Explanipedia

Sensitivity to TDP-43 loss and degradation resistance determine cryptic exon biomarker potential Open

Anna‐Leigh Brown, Alla Mikheenko, Dario Dattilo, Sam Bryce-Smith, Puja R. Mehta , et al. · 2025

Cryptic splicing caused by TDP-43 proteinopathy is a hallmark of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, which cryptic splicing events (CEs) are the most sensitive to T…

TDP-43 loss induces cryptic polyadenylation in ALS/FTD Open

Sam Bryce-Smith, Anna‐Leigh Brown, Max Z. Y. J. Chien, Dario Dattilo, Puja R. Mehta , et al. · 2025

Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 are cellular hallmarks of amyotrophic lateral sclerosis (ALS). TDP-43 nuclear loss causes de-repression of cryptic exons, yet cryptic alternative polyadenylati…

Altered mRNA transport and local translation in i3Neurons with RNA-binding protein knockdown Open

Rachael Dargan, Alla Mikheenko, Nicholas L. Johnson, Benjamin Packer, Ziyi Li , et al. · 2025

Neurons rely on messenger RNA (mRNA) transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by R…

A multimodal screening platform for endogenous dipeptide repeat proteins in C9orf72 patient iPSC neurons Open

Benedikt V. Hölbling, Yashwant Gupta, Paolo Marchi, Magda L. Atilano, Michael Flower , et al. · 2025

Repeat expansions in C9orf72 are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation generates neurotoxic dipeptide repeat proteins (DPRs). To study endogenous DPR…

Author Correction: Neuronal polyunsaturated fatty acids are protective in ALS/FTD Open

Ashling Giblin, Alexander J. Cammack, Niek Blomberg, Sharifah Anoar, Alla Mikheenko , et al. · 2025

Neuronal polyunsaturated fatty acids are protective in ALS/FTD Open

Ashling Giblin, Alexander J. Cammack, Niek Blomberg, Sharifah Anoar, Alla Mikheenko , et al. · 2025

Dual-targeting CRISPR-CasRx reduces C9orf72 ALS/FTD sense and antisense repeat RNAs in vitro and in vivo Open

Liam Kempthorne, Deniz Vaizoglu, Alexander J. Cammack, Mireia Carcolé, Maxine P. Roberts , et al. · 2025

The most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is an intronic G 4 C 2 repeat expansion in C9orf72 . The repeats undergo bidirectional transcription to produce sense and antisense repe…

Altered mRNA transport and local translation in iNeurons with RNA binding protein knockdown Open

Rachael Dargan, Alla Mikheenko, Nicholas L. Johnson, Benjamin Packer, Ziyi Li , et al. · 2024

Neurons rely on mRNA transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA binding prote…

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

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala , et al. · 2024

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated…

PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons Open

Carmelo Milioto, Mireia Carcolé, Ashling Giblin, Rachel Coneys, Olivia N. Attrebi , et al. · 2024

Dual-targeting CRISPR-CasRx reduces<i>C9orf72</i>ALS/FTD sense and antisense repeat RNAs in vitro and in vivo Open

Liam Kempthorne, Deniz Vaizoglu, Alexander J. Cammack, Mireia Carcolé, Pacharaporn Suklai , et al. · 2024

The most common genetic cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is a G 4 C 2 repeat expansion in intron 1 of the C9orf72 gene. This repeat expansion undergoes bidirectional transcription to produ…

TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD Open

Sam Bryce-Smith, Anna‐Leigh Brown, Puja R. Mehta, Francesca Mattedi, Alla Mikheenko , et al. · 2024

Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated…

Neuronal polyunsaturated fatty acids are protective in FTD/ALS Open

Ashling Giblin, AJ Cammack, N. Blomberg, Alla Mikheenko, Mireia Carcolé , et al. · 2024

We report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in human post-mortem ALS spinal cord and a Drosophila model of the most common genetic cause of FTD/ALS, a repeat expansion in C9orf7…

The complete sequence of a human Y chromosome Open

Arang Rhie, Sergey Nurk, Monika Čechová, Savannah J. Hoyt, Dylan J. Taylor , et al. · 2023

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

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala , et al. · 2023

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from …

PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in<i>C9orf72</i>ALS/FTD neurons Open

Carmelo Milioto, Mireia Carcolé, Ashling Giblin, Rachel Coneys, Olivia N. Attrebi , et al. · 2023

A GGGGCC repeat expansion in C9orf72 is the most common genetic cause of ALS and FTD (C9ALS/FTD). The presence of dipeptide repeat (DPR) proteins, generated by translation of the expanded repeat, is a major pathogenic feature of C9ALS/FTD …

WebQUAST: online evaluation of genome assemblies Open

Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich · 2023

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluati…

Supplementary data for "WebQUAST: online evaluation of genome assemblies" Open

Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich · 2023

Supplementary data for A. Mikheenko, V. Saveliev, P. Hirsch, A. Gurevich. WebQUAST: online evaluation of genome assemblies. Reference genomes of two Escherichia coli K-12 substrains (MG1655 and W3110) and genome annotation of MG1…

Supplementary data for "WebQUAST: online evaluation of genome assemblies" Open

Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich · 2023

Supplementary data for A. Mikheenko, V. Saveliev, P. Hirsch, A. Gurevich. WebQUAST: online evaluation of genome assemblies. Reference genomes of two Escherichia coli K-12 substrains (MG1655 and W3110) and genome annotation of MG1…

Supplementary data for "WebQUAST: online evaluation of genome assemblies" Open

Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich · 2023

Supplementary data for A. Mikheenko, V. Saveliev, P. Hirsch, A. Gurevich. WebQUAST: online evaluation of genome assemblies. Reference genomes of two Escherichia coli K-12 substrains (MG1655 and W3110) and genome annotation of MG1…

Mouse SIRV and simulated data used in the IsoQuant publication Open

Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Julien Jarroux, Hagen Tilgner · 2023

This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. - Reduced mouse GENCODE vM26 annotation: 15% of expressed isoforms removed, expression profile based on real mouse brain sequencing data; also c…

Mouse SIRV and simulated data used in the IsoQuant publication Open

Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Julien Jarroux, Hagen Tilgner · 2023

This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. - Reduced mouse GENCODE vM26 annotation: 15% of expressed isoforms removed, expression profile based on real mouse brain sequencing data; also c…

Accurate isoform discovery with IsoQuant using long reads Open

Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux , et al. · 2023

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs tr…

The complete sequence of a human Y chromosome Open

Arang Rhie, Sergey Nurk, Monika Čechová, Savannah J. Hoyt, Dylan J. Taylor , et al. · 2022

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications 1–3 . As a result, more than half of the Y chromo…

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap Open

Andrey V. Bzikadze, Alla Mikheenko, Pavel A. Pevzner · 2022

Recent advancements in long-read sequencing have enabled the telomere-to-telomere (complete) assembly of a human genome and are now contributing to the haplotype-resolved complete assemblies of multiple human genomes. Because the accuracy …

Mouse SIRV and simulated data used in the IsoQuant publication Open

Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Julien Jarroux, Hagen Tilgner · 2022

This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. NOTE: SIRVs BAM file contains ONT R9.4 data, R10.4 data that was used in the publication is available in the newer version. - R…

NPvis: An Interactive Visualizer of Peptidic Natural Product–MS/MS Matches Open

Olga Kunyavskaya, Alla Mikheenko, Alexey Gurevich · 2022

Peptidic natural products (PNPs) represent a medically important class of secondary metabolites that includes antibiotics, anti-inflammatory and antitumor agents. Advances in tandem mass spectra (MS/MS) acquisition and in silico database s…

IsoQuant: a tool for accurate novel isoform discovery with long reads Open

Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux , et al. · 2022

Long reads are reshaping RNA biology. However, determining alternative isoforms from long-read RNA data is a complex and incompletely solved problem even when the reference genome is known. Here we present IsoQuant - a reference-based tool…

VerityMap: fast and accurate mapping of long reads to complete genome assemblies Open

Andrey V. Bzikadze, Alla Mikheenko, Pavel A. Pevzner · 2022

Recent advancements in long-read sequencing have enabled the telomere-to-telomere (T2T) assembly of a human genome and are now contributing to the haplotype-resolved T2T assemblies of multiple human genomes. Since the accuracy of read mapp…

VerityMap: fast and accurate mapping of long reads to complete genome assemblies Open

Andrey V. Bzikadze, Alla Mikheenko, Pavel A. Pevzner · 2022

Recent advancements in long-read sequencing have enabled the telomere-to-telomere (T2T) assembly of a human genome and are now contributing to the haplotype-resolved T2T assemblies of multiple human genomes. Since the accuracy of read mapp…

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