Ezra Herman

Experience

• 

  Edinburgh University Dance Music Society

  May 2015 - May 2018

  Vice President (15-17) & President (17-18)

  • Led the organisation of club nights and workshops, including the booking of a Dutch international DJ.• Organised society trips to Glasgow and Berlin for approximately ten people.

• 

  Weizmann Institute of Science

  Jun 2016 - Aug 2016

  Summer Research Student (Stavans lab)

  "Investigating the patterns of heterocyst formation in Anabaena."• Set up time-lapse microscopy experiments to track cyanobacterial filament development.• Prepared a protocol for time-lapse microscopy assays. • Processed microscopy images through a graphical user interface.• Offered guidance to a student that continued my work after my placement.

• 

  The University of Edinburgh

  Jun 2017 - Aug 2017

  Summer Research Student (Bayne lab)

  "Investigating the importance of RNAi in yeast DNA double-stranded break repair."• Constructed three yeast mutants by transformation.• Analysed strain genotypes by PCR and gel electrophoresis. • Determined an optimal drug concentration for yeast growth.• Analysed the DNA double-stranded break repair efficiency of the mutants through plate assays.

• 

  Educational Institution

  Oct 2017 - Oct 2017

  Student symposium co-lead

  • Identified the need for students to receive feedback on their research project talks.• Invited a member of staff to provide feedback to the seven speakers.• Secured funding for refreshments from the Edinburgh University Biology Society.

• 

  The University of Edinburgh

  Jan 2018 - May 2018

  Honours Project Student (McNally lab)

  “What game are they playing? Meta-analysis of microbial cooperator-cheater dynamics.”• Collected raw data from 4924 competition experiments between cooperating and non-cooperating microbes.• Applied game theory and linear mixed effects modelling in RStudio.• Found strong effects of spatial structure and type of cooperation on competition outcome.

• 

  University of Glasgow

  Jun 2019 - Aug 2019

  Master Thesis Student (Robertson lab)

  “Local adaptation, modularity and nestedness in a network of natural Ralstonia solanacearum bacteria and their phages” • Applied generalized linear mixed modelling and modularity analysis to detect local adaptation.• Applied nestedness analysis, finding a strong dependency of statistical significance on the chosen null model.

• 

  University of York

  Oct 2019 - Sept 2023

  I developed skills in bioinformatics and data analysis throughout my PhD, in addition to experimental design and communication of results to non-technical audiences. All my projects have involved Snakemake pipeline construction and working with an HPC cluster. I have also deployed my work on Azure VMs. Projects included:- Characterising the immune system repertoire of clinical Pseudomonas aeruginosa isolates. This involved the design of a nanopore-illumina hybrid assembly pipeline, construction of a pangenome of 460 isolates using PPanGGOLiN and generating insights from the outputs of various gene prediction tools. In addition, I communicated the complex results to a non-bioinformatics audience.- Characterising the interactions between individual phage-bacteria pairs. This involved the design and execution of a large wet-lab experiment. This project also involved measuring the association between genomic features and phenotypic data through generalised linear mixed modelling.- Testing the effect of null hypothesis choice in nestedness tests. This involved simulation of phage-bacteria infection networks in R and communication of complex results to a non-statistical audience. Show less

  • PhD student (Friman lab)

    Oct 2019 - Sept 2023

  • Graduate Teaching Assistant [Maths Skills Centre & Biology Department]

    Oct 2019 - Jun 2022
• 

  Software Sustainability Institute

  Jan 2021 - Oct 2021

  Graduate Lead [Developing Training Materials for Data Science]

  A Software Sustainability Institute funded project to develop and pilot Data Carpentry course material, under supervision of Emma Rand (University of York) and Andrew Stewart (University of Manchester). - Created and taught a three-day Data Carpentry workshop on statistics in R for public health research.The four modules can be found at the following pages:- Statistical thinking for public health: https://carpentries-incubator.github.io/statistical-thinking-public-health/- Simple linear regression for public health: https://carpentries-incubator.github.io/simple-linear-regression-public-health/- Multiple linear regression for public health: https://carpentries-incubator.github.io/multiple-linear-regression-public-health/- Logistic regression for public health: https://carpentries-incubator.github.io/logistic-regression-public-health/ Show less

• 

  Ed-DaSH

  Sept 2021 - Sept 2022

  Instructor

  Instructor on the Introductory Statistics and Snakemake courses run by Ed-DaSH: https://edcarp.github.io/Ed-DaSH/index.html.

• 

  The Alan Turing Institute

  Oct 2022 - Mar 2023

  Enrichment Placement Student

  Six-month relocation to work on network analysis as part of my PhD. I also presented at the "Data Hazards, Ethics and Reproducibility" symposium on how to combine Snakemake and RMarkdown for reproducible analyses and reports.More details on the Turing website: https://www.turing.ac.uk/people/enrichment-students/ezra-herman

• 

  Bactobio

  Apr 2023 - Jun 2023

  Intern (Scientific Software Engineering)

  - Wrote queries in mySQL and SQLAlchemy ORM. - Met with wet lab scientists to understand their database needs. - Built Dash interfaces with Python for lab scientists to easily interact with the company's database. - Reviewed colleague's PRs and contributed to the wider codebase.

• 

  Esox Biologics

  Nov 2023 - now

  - Leading the development and maintenance of pipelines for metagenomic taxonomic classification, MAG assembly and automated client report generation. - Performing hiring and management for the bioinformatics team and its objectives.- Ensuring complex bioinformatics concepts and results are clearly communicated to clients through reports and presentations.- Overseeing and performing bioinformatics support to the rest of the organisation. - Managing our relationships with service providers and consultants. Show less

  • Lead Bioinformatician

    Jan 2025 - now

  • Senior Bioinformatician

    Nov 2023 - Dec 2024