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USD 40 /hr

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Hire Dr. Joshua C.

United Kingdom

USD 40 /hr

Biostatistics & Bioinformatics Consultant | Expert in High-Dimensional Data Science Using R & Python

Profile Summary

I am a bioinformatics and data science consultant with a PhD from the Earlham Institute, where I developed machine learning models to predict complex traits from omics data. My expertise covers the analysis of high-dimensional biological and experimental datasets, robust statistical modelling, cross-validation design, feature selection, and predictive modelling under varying environmental conditions. I also have extensive experience with RNA-Seq and other omics analyses, including quality control, normalisation, differential expression, and biomarker discovery, as well as data visualisation and reproducible pipeline development in R and Python.

Subject Matter Expertise

• ☆ Biostatistics
• ☆ Data Analysis
• ☆ Machine Learning
• ☆ Artificial Intelligence
• ☆ Statistics
• ☆ Bioinformatics
• ☆ Python
• ☆ R

Services

• Writing
• Consulting
• Data & AI

Writing Technical Writing, General Proofreading & Editing

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Data Processing, Data Insights

Work Experience

CEO

Traitseq Ltd

February 2023 - Present

Data Scientist

bloods.ai

March 2022 - Present

Postgraduate Researcher

Earlham Institute

September 2018 - July 2023

Computer Vision Research Engineer (Intern)

Syngenta

February 2022 - May 2022

Education

Mathematics and Statistics (First Class Honours) (Mathematics)

University of York

- Present

PhD (Data Science and Bioinformatics)

Earlham Institute

- Present

Certifications

• PhD in Computational Biology and Bioinformatics

  Earlham Institute, University of East Anglia

  https://orcid.org/0000-0002-0511-685X

  August 2023 - Present

Publications

PREPRINT

Joshua Colmer, Connor Reynolds, Hannah Rees, Ehsan Khajouei, Rachel Rusholme-Pilcher, Hiroshi Kudoh, Antony N. Dodd, Anthony Hall (2024). Machine learning models reveal environmental and genetic factors associated with the plant circadian clock .

Benjamen White, Thomas Lux, Rachel Rusholme-Pilcher, Angéla Juhász, Gemy Kaithakottil, Susan Duncan, James Simmonds, Hannah Rees, Jonathan Wright, Josh Colmer, et al. (2024). De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome .

Joshua Colmer, Hannah Rees, Rachel Rusholme-Pilcher, Paul Bailey, Benjamen White, Connor Reynolds, Sabrina Jaye Ward, Calum A. Graham, Luíza Lane de Barros Dantas, Antony N. Dodd, et al.(2021). Circadian regulation of the transcriptome in a complex polyploid crop . Cold Spring Harbor Laboratory

JOURNAL ARTICLE

Joshua Colmer, Gang Sun, Hengyun Lu, Yan Zhao, Jie Zhou, Robert Jackson, Yongchun Wang, Ling‐xiang Xu, Ahong Wang, Eric Ober, et al. (2022). AirMeasurer: open‐source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice . New Phytologist.

Joshua Colmer, Yulei Zhu, Gang Sun, Guohui Ding, Jie Zhou, Mingxing Wen, Shichao Jin, Qiang Zhao, Yanfeng Ding, Eric S. Ober, et al.(2021). Large-scale field phenotyping using backpack LiDAR and CropQuant-3D to measure structural variation in wheat . Plant Physiology. 187. (2). p. 716--738. Oxford University Press ({OUP})

Laura-Jayne Gardiner, Rachel Rusholme-Pilcher, Josh Colmer, Hannah Rees, Juan Manuel Crescente, Anna Paola Carrieri, Susan Duncan, Edward O. Pyzer-Knapp, Ritesh Krishna, Anthony Hall(2021). Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function . Proceedings of the National Academy of Sciences. 118. (32). Proceedings of the National Academy of Sciences

Joshua Colmer, Carmel M. O'Neill, Rachel Wells, Aaron Bostrom, Daniel Reynolds, Danny Websdale, Gagan Shiralagi, Wei Lu, Qiaojun Lou, Thomas Le Cornu, et al.(2020). SeedGerm: a cost‐effective phenotyping platform for automated seed imaging and machine‐learning based phenotypic analysis of crop seed germination . New Phytologist. 228. (2). p. 778--793. Wiley

OTHER

Joshua Colmer, Yulei Zhu, Gang Sun, Guohui Ding, Jie Zhou, Mingxing Wen, Shichao Jin, Qiang Zhao, Yanfeng Ding, Eric S. Ober, et al.(2021). Large-scale field phenotyping using backpack LiDAR and GUI-based CropQuant-3D to measure structural responses to different nitrogen treatments in wheat . Cold Spring Harbor Laboratory