Alberto Paccanaro

Professor in Machine Learning & Computational Biology

Centre for Systems and Synthetic Biology &
Department of Computer Science
Royal Holloway, University of London

To answer many important questions in biology and medicine we need to integrate diverse sets of data from different sources, and these data sets are often large and very noisy. My research interests are in applying and developing novel computational methods that make use of these diverse biological data sets to answer biological questions. Particularly, the focus of my research is in developing machine learning and pattern recognition techniques for solving problems in molecular computational biology. Such techniques can provide an answer to many of the current challenges in the field because they offer a natural way to integrate different types of data and to handle large amounts of noisy information.

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University of Milan
Laurea, 1990

Catholic University
of Asuncion

University of Toronto
PhD, 2002

Gatsby Computational
Neuroscience Unit, UCL

Queen Mary
University of London

Yale University

Royal Holloway
University of London



List of publications


Overview of selected research projects

A network medicine approach to quantify distance between hereditary disease modules on the interactome (more...)
An overlapping clustering method for protein interaction data (more...)
Computational selection of transcriptomics experiments (more...)

Automatic annotation of gene families (more...)
Semantic similarity measures (more...)
Spectral methods for clustering protein sequences (
Techniques for integrating different protein-protein interaction experiments (
Methods for de-noising large scale protein-protein interaction experiments (
Protein-protein interaction prediction (
Prediction of gene essentiality from genomic features (more...)
Prediction of protein function in E. Coli (more...)
Quantifying environmental adaptation of metabolic pathways in metagenomics (more...)

Selected publications

A network medicine approach to quantify distance between hereditary disease modules on the interactome,
Nature Scientific Reports, 2015, 5, 17658

A census of human soluble protein complexes Cell, 2012 Aug 31;150(5):1068-81.

Detecting overlapping protein complexes in protein-protein interaction networks  Nature Methods, 2012 Mar 18;9(5):471-2. doi: 10.1038/nmeth.1938.

Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty  Bioinformatics, 2012, 28, 1383

GFam: a platform for automatic annotation of gene families  Nucleic Acids Res. 2012 Jul 11.

Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses  PLoS ONE, 2012, vol. 7, iss. 8, p. 39681

Exploring the evolutionary path of plant MAPK networks  Trends Plant Sci. 2012 Sep;17(9):518-25. Epub 2012 Jun 8.

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins, PLoS Biol. 2009 Apr 28;7(4)
Quantifying environmental adaptation of metabolic pathways in metagenomics
, Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions, Genome Research, 2007,17(6):787
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, Nature, 2006, Mar 30,440(7084):637-43
Spectral Clustering of Proteins Sequences, Nucleic Acids Research 2006, Mar 17;34(5):1571-80
Predicting Essential Genes in Fungal Genomes, Genome Research, 2006, 16 (9): 1126-35
Predicting interactions in protein networks by completing defective cliques, Bioinformatics 2006, Apr 1;22(7):823-9
Integration of curated databases to identify genotype-phenotype associations, BMC Genomics. 2006, Oct 12;7:257
Assessing the Limits of Genomic Data Integration for Protein-Protein Interactions,
Genome Research, Jul 2005, 15: 945 953


- Translational landscape to link cell growth with proliferation in the root meristem, NSF/BIO-BBSRC (with Prof Laszlo Bogre and Albrecht G. von Arnim),
733,230 started in September 2015
- Inference of RBR network and dynamic RBR complexes during leaf development, EU, Marie Curie Fellowship to Dr Beatrix Horvath, 309,235 started in March 2013
- MAPK signalling network to adapt leaf growth to drought condition, EU, Marie Curie Fellowship to Dr Papdi Csaba (with Prof Laszlo Bogre), 221,606 started in April 2013
- A GPU-based high performance system for discovering consensus domain architecture and functional annotation of protein families, BBSRC, 142,000 started in July 2012
- Overlapping community detection methods for biological applications, Newton International Fellowship, 98,000 started in February 2009
- Development of graph theoretic approaches to predict protein function by integrating large scale heterogeneous data, BBSRC New Investigator Grant, 517,000 started in October 2008

- BioSynLab: a software platform for the analysis of metabolic data, Park (Partnership in Accessible Research and Knowledge), 53,202 started in October 2007

Contact information

Prof. Alberto Paccanaro
Department of Computer Science
Royal Holloway, University of London
Egham, TW20 0EX

Phone: +44 1784 414239
Fax: +44 1784 439786
Email: alberto - at -
(replace -at- with @ )