A. Prjibelski

发表

Andrey D. Prjibelski, Anton I. Korobeynikov, Alla L. Lapidus, 2019, Encyclopedia of Bioinformatics and Computational Biology.

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

Elena Bushmanova, Dmitry Antipov, Andrey D. Prjibelski, 2018, bioRxiv.

Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish

R. Gainetdinov, A. Kalueff, T. Strekalova, 2020, Scientific Reports.

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

Stephen R. Williams, Hagen U. Tilgner, A. Frankish, 2020, bioRxiv.

Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)

S. A. Raccuia, K. Schmid, A. Prjibelski, 2020, BMC Genomics.

De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

Mark F. Fisher, P. Pevzner, P. Dorrestein, 2019, bioRxiv.

De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments.

Mark F. Fisher, P. Pevzner, P. Dorrestein, 2019, Cell systems.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

R. Finn, A. Lapidus, A. Korobeynikov, 2022, Frontiers in Microbiology.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Sergey I. Nikolenko, Dmitry Antipov, Andrey D. Prjibelski, 2012, J. Comput. Biol..

Using SPAdes De Novo Assembler

Dmitry Antipov, Alla Lapidus, Anton Korobeynikov, 2020, Current protocols in bioinformatics.

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Dmitry Antipov, Alla Lapidus, Andrey D. Prjibelski, 2013, J. Comput. Biol..

SGTK: a toolkit for visualization and assessment of scaffold graphs

Andrey D Prjibelski, Olga Kunyavskaya, A. Prjibelski, 2018, Bioinform..

Icarus: visualizer for de novo assembly evaluation

Andrey D. Prjibelski, Alexey A. Gurevich, Vladislav Saveliev, 2016, Bioinform..

Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns

Hagen U. Tilgner, Anoushka Joglekar, A. Prjibelski, 2022, bioRxiv.

Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns

Hagen U. Tilgner, Anoushka Joglekar, A. Prjibelski, 2022, Genome research.

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

Hagen U. Tilgner, J. Trojanowski, M. Palkovits, 2022, Nature Biotechnology.

Human pericentromeric tandemly repeated DNA is transcribed at the end of oocyte maturation and is associated with membraneless mitochondria-associated structures

I. Stepanova, A. Prjibelski, O. Podgornaya, 2020, Scientific Reports.

Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis

R. Gainetdinov, A. Prjibelski, N. Katolikova, 2021, International journal of molecular sciences.

Accurate isoform discovery with IsoQuant using long reads

Hagen U. Tilgner, A. Lapidus, Anoushka Joglekar, 2023, Nature Biotechnology.

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Stephen R. Williams, Weill Cornell Medicine, Hagen U. Tilgner, 2021, Nature Communications.

Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis

U. Klingmüller, T. Stiewe, P. Pfefferle, 2023, Cell Death & Disease.

Assembling short reads from jumping libraries with large insert sizes

Andrey D. Prjibelski, Pavel A. Pevzner, Alexey A. Gurevich, 2015, Bioinform..

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Alla Lapidus, Andrey D. Prjibelski, Pavel A. Pevzner, 2014, Bioinform..

Versatile genome assembly evaluation with QUAST-LG

Dmitry Antipov, Andrey D. Prjibelski, Alexey A. Gurevich, 2018, Bioinform..

Liquid drop of DNA libraries reveals total genome information

S. Altman, K. Severinov, S. Terekhov, 2020, Proceedings of the National Academy of Sciences.

Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types

Hagen U. Tilgner, J. Trojanowski, V. Lee, 2021, bioRxiv.

Extending rnaSPAdes functionality for hybrid transcriptome assembly

Elena Bushmanova, Dmitry Antipov, Alla Lapidus, 2020, BMC Bioinformatics.

Modulation of Notch Signaling at Early Stages of Differentiation of Human Induced Pluripotent Stem Cells to Dopaminergic Neurons

R. Gainetdinov, I. Neganova, A. Malashicheva, 2023, International journal of molecular sciences.

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies

Elena Bushmanova, Dmitry Antipov, Alla Lapidus, 2016, Bioinform..

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2023, bioRxiv.

Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"

A. Gurevich, A. Prjibelski, D. Antipov, 2018 .

Systematic assessment of long-read RNA-seq methods for transcript identi cation and quanti cation

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

Mark F. Fisher, P. Pevzner, P. Dorrestein, 2019, bioRxiv.

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

P. Pevzner, G. Tesler, R. Stepanauskas, 2013, J. Comput. Biol..

Sequence Analysis

S. Mirarab, A. Korobeynikov, Bo Liu, 2020, Encyclopedia of Bioinformatics and Computational Biology.

Seed Transcriptome Annotation Reveals Enhanced Expression of Genes Related to ROS Homeostasis and Ethylene Metabolism at Alternating Temperatures in Wild Cardoon

S. A. Raccuia, A. Prjibelski, G. Puglia, 2020, Plants.

Significant speedup of database searches with HMMs by search space reduction with PSSM family models

Michael Beckstette, Robert Giegerich, Robert Homann, 2009, Bioinform..

Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience

T. Venesio, D. Calistri, E. Pierpaoli, 2024, Oncology and therapy.

SGTK: a toolkit for visualization and assessment of scaffold graphs

A. Prjibelski, Olga Kunyavskaya, 2018, Bioinform..