Wei Y, Zhou T, Zhai Y, Yu L, Zou Q
Brief Bioinform. 2025; 26(1).
PMID: 39987460
PMC: 11846685.
DOI: 10.1093/bib/bbaf061.
Hu Y, Huang B, Zang C, Xu J
Comput Struct Biotechnol J. 2025; 27:214-220.
PMID: 39866668
PMC: 11757225.
DOI: 10.1016/j.csbj.2024.12.029.
Zong P, Deng W, Liu J, Ruan J
GigaByte. 2024; 2024:gigabyte141.
PMID: 39539520
PMC: 11558659.
DOI: 10.46471/gigabyte.141.
Makino J, Ebisuzaki T, Himeno R, Hayashizaki Y
Genomics Inform. 2024; 22(1):19.
PMID: 39472988
PMC: 11520436.
DOI: 10.1186/s44342-024-00012-5.
Alonso-Marin A, Fernandez I, Aguado-Puig Q, Gomez-Luna J, Marco-Sola S, Mutlu O
Bioinformatics. 2024; 40(11).
PMID: 39432682
PMC: 11576351.
DOI: 10.1093/bioinformatics/btae631.
Jointly benchmarking small and structural variant calls with vcfdist.
Dunn T, Zook J, Holt J, Narayanasamy S
Genome Biol. 2024; 25(1):253.
PMID: 39358801
PMC: 11446017.
DOI: 10.1186/s13059-024-03394-5.
Gene-level alignment of single-cell trajectories.
Sumanaweera D, Suo C, Cujba A, Muraro D, Dann E, Polanski K
Nat Methods. 2024; 22(1):68-81.
PMID: 39300283
PMC: 11725504.
DOI: 10.1038/s41592-024-02378-4.
SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects.
Ferrer Florensa A, Almagro Armenteros J, Nielsen H, Aarestrup F, Clausen P
NAR Genom Bioinform. 2024; 6(3):lqae106.
PMID: 39157582
PMC: 11327874.
DOI: 10.1093/nargab/lqae106.
Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.
Iglhaut C, Pecerska J, Gil M, Anisimova M
Mol Biol Evol. 2024; 41(7).
PMID: 38842253
PMC: 11221656.
DOI: 10.1093/molbev/msae109.
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.
Scholten N, Haandrikman D, Tolhuis J, Morandi E, Incarnato D
Nucleic Acids Res. 2024; 52(W1):W362-W367.
PMID: 38709889
PMC: 11223795.
DOI: 10.1093/nar/gkae348.
RecGraph: recombination-aware alignment of sequences to variation graphs.
Avila Cartes J, Bonizzoni P, Ciccolella S, Della Vedova G, Denti L, Didelot X
Bioinformatics. 2024; 40(5).
PMID: 38676570
PMC: 11256948.
DOI: 10.1093/bioinformatics/btae292.
Infrared: a declarative tree decomposition-powered framework for bioinformatics.
Yao H, Marchand B, Berkemer S, Ponty Y, Will S
Algorithms Mol Biol. 2024; 19(1):13.
PMID: 38493130
PMC: 10943887.
DOI: 10.1186/s13015-024-00258-2.
Exact global alignment using A* with chaining seed heuristic and match pruning.
Groot Koerkamp R, Ivanov P
Bioinformatics. 2024; 40(3).
PMID: 38265119
PMC: 10932610.
DOI: 10.1093/bioinformatics/btae032.
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.
Genovese G, Rockweiler N, Gorman B, Bigdeli T, Pato M, Pato C
Bioinformatics. 2024; 40(2).
PMID: 38261650
PMC: 10832354.
DOI: 10.1093/bioinformatics/btae038.
vcfdist: accurately benchmarking phased small variant calls in human genomes.
Dunn T, Narayanasamy S
Nat Commun. 2023; 14(1):8149.
PMID: 38071244
PMC: 10710436.
DOI: 10.1038/s41467-023-43876-x.
Kabirian-based optinalysis: A conceptually grounded framework for symmetry/asymmetry, similarity/dissimilarity and identity/unidentity estimations in mathematical structures and biological sequences.
Abdullahi K
MethodsX. 2023; 11:102400.
PMID: 37928104
PMC: 10622715.
DOI: 10.1016/j.mex.2023.102400.
Seedability: optimizing alignment parameters for sensitive sequence comparison.
Ayad L, Chikhi R, Pissis S
Bioinform Adv. 2023; 3(1):vbad108.
PMID: 37621456
PMC: 10444664.
DOI: 10.1093/bioadv/vbad108.
Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.
Liu D, Steinegger M
Bioinformatics. 2023; 39(8).
PMID: 37535681
PMC: 10457662.
DOI: 10.1093/bioinformatics/btad487.
Effects of spaced k-mers on alignment-free genotyping.
Hantze H, Horton P
Bioinformatics. 2023; 39(39 Suppl 1):i213-i221.
PMID: 37387138
PMC: 10311327.
DOI: 10.1093/bioinformatics/btad202.
A framework for high-throughput sequence alignment using real processing-in-memory systems.
Diab S, Nassereldine A, Alser M, Gomez Luna J, Mutlu O, El Hajj I
Bioinformatics. 2023; 39(5).
PMID: 36971586
PMC: 10159653.
DOI: 10.1093/bioinformatics/btad155.
