Ira W. Deveson

发表

ANAQUIN: a software toolkit for the analysis of spike‐in controls for next generation sequencing

Tim R. Mercer, Ted Wong, Ira W. Deveson, 2017, Bioinform..

Use of synthetic DNA spike-in controls (sequins) for human genome sequencing

Chris Barker, Tim R. Mercer, Ted Wong, 2019, Nature Protocols.

Chiral DNA sequences as commutable reference standards for clinical genomics

Chris Barker, Tim R. Mercer, Martin A. Smith, 2018, bioRxiv.

Extensive DNA methylome rearrangement during early lamprey embryogenesis

Ira W. Deveson, R. Klose, I. Deveson, 2023, bioRxiv.

Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation

Ira W. Deveson, J. Graves, I. Deveson, 2022, Proceedings of the National Academy of Sciences.

Reference standards for next-generation sequencing

Ira W. Deveson, T. Mercer, S. Hardwick, 2017, Nature Reviews Genetics.

The landscape of genomic structural variation in Indigenous Australians

Ira W. Deveson, B. Llamas, O. Siggs, 2023, bioRxiv.

Gene expression of male pathway genes sox9 and amh during early sex differentiation in a reptile departs from the classical amniote model

Ira W. Deveson, I. Deveson, J. Blackburn, 2023, BMC Genomics.

Universal alternative splicing of noncoding exons

Ira W. Deveson, Tyson A. Clark, J. Mattick, 2017, bioRxiv.

Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition

Ira W. Deveson, I. Deveson, I. McGregor, 2021, bioRxiv.

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Ira W. Deveson, Nikki E. Freed, Nuno R. Faria, 2021, Wellcome open research.

Both phenotypic and genotypic sex influence sex chromosome dosage compensation in a sex reversing lizard

Ira W. Deveson, H. Patel, A. Georges, 2023, bioRxiv.

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity.

Ira W. Deveson, Cathryn M. Gould, E. Zotenko, 2021, Cell reports.

A universal molecular control for DNA, mRNA and protein expression

Ira W. Deveson, Ted Wong, Scott E. Youlten, 2024, Nature communications.

Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing

Ira W. Deveson, T. Mercer, Ted Wong, 2022, Nature Communications.

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome.

Ira W. Deveson, J. Mattick, T. Mercer, 2017, Trends in genetics : TIG.

Spliced synthetic genes as internal controls in RNA sequencing experiments

Ira W. Deveson, J. Mattick, L. Nielsen, 2016, Nature Methods.

The retroelement Lx9 puts a brake on the immune response to virus infection

Ira W. Deveson, Robert J. Weatheritt, J. Mattick, 2022, Nature.

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)

Ira W. Deveson, Alastair J. Ludington, Jillian M. Hammond, 2023, BMC Biology.

Streamlining remote nanopore data access with slow5curl

Ira W. Deveson, Hasindu Gamaarachchi, James M. Ferguson, 2023, bioRxiv.

Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters

Ira W. Deveson, I. Deveson, Hasindu Gamaarachchi, 2023, bioRxiv.

Accelerated nanopore basecalling with SLOW5 data format

Ira W. Deveson, I. Deveson, Hasindu Gamaarachchi, 2023, bioRxiv.

Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Ira W. Deveson, I. Deveson, S. Parameswaran, 2022, bioRxiv.

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

Ira W. Deveson, Cathryn M. Gould, E. Zotenko, 2020, bioRxiv.

Genopo: a nanopore sequencing analysis toolkit for portable Android devices

Hasindu Gamaarachchi, Hiruna Samarakoon, Ira W. Deveson, 2020, Communications Biology.

Simulation of nanopore sequencing signal data with tunable parameters

Ira W. Deveson, Hasindu Gamaarachchi, Hiruna Samarakoon, 2024, Genome research.

Fast nanopore sequencing data analysis with SLOW5

Ira W. Deveson, I. Deveson, Martin A. Smith, 2022, Nature Biotechnology.

Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

Ira W. Deveson, G. Ravenscroft, N. Laing, 2021, medRxiv.

SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

Ira W. Deveson, I. Deveson, Martin A. Smith, 2021, bioRxiv.

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

Ted Wong, Ira W. Deveson, Martin A Smith, 2018, Nature Communications.

SLOW5: a new �le format enables massive acceleration of nanopore sequencing data analysis

Ira W. Deveson, I. Deveson, Martin A. Smith, 2021 .

Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia

Ira W. Deveson, W. Tam, R. Dickins, 2021, Nature Communications.

Diagnosis of fusion genes using targeted RNA sequencing

David M. Thomas, Ira W. Deveson, S. O'toole, 2019, Nature Communications.

Sequencing and characterizing short tandem repeats in the human genome

Ira W. Deveson, Harriet Dashnow, D. MacArthur, 2024, Nature reviews. Genetics.

Chiral DNA sequences as commutable controls for clinical genomics

Chris Barker, Ted Wong, Ira W. Deveson, 2019, Nature Communications.

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination

Ira W. Deveson, J. Graves, I. Deveson, 2021, bioRxiv.

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

Ira W. Deveson, G. Faulkner, I. Deveson, 2021, Cell Reports.

An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics

Ira W. Deveson, I. Deveson, K. Kumar, 2021, Acta neuropathologica communications.

A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics

Ira W. Deveson, B. Llamas, Matthew P. Williams, 2022, The Lancet.

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Ira W. Deveson, J. Bader, J. Boeke, 2023, Cell genomics.

Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements

Ira W. Deveson, J. Bader, J. Boeke, 2022, bioRxiv.

Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA

Ira W. Deveson, Thomas M. Blomquist, W. Jones, 2021, Cell reports methods.

Representing genetic variation with synthetic DNA standards

Ted Wong, Ira W. Deveson, John S Mattick, 2016, Nature Methods.

Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination

Ira W. Deveson, J. Mattick, I. Deveson, 2017, Science Advances.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Paul M. Rindler, Ira W. Deveson, S. Cawley, 2021, Nature Biotechnology.

CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies

Ira W. Deveson, M. Ruella, J. Samir, 2023, Nature communications.

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome

Ira W. Deveson, N. Lennon, W. Tong, 2022, Genome biology.

Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response

Ira W. Deveson, David R. Croucher, P. Timpson, 2024, Science advances.

HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women

Ira W. Deveson, A. Adimora, N. Archin, 2023, Journal of virology.