プロフィール詳細

プロジェクトを作成

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Andrew S.に依頼

Australia

Lead Bioinformatician | Industry & Clinical Applied Bioinformatics

プロフィール概要

I am an experienced lead bioinformatician with over a decade of expertise in clinical, public health, and research data analysis. I have supported projects ranging from motor neuron disease research to large-scale public health genomics, collaborating with organizations such as the UK NHS, biotech startups, and academic institutions. In addition to my technical skills, I have served as a Quality Lead, ensuring the delivery of high-quality, reproducible workflows and analyses that meet rigorous standards in clinical and research environments. My work has included developing and maintaining pipelines using Nextflow, Snakemake, Python, R, Bash, Rust, containerizing workflows with Docker and Singularity, and scaling analyses on cloud platforms (AWS, GCP) and HPC clusters. I specialize in analysing whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA-seq data, as well as integrating bioinformatics solutions with healthcare systems, databases, electronic health records (EHRs) and genomic repositories.

専門分野

• ☆ Molecular Biology
• ☆ Genetics
• ☆ Omics
• ☆ Genomics
• ☆ Computer Science
• ☆ Parallel Computing
• ☆ Software Engineering
• ☆ Information Technology
• ☆ Database Management
• ☆ Software Architecture
• ☆ Bioinformatics
• ☆ Python
• ☆ SQL
• ☆ Quality Assurance & Quality Control (QA/QC)
• ☆ Software Development
• ☆ DevOps

サービス

• Consulting
• Data & AI
• Product Development

Consulting Digital Strategy Consulting, Scientific and Technical Consulting

Data & AI Statistical Analysis, Big Data Analytics, Text Mining & Analytics

Product Development Formulation, Product Evaluation, Quality Assurance & Control (QA/QC), Product Compliance , Concept Development, Prototyping, Reverse Engineering

職務経験

Macquarie University

- 現在

Clinical Bioinformatician

Public Health Wales

9月 2021 - 2月 2022

Clinical Bioinformatician STP

North Bristol NHS Trust

9月 2018 - 8月 2021

学歴

Clinical Science (Clinical Bioinformatics) - Genomics (Faculty of Biology, Medicine & Health)

University of Manchester

9月 2018 - 8月 2021

BSc (Hons) Biomedical Science (Department of Life Sciences)

University of Lincoln

9月 2011 - 8月 2014

認定資格

• MSc Clinical Science - Bioinformatics (Genomics)

  University of Manchester

  9月 2021 - 現在

出版物

JOURNAL ARTICLE

Short tandem repeat expansions in LRP12 are absent in cohorts of familial and sporadic amyotrophic lateral sclerosis patients of European ancestry @article{e8a1c25725d948cfb5bbaa4e6d5e1a94, title = "Short tandem repeat expansions in LRP12 are absent in cohorts of familial and sporadic amyotrophic lateral sclerosis patients of European ancestry", abstract = "In patients of Asian ancestry, a heterozygous CGG repeat expansion of >100 units in LRP12 is the cause of oculopharyngodistal myopathy type 1 (OPDM1). Repeat lengths of between 61 and 100 units have been associated with rare amyotrophic lateral sclerosis (ALS) cases of Asian ancestry, although with unusually long disease duration and without significant upper motor neuron involvement. This study sought to determine whether LRP12 CGG repeat expansions were also present in ALS patients of European ancestry. Whole-genome sequencing data from 608 sporadic ALS patients, 35 familial ALS probands, and 4703 neurologically normal controls were screened for LRP12 CGG expansions using ExpansionHunter v4. All individuals had LRP12 CGG repeat lengths within the normal range of 3-25 units. To date, LRP12 CGG repeat expansions have not been reported in ALS patients of European ancestry and may be limited to rare ALS patients of Asian ancestry and atypical clinical presentations.", keywords = "Amyotrophic lateral sclerosis, LRP12, short tandem repeat expansions", author = "Lyndal Henden and Fearnley, {Liam G.} and Dean Southwood and Andrew Smith and Rowe, {Dominic B.} and Kiernan, {Matthew C.} and Roger Pamphlett and Melanie Bahlo and Blair, {Ian P.} and Williams, {Kelly L.}", note = "Copyright the Author(s) 2024. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2024", month = aug, doi = "10.1080/21678421.2024.2348636", language = "English", volume = "25", pages = "644--647", journal = "Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration", issn = "2167-8421", publisher = "Taylor & Francis", number = "5-6", } . Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration.

Localization of protoporphyrin IX during glioma-resection surgery via paired stimulated Raman histology and fluorescence microscopy @article{f514ffa99a144c5a9770a704fbfd9de9, title = "Localization of protoporphyrin IX during glioma-resection surgery via paired stimulated Raman histology and fluorescence microscopy", abstract = "The most widely used fluorophore in glioma-resection surgery, 5-aminolevulinic acid (5-ALA), is thought to cause the selective accumulation of fluorescent protoporphyrin IX (PpIX) in tumour cells. Here we show that the clinical detection of PpIX can be improved via a microscope that performs paired stimulated Raman histology and two-photon excitation fluorescence microscopy (TPEF). We validated the technique in fresh tumour specimens from 115 patients with high-grade gliomas across four medical institutions. We found a weak negative correlation between tissue cellularity and the fluorescence intensity of PpIX across all imaged specimens. Semi-supervised clustering of the TPEF images revealed five distinct patterns of PpIX fluorescence, and spatial transcriptomic analyses of the imaged tissue showed that myeloid cells predominate in areas where PpIX accumulates in the intracellular space. Further analysis of external spatially resolved metabolomics, transcriptomics and RNA-sequencing datasets from glioblastoma specimens confirmed that myeloid cells preferentially accumulate and metabolize PpIX. Our findings question 5-ALA-induced fluorescence in glioma cells and show how 5-ALA and TPEF imaging can provide a window into the immune microenvironment of gliomas.", author = "Mustafa Nasir-Moin and Wadiura, {Lisa Irina} and Vlad Sacalean and Devin Juros and Misha Movahed-Ezazi and Lock, {Emily K.} and Andrew Smith and Matthew Lee and Hannah Weiss and Michael M{\"u}ther and Daniel Alber and Sujay Ratna and Camila Fang and Eric Suero-Molina and S{\"o}nke Hellwig and Walter Stummer and Karl R{\"o}ssler and Hainfellner, {Johannes A.} and Georg Widhalm and Barbara Kiesel and David Reichert and Mario Mischkulnig and Rajan Jain and Jakob Straehle and Nicolas Neidert and Oliver Schnell and J{\"u}rgen Beck and Jay Trautman and Steve Pastore and Donato Pacione and Dimitris Placantonakis and Oermann, {Eric Karl} and Golfinos, {John G.} and Hollon, {Todd C.} and Matija Snuderl and Freudiger, {Christian W.} and Heiland, {Dieter Henrik} and Orringer, {Daniel A.}", year = "2024", month = jun, doi = "10.1038/s41551-024-01217-3", language = "English", volume = "8", pages = "672--688", journal = "Nature Biomedical Engineering", issn = "2157-846X", publisher = "Springer, Springer Nature", number = "6", } . Nature Biomedical Engineering.

Andrew Smith, Natalie Grima, Sidong Liu, Dean Southwood, Lyndal Henden, Albert Lee, Dominic B. Rowe, Susan D'Silva, Ian P. Blair, Kelly L. Williams (2023). RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery . Neuropathology and Applied Neurobiology.

RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes @article{bf418bf6d6b94e99b8c8e658c8363de3, title = "RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: considerations for biomarker discovery", abstract = "Aim: Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. Methods: Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS–control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. Results: Two hundred and forty-five differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress-related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS patients from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. Conclusions: Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.", keywords = "amyotrophic lateral sclerosis, biomarker, ferroptosis, immune response, metabolism, peripheral blood, RNA-seq, transcriptome", author = "Natalie Grima and Sidong Liu and Dean Southwood and Lyndal Henden and Andrew Smith and Albert Lee and Rowe, {Dominic B.} and Susan D'Silva and Blair, {Ian P.} and Williams, {Kelly L.}", note = "Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2023", month = dec, doi = "10.1111/nan.12943", language = "English", volume = "49", pages = "1--16", journal = "Neuropathology and Applied Neurobiology", issn = "0305-1846", publisher = "Wiley-Blackwell, Wiley", number = "6", } . Neuropathology and Applied Neurobiology.