Hello! I’m Sam Nicholls.

A twenty-six year old Computational Biology PhD student at Aberystwyth University. Previously a first class Computer Science and Statistics graduate, during the study for which I spent a year out with the Numerical Algorithms Group and Wellcome Trust Sanger Institute. One time I worked at Google.

I like telling computers to do things, statistics, fries, and owls.

Say Hello: sam [at] samnicholls [dot] net
See also; @samstudio8, LinkedIn

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Publications

• Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7
  Yang Luo, Katrina M de Lange, Luke Jostins, Loukas Moutsianas, Joshua Randall, Nicholas A Kennedy, Christopher A Lamb, Shane McCarthy, Tariq Ahmad, Cathryn Edwards, Eva Goncalves Serra, Ailsa Hart, Chris Hawkey, John C Mansfield, Craig Mowat, William G Newman, Sam Nichols, Martin Pollard, Jack Satsangi, Alison Simmons, Mark Tremelling, Holm Uhlig, David C Wilson, James C Lee, Natalie J Prescott et al.
  Nature Genetics (2017) 49, 186–192.
• Goldilocks: a tool for identifying genomic regions that are “just right.”
  Nicholls, S. M., Clare, A., & Randall, J. C.
  Bioinformatics (2016) 32 (13): 2047-2049.

Pre-Prints

• Probabilistic Recovery Of Cryptic Haplotypes From Metagenomic Data
  Samuel M. Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare.
• Advances in the recovery of haplotypes from the metagenome
  Samuel M. Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare.

Posters

• Towards an algorithm for extracting exciting enzymes from metagenomic data
  Samuel M. Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare.
  15th European Conference on Computational Biology, July 2016 in The Hague, Netherlands
• A data structure and algorithm for recovering haplotypes from metagenomes (with Hansel and Gretel)
  Samuel M. Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare.
  Computational Pan-Genomics Workshop, 15th European Conference on Computational Biology, July 2016 in The Hague, Netherlands
• Meet the Metahaplome: A definition of functional haplotype resolution in the metagenome
  Samuel M. Nicholls
  2nd UK Bioinformatics Student Symposium, October 2015 in Norwich, UK
• Goldilocks: Locating genomic regions that are “just right”
  Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
  23rd Annual International Conference on Intelligent Systems for Molecular Biology and 14th European Conference on Computational Biology, July 2015 in Dublin, Ireland
• Application of Machine Learning Techniques to Next Generation Sequencing Quality Control
  Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
  64th Annual Meeting of The American Society of Human Genetics, October 20, 2014 in San Diego, CA

Grants

• Aberystwyth University Research Fund 2016
  Extracting exciting commercially exploitable enzymes from metagenomic data sets
  Co-authored £4,500 grant to cover lab and sequencing costs for proof of concept of my PhD algorithm.
• Aberystwyth University Doctoral Career Development Scholarship
  50% PhD fees and stipend awarded by competition
• Aberystwyth University IBERS Scholarship
  50% PhD fees and stipend awarded by IBERS scholarship

Awards

• Best Poster
  2016 Annual IMPACS PhD Conference
  Aberystwyth University. Institute of Mathematics, Physics and Computer Science
• Runner-Up Poster
  Excellence with Impact Poster Presentation
  Aberystwyth University. Institute of Biological, Environmental and Rural Sciences
• Best Student Presentation
  2014 Student Symposium on Computational Biology and Life Sciences, Cardiff
• Best Minor Dissertation Project 2014
  Aberystwyth University. Department of Computer Science
• 2012 O.L. Davies Prize in Statistics
  Aberystwyth University. Department of Mathematics
  Awarded to the undergraduate student with the best performance in Statistics in memory of the Professor Owen L. Davies