The paper demonstrates that long-read RNA-seq with quality control measures reduces bias in allele counts across four species, improving accuracy in allelic imbalance studies.

NAR Genomics and Bioinformatics · Jun 27, 2026Peer-reviewedGenetics

Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines

Logan Mulroney, Henry J. Taylor, Angela Lee, Amy J. Swift, Mihail Zdravkov, Lori L. Bonnycastle, Shelise Y. Brooks, Brian N. Lee, Tomas W. Fitzgerald, Narisu Narisu, Leslie G. Biesecker, Michael R. Erdos, Francesco Nicassio, Ewan Birney, Francis S. Collins, D. Leland Taylor

The paper uses direct RNA nanopore sequencing to identify RNA modification changes in human pancreatic beta-cells after glucose stimulation, finding 1,697 differentially modified sites linked to type 2 diabetes genes.

bioRxiv · Jun 12, 2025 · PreprintGenomics

Simultaneous detection of RNA modifications using In Vitro Transcription and Direct RNA Nanopore sequencing

Logan Mulroney, Lucia Coscujuela Tarrero, Paola Maragno, Carmela Rubolino, Simone Maestri, Mattia Furlan, Matteo Jacopo Marzi, Tomas W. Fitzgerald, Tommaso Leonardi, Mattia Pelizzola, Ewan Birney, Francesco Nicassio

The paper introduces an IVT-based method with dRNA-seq to detect RNA modifications across the transcriptome, identifying 26,619 modification sites and revealing non-random co-occurrence and isoform-specific patterns.

bioRxiv · Oct 22, 2024 · PreprintGenomics

Discovering host protein interactions specific for SARS-CoV-2 RNA genome

Roberto Giambruno, Elsa Zacco, Camilla Ugolini, Andrea Vandelli, Logan Mulroney, Manfredi D’Onghia, Bianca Giuliani, Elena Criscuolo, Matteo Castelli, Nicola Clementi, Massimo Clementi, Nicasio Mancini, Tiziana Bonaldi, Stefano Gustincich, Tommaso Leonardi, , Francesco Nicassio

The paper identifies host proteins interacting with SARS-CoV-2 RNA ends, highlighting pseudouridine synthase PUS7 and post-transcriptional modifications in viral RNA structure and function.

bioRxiv · Jul 18, 2022 · PreprintMolecular Biology

Nanopore ReCappable Sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs

Camilla Ugolini, Logan Mulroney, Adrien Léger, Matteo Castelli, Elena Criscuolo, Maia Kavanagh Williamson, Andrew D. Davidson, Abdulaziz Almuqrin, Roberto Giambruno, Miten Jain, Gianmaria Frigè, Hugh E. Olsen, George Tzertzinis, Ira Schildkraut, Madalee G. Wulf, , Tommaso Leonardi

This study introduces NRCeq, a method to identify capped full-length SARS-CoV-2 transcripts, revealing new insights into sgRNA structure and expression.

Nucleic Acids Research · Feb 16, 2022Peer-reviewedGenomics

Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

Logan Mulroney, Madalee G. Wulf, Ira Schildkraut, George Tzertzinis, John Buswell, Miten Jain, Hugh E. Olsen, Mark Diekhans, Ivan Reis Correa Junior, Mark A. Akeson, Laurence M. Ettwiller

The paper identifies high-confidence full-length human RNA isoform scaffolds using nanopore sequencing by improving 5' cap detection and 3' polyadenylation site identification.

RNA · Nov 2, 2021Peer-reviewedGenomics

Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: Application to direct RNA sequencing on nanopores.

Jenny Mai Vo, Logan Mulroney, Jen Quick-Cleveland, Miten Jain, Mark A. Akeson, Manuel Ares

This paper tests the use of Cid1 to add poly(I) tails to RNA for direct nanopore sequencing, enabling detection of both poly(A) and non-poly(A) RNAs and nascent transcripts.

RNA · Aug 26, 2021Peer-reviewedMolecular Biology

Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing

Andrew M. Smith, Miten Jain, Logan Mulroney, Daniel R. Garalde, Mark Akeson

This paper uses nanopore direct RNA sequencing to detect modified nucleotides in 16S rRNA, revealing a 7-methylguanosine modification linked to aminoglycoside resistance in E. coli.

bioRxiv · Apr 29, 2017 · PreprintBioengineering