Speakers

 

Miguel Andrade

Johannes Gutenberg University of Mainz, DE

Website

Miguel Andrade received his PhD in Biochemistry at the Universidad Complutense de Madrid in 1994. He trained at the post-doctoral level at the European Molecular Biology Laboratory in Heidelberg and Cambridge with Chris Sander and Peer Bork. His postdoctoral studies involved the development and application of computational methods for the analysis of gene and protein function and structure. He has led computational biology groups at the Ottawa Health Research Institute in Ottawa and at the Max Delbrück Center for Molecular Medicine in Berlin. Since April 2014 he is member of the Faculty of Biology of the Johannes Gutenberg University and of the Institute of Molecular Biology (Mainz). His group focuses on computational methods to research the molecular and genetic components of human disease.

 

Aidan Budd

EMBL Heidelberg, DE

Website

Aidan Budd is a Senior Project Manager for Bioinformatics at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he works in the group of Toby Gibson. His work focuses on managing a range of projects linked to community building and training in bioinformatics. In the past, his research focused on protein sequence analysis and phylogenies. He is one of the organisers of Heidelberg Unseminars in Bioinformatics hub-hub.de. After studying for his undergraduate degree in Zoology at Cambridge University, Aidan worked as a research assistant with Torsten Krude in the lab of Ron Laskey at the Gurdon Institute in Cambridge. He went on to obtain his PhD at EMBL Heidelberg focusing on the evolution of gene families expected to have similar evolutionary histories. Between completing his PhD and rejoining EMBL, Aidan worked as the commissioning editor for life science books at Wiley-VCH in Weinheim, Germany.

 

Holger Dinkel

EMBL Heidelberg, DE

Website

Holger Dinkel is a member of staff at the European Molecular Biology Laboratory (EMBL). He is a Biologist by training and a computer scientist by passion, fascinated by the biology of short linear motifs. He started working on these small protein modules during his PhD by studying the interplay between linear motifs and globular domains. Since 2009 he has been working at the European Molecular Biology Laboratory as a software engineer, developing methods to study short linear motifs. He is also taking care of the ELM, Phospho.ELM and Switches.ELM databases & web services. He is focused on the technical aspects of science and loves to use & teach Linux, Python, git, Django and more.

Nadezhda T. Doncheva

Max Planck Institute for Informatics, Saarbrücken, DE

Website

Nadezhda is a PhD student at the Max Planck Institute for Informatics (MPII), Saarbrücken, Germany. She received her MSc in Bioinformatics from the Saarland University, Germany, in 2009, after completing her thesis under the supervision of Mario Albrecht in the Department of Computational Biology and Applied Algorithmics at the MPII. Nadezhda developed a novel method for the interactive analysis and visualization of residue interaction networks for understanding complex protein structure-function relationships. Her research involves the development of methods and accompanying software tools for the analysis and visualization of molecular interaction networks with a special focus on visual analytics and their application to biomedical data for understanding complex diseases. In particular, she has been using Cytoscape for a number of years both as user and developer.

Zsuzsanna Dosztányi

Department of Biochemistry, Eötvös Loránd University, Budapest, HU

Website

Zsuzsanna Dosztányi is just starting her own lab at the Department of Biochemistry at the Eotvos Lorand University in Budapest. Her primary research interests focus on instrinsically disordered proteins. She developed the IUPred method for predicting disordered regions and the ANCHOR method for predicting disordered binding regions in proteins. Her current research follows three main directions: describing the thermodynamic basis of protein disorder that would enable a more detailed description of this phenomenon; developing methods to identify functional regions in IDPs; understanding the role of disordered proteins in diseases. Zsuzsanna graduated from the Eötvös Loránd University in Budapest with a degree in physics and biophysics. She worked in the lab of István Simon at the Institute of Enzymology investigating diverse aspects of proteins using computational methods. She also obtained post-doc experience in the lab of Andrew Torda at the Australian National University and the lab of Burkhard Rost at Columbia University.

Toby Gibson

EMBL Heidelberg, DE

Website

Toby Gibson is at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. He studied Biology at Edinburgh University and did his PhD with Bart Barrell at the LMB, Cambridge. He is a computational biologist: i.e. a biologist who finds computers to be useful adjuncts to biological research. He is a co-developer of the widely used Clustal series of multiple sequence alignment software. He oversees the development of ELM, the Eukaryotic Linear Motif resource (http://elm.eu.org/) devoted to protein sequence motifs involved in cell signalling and regulation. Toby is currently fascinated by the developing structure-function paradigm for the massively interacting hub proteins such as P53, IRS-1, sundry AKAPs and many, many more. These are characterised by large natively unstructured protein segments that are repositories of abundant "linear motifs" - short regulatory sites that interact with other proteins. These low affinity interacting modules allow for co-operative and combinatorial regulatory interactions in the assembly of large regulatory protein complexes in response to signals received at the cell membrane. Multiple input parameters can be sampled by direct interaction so that regulatory decisions are made by in-complex molecular switching (http://switches.elm.eu.org) often returning multiple outputs into the regulatory networks. This discrete switching model contrasts with the more prevalent and diffusionist signalling cascade metaphor. The latter perspective would seem to be in need of replacement by a model that allows for more spatially and temporally discrete operations.

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research,

University of Copenhagen, DK

Website

Lars Juhl Jensen is professor and group leader at the NNF Center for Protein Research in Copenhagen as well as co-founder and scientific advisor of Intomics A/S. His group focuses on using data integration and text mining for network analysis of cellular regulation and phenotypes, especially in the context of diseases. He is also heavily involved in the development several bioinformatics web resources, the most famous of which is the STRING database.

John "Scooter" Morris

University of California San Francisco, USA

Website

John "Scooter" Morris is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. Before finding his home in academia, he was a Distinguished Systems Architect at Genentech, Inc., where for 19 years, he participated in the joys and trials of life in industry. He received his Ph.D. in Medical Information Science from UCSF in 1990, and has bachelors degrees in Physics, Biology, and Computer Science from UC Irvine. Scooter is a member of the Cytoscape core development team, and author of several Cytoscape plugins and core features. In his "spare time" he is the Vice President for Conferences of the ACM Special Interest Group for Computers and Human Interaction (SIGCHI) and he is known to voluntarily jump off perfectly good boats near Alcatraz Island for a brisk swim to shore.

Nicola Mulder

University of Cape Town, ZA

Website

Associate Prof Mulder heads the Computational Biology Group at the University of Cape Town (UCT). After her PhD in Medical Microbiology, she spent 8 years at the European Bioinformatics Institute (EBI) in Cambridge, moving into the area of bioinformatics. At UCT A/Prof Mulder works in the area of bioinformatics of infectious diseases, including pathogen and host genomics and biological networks, human variation studies and disease associations. The group also provides bioinformatics support and training for postgraduate students and local researchers. A/Prof Mulder is coordinating H3ABioNet, a pan-African Bioinformatics Network, which is working on building bioinformatics capacity in Africa.

 

Marco Punta

Wellcome Trust Sanger Institute and EMBL-EBI, UK

Website

Marco Punta is Project Leader for the Pfam protein family database at the Wellcome Trust Sanger Institute and the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Marco has a degree in Physics from the University of Rome “La Sapienza” and a Ph.D. in Biophysics from the International School for Advanced Studies (SISSA) in Trieste, Italy. He did his post-doctoral work in the lab of Prof. Burkhard Rost at Columbia University New York, USA. Marco’s background includes development of prediction methods for protein structural and functional features (transmembrane helices, residue contacts, intrinsic disorder, metal binding), structural genomics (structure-based annotation of protein function and development of target selection pipelines), database management (Pfam) and application of remote homology searches to compositionally biased regions and to analysis of complete proteomes. Pfam Website.

 

Gustavo Salazar

University of Cape Town, ZA

Website

Gustavo was awarded his bachelors degree in Systems engineering in 2002 at the Universidad del Valle in Colombia, and for over 10 years he has taken part of multiple software projects for both academia and private companies. Gustavo has developed software as a Freelancer for companies in Colombia, USA, South Africa and the UK. He moved to South Africa in 2007 as a member of the central node at National Bioinformatics Network located in Cape Town. He started his MSc in Computer Science in 2008 and finished in 2010, the topic of this research was about collaborative annotations for biological data. The collaborations held during this time allowed him to visit the European Bioinformatics Institute and work there as an intern at the proteomics Services team. Gustavo started a PhD in Bioinformatics under the supervision of Dr. Nicola Mulder at the end of 2010, the current focus of this research is on the visualization of protein-protein interactions using recent web technologies such as HTML5

 

Natasha Wood

South African National Bioinformatics Institute,

Cape Town, ZA

Website

Natasha is a postdoctoral research fellow at the South African National Bioinformatics Institute located at the University of the Western Cape. She received her PhD in 2010 from the University of Cape Town for research on the evolution of HIV protein coding sequences during the early stages of infection. Her current work is focused on understanding the molecular dynamics of the HIV envelope protein under different glycosylated states. Further information is available at http://hiv.sanbi.ac.za/.