Andrey Prjibelski
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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
A Bankevich, S Nurk, D Antipov, AA Gurevich, M Dvorkin, AS Kulikov, ...
Journal of computational biology 19 (5), 455-477, 2012
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products
S Nurk, A Bankevich, D Antipov, AA Gurevich, A Korobeynikov, A Lapidus, ...
Journal of Computational Biology 20 (10), 714-737, 2013
Using SPAdes de novo assembler
A Prjibelski, D Antipov, D Meleshko, A Lapidus, A Korobeynikov
Current protocols in bioinformatics 70 (1), e102, 2020
Assembling genomes and mini-metagenomes from highly chimeric reads
S Nurk, A Bankevich, D Antipov, A Gurevich, A Korobeynikov, A Lapidus, ...
Annual International Conference on Research in Computational Molecular …, 2013
Versatile genome assembly evaluation with QUAST-LG
A Mikheenko, A Prjibelski, V Saveliev, D Antipov, A Gurevich
Bioinformatics 34 (13), i142-i150, 2018
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
E Bushmanova, D Antipov, A Lapidus, AD Prjibelski
GigaScience 8 (9), giz100, 2019
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
E Bushmanova, D Antipov, A Lapidus, V Suvorov, AD Prjibelski
Bioinformatics 32 (14), 2210-2212, 2016
Icarus: visualizer for de novo assembly evaluation
A Mikheenko, G Valin, A Prjibelski, V Saveliev, A Gurevich
Bioinformatics 32 (21), 3321-3323, 2016
A spatially resolved brain region-and cell type-specific isoform atlas of the postnatal mouse brain
A Joglekar, A Prjibelski, A Mahfouz, P Collier, S Lin, AK Schlusche, ...
Nature Communications 12 (1), 463, 2021
ExSPAnder: a universal repeat resolver for DNA fragment assembly
AD Prjibelski, I Vasilinetc, A Bankevich, A Gurevich, T Krivosheeva, ...
Bioinformatics 30 (12), i293-i301, 2014
Assembling short reads from jumping libraries with large insert sizes
I Vasilinetc, AD Prjibelski, A Gurevich, A Korobeynikov, PA Pevzner
Bioinformatics 31 (20), 3262-3268, 2015
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
SA Hardwick, W Hu, A Joglekar, L Fan, PG Collier, C Foord, J Balacco, ...
Nature biotechnology 40 (7), 1082-1092, 2022
De novo peptide sequencing reveals many cyclopeptides in the human gut and other environments
B Behsaz, H Mohimani, A Gurevich, A Prjibelski, M Fisher, F Vargas, ...
Cell systems 10 (1), 99-108. e5, 2020
Accurate isoform discovery with IsoQuant using long reads
AD Prjibelski, A Mikheenko, A Joglekar, A Smetanin, J Jarroux, ...
Nature Biotechnology, 1-4, 2023
Extending rnaSPAdes functionality for hybrid transcriptome assembly
AD Prjibelski, GD Puglia, D Antipov, E Bushmanova, D Giordano, ...
BMC Bioinformatics 21 (302), 2020
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
FJ Pardo-Palacios, D Wang, F Reese, M Diekhans, S Carbonell-Sala, ...
bioRxiv, 2021
Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish
KA Demin, AM Lakstygal, NA Krotova, A Masharsky, N Tagawa, ...
Scientific reports 10 (1), 19981, 2020
Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)
GD Puglia, AD Prjibelski, D Vitale, E Bushmanova, KJ Schmid, ...
BMC genomics 21 (1), 1-17, 2020
Sequence analysis
AD Prjibelski, AI Korobeynikov, AL Lapidus
Encyclopedia of Bioinformatics and Computational Biology: ABC of …, 2018
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
A Mikheenko, AD Prjibelski, A Joglekar, HU Tilgner
Genome Research 32 (4), 726-737, 2022
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