Accueil
Andrey D Prjibelski
Andrey D Prjibelski
Affiliations
Department of Computer Science, University of Helsinki, Helsinki, Finland.
Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
These authors contributed equally to this work.
Publications (18)
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
bioRxiv : the preprint server for biology
Avec:
Francisco J Pardo-Palacios
,
Dingjie Wang
,
Fairlie Reese
,
Mark Diekhans
,
Sílvia Carbonell-Sala
,
Brian Williams
,
Jane E Loveland
,
Maite De María
,
Matthew S Adams
,
Gabriela Balderrama-Gutierrez
,
Amit K Behera
,
Jose M Gonzalez
,
Toby Hunt
,
Julien Lagarde
,
Cindy E Liang
,
Haoran Li
,
Marcus Jerryd Meade
,
David A Moraga Amador
,
Inanc Birol
,
Hamed Bostan
,
Ashley M Brooks
,
Muhammed Hasan Çelik
,
Ying Chen
,
Mei R M Du
,
Colette Felton
,
Jonathan Göke
,
Saber Hafezqorani
,
Ralf Herwig
,
Hideya Kawaji
,
Joseph Lee
,
Jian Liang Li
,
Matthias Lienhard
,
Alla Mikheenko
,
Dennis Mulligan
,
Ka Ming Nip
,
Mihaela Pertea
,
Matthew E Ritchie
,
Andre D Sim
,
Alison D Tang
,
Yuk Kei Wan
,
Changqing Wang
,
Brandon Y Wong
,
Chen Yang
,
If Barnes
,
Andrew Berry
,
Salvador Capella
,
Namrita Dhillon
,
Jose M Fernandez-Gonzalez
,
Luis Ferrández-Peral
,
Natàlia Garcia-Reyero
,
Stefan Goetz
,
Carles Hernández-Ferrer
,
Liudmyla Kondratova
,
Tianyuan Liu
,
Alessandra Martinez-Martin
,
Carlos Menor
,
Jorge Mestre-Tomás
,
Jonathan M Mudge
,
Nedka G Panayotova
,
Alejandro Paniagua
,
Dmitry Repchevsky
,
Eric Rouchka
,
Brandon Saint-John
,
Enrique Sapena
,
Leon Sheynkman
,
Melissa Laird Smith
,
Marie-Marthe Suner
,
Hazuki Takahashi
,
Ingrid Ashley Youngworth
,
Piero Carninci
,
Nancy D Denslow
,
Roderic Guigó
,
Margaret E Hunter
,
Hagen U Tilgner
,
Barbara J Wold
,
Christopher Vollmers
,
Adam Frankish
,
Kin Fai Au
,
Gloria M Sheynkman
,
Ali Mortazavi
,
Ana Conesa
,
Angela N Brooks
Extending rnaSPAdes functionality for hybrid transcriptome assembly.
BMC bioinformatics
Avec:
Giuseppe D Puglia
,
Dmitry Antipov
,
Elena Bushmanova
,
Daniela Giordano
,
Alla Mikheenko
,
Domenico Vitale
,
Alla Lapidus
Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.).
BMC genomics
Avec:
Giuseppe D Puglia
,
Domenico Vitale
,
Elena Bushmanova
,
Karl J Schmid
,
Salvatore A Raccuia
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data.
GigaScience
Avec:
Elena Bushmanova
,
Dmitry Antipov
,
Alla Lapidus
,
Liquid drop of DNA libraries reveals total genome information.
Proceedings of the National Academy of Sciences of the United States of America
Avec:
Stanislav S Terekhov
,
Igor E Eliseev
,
Leyla A Ovchinnikova
,
Marsel R Kabilov
,
Alexey E Tupikin
,
Ivan V Smirnov
,
Alexey A Belogurov
,
Konstantin V Severinov
,
Yakov A Lomakin
,
Sidney Altman
,
Alexander G Gabibov
Human pericentromeric tandemly repeated DNA is transcribed at the end of oocyte maturation and is associated with membraneless mitochondria-associated structures.
Scientific reports
Avec:
M A Dobrynin
,
N M Korchagina
,
A D Prjibelski
,
D Shafranskaya
,
D I Ostromyshenskii
,
K Shunkina
,
I Stepanova
,
A V Kotova
,
O I Podgornaya
,
N I Enukashvily
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.
Genome research
Avec:
Alla Mikheenko
,
Anoushka Joglekar
,
Hagen U Tilgner
SGTK: a toolkit for visualization and assessment of scaffold graphs.
Bioinformatics (Oxford, England)
Avec:
Olga Kunyavskaya
,
Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis.
International journal of molecular sciences
Avec:
Anastasia N Vaganova
,
Ramilya Z Murtazina
,
Taisiia S Shemyakova
,
Nataliia V Katolikova
,
Raul R Gainetdinov
Accurate isoform discovery with IsoQuant using long reads.
Nature biotechnology
Avec:
Alla Mikheenko
,
Anoushka Joglekar
,
Alexander Smetanin
,
Julien Jarroux
,
Alla L Lapidus
,
Hagen U Tilgner
Seed Transcriptome Annotation Reveals Enhanced Expression of Genes Related to ROS Homeostasis and Ethylene Metabolism at Alternating Temperatures in Wild Cardoon.
Plants (Basel, Switzerland)
Avec:
Hector R Huarte
,
Giuseppe D Puglia
,
Salvatore A Raccuia
Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish.
Scientific reports
Avec:
Konstantin A Demin
,
Anton M Lakstygal
,
Nataliya A Krotova
,
Alexey Masharsky
,
Natsuki Tagawa
,
Maria V Chernysh
,
Nikita P Ilyin
,
Alexander S Taranov
,
David S Galstyan
,
Ksenia A Derzhavina
,
Nataliia A Levchenko
,
Tatiana O Kolesnikova
,
Mikael S Mor
,
Marina L Vasyutina
,
Evgeniya V Efimova
,
Nataliia Katolikova
,
Raul R Gainetdinov
,
Murilo S de Abreu
,
Tamara G Amstislavskaya
,
Tatyana Strekalova
,
Allan V Kalueff
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology
Avec:
Simon A Hardwick
,
Wen Hu
,
Anoushka Joglekar
,
Li Fan
,
Paul G Collier
,
Careen Foord
,
Jennifer Balacco
,
Samantha Lanjewar
,
Maureen McGuirk Sampson
,
Frank Koopmans
,
Alla Mikheenko
,
Natan Belchikov
,
Julien Jarroux
,
Anne Bergstrom Lucas
,
Miklós Palkovits
,
Wenjie Luo
,
Teresa A Milner
,
Lishomwa C Ndhlovu
,
August B Smit
,
John Q Trojanowski
,
Virginia M Y Lee
,
Olivier Fedrigo
,
Steven A Sloan
,
Dóra Tombácz
,
M Elizabeth Ross
,
Erich Jarvis
,
Zsolt Boldogkői
,
Li Gan
,
Hagen U Tilgner
Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience.
Oncology and therapy
Avec:
Francesco Pepe
,
Gianluca Russo
,
Alessandro Venuta
,
Claudia Scimone
,
Mariantonia Nacchio
,
Pasquale Pisapia
,
Gaia Goteri
,
Francesca Barbisan
,
Caterina Chiappetta
,
Angelina Pernazza
,
Domenico Campagna
,
Marco Giordano
,
Giuseppe Perrone
,
Giovanna Sabarese
,
Annalisa Altimari
,
Dario de Biase
,
Giovanni Tallini
,
Daniele Calistri
,
Elisa Chiadini
,
Laura Capelli
,
Alfredo Santinelli
,
Anna Elisa Gulini
,
Elisa Pierpaoli
,
Manuela Badiali
,
Stefania Murru
,
Riccardo Murgia
,
Elena Guerini Rocco
,
Konstantinos Venetis
,
Nicola Fusco
,
Denise Morotti
,
Andrea Gianatti
,
Daniela Furlan
,
Giulio Rossi
,
Laura Melocchi
,
Maria Russo
,
Caterina De Luca
,
Lucia Palumbo
,
Saverio Simonelli
,
Antonella Maffè
,
Paola Francia di Celle
,
Tiziana Venesio
,
Maria Scatolini
,
Enrico Grosso
,
Sara Orecchia
,
Matteo Fassan
,
Mariangela Balistreri
,
Elisabetta Zulato
,
Daniela Reghellin
,
Elena Lazzari
,
Maria Santacatterina
,
Maria Liliana Piredda
,
Manuela Riccardi
,
Licia Laurino
,
Elena Roz
,
Domenico Longo
,
Daniela Petronilla Romeo
,
Carmine Fazzari
,
Andrea Moreno-Manuel
,
Giuseppe Diego Puglia
,
Daria Shafranskaya
,
Luisella Righi
,
Angela Listì
,
Domenico Vitale
,
Antonino Iaccarino
,
Umberto Malapelle
,
Giancarlo Troncone
Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis.
Cell death & disease
Avec:
Natella I Enukashvily
,
Nikita V Ponomartsev
,
Avanee Ketkar
,
Roman Suezov
,
Anna V Chubar
,
Daria D Shafranskaya
,
Sabrina Elmshäuser
,
Corinna U Keber
,
Vera N Stefanova
,
Andrey L Akopov
,
Ursula Klingmüller
,
Petra I Pfefferle
,
Thorsten Stiewe
,
Matthias Lauth
,
Anna I Brichkina
Modulation of Notch Signaling at Early Stages of Differentiation of Human Induced Pluripotent Stem Cells to Dopaminergic Neurons.
International journal of molecular sciences
Avec:
Nataliia V Katolikova
,
Aleksandr A Khudiakov
,
Daria D Shafranskaya
,
Alexey E Masharskiy
,
Mikael S Mor
,
Alexey S Golovkin
,
Anastasia K Zaytseva
,
Irina E Neganova
,
Evgeniya V Efimova
,
Raul R Gainetdinov
,
Anna B Malashicheva
MetaGT: A pipeline for
Frontiers in microbiology
Avec:
Daria Shafranskaya
,
Varsha Kale
,
Rob Finn
,
Alla L Lapidus
,
Anton Korobeynikov
,
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Nature methods
Avec:
Francisco J Pardo-Palacios
,
Dingjie Wang
,
Fairlie Reese
,
Mark Diekhans
,
Sílvia Carbonell-Sala
,
Brian Williams
,
Jane E Loveland
,
Maite De María
,
Matthew S Adams
,
Gabriela Balderrama-Gutierrez
,
Amit K Behera
,
Jose M Gonzalez Martinez
,
Toby Hunt
,
Julien Lagarde
,
Cindy E Liang
,
Haoran Li
,
Marcus Jerryd Meade
,
David A Moraga Amador
,
Inanc Birol
,
Hamed Bostan
,
Ashley M Brooks
,
Muhammed Hasan Çelik
,
Ying Chen
,
Mei R M Du
,
Colette Felton
,
Jonathan Göke
,
Saber Hafezqorani
,
Ralf Herwig
,
Hideya Kawaji
,
Joseph Lee
,
Jian-Liang Li
,
Matthias Lienhard
,
Alla Mikheenko
,
Dennis Mulligan
,
Ka Ming Nip
,
Mihaela Pertea
,
Matthew E Ritchie
,
Andre D Sim
,
Alison D Tang
,
Yuk Kei Wan
,
Changqing Wang
,
Brandon Y Wong
,
Chen Yang
,
If Barnes
,
Andrew E Berry
,
Salvador Capella-Gutierrez
,
Alyssa Cousineau
,
Namrita Dhillon
,
Jose M Fernandez-Gonzalez
,
Luis Ferrández-Peral
,
Natàlia Garcia-Reyero
,
Stefan Götz
,
Carles Hernández-Ferrer
,
Liudmyla Kondratova
,
Tianyuan Liu
,
Alessandra Martinez-Martin
,
Carlos Menor
,
Jorge Mestre-Tomás
,
Jonathan M Mudge
,
Nedka G Panayotova
,
Alejandro Paniagua
,
Dmitry Repchevsky
,
Xingjie Ren
,
Eric Rouchka
,
Brandon Saint-John
,
Enrique Sapena
,
Leon Sheynkman
,
Melissa Laird Smith
,
Marie-Marthe Suner
,
Hazuki Takahashi
,
Ingrid A Youngworth
,
Piero Carninci
,
Nancy D Denslow
,
Roderic Guigó
,
Margaret E Hunter
,
Rene Maehr
,
Yin Shen
,
Hagen U Tilgner
,
Barbara J Wold
,
Christopher Vollmers
,
Adam Frankish
,
Kin Fai Au
,
Gloria M Sheynkman
,
Ali Mortazavi
,
Ana Conesa
,
Angela N Brooks
Réseau de co-auteurs
Alla Mikheenko
6 collaborations
Hagen U Tilgner
5 collaborations
Giuseppe D Puglia
3 collaborations
Elena Bushmanova
3 collaborations
Domenico Vitale
3 collaborations
Anoushka Joglekar
3 collaborations
Raul R Gainetdinov
3 collaborations
Francisco J Pardo-Palacios
2 collaborations
Dingjie Wang
2 collaborations
Fairlie Reese
2 collaborations
Mark Diekhans
2 collaborations
Sílvia Carbonell-Sala
2 collaborations
Brian Williams
2 collaborations
Jane E Loveland
2 collaborations
Maite De María
2 collaborations
Matthew S Adams
2 collaborations
Gabriela Balderrama-Gutierrez
2 collaborations
Amit K Behera
2 collaborations
Toby Hunt
2 collaborations
Julien Lagarde
2 collaborations
Cindy E Liang
2 collaborations
Haoran Li
2 collaborations
Marcus Jerryd Meade
2 collaborations
David A Moraga Amador
2 collaborations
Inanc Birol
2 collaborations
Hamed Bostan
2 collaborations
Ashley M Brooks
2 collaborations
Muhammed Hasan Çelik
2 collaborations
Ying Chen
2 collaborations
Mei R M Du
2 collaborations
Colette Felton
2 collaborations
Jonathan Göke
2 collaborations
Saber Hafezqorani
2 collaborations
Ralf Herwig
2 collaborations
Hideya Kawaji
2 collaborations
Joseph Lee
2 collaborations
Matthias Lienhard
2 collaborations
Dennis Mulligan
2 collaborations
Ka Ming Nip
2 collaborations
Mihaela Pertea
2 collaborations
Matthew E Ritchie
2 collaborations
Andre D Sim
2 collaborations
Alison D Tang
2 collaborations
Yuk Kei Wan
2 collaborations
Changqing Wang
2 collaborations
Brandon Y Wong
2 collaborations
Chen Yang
2 collaborations
If Barnes
2 collaborations
Namrita Dhillon
2 collaborations
Jose M Fernandez-Gonzalez
2 collaborations
Luis Ferrández-Peral
2 collaborations
Natàlia Garcia-Reyero
2 collaborations
Carles Hernández-Ferrer
2 collaborations
Liudmyla Kondratova
2 collaborations
Tianyuan Liu
2 collaborations
Alessandra Martinez-Martin
2 collaborations
Carlos Menor
2 collaborations
Jorge Mestre-Tomás
2 collaborations
Jonathan M Mudge
2 collaborations
Nedka G Panayotova
2 collaborations
Alejandro Paniagua
2 collaborations
Dmitry Repchevsky
2 collaborations
Eric Rouchka
2 collaborations
Brandon Saint-John
2 collaborations
Enrique Sapena
2 collaborations
Leon Sheynkman
2 collaborations
Melissa Laird Smith
2 collaborations
Marie-Marthe Suner
2 collaborations
Hazuki Takahashi
2 collaborations
Piero Carninci
2 collaborations
Nancy D Denslow
2 collaborations
Roderic Guigó
2 collaborations
Margaret E Hunter
2 collaborations
Barbara J Wold
2 collaborations
Christopher Vollmers
2 collaborations
Adam Frankish
2 collaborations
Kin Fai Au
2 collaborations
Gloria M Sheynkman
2 collaborations
Ali Mortazavi
2 collaborations
Ana Conesa
2 collaborations
Angela N Brooks
2 collaborations
Dmitry Antipov
2 collaborations
Alla Lapidus
2 collaborations
Salvatore A Raccuia
2 collaborations
Nataliia V Katolikova
2 collaborations
Julien Jarroux
2 collaborations
Alla L Lapidus
2 collaborations
Mikael S Mor
2 collaborations
Evgeniya V Efimova
2 collaborations
Daria Shafranskaya
2 collaborations
Daria D Shafranskaya
2 collaborations
Jose M Gonzalez
1 collaboration
Jian Liang Li
1 collaboration
Andrew Berry
1 collaboration
Salvador Capella
1 collaboration
Stefan Goetz
1 collaboration
Ingrid Ashley Youngworth
1 collaboration
Daniela Giordano
1 collaboration
Karl J Schmid
1 collaboration
Stanislav S Terekhov
1 collaboration
Igor E Eliseev
1 collaboration
Leyla A Ovchinnikova
1 collaboration
Marsel R Kabilov
1 collaboration
Alexey E Tupikin
1 collaboration
Ivan V Smirnov
1 collaboration
Alexey A Belogurov
1 collaboration
Konstantin V Severinov
1 collaboration
Yakov A Lomakin
1 collaboration
Sidney Altman
1 collaboration
Alexander G Gabibov
1 collaboration
M A Dobrynin
1 collaboration
N M Korchagina
1 collaboration
A D Prjibelski
1 collaboration
D Shafranskaya
1 collaboration
D I Ostromyshenskii
1 collaboration
K Shunkina
1 collaboration
I Stepanova
1 collaboration
A V Kotova
1 collaboration
O I Podgornaya
1 collaboration
N I Enukashvily
1 collaboration
Olga Kunyavskaya
1 collaboration
Anastasia N Vaganova
1 collaboration
Ramilya Z Murtazina
1 collaboration
Taisiia S Shemyakova
1 collaboration
Alexander Smetanin
1 collaboration
Hector R Huarte
1 collaboration
Konstantin A Demin
1 collaboration
Anton M Lakstygal
1 collaboration
Nataliya A Krotova
1 collaboration
Alexey Masharsky
1 collaboration
Natsuki Tagawa
1 collaboration
Maria V Chernysh
1 collaboration
Nikita P Ilyin
1 collaboration
Alexander S Taranov
1 collaboration
David S Galstyan
1 collaboration
Ksenia A Derzhavina
1 collaboration
Nataliia A Levchenko
1 collaboration
Tatiana O Kolesnikova
1 collaboration
Marina L Vasyutina
1 collaboration
Nataliia Katolikova
1 collaboration
Murilo S de Abreu
1 collaboration
Tamara G Amstislavskaya
1 collaboration
Tatyana Strekalova
1 collaboration
Allan V Kalueff
1 collaboration
Simon A Hardwick
1 collaboration
Wen Hu
1 collaboration
Li Fan
1 collaboration
Paul G Collier
1 collaboration
Careen Foord
1 collaboration
Jennifer Balacco
1 collaboration
Samantha Lanjewar
1 collaboration
Maureen McGuirk Sampson
1 collaboration
Frank Koopmans
1 collaboration
Natan Belchikov
1 collaboration
Anne Bergstrom Lucas
1 collaboration
Miklós Palkovits
1 collaboration
Wenjie Luo
1 collaboration
Teresa A Milner
1 collaboration
Lishomwa C Ndhlovu
1 collaboration
August B Smit
1 collaboration
John Q Trojanowski
1 collaboration
Virginia M Y Lee
1 collaboration
Olivier Fedrigo
1 collaboration
Steven A Sloan
1 collaboration
Dóra Tombácz
1 collaboration
M Elizabeth Ross
1 collaboration
Erich Jarvis
1 collaboration
Zsolt Boldogkői
1 collaboration
Li Gan
1 collaboration
Francesco Pepe
1 collaboration
Gianluca Russo
1 collaboration
Alessandro Venuta
1 collaboration
Claudia Scimone
1 collaboration
Mariantonia Nacchio
1 collaboration
Pasquale Pisapia
1 collaboration
Gaia Goteri
1 collaboration
Francesca Barbisan
1 collaboration
Caterina Chiappetta
1 collaboration
Angelina Pernazza
1 collaboration
Domenico Campagna
1 collaboration
Marco Giordano
1 collaboration
Giuseppe Perrone
1 collaboration
Giovanna Sabarese
1 collaboration
Annalisa Altimari
1 collaboration
Dario de Biase
1 collaboration
Giovanni Tallini
1 collaboration
Daniele Calistri
1 collaboration
Elisa Chiadini
1 collaboration
Laura Capelli
1 collaboration
Alfredo Santinelli
1 collaboration
Anna Elisa Gulini
1 collaboration
Elisa Pierpaoli
1 collaboration
Manuela Badiali
1 collaboration
Stefania Murru
1 collaboration
Riccardo Murgia
1 collaboration
Elena Guerini Rocco
1 collaboration
Konstantinos Venetis
1 collaboration
Nicola Fusco
1 collaboration
Denise Morotti
1 collaboration
Andrea Gianatti
1 collaboration
Daniela Furlan
1 collaboration
Giulio Rossi
1 collaboration
Laura Melocchi
1 collaboration
Maria Russo
1 collaboration
Caterina De Luca
1 collaboration
Lucia Palumbo
1 collaboration
Saverio Simonelli
1 collaboration
Antonella Maffè
1 collaboration
Paola Francia di Celle
1 collaboration
Tiziana Venesio
1 collaboration
Maria Scatolini
1 collaboration
Enrico Grosso
1 collaboration
Sara Orecchia
1 collaboration
Matteo Fassan
1 collaboration
Mariangela Balistreri
1 collaboration
Elisabetta Zulato
1 collaboration
Daniela Reghellin
1 collaboration
Elena Lazzari
1 collaboration
Maria Santacatterina
1 collaboration
Maria Liliana Piredda
1 collaboration
Manuela Riccardi
1 collaboration
Licia Laurino
1 collaboration
Elena Roz
1 collaboration
Domenico Longo
1 collaboration
Daniela Petronilla Romeo
1 collaboration
Carmine Fazzari
1 collaboration
Andrea Moreno-Manuel
1 collaboration
Giuseppe Diego Puglia
1 collaboration
Luisella Righi
1 collaboration
Angela Listì
1 collaboration
Antonino Iaccarino
1 collaboration
Umberto Malapelle
1 collaboration
Giancarlo Troncone
1 collaboration
Natella I Enukashvily
1 collaboration
Nikita V Ponomartsev
1 collaboration
Avanee Ketkar
1 collaboration
Roman Suezov
1 collaboration
Anna V Chubar
1 collaboration
Sabrina Elmshäuser
1 collaboration
Corinna U Keber
1 collaboration
Vera N Stefanova
1 collaboration
Andrey L Akopov
1 collaboration
Ursula Klingmüller
1 collaboration
Petra I Pfefferle
1 collaboration
Thorsten Stiewe
1 collaboration
Matthias Lauth
1 collaboration
Anna I Brichkina
1 collaboration
Aleksandr A Khudiakov
1 collaboration
Alexey E Masharskiy
1 collaboration
Alexey S Golovkin
1 collaboration
Anastasia K Zaytseva
1 collaboration
Irina E Neganova
1 collaboration
Anna B Malashicheva
1 collaboration
Varsha Kale
1 collaboration
Rob Finn
1 collaboration
Anton Korobeynikov
1 collaboration
Jose M Gonzalez Martinez
1 collaboration
Jian-Liang Li
1 collaboration
Andrew E Berry
1 collaboration
Salvador Capella-Gutierrez
1 collaboration
Alyssa Cousineau
1 collaboration
Stefan Götz
1 collaboration
Xingjie Ren
1 collaboration
Ingrid A Youngworth
1 collaboration
Rene Maehr
1 collaboration
Yin Shen
1 collaboration