Development of an Easy-to-use Metagenomics Platform for Agricultural Science

Deliverables

Current Algorithm evolution – Review/position publication

A report on Current Algorithm evolution will be produced

Technical reports and Platform Integration of WP4 pipelines
Academic Papers

Papers will be submitted for publication to peer reviewed journals

Academic papers & technical reports

Academic papers and technical reports will be published

Publications

Papers will be submitted for publication to peer reviewed journals and international conferences

Academic papers on changes in rumen microbial population due to chronic stress

Academic papers on changes in rumen microbial population due to chronic stress will be published

Academic papers and technical reports

Academic papers and technical reports will be produced

Technical reports and Platform Integration of WP2 results and databases

Technical reports and Platform Integration of WP2 results and databases will be produced

Technical reports and Platform Integration of WP3 pipelines

Submission to EBI ENA database of the raw sequence files

Raw sequence files will be submitted to EBI ENA database

Implementation of next software platform

New software platform will be rolled out

Implementation of Software platform

NSilico will demonstrated the software platform

Public release of the meta-genomic analysis platform

A Public release of the meta-genomic analysis platform will be undertaken

Publications

Analysis of rumen microbial community in cattle through the integration of metagenomic and network-based approaches

Author(s): Haiying Wang, Huiru Zheng, Fiona Browne, Rainer Roehe, Richard J. Dewhurst, Felix Engel, Matthias Hemmje, Paul Walsh
Published in: 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016, Page(s) 198-203, ISBN 978-1-5090-1611-2
Publisher: IEEE
DOI: 10.1109/bibm.2016.7822518

An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes

Author(s): Jyotsna Talreja Wassan, Huiru Zheng, Fiona Browne, Jenna Bowen, Paul Walsh, Rainer Roehe, Richard Dewhurst, Cintia Palu, Brian Kelly, Haiying Wang
Published in: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018, Page(s) 1854-1860, ISBN 978-1-5386-5488-0
Publisher: IEEE
DOI: 10.1109/bibm.2018.8621104

A metagenomics analysis of rumen microbiome

Author(s): Paul Walsh, Cintia Palu, Brian Kelly, Brendan Lawor, Jyotsna Talreja Wassan, Huiru Zheng, Haiying Wang
Published in: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017, Page(s) 2077-2082, ISBN 978-1-5090-3050-7
Publisher: IEEE
DOI: 10.1109/bibm.2017.8217980

Microbial co-presence and mutual-exclusion networks in the Bovine rumen microbiome

Author(s): Haiying Wang, Huiru Zheng, Richard J. Dewhurst, Rainer Roehe
Published in: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017, Page(s) 114-119, ISBN 978-1-5090-3050-7
Publisher: IEEE
DOI: 10.1109/bibm.2017.8217635

Microbial abundance analysis and phylogenetic adoption in functional metagenomics

Author(s): Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
Published in: 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2017, Page(s) 1-8, ISBN 978-1-4673-8988-4
Publisher: IEEE
DOI: 10.1109/cibcb.2017.8058557

A network analysis of methane and feed conversion genes in the rumen microbial community

Author(s): Fiona Browne, Haiying Wang, Huiru Zheng, Rainer Roehe, Richard J. Dewhurst, Paul Walsh
Published in: 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016, Page(s) 1477-1484, ISBN 978-1-5090-1611-2
Publisher: IEEE
DOI: 10.1109/bibm.2016.7822741

PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification

Author(s): Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
Published in: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018, Page(s) 44-49, ISBN 978-1-5386-5488-0
Publisher: IEEE
DOI: 10.1109/bibm.2018.8621382

An Interface to Heterogeneous Data Sources Based on the Mediator/Wrapper Architecture in the Hadoop Ecosystem

Author(s): Klaus-Dieter Schmatz, Kevin Berwind, Felix Engel, Matthias L. Hemmje
Published in: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018, Page(s) 1838-1845, ISBN 978-1-5386-5488-0
Publisher: IEEE
DOI: 10.1109/bibm.2018.8621111

Phylogeny-Aware Deep 1-Dimensional Convolutional Neural Network for the Classification of Metagenomes

Author(s): Timmy Manning, Jyotsna Talreja Wassan, Cintia Palu, Haiying Wang, Fiona Browne, Huiru Zheng, Brian Kelly, Paul Walsh
Published in: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018, Page(s) 1826-1831, ISBN 978-1-5386-5488-0
Publisher: IEEE
DOI: 10.1109/bibm.2018.8621543

A Metagenomic Content and Knowledge Management Ecosystem Platform

Author(s): Binh Vu, Yanxin Wu, Haithem Afli, Paul Mc Kevitt, Paul Walsh, Felix Engel, Michael Fuchs, Matthias Hemmje
Published in: 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Publisher: IEEE

Automated Object Tracking for Animal Behaviour Studies

Author(s): Timmy Manning, Miguel Somarriba, Rainer Roehe, Simon Turner, Haiying Wang, Huiru Zheng, Brian Kelly, Jennifer Lynch, Paul Walsh
Published in: 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Publisher: IEEE

A Phylogeny-aware Feature Ranking for Classification of Cattle Rumen Microbiome

Author(s): Jyotsna Talreja Wassan, Huiru Zheng, Haiying Wang, Fiona Browne, Paul Walsh, Tim Manning, Richard Dewhurst, Rainer Roehe
Published in: 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Publisher: IEEE

A knowledge driven mutual information-based analytical framework for the identification of rumen metabolites

Author(s): Mengyuan Wang, Huiru Zheng, Haiying Wang, Richard Dewhurst, Rainer Roehe,
Published in: 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Publisher: IEEE

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods

Author(s): Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2018.2858808

Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome

Author(s): Huiru Zheng, Haiying Wang, Richard Dewhurst, Rainer Roehe
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2018.2879342

Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits

Author(s): Haiying Wang, Huiru Zheng, Fiona Browne, Rainer Roehe, Richard J. Dewhurst, Felix Engel, Matthias Hemmje, Xiangwu Lu, Paul Walsh
Published in: Methods, Issue 124, 2017, Page(s) 108-119, ISSN 1046-2023
Publisher: Academic Press
DOI: 10.1016/j.ymeth.2017.05.029

Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance

Author(s): Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
Published in: IEEE Transactions on NanoBioscience, Issue 18/3, 2019, Page(s) 273-282, ISSN 1536-1241
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tnb.2019.2912824

An Integrative Approach for the Functional Analysis of Metagenomic Studies

Author(s): Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Paul Wash, Brain Kelly, Cintia Palu, Nina Konstantinidou, Rainer Roehe, Richard Dewhurst, Huiru Zheng
Published in: Intelligent Computing Theories and Application, Issue 10362, 2017, Page(s) 421-427, ISBN 978-3-319-63311-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-63312-1_37

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