139 related articles for article (PubMed ID: 37790531)
1. Pangenome graph layout by Path-Guided Stochastic Gradient Descent.
Heumos S; Guarracino A; Schmelzle JM; Li J; Zhang Z; Hagmann J; Nahnsen S; Prins P; Garrison E
bioRxiv; 2023 Oct; ():. PubMed ID: 37790531
[TBL] [Abstract][Full Text] [Related]
2. Pangenome graph layout by Path-Guided Stochastic Gradient Descent.
Heumos S; Guarracino A; Schmelzle JM; Li J; Zhang Z; Hagmann J; Nahnsen S; Prins P; Garrison E
Bioinformatics; 2024 Jul; 40(7):. PubMed ID: 38960860
[TBL] [Abstract][Full Text] [Related]
3. ODGI: understanding pangenome graphs.
Guarracino A; Heumos S; Nahnsen S; Prins P; Garrison E
Bioinformatics; 2022 Jun; 38(13):3319-3326. PubMed ID: 35552372
[TBL] [Abstract][Full Text] [Related]
4. Panacus: fast and exact pangenome growth and core size estimation.
Parmigiani L; Garrison E; Stoye J; Marschall T; Doerr D
bioRxiv; 2024 Jun; ():. PubMed ID: 38915671
[TBL] [Abstract][Full Text] [Related]
5. Unbiased pangenome graphs.
Garrison E; Guarracino A
Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36448683
[TBL] [Abstract][Full Text] [Related]
6. Multicriteria Scalable Graph Drawing via Stochastic Gradient Descent, (SGD)
Ahmed R; De Luca F; Devkota S; Kobourov S; Li M
IEEE Trans Vis Comput Graph; 2022 Jun; 28(6):2388-2399. PubMed ID: 35230951
[TBL] [Abstract][Full Text] [Related]
7. Graph Drawing by Stochastic Gradient Descent.
Zheng JX; Pawar S; Goodman DFM
IEEE Trans Vis Comput Graph; 2019 Sep; 25(9):2738-2748. PubMed ID: 30047888
[TBL] [Abstract][Full Text] [Related]
8. Taurus: Towards a Unified Force Representation and Universal Solver for Graph Layout.
Xue M; Wang Z; Zhong F; Wang Y; Xu M; Deussen O; Wang Y
IEEE Trans Vis Comput Graph; 2023 Jan; 29(1):886-895. PubMed ID: 36166546
[TBL] [Abstract][Full Text] [Related]
9. Co-linear chaining on pangenome graphs.
Rajput J; Chandra G; Jain C
Algorithms Mol Biol; 2024 Jan; 19(1):4. PubMed ID: 38279113
[TBL] [Abstract][Full Text] [Related]
10. Efficient short read mapping to a pangenome that is represented by a graph of ED strings.
Büchler T; Olbrich J; Ohlebusch E
Bioinformatics; 2023 May; 39(5):. PubMed ID: 37171844
[TBL] [Abstract][Full Text] [Related]
11. Pan-genome de Bruijn graph using the bidirectional FM-index.
Depuydt L; Renders L; Abeel T; Fostier J
BMC Bioinformatics; 2023 Oct; 24(1):400. PubMed ID: 37884897
[TBL] [Abstract][Full Text] [Related]
12. Exploring gene content with pangene graphs.
Li H; Marin M; Farhat MR
ArXiv; 2024 May; ():. PubMed ID: 38463499
[TBL] [Abstract][Full Text] [Related]
13. Efficient dynamic variation graphs.
Eizenga JM; Novak AM; Kobayashi E; Villani F; Cisar C; Heumos S; Hickey G; Colonna V; Paten B; Garrison E
Bioinformatics; 2021 Jan; 36(21):5139-5144. PubMed ID: 33040146
[TBL] [Abstract][Full Text] [Related]
14. Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of
Yang Z; Guarracino A; Biggs PJ; Black MA; Ismail N; Wold JR; Merriman TR; Prins P; Garrison E; de Ligt J
Front Genet; 2023; 14():1225248. PubMed ID: 37636268
[TBL] [Abstract][Full Text] [Related]
15. Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G; Monlong J; Ebler J; Novak AM; Eizenga JM; Gao Y; ; Marschall T; Li H; Paten B
Nat Biotechnol; 2024 Apr; 42(4):663-673. PubMed ID: 37165083
[TBL] [Abstract][Full Text] [Related]
16. Detecting high-scoring local alignments in pangenome graphs.
Schulz T; Wittler R; Rahmann S; Hach F; Stoye J
Bioinformatics; 2021 Aug; 37(16):2266-2274. PubMed ID: 33532821
[TBL] [Abstract][Full Text] [Related]
17. WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.
Chao KH; Chen PW; Seshia SA; Langmead B
iScience; 2023 Aug; 26(8):107402. PubMed ID: 37575187
[TBL] [Abstract][Full Text] [Related]
18. GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
Tognon M; Bonnici V; Garrison E; Giugno R; Pinello L
PLoS Comput Biol; 2021 Sep; 17(9):e1009444. PubMed ID: 34570769
[TBL] [Abstract][Full Text] [Related]
19. Haplotype-aware graph indexes.
Sirén J; Garrison E; Novak AM; Paten B; Durbin R
Bioinformatics; 2020 Jan; 36(2):400-407. PubMed ID: 31406990
[TBL] [Abstract][Full Text] [Related]
20. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
Gautreau G; Bazin A; Gachet M; Planel R; Burlot L; Dubois M; Perrin A; Médigue C; Calteau A; Cruveiller S; Matias C; Ambroise C; Rocha EPC; Vallenet D
PLoS Comput Biol; 2020 Mar; 16(3):e1007732. PubMed ID: 32191703
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]