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A. Prjibelski · SciRah

Researcher profile · Semantic Scholar

A. Prjibelski

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A. Prjibelski — researcher profile on SciRah

h-index: 19
Works: 56
Citations: 32K

Most-cited papers

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
A. Bankevich, S. Nurk, D. Antipov, A. Gurevich +12 more
2012J. Comput. Biol.24K citations Open access
Semantic Scholar
Using SPAdes De Novo Assembler
A. Prjibelski, D. Antipov, Dmitry Meleshko, A. Lapidus +1 more
2020Current Protocols in Bioinformatics3,147 citations
Semantic Scholar
Versatile genome assembly evaluation with QUAST-LG
Alla Mikheenko, A. Prjibelski, V. Saveliev, D. Antipov +1 more
2018Bioinform.1,359 citations Open access
Semantic Scholar
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
S. Nurk, A. Bankevich, D. Antipov, A. Gurevich +14 more
2013J. Comput. Biol.1,132 citations Open access
Semantic Scholar
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Elena Bushmanova, D. Antipov, A. Lapidus, A. Prjibelski
2018bioRxiv737 citations Open access
Semantic Scholar
Accurate isoform discovery with IsoQuant using long reads
A. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin +3 more
2023Nature Biotechnology248 citations Open access
Semantic Scholar
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, M. Diekhans +83 more
2024Nature Methods207 citations Open access
Semantic Scholar
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Anoushka Joglekar, A. Prjibelski, A. Mahfouz, Paul G Collier +26 more
2021Nature Communications188 citations Open access
Semantic Scholar
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
Elena Bushmanova, D. Antipov, A. Lapidus, V. Suvorov +1 more
2016Bioinform.144 citations
Semantic Scholar
Icarus: visualizer for de novo assembly evaluation
Alla Mikheenko, G. Valin, A. Prjibelski, V. Saveliev +1 more
2016Bioinform.141 citations Open access
Semantic Scholar
ExSPAnder: a universal repeat resolver for DNA fragment assembly
A. Prjibelski, Irina Vasilinetc, A. Bankevich, A. Gurevich +6 more
2014Bioinform.126 citations Open access
Semantic Scholar
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
S. Hardwick, Wengian Hu, Anoushka Joglekar, Li Fan +26 more
2022Nature Biotechnology118 citations Open access
Semantic Scholar
Assembling short reads from jumping libraries with large insert sizes
Irina Vasilinetc, A. Prjibelski, A. Gurevich, Anton I. Korobeynikov +1 more
2015Bioinform.74 citations Open access
Semantic Scholar
Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish
K. Demin, A. Lakstygal, N. Krotova, A. Masharsky +18 more
2020Scientific Reports48 citations Open access
Semantic Scholar
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
Alla Mikheenko, A. Prjibelski, Anoushka Joglekar, H. Tilgner
2022Genome Research33 citations Open access
Semantic Scholar
De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments.
B. Behsaz, H. Mohimani, A. Gurevich, A. Prjibelski +6 more
2019Cell Systems33 citations Open access
Semantic Scholar
Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)
G. Puglia, A. Prjibelski, D. Vitale, Elena Bushmanova +2 more
2020BMC Genomics29 citations Open access
Semantic Scholar
Extending rnaSPAdes functionality for hybrid transcriptome assembly
A. Prjibelski, G. Puglia, D. Antipov, Elena Bushmanova +4 more
2020BMC Bioinformatics27 citations Open access
Semantic Scholar
Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis
A. Vaganova, R. Murtazina, T. Shemyakova, A. Prjibelski +2 more
2021International Journal of Molecular Sciences19 citations Open access
Semantic Scholar
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
Careen Foord, A. Prjibelski, Wengian Hu, Lieke Michielsen +13 more
2025Nature Communications18 citations Open access
Semantic Scholar
Human pericentromeric tandemly repeated DNA is transcribed at the end of oocyte maturation and is associated with membraneless mitochondria-associated structures
M. Dobrynin, N. Korchagina, A. Prjibelski, D. Shafranskaya +6 more
2020Scientific Reports18 citations Open access
Semantic Scholar
Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis
N. Enukashvily, N. Ponomartsev, A. Ketkar, R. Suezov +12 more
2023Cell Death and Disease17 citations Open access
Semantic Scholar
Seed Transcriptome Annotation Reveals Enhanced Expression of Genes Related to ROS Homeostasis and Ethylene Metabolism at Alternating Temperatures in Wild Cardoon
H. R. Huarte, G. Puglia, A. Prjibelski, S. A. Raccuia
2020Plants15 citations Open access
Semantic Scholar
Liquid drop of DNA libraries reveals total genome information
S. Terekhov, I. Eliseev, L. A. Ovchinnikova, Marsel R Kabilov +8 more
2020Proceedings of the National Academy of Sciences of the United States of America14 citations Open access
Semantic Scholar
SGTK: a toolkit for visualization and assessment of scaffold graphs
Olga Kunyavskaya, A. Prjibelski
2018Bioinform.13 citations
Semantic Scholar
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data
D. Shafranskaya, Varsha Kale, R. Finn, A. Lapidus +2 more
2022Frontiers in Microbiology11 citations Open access
Semantic Scholar
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain
Natan Belchikov, Wengian Hu, Li Fan, Anoushka Joglekar +26 more
2025Cell Reports10 citations Open access
Semantic Scholar
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
Careen Foord, A. Prjibelski, Wengian Hu, Lieke Michielsen +13 more
2025bioRxiv9 citations Open access
Semantic Scholar
Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience
F. Pepe, G. Russo, A. Venuta, C. Scimone +63 more
2024Oncology and Therapy9 citations Open access
Semantic Scholar
Modulation of Notch Signaling at Early Stages of Differentiation of Human Induced Pluripotent Stem Cells to Dopaminergic Neurons
N. Katolikova, A. Khudiakov, Daria D Shafranskaya, A. Prjibelski +8 more
2023International Journal of Molecular Sciences8 citations Open access
Semantic Scholar
IsoQuant: a tool for accurate novel isoform discovery with long reads
A. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin +3 more
20227 citations
Semantic Scholar
Peer Review #2 of "Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces (v0.1)"
S. Ghimire, S. Wongkuna, J. Scaria, M. Alcaide +255 more
20207 citations Open access
Semantic Scholar
Knocking Out TAAR5: A Pathway to Enhanced Neurogenesis and Dopamine Signaling in the Striatum
A. Vaganova, Z. Fesenko, E. Efimova, Sergei A. Chekrygin +4 more
2024Cells6 citations Open access
Semantic Scholar
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Fairlie Reese, Sílvia Carbonell-Sala, M. Diekhans +33 more
20215 citations Open access
Semantic Scholar
Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development
Anoushka Joglekar, A. Prjibelski, A. Mahfouz, Paul G Collier +24 more
2020bioRxiv5 citations Open access
Semantic Scholar
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
B. Behsaz, H. Mohimani, A. Gurevich, A. Prjibelski +5 more
2019bioRxiv5 citations Open access
Semantic Scholar
Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types
Lieke Michielsen, A. Prjibelski, Careen Foord, Yelizaveta Spiegelman +10 more
2025bioRxiv4 citations Open access
Semantic Scholar
Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types
Lieke Michielsen, A. Prjibelski, Careen Foord, Yelizaveta Spiegelman +10 more
2026Nature Methods2 citations Open access
Semantic Scholar
Flowtigs: Safety in flow decompositions for assembly graphs
Francisco Sena, Eliel Ingervo, Shahbaz Khan, A. Prjibelski +2 more
2024bioRxiv2 citations Open access
Semantic Scholar
PABLOG: a Primer Analysis tool using a Bee-Like approach on Orthologous Genes.
Michele Ferrigno, Paola Frazzetto, A. Prjibelski, Alexandru I. Tomescu +1 more
2024Physiologia Plantarum : An International Journal for Plant Biology2 citations Open access
Semantic Scholar
Technical feasibility of a long read, fourth generation sequencing platform in diagnostic profiling of clinical routine samples: a proof-of-concept study
D. Vitale, L. Colarossi, G. Russo, C. Scimone +11 more
2026Pathologica1 citations Open access
Semantic Scholar
Light and Alternating Temperatures Release Seed Dormancy in the Invasive Dipsacus fullonum L. Through ROS Homeostasis and ABA Regulation
Paola Frazzetto, H. R. Huarte, G. D. Puglia, A. Prjibelski +4 more
2025Physiologia Plantarum : An International Journal for Plant Biology1 citations Open access
Semantic Scholar
Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types
S. Hardwick, Wengian Hu, Anoushka Joglekar, Li Fan +19 more
2021bioRxiv1 citations Open access
Semantic Scholar
Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"
Alla Mikheenko, A. Prjibelski, V. Saveliev, D. Antipov +1 more
20181 citations
Semantic Scholar
Real-time Targeted Enrichment in Single-cell Long-read Sequencing.
Xiang-Jen-Nie Li, Careen Foord, A. Prjibelski, Natan Belchikov +6 more
2026Genomics, Proteomics & Bioinformatics0 citations Open access
Semantic Scholar
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, M. Diekhans +79 more
2023bioRxiv0 citations Open access
Semantic Scholar
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns
A. Mikheenko, A. Prjibelski, Anoushka Joglekar, H. Tilgner
2022bioRxiv0 citations Open access
Semantic Scholar
Peer Review #3 of "Empirical evaluation of methods for de novo genome assembly (v0.1)"
F. Dida, G. Yi, A. Abate, T. Hung +346 more
20210 citations Open access
Semantic Scholar
Peer Review #2 of "Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana (v0.1)"
Lauren K. Hudson, Lisha Constantine-Renna, Linda S. Thomas, Christina Moore +496 more
20200 citations Open access
Semantic Scholar
Peer Review #1 of "Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution (v0.2)"
Su-Nan Huang, Xue-Jun Ge, A. Cano, B. Salazar +351 more
20200 citations Open access
Semantic Scholar

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