Alexander V Predeus

Affiliations

Bioinformatics Institute, St. Petersburg 197342, Russia.
University of Liverpool, Liverpool, UK, L7 3EA.

Publications (24)

Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage.

G3 (Bethesda, Md.)

Avec: Yury A Barbitoff , Andrew G Matveenko , Anton B Matiiv , Evgeniia M Maksiutenko , Svetlana E Moskalenko , Polina B Drozdova , Dmitrii E Polev , Alexandra Y Beliavskaia , Lavrentii G Danilov , Alexander V Predeus , Galina A Zhouravleva

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.

Genome biology

Avec: Blanca M Perez-Sepulveda , Darren Heavens , Caisey V Pulford , Alexander V Predeus , Ross Low , Hermione Webster , Gregory F Dykes , Christian Schudoma , Will Rowe , James Lipscombe , Chris Watkins , Benjamin Kumwenda , Neil Shearer , Karl Costigan , Kate S Baker , Nicholas A Feasey , Jay C D Hinton , Neil Hall , Auteur inconnu

A spatial human thymus cell atlas mapped to a continuous tissue axis.

bioRxiv : the preprint server for biology

Avec: Nadav Yayon , Veronika R Kedlian , Lena Boehme , Chenqu Suo , Brianna Wachter , Rebecca T Beuschel , Oren Amsalem , Krzysztof Polanski , Simon Koplev , Elizabeth Tuck , Emma Dann , Jolien Van Hulle , Shani Perera , Tom Putteman , Alexander V Predeus , Monika Dabrowska , Laura Richardson , Catherine Tudor , Alexandra Y Kreins , Justin Engelbert , Emily Stephenson , Vitalii Kleshchevnikov , Fabrizio De Rita , David Crossland , Marita Bosticardo , Francesca Pala , Elena Prigmore , Nana-Jane Chipampe , Martin Prete , Lijiang Fei , Ken To , Roger A Barker , Xiaoling He , Filip Van Nieuwerburgh , Omer Bayraktar , Minal Patel , Graham E Davies , Muzlifah A Haniffa , Virginie Uhlmann , Luigi D Notarangelo , Ronald N Germain , Andrea J Radtke , John C Marioni , Tom Taghon , Sarah A Teichmann

Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits.

Scientific reports

Avec: Anton E Shikov , Rostislav K Skitchenko , Alexander V Predeus , Yury A Barbitoff

RNA Sequencing of Whole Blood Defines the Signature of High Intensity Exercise at Altitude in Elite Speed Skaters.

Genes

Avec: Andrey S Glotov , Irina E Zelenkova , Elena S Vashukova , Anna R Shuvalova , Alexandra D Zolotareva , Dmitrii E Polev , Yury A Barbitoff , Oleg S Glotov , Andrey M Sarana , Sergey G Shcherbak , Mariya A Rozina , Victoria L Gogotova , Alexander V Predeus

Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors.

Scientific reports

Avec: Rama P Bhatia , Hande A Kirit , Alexander V Predeus , Jonathan P Bollback

Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery.

BMC genomics

Avec: Yury A Barbitoff , Ruslan Abasov , Varvara E Tvorogova , Andrey S Glotov , Alexander V Predeus

Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Clarisse Ganier , Pavel Mazin , Gabriel Herrera-Oropeza , Xinyi Du-Harpur , Matthew Blakeley , Jeyrroy Gabriel , Alexander V Predeus , Batuhan Cakir , Martin Prete , Nasrat Harun , Jean-Francois Darrigrand , Alexander Haiser , Saranya Wyles , Tanya Shaw , Sarah A Teichmann , Muzlifah Haniffa , Fiona M Watt , Magnus D Lynch

Whole‑exome sequencing in Russian children with non‑type 1 diabetes mellitus reveals a wide spectrum of genetic variants in MODY‑related and unrelated genes.

Molecular medicine reports

Avec: Oleg S Glotov , Elena A Serebryakova , Mariia E Turkunova , Olga A Efimova , Andrey S Glotov , Yury A Barbitoff , Yulia A Nasykhova , Alexander V Predeus , Dmitrii E Polev , Mikhail A Fedyakov , Irina V Polyakova , Tatyana E Ivashchenko , Natalia Y Shved , Elena S Shabanova , Alena V Tiselko , Olga V Romanova , Andrey M Sarana , Anna A Pendina , Sergey G Scherbak , Ekaterina V Musina , Anastasiia V Petrovskaia-Kaminskaia , Liubov R Lonishin , Liliya V Ditkovskaya , Liudmila А Zhelenina , Ludmila V Tyrtova , Olga S Berseneva , Rostislav K Skitchenko , Evgenii N Suspitsin , Elena B Bashnina , Vladislav S Baranov

Data on RNA-seq analysis of the oviducts of five closely related species genus

Data in brief

Avec: Arseniy A Lobov , Lavrentii G Danilov , Alexey E Masharskiy , Alexander V Predeus , Natalia A Mikhailova , Andrei I Granovitch , Arina L Maltseva

Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.

Briefings in bioinformatics

Avec: Yury A Barbitoff , Mikhail O Ushakov , Tatyana E Lazareva , Yulia A Nasykhova , Andrey S Glotov , Alexander V Predeus

Acute response to pathogens in the early human placenta at single-cell resolution.

Cell systems

Avec: Regina Hoo , Elias R Ruiz-Morales , Iva Kelava , Mukul Rawat , Cecilia Icoresi Mazzeo , Elizabeth Tuck , Carmen Sancho-Serra , Sara Chelaghma , Alexander V Predeus , Simon Murray , David Fernandez-Antoran , Ross F Waller , Damiana Álvarez-Errico , Marcus C S Lee , Roser Vento-Tormo

Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580.

PLoS biology

Avec: Rocío Canals , Disa L Hammarlöf , Carsten Kröger , Siân V Owen , Wai Yee Fong , Lizeth Lacharme-Lora , Xiaojun Zhu , Nicolas Wenner , Sarah E Carden , Jared Honeycutt , Denise M Monack , Robert A Kingsley , Philip Brownridge , Roy R Chaudhuri , Will P M Rowe , Alexander V Predeus , Karsten Hokamp , Melita A Gordon , Jay C D Hinton

Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage.

Scientific reports

Avec: Yury A Barbitoff , Dmitrii E Polev , Andrey S Glotov , Elena A Serebryakova , Irina V Shcherbakova , Artem M Kiselev , Anna A Kostareva , Oleg S Glotov , Alexander V Predeus

Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets.

PLoS neglected tropical diseases

Avec: Catherine N Wilson , Caisey V Pulford , James Akoko , Blanca Perez Sepulveda , Alexander V Predeus , Jessica Bevington , Patricia Duncan , Neil Hall , Paul Wigley , Nicholas Feasey , Gina Pinchbeck , Jay C D Hinton , Melita A Gordon , Eric M Fèvre

Complete Genome Sequences of African Salmonella enterica Serovar Enteritidis Clinical Isolates Associated with Bloodstream Infection.

Microbiology resource announcements

Avec: Blanca M Perez-Sepulveda , Alexander V Predeus , Wai Yee Fong , Christopher M Parry , John Cheesbrough , Paul Wigley , Nicholas A Feasey , Jay C D Hinton

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa.

Nature microbiology

Avec: Caisey V Pulford , Blanca M Perez-Sepulveda , Rocío Canals , Jessica A Bevington , Rebecca J Bengtsson , Nicolas Wenner , Ella V Rodwell , Benjamin Kumwenda , Xiaojun Zhu , Rebecca J Bennett , George E Stenhouse , P Malaka De Silva , Hermione J Webster , Jose A Bengoechea , Amy Dumigan , Alicia Tran-Dien , Reenesh Prakash , Happy C Banda , Lovemore Alufandika , Mike P Mautanga , Arthur Bowers-Barnard , Alexandra Y Beliavskaia , Alexander V Predeus , Will P M Rowe , Alistair C Darby , Neil Hall , François-Xavier Weill , Melita A Gordon , Nicholas A Feasey , Kate S Baker , Jay C D Hinton

Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia.

Molecular genetics & genomic medicine

Avec: Yury A Barbitoff , Rostislav K Skitchenko , Olga I Poleshchuk , Anton E Shikov , Elena A Serebryakova , Yulia A Nasykhova , Dmitrii E Polev , Anna R Shuvalova , Irina V Shcherbakova , Mikhail A Fedyakov , Oleg S Glotov , Andrey S Glotov , Alexander V Predeus

Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of

Biology

Avec: Arseniy A Lobov , Irina Y Babkina , Lavrentii G Danilov , Alexey E Masharskiy , Alexander V Predeus , Natalia A Mikhailova , Andrei I Granovitch , Arina L Maltseva

Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features.

Mitochondrion

Avec: Vladimir A Kutyumov , Alexander V Predeus , Viktor V Starunov , Arina L Maltseva , Andrew N Ostrovsky

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica.

PLoS pathogens

Avec: TuShun R Powers , Amanda L Haeberle , Alexander V Predeus , Disa L Hammarlöf , Jennifer A Cundiff , Zeus Saldaña-Ahuactzi , Karsten Hokamp , Jay C D Hinton , Leigh A Knodler

microLife

Avec: Benjamin Kumwenda , Rocío Canals , Alexander V Predeus , Xiaojun Zhu , Carsten Kröger , Caisey Pulford , Nicolas Wenner , Lizeth Lacharme Lora , Yan Li , Siân V Owen , Dean Everett , Karsten Hokamp , Robert S Heyderman , Philip M Ashton , Melita A Gordon , Chisomo L Msefula , Jay C D Hinton

Modulation of

mBio

Avec: Xiu-Jun Yu , Haixia Xie , Yan Li , Mei Liu , Ruhong Hou , Alexander V Predeus , Blanca M Perez Sepulveda , Jay C D Hinton , David W Holden , Teresa L M Thurston

Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis.

Nature communications

Avec: Quinn T Easter , Bruno Fernandes Matuck , Germán Beldorati Stark , Catherine L Worth , Alexander V Predeus , Brayon Fremin , Khoa Huynh , Vaishnavi Ranganathan , Zhi Ren , Diana Pereira , Brittany T Rupp , Theresa Weaver , Kathryn Miller , Paola Perez , Akira Hasuike , Zhaoxu Chen , Mandy Bush , Xufeng Qu , Janice Lee , Scott H Randell , Shannon M Wallet , Inês Sequeira , Hyun Koo , Katarzyna M Tyc , Jinze Liu , Kang I Ko , Sarah A Teichmann , Kevin M Byrd

Réseau de co-auteurs

Yury A Barbitoff 8 collaborations

Jay C D Hinton 8 collaborations

Andrey S Glotov 6 collaborations

Dmitrii E Polev 5 collaborations

Oleg S Glotov 4 collaborations

Melita A Gordon 4 collaborations

Lavrentii G Danilov 3 collaborations

Blanca M Perez-Sepulveda 3 collaborations

Caisey V Pulford 3 collaborations

Benjamin Kumwenda 3 collaborations

Nicholas A Feasey 3 collaborations

Neil Hall 3 collaborations

Sarah A Teichmann 3 collaborations

Rostislav K Skitchenko 3 collaborations

Elena A Serebryakova 3 collaborations

Yulia A Nasykhova 3 collaborations

Arina L Maltseva 3 collaborations

Rocío Canals 3 collaborations

Xiaojun Zhu 3 collaborations

Nicolas Wenner 3 collaborations

Karsten Hokamp 3 collaborations

Alexandra Y Beliavskaia 2 collaborations

Kate S Baker 2 collaborations

Elizabeth Tuck 2 collaborations

Martin Prete 2 collaborations

Anton E Shikov 2 collaborations

Anna R Shuvalova 2 collaborations

Andrey M Sarana 2 collaborations

Mikhail A Fedyakov 2 collaborations

Arseniy A Lobov 2 collaborations

Alexey E Masharskiy 2 collaborations

Natalia A Mikhailova 2 collaborations

Andrei I Granovitch 2 collaborations

Disa L Hammarlöf 2 collaborations

Carsten Kröger 2 collaborations

Siân V Owen 2 collaborations

Wai Yee Fong 2 collaborations

Will P M Rowe 2 collaborations

Irina V Shcherbakova 2 collaborations

Paul Wigley 2 collaborations

Yan Li 2 collaborations

Andrew G Matveenko 1 collaboration

Anton B Matiiv 1 collaboration

Evgeniia M Maksiutenko 1 collaboration

Svetlana E Moskalenko 1 collaboration

Polina B Drozdova 1 collaboration

Galina A Zhouravleva 1 collaboration

Darren Heavens 1 collaboration

Ross Low 1 collaboration

Hermione Webster 1 collaboration

Gregory F Dykes 1 collaboration

Christian Schudoma 1 collaboration

Will Rowe 1 collaboration

James Lipscombe 1 collaboration

Chris Watkins 1 collaboration

Neil Shearer 1 collaboration

Karl Costigan 1 collaboration

None None 1 collaboration

Nadav Yayon 1 collaboration

Veronika R Kedlian 1 collaboration

Lena Boehme 1 collaboration

Chenqu Suo 1 collaboration

Brianna Wachter 1 collaboration

Rebecca T Beuschel 1 collaboration

Oren Amsalem 1 collaboration

Krzysztof Polanski 1 collaboration

Simon Koplev 1 collaboration

Emma Dann 1 collaboration

Jolien Van Hulle 1 collaboration

Shani Perera 1 collaboration

Tom Putteman 1 collaboration

Monika Dabrowska 1 collaboration

Laura Richardson 1 collaboration

Catherine Tudor 1 collaboration

Alexandra Y Kreins 1 collaboration

Justin Engelbert 1 collaboration

Emily Stephenson 1 collaboration

Vitalii Kleshchevnikov 1 collaboration

Fabrizio De Rita 1 collaboration

David Crossland 1 collaboration

Marita Bosticardo 1 collaboration

Francesca Pala 1 collaboration

Elena Prigmore 1 collaboration

Nana-Jane Chipampe 1 collaboration

Lijiang Fei 1 collaboration

Ken To 1 collaboration

Roger A Barker 1 collaboration

Xiaoling He 1 collaboration

Filip Van Nieuwerburgh 1 collaboration

Omer Bayraktar 1 collaboration

Minal Patel 1 collaboration

Graham E Davies 1 collaboration

Muzlifah A Haniffa 1 collaboration

Virginie Uhlmann 1 collaboration

Luigi D Notarangelo 1 collaboration

Ronald N Germain 1 collaboration

Andrea J Radtke 1 collaboration

John C Marioni 1 collaboration

Tom Taghon 1 collaboration

Irina E Zelenkova 1 collaboration

Elena S Vashukova 1 collaboration

Alexandra D Zolotareva 1 collaboration

Sergey G Shcherbak 1 collaboration

Mariya A Rozina 1 collaboration

Victoria L Gogotova 1 collaboration

Rama P Bhatia 1 collaboration

Hande A Kirit 1 collaboration

Jonathan P Bollback 1 collaboration

Ruslan Abasov 1 collaboration

Varvara E Tvorogova 1 collaboration

Clarisse Ganier 1 collaboration

Pavel Mazin 1 collaboration

Gabriel Herrera-Oropeza 1 collaboration

Xinyi Du-Harpur 1 collaboration

Matthew Blakeley 1 collaboration

Jeyrroy Gabriel 1 collaboration

Batuhan Cakir 1 collaboration

Nasrat Harun 1 collaboration

Jean-Francois Darrigrand 1 collaboration

Alexander Haiser 1 collaboration

Saranya Wyles 1 collaboration

Tanya Shaw 1 collaboration

Muzlifah Haniffa 1 collaboration

Fiona M Watt 1 collaboration

Magnus D Lynch 1 collaboration

Mariia E Turkunova 1 collaboration

Olga A Efimova 1 collaboration

Irina V Polyakova 1 collaboration

Tatyana E Ivashchenko 1 collaboration

Natalia Y Shved 1 collaboration

Elena S Shabanova 1 collaboration

Alena V Tiselko 1 collaboration

Olga V Romanova 1 collaboration

Anna A Pendina 1 collaboration

Sergey G Scherbak 1 collaboration

Ekaterina V Musina 1 collaboration

Anastasiia V Petrovskaia-Kaminskaia 1 collaboration

Liubov R Lonishin 1 collaboration

Liliya V Ditkovskaya 1 collaboration

Liudmila А Zhelenina 1 collaboration

Ludmila V Tyrtova 1 collaboration

Olga S Berseneva 1 collaboration

Evgenii N Suspitsin 1 collaboration

Elena B Bashnina 1 collaboration

Vladislav S Baranov 1 collaboration

Mikhail O Ushakov 1 collaboration

Tatyana E Lazareva 1 collaboration

Regina Hoo 1 collaboration

Elias R Ruiz-Morales 1 collaboration

Iva Kelava 1 collaboration

Mukul Rawat 1 collaboration

Cecilia Icoresi Mazzeo 1 collaboration

Carmen Sancho-Serra 1 collaboration

Sara Chelaghma 1 collaboration

Simon Murray 1 collaboration

David Fernandez-Antoran 1 collaboration

Ross F Waller 1 collaboration

Damiana Álvarez-Errico 1 collaboration

Marcus C S Lee 1 collaboration

Roser Vento-Tormo 1 collaboration

Lizeth Lacharme-Lora 1 collaboration

Sarah E Carden 1 collaboration

Jared Honeycutt 1 collaboration

Denise M Monack 1 collaboration

Robert A Kingsley 1 collaboration

Philip Brownridge 1 collaboration

Roy R Chaudhuri 1 collaboration

Artem M Kiselev 1 collaboration

Anna A Kostareva 1 collaboration

Catherine N Wilson 1 collaboration

James Akoko 1 collaboration

Blanca Perez Sepulveda 1 collaboration

Jessica Bevington 1 collaboration

Patricia Duncan 1 collaboration

Nicholas Feasey 1 collaboration

Gina Pinchbeck 1 collaboration

Eric M Fèvre 1 collaboration

Christopher M Parry 1 collaboration

John Cheesbrough 1 collaboration

Jessica A Bevington 1 collaboration

Rebecca J Bengtsson 1 collaboration

Ella V Rodwell 1 collaboration

Rebecca J Bennett 1 collaboration

George E Stenhouse 1 collaboration

P Malaka De Silva 1 collaboration

Hermione J Webster 1 collaboration

Jose A Bengoechea 1 collaboration

Amy Dumigan 1 collaboration

Alicia Tran-Dien 1 collaboration

Reenesh Prakash 1 collaboration

Happy C Banda 1 collaboration

Lovemore Alufandika 1 collaboration

Mike P Mautanga 1 collaboration

Arthur Bowers-Barnard 1 collaboration

Alistair C Darby 1 collaboration

François-Xavier Weill 1 collaboration

Olga I Poleshchuk 1 collaboration

Irina Y Babkina 1 collaboration

Vladimir A Kutyumov 1 collaboration

Viktor V Starunov 1 collaboration

Andrew N Ostrovsky 1 collaboration

TuShun R Powers 1 collaboration

Amanda L Haeberle 1 collaboration

Jennifer A Cundiff 1 collaboration

Zeus Saldaña-Ahuactzi 1 collaboration

Leigh A Knodler 1 collaboration

Caisey Pulford 1 collaboration

Lizeth Lacharme Lora 1 collaboration

Dean Everett 1 collaboration

Robert S Heyderman 1 collaboration

Philip M Ashton 1 collaboration

Chisomo L Msefula 1 collaboration

Xiu-Jun Yu 1 collaboration

Haixia Xie 1 collaboration

Mei Liu 1 collaboration

Ruhong Hou 1 collaboration

Blanca M Perez Sepulveda 1 collaboration

David W Holden 1 collaboration

Teresa L M Thurston 1 collaboration

Quinn T Easter 1 collaboration

Bruno Fernandes Matuck 1 collaboration

Germán Beldorati Stark 1 collaboration

Catherine L Worth 1 collaboration

Brayon Fremin 1 collaboration

Khoa Huynh 1 collaboration

Vaishnavi Ranganathan 1 collaboration

Zhi Ren 1 collaboration

Diana Pereira 1 collaboration

Brittany T Rupp 1 collaboration

Theresa Weaver 1 collaboration

Kathryn Miller 1 collaboration

Paola Perez 1 collaboration

Akira Hasuike 1 collaboration

Zhaoxu Chen 1 collaboration

Mandy Bush 1 collaboration

Xufeng Qu 1 collaboration

Janice Lee 1 collaboration

Scott H Randell 1 collaboration

Shannon M Wallet 1 collaboration

Inês Sequeira 1 collaboration

Hyun Koo 1 collaboration

Katarzyna M Tyc 1 collaboration

Jinze Liu 1 collaboration

Kang I Ko 1 collaboration

Kevin M Byrd 1 collaboration