan-genome de Bruijn graph using the bidirectional FM-index.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05531-6

By:

Depuydt, Lore;
Renders, Luca;
Abeel, Thomas;
Fostier, Jan

Publication type:

Article

RegCloser: a robust regression approach to closing genome gaps.

Published in:

BMC Bioinformatics, 2023, v. 23, n. 11, p. 1, doi. 10.1186/s12859-023-05367-0

By:

Cao, Shenghao;
Li, Mengtian;
Li, Lei M.

Publication type:

Article

Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009229

By:

Liu, Yuansheng;
Li, Jinyan

Publication type:

Article

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Published in:

PLoS Computational Biology, 2021, v. 17, n. 5, p. 1, doi. 10.1371/journal.pcbi.1008928

By:

Medvedev, Paul;
Pop, Mihai

Publication type:

Article

Genome-wide somatic variant calling using localized colored de Bruijn graphs.

Published in:

Communications Biology, 2018, v. 1, n. 1, p. N.PAG, doi. 10.1038/s42003-018-0023-9

By:

Narzisi, Giuseppe;
Corvelo, André;
Arora, Kanika;
Bergmann, Ewa A.;
Shah, Minita;
Musunuri, Rajeeva;
Emde, Anne-Katrin;
Robine, Nicolas;
Vacic, Vladimir;
Zody, Michael C.

Publication type:

Article

Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.

Published in:

Frontiers in Genetics, 2023, p. 1, doi. 10.3389/fgene.2023.1250907

By:

Fiedler, Lisa;
Middendorf, Martin;
Bernt, Matthias

Publication type:

Article

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach.

Published in:

PLoS ONE, 2014, v. 9, n. 12, p. 1, doi. 10.1371/journal.pone.0114253

By:

Zhu, Xiao;
Leung, Henry C. M.;
Chin, Francis Y. L.;
Yiu, Siu Ming;
Quan, Guangri;
Liu, Bo;
Wang, Yadong

Publication type:

Article

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs.

Published in:

PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0060058

By:

Leggett, Richard M.;
Ramirez-Gonzalez, Ricardo H.;
Verweij, Walter;
Kawashima, Cintia G.;
Iqbal, Zamin;
Jones, Jonathan D. G.;
Caccamo, Mario;
MacLean, Daniel

Publication type:

Article

Explicit substitution calculi with de Bruijn indices and intersection type systems.

Published in:

Logic Journal of the IGPL, 2015, v. 23, n. 2, p. 295, doi. 10.1093/jigpal/jzu044

By:

VENTURA, DANIEL LIMA;
KAMAREDDINE, FAIROUZ;
AYALA-RINCÓN, MAURICIO

Publication type:

Article

Detecting circular RNA from high-throughput sequence data with de Bruijn graph.

Published in:

BMC Genomics, 2020, v. 21, p. 1, doi. 10.1186/s12864-019-6154-7

By:

Li, Xin;
Wu, Yufeng

Publication type:

Article

A hybrid and scalable error correction algorithm for indel and substitution errors of long reads.

Published in:

BMC Genomics, 2019, v. 20, n. 11, p. 1, doi. 10.1186/s12864-019-6286-9

By:

Das, Arghya Kusum;
Goswami, Sayan;
Lee, Kisung;
Park, Seung-Jong

Publication type:

Article

Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus.

Published in:

BMC Genomics, 2019, v. 20, n. 5, p. N.PAG, doi. 10.1186/s12864-019-5702-5

By:

Fu, Shuhua;
Chang, Peter L.;
Friesen, Maren L.;
Teakle, Natasha L.;
Tarone, Aaron M.;
Sze, Sing-Hoi

Publication type:

Article

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics.

Published in:

Molecular Ecology, 2019, v. 28, n. 21, p. 4737, doi. 10.1111/mec.15253

By:

Rochette, Nicolas C.;
Rivera‐Colón, Angel G.;
Catchen, Julian M.

Publication type:

Article

Robust data storage in DNA by de Bruijn graph-based de novo strand assembly.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33046-w

By:

Song, Lifu;
Geng, Feng;
Gong, Zi-Yi;
Chen, Xin;
Tang, Jijun;
Gong, Chunye;
Zhou, Libang;
Xia, Rui;
Han, Ming-Zhe;
Xu, Jing-Yi;
Li, Bing-Zhi;
Yuan, Ying-Jin

Publication type:

Article

A New Approach to Sequence Construction With Good Correlation by Particle Swarm Optimization.

Published in:

Journal of Communications Software & Systems, 2015, v. 11, n. 3, p. 127, doi. 10.24138/jcomss.v11i3.101

By:

Sarayloo, Mahdiyar;
Gambi, Ennio;
Spinsante, Susanna

Publication type:

Article

Using earth mover's distance for viral outbreak investigations.

Published in:

BMC Genomics, 2020, v. 21, p. 1, doi. 10.1186/s12864-020-06982-4

By:

Melnyk, Andrew;
Knyazev, Sergey;
Vannberg, Fredrik;
Bunimovich, Leonid;
Skums, Pavel;
Zelikovsky, Alex

Publication type:

Article

Read mapping on de Bruijn graphs.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1103-9

By:

Limasset, Antoine;
Cazaux, Bastien;
Rivals, Eric;
Peterlongo, Pierre

Publication type:

Article

Sealer: a scalable gap-closing application for finishing draft genomes.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0663-4

By:

Paulino, Daniel;
Warren, René L.;
Vandervalk, Benjamin P.;
Raymond, Anthony;
Jackman, Shaun D.;
Birol, Inanç

Publication type:

Article

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0709-7

By:

Benoit, Gaëtan;
Lemaitre, Claire;
Lavenier, Dominique;
Drezen, Erwan;
Dayris, Thibault;
Uricaru, Raluca;
Rizk, Guillaume

Publication type:

Article

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07376-y

By:

Liu, Yuansheng;
Li, Yichen;
Chen, Enlian;
Xu, Jialu;
Zhang, Wenhai;
Zeng, Xiangxiang;
Luo, Xiao

Publication type:

Article

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.

Published in:

Microbiome, 2024, v. 12, n. 1, p. 1, doi. 10.1186/s40168-024-01904-y

By:

Jochheim, Annika;
Jochheim, Florian A.;
Kolodyazhnaya, Alexandra;
Morice, Étienne;
Steinegger, Martin;
Söding, Johannes

Publication type:

Article

A history of DNA sequence assembly.

Published in:

IT: Information Technology, 2016, v. 58, n. 3, p. 126, doi. 10.1515/itit-2015-0047

By:

Myers Jr, Eugene W.

Publication type:

Article

A Novel 3D Mesh-Based NoC Architecture for Performance Improvement.

Published in:

Majlesi Journal of Electrical Engineering, 2022, v. 16, n. 2, p. 85, doi. 10.52547/mjee.16.2.85

By:

Habibi, Navid;
Salehnamadi, Mohammad Reza;
Khademzadeh, Ahmad

Publication type:

Article

High-Performance 3D Mesh-Based NOC Architecture Using Node-Layer Clustering.

Published in:

IETE Journal of Research, 2023, v. 69, n. 1, p. 509, doi. 10.1080/03772063.2020.1830864

By:

Habibi, Navid;
Salehnamadi, M. Reza;
Khademzadeh, Ahmad

Publication type:

Article

Sink Mobility Model for Wireless Sensor Networks.

Published in:

Arabian Journal for Science & Engineering (Springer Science & Business Media B.V. ), 2014, v. 39, n. 3, p. 1775, doi. 10.1007/s13369-013-0811-y

By:

Taleb, Anas;
Alhmiedat, Tareq;
Taleb, Reem;
Hassan, Osama

Publication type:

Article

GAIA ASTROMETRIC SCIENCE PERFORMANCE - POST-LAUNCH PREDICTIONS.

Published in:

EAS Publications Series, 2014, v. 67/68, p. 23, doi. 10.1051/eas/1567004

By:

de Bruijne, J. H. J.;
Rygl, K. L. J.;
Antoja, T.

Publication type:

Article

A New Universal Cycle for Permutations.

Published in:

Graphs & Combinatorics, 2017, v. 33, n. 6, p. 1393, doi. 10.1007/s00373-017-1778-3

By:

Wong, Dennis

Publication type:

Article

An Unoriented Variation on de Bruijn Sequences.

Published in:

Graphs & Combinatorics, 2017, v. 33, n. 4, p. 845, doi. 10.1007/s00373-017-1793-4

By:

Burris, Christie;
Motta, Francis;
Shipman, Patrick

Publication type:

Article

De Bruijn Graph Based Solution for Lookup Acceleration and Optimization in P2P Networks.

Published in:

Wireless Personal Communications, 2015, v. 85, n. 3, p. 1471, doi. 10.1007/s11277-015-2851-y

By:

Amad, Mourad;
Aïssani, Djamil;
Meddahi, Ahmed;
Benkerrou, Makhlouf;
Amghar, Farouk

Publication type:

Article

BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs.

Published in:

PeerJ, 2018, p. 1, doi. 10.7717/peerj.5611

By:

Rongjie Wang;
Junyi Li;
Yang Bai;
Tianyi Zang;
Yadong Wang

Publication type:

Article

The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbae627

By:

Wei, Yuxiao;
Zhang, Qi;
Liu, Liwei

Publication type:

Article

Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae363

By:

Dou, Chang;
Yang, Yijie;
Zhu, Fei;
Li, BingZhi;
Duan, Yuping

Publication type:

Article