Mathematical, statistical and computational aspects of the new science of metagenomics

Programme theme

Metagenomics is the study of the total genomic content of microbial communities. In metagenomic studies, DNA material is sampled collectively from the microorganisms that populate the environment of interest (e.g. agricultural soil, ocean water, or the human gut). The extracted DNA sequences are subsequently used to profile the environment and its biodiversity, its dominant microbial classes or biological functions, and whether and how this profile differs from those of other environments.

The impact of metagenomics in our understanding of the natural world has been, and will continue to be, revolutionary and profound. Insights derived from metagenomic studies have become increasingly relevant in areas as diverse as human health, bioenergy, environmental sciences and paleontology.

This research programme will bring together leading expertise in the multiple disciplines involved in metagenomics including mathematics, computer science, probability and statistics, biomedical research and biology.

The brief of the programme will be to explore the major current analytical and computational open problems in metagenomics, and to identify opportunities for application and development of theory and methods, with an emphasis on synergy between disciplines.

Particular themes will include:

Community profiling and comparative metagenomics
Assembly of metagenomic data in the context of evolving NGS platforms
Community structure and dynamics: beyond taxonomic and functional characterisation
Analysis of microbial community transcriptomes, proteomes and metabolomes

These themes provide a rich source of mathematical problems in areas such as probability and statistics theory, dynamic programming, combinatorics and graph theory.

Click here to download the programme's final scientific report

Workshops

MTGW01

Mathematical, statistical and computational aspects of the new science of metagenomics

24 March 2014 to 28 March 2014

MTGW04

Evaluation workshop of the first CAMI challenge

10 May 2016 to 13 May 2016

Seminars

Monday 24th March 2014
10:15 to 11:15	Registration and Morning Coffee	No Room Required
11:15 to 11:25	Welcome from John Toland (INI Director)	No Room Required
11:25 to 11:30	Welcome by the Programme Organisers	No Room Required
12:30 to 13:45	Lunch at Wolfson Court	No Room Required
14:45 to 15:30	Afternoon Tea	No Room Required
15:30 to 16:15	Fast and accurate analysis of metagenomic data	Room 1
16:15 to 17:00	TIPP: Taxon Identification and Phylogenetic Profiling	Room 1
17:00 to 18:00	Welcome Wine Reception	No Room Required

Tuesday 25th March 2014
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Estimating within-host viral genetic diversity from next-generation sequencing data	Room 1
11:45 to 12:30	Metagenomic assembly and characterisation of viral signatures with MetaCortex	Room 1
12:30 to 13:45	Lunch at Wolfson Court	No Room Required
13:45 to 14:45	tba	Room 1
14:45 to 15:30	Afternoon Tea	No Room Required
15:30 to 16:15	Species identification from medical metagenomic sequence data	Room 1
16:15 to 17:00	NGS Sequence Assembly for Metagenomic Data	Room 1

Wednesday 26th March 2014
09:30 to 10:30	Understanding Biology from the Sequence Data of Uncultured Organisms	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Predictability and unpredictability in the dynamics of nutrient-cycling microbial ecosystems	Room 1
12:30 to 13:45	Lunch at Wolfson Court	No Room Required
15:00 to 15:45	Afternoon Tea	No Room Required
15:45 to 16:30	The living layer: the microbial interface between superior organisms and the environment as revealed by metagenomics	Room 1
16:30 to 17:00	Metagenome, metatranscriptome and single cell genome sequencing of biogas-producing microbial communities from production-scale biogas plants	Room 1
19:30 to 22:30	Conference Dinner at Cambridge Union Society hosted by Cambridge Dining Company	No Room Required

Thursday 27th March 2014
09:30 to 10:30	Inferring genotype-phenotype relationships from (meta-)genomes	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:45 to 12:30	Using metatranscriptomics to make global predictions: The impact of temperature on marine phytoplankton resource allocation and metabolism	Room 1
12:30 to 13:45	Lunch at Wolfson Court	No Room Required
13:45 to 14:15	Quikr: Rapid Bacterial Community Reconstruction Via Compressive Sensing	Room 1
14:15 to 14:45	New bioinformatic resources for taxonomic assignment of metagenomic NGS data: BioMaS, ITSoneDB and SARMA	Room 1
14:45 to 15:15	Webserver-supported storage of metagenomic datasets using MEGANv5	Room 1
15:15 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:30	Inferring Mixed Viral Populations	Room 1
16:30 to 17:30	Open discussion	Room 1

Friday 28th March 2014
09:30 to 10:15	Microbiome, Metagenomics and High-dimensional Compositional Data Analysis	Room 1
10:15 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Statistical Machine Learning for Modeling Early Respiratory Microbiota Composition	Room 1
11:00 to 11:45	Statistical Machine Learning for Modeling Early Respiratory Microbiota Composition	Room 1
11:00 to 11:45	Statistical Machine Learning for Modeling Early Respiratory Microbiota Composition	Room 1
12:30 to 13:45	Lunch at Wolfson Court	No Room Required
13:45 to 14:30	Linking taxa to function through contig clustering of microbial metagenomes	Room 1
14:30 to 15:00	Application of Bayesian model averaging and population Monte Carlo to inference from metagenomic mixture	Room 1
15:00 to 15:45	Afternoon Tea	No Room Required

Sunday 30th March 2014
09:00 to 17:00	Informal discussion	Discussion Room

Monday 31st March 2014
09:00 to 17:00	Informal discussion	Discussion Room

Tuesday 1st April 2014
15:00 to 16:00	Modelling macroecological patterns: Neutral theory and beyond	Room 2

Wednesday 2nd April 2014
15:00 to 16:30	Why mixture modelling?	Room 1

Thursday 3rd April 2014
14:00 to 17:00	Hands-on tutorial on the MEGAN software	Discussion Room

Friday 4th April 2014
09:30 to 12:30	Hands-on tutorial on R	Room 1
14:00 to 17:00	Discussion meeting	Discussion Room

Wednesday 9th April 2014
15:00 to 17:00	Forth Demain Discussion	Discussion Room

Friday 11th April 2014
14:00 to 17:00	Discussion meeting	Discussion Room

Monday 14th April 2014
11:00 to 12:00	C Quince - MTG informal discussion	Room 2
14:00 to 12:00	Open for Business -Metegenomics	Discussion Room
14:40 to 15:00	Challenges - The Kitten Microbiome	Room 1
15:00 to 15:20	The Oil Field Microbiome - How can Metagenomics Help the Oil Industry?	Room 1
15:40 to 16:00	Metagenomics at Second Genome	Room 1
16:00 to 16:20	Challenges at Illumina	Room 1
17:00 to 12:30	Metagenomics Industrial Applications, Open for Business	Room 1

Wednesday 16th April 2014
10:30 to 12:00	Susan Holmes informal discussion	Room 1
13:00 to 14:00	Skype - Richard Leggett	Discussion Room

Thursday 17th April 2014
09:00 to 11:00	Forth Demain Discussion	Discussion Room
14:00 to 17:00	Discussion meeting	Discussion Room

Wednesday 17th September 2014
15:00 to 17:00	MTGW03 workshop	Room 2

Mathematical, statistical and computational aspects of the new science of metagenomics

Organisers

Wally Gilks University of Leeds
Daniel Huson Eberhard Karls Universität Tübingen
Elisa Loza Rothamsted Research
Simon Tavaré University of Cambridge
Gabriel Valiente Technical University of Catalonia
Tandy Warnow Japan Atomic Energy Agency & University of Texas at Austin

Mathematical, statistical and computational aspects of the new science of metagenomics

Programme theme

Workshops

Mathematical, statistical and computational aspects of the new science of metagenomics

Evaluation workshop of the first CAMI challenge

Seminars

Organisers

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