Resources

Resources

Human Ageing Genomic Resources

Useful Links

We are committed to open access and sharing of data, methods, materials and publications resulting from our work.

HAGR

An important element of our work is the development of tools and methods for aiding research on the biology and genetics of ageing, in particular, computational tools like databases and algorithms. These are made available on the Human Ageing Genomic Resources (HAGR). Most notably, HAGR features six core databases: 1) the GenAge database of ageing-related genes; 2) the AnAge database of animal ageing and longevity, featuring >4000 species; 3) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; 4) the LongevityMap database of human genetic association studies of longevity with >500 entries; 5) the DrugAge  database of longevity-associated drugs or compounds; 6) the CellAge database of genes associated with cell senescence. Bioinformatics tools and software are also available on HAGR.

HAGR has been featured in Science (307:187) and Nature Reviews Genetics (5:1362), among other journals, and its resources have been cited hundreds of times.

Digital Ageing Atlas

A complementary resource to HAGR is the Digital Ageing Atlas, a web portal combining molecular, physiological and pathological age-related data. Our goal is for this portal to serve as the first centralized collection of human ageing changes and pathologies.

Genome Resources

To facilitate analyses and studies in long-lived, exotic animals we developed two genome resources: The Naked Mole Rat Genome Resource, focused on this unique long-lived, cancer-resistant species; and the Bowhead Whale Genome Resource focused on the longest living mammal.

Research Training and Tutorials

In addition to conducting innovative research, our group aims to train and inspire students to study the biology of ageing. Therefore, in parallel to HAGR, we maintain the senescence.info website, which is an educational resource on the science of ageing. It includes numerous tutorials, essays on the biology of ageing, a list of companies and researchers working on ageing, and other resources related to the study of ageing.

Students and researchers wishing to learn more about ageing are encouraged to visit senescence.info. Our group’s website also features extensive cross-links with senescence.info which thus serves as an additional source of information.

Tools for Functional Genomics

Although our research is primarily focused on ageing, we also develop broader bioinformatics tools for functional genomics and systems biology. In particular, we developed a co-expression tool called GeneFriends. Briefly, we constructed genome-wide co-expression maps for various organisms, including humans and mice.

Using a guilt-by-association method, we then developed the GeneFriends tool for candidate gene prioritization based on a seed list of genes (which can be associated with any process or disease of interest) and to derive putative functions of unstudied genes.

Supplementary

Materials and Data Sharing

For supplementary materials resulting from our research projects, please refer to our publications. If you require any data, reagent, protocol or software mentioned in a publication that is not provided on our website or publication please contact us.

We are committed to open access and sharing of data, methods, materials and publications resulting from our work.

joao pedro de magalhaes

Lab Links

Roster of lab meetings
GitHub

(lab data repositories, supplementary materials, etc.)

Lab wiki

at OpenWetWare

Maglab mailing-list

(for lab members only)

Birmingham & Liverpool Links

Birmingham Centre for Genome Biology
Centre for Computational Biology
Centre for Genomic Research
Centre for Integrated Research into Musculoskeletal Ageing (CIMA)
Genomics Birmingham
Library at University of Liverpool
Liverpool Neuroscience Group
NIHR Birmingham Biomedical Research Centre

External Colleagues and Collaborators (non-exhaustive list)

Alex Freitas

at the University of Kent.

Alexandra Stolzing

at Loughborough University.

Barshop Institute

in San Antonio with whom we have several collaborations.

Broad Institute

of Harvard and MIT.

Buck Institute

near San Francisco, with whom we collaborate.

Caleb Finch

at the University of Southern California.

Center for Neuroscience and Cell Biology

at the University of Coimbra in Portugal.

Chris Faulkes

at Queen Mary, University of London.

Collin Ewald

at ETH Zurich.

Evolutionary Genomics Lab

in Barcelona.

George Church

in Boston.

The Gorbunova & Seluanov Laboratory

at the University of Rochester.

Institute of Healthy Ageing

at University College London.

Jia Meng

at the Xi’an Jiaotong-Liverpool University in China.

Ocampo Lab

at the University of Lausanne.

Opazo Lab

at the Universidad Austral de Chile.

Peter Van Loo

at the Francis Crick Institute.

Rejuvenome

project from the Astera Institute.

Singapore Immunology Network
Systems Biology of Aging Group

led by lab alumni Robi Tacutu at the Romanian Academy.

Informational Sources and Useful Websites

Engage

resource mostly aimed at bioscience undergraduates but could be useful for first year graduate students as well.

Gulbenkian Training Programme in Bioinformatics

offering a number of training courses near Lisbon.

Kimball's Biology Pages
Java applets for power and sample size
National Academy Press

a US-based institution with many scientific books online.

OpenAcademics
The laws list
THE REALLY EASY STATISTICS SITE