Timothy
Ravasi

  Professor, Bioscience ​

  Office Location: Ibn Al Haytham (Building 2) · Level 4 · Room 4219​
  Email: timothy.ravasi@kaust.edu.sa
  Faculty lab website: http://systemsbiology.kaust.edu.sa


Research Keywords
Systems Biology, Genomics, Computational Biology, Complex Networks, Bioinformatics, Machine Learning


Research Interests
Prof. Ravasi is working to develop large-scale, computer-aided models of biological signaling, transcription regulatory networks, and regulatory pathways. He applies new experimental strategies and statistical frameworks with the aim to integrate, model, and visualize the enormous amount of measurements derived from genome-wide experiments, such as ultra-high-throughput DNA and RNA sequencing, proteins and mRNAs expression, and protein-protein interactions arising in the wake of Genome Projects. These tools are crucial to the success of systems biology, an approach that aims to understand biological systems as more than merely the sum of their parts. He is also using Massively Parallel Genomes Sequencing to explore the biodiversity in the Red Sea Ecosystem such as reef-building corals and marine sponges.


Main Techniques
Machine Learning, Graph Theory, Next Generation Sequencing (NGS), CAGE

Members of the Lab

Dr. Taewoo Ryu: Research Scientist theme is identifying transcriptional regulatory networks in marine organisms, especially in Red Sea coral, fish and sponge. In particular, he’s interested in elucidating spatiotemporal regulatory networks during development using genome-scale high-throughput data and integrative systems biology approaches.

Dr. Anders J. Eriksson: Postdoctoral fellow has a broad interest in understanding how different types of population dynamics and structure, combined with the effects of selection, mutation and recombination, shape the patterns of genetic variation observed in animal and human populations. A key complication with reconstructing the history of adaptation in a population is that neutral processes (such as bottlenecks and migration) can leave signatures in the genome that are very similar to those arising from natural selection.

Dr. Kondethimmanahalli Chandramouli (Chandra): Postdoctoral fellow research interest includes developmental biology, proteomics and transcriptomics. He is using 'omics’ technologies to identify genes/proteins function both in model and non-model organisms. His current research focused on understanding the proteomic patterns of Red Sea Barnacles larvae. The barnacle Balanus amphitrite is a worldwide distributed biofouler and a model species in marine ecology research.  While little is known about these species in Red Sea Arabian Peninsula, his research helps elucidate the adaptation strategy of these species in relation to evolutionary contexts.

Mr. Gregorio Alanis-Lobato: PhD candidate (Computer Sciences) is developing novel and powerful approaches for the prediction of interactions in biological and social networks.

Mr. Yanal Ghosheh: PhD candidate (Computer Sciences) is currently working in the field of bioinformatics. Interests include transcriptional networks and neuroscience.

Mr. Loqmane Seridi: PhD candidate (Computer Sciences) is interested in studying biological networks like regulatory networks and protein-protein interactions networks. My general research interests lie within the areas of System Biology, Machine Learning, Graph Theory, and Data Mining.

Ms. Dina Hajar: PhD Student candidate (Chemical Biological Engineering) is interested in Marine Natural Products that show great potential in upcoming drug development.  I am currently working in a joint project with Dr. Timothy Ravasi and Dr. Christian Voolstra on discovering new bioactive compounds from Red Sea marine animals able to inhibit the Dengue replicon system.  My objectives are to help improving my country and to invent new ways to improve industry, health and the natural environment in Saudi Arabia.

Ms. Maria Fernanda Contreras: PhD Student candidate (Chemical Biological Engineering) has always liked physics and biology. She started working as an undergrad student in a membrane biophysics project that included studying the thermodynamic properties of the lipids that form bacterial cell membranes in a biofilm. She is currently working in an interdisciplinary project with prof. Timothy Ravasi and prof. Jürgen Kosel that involves fabrication of micro and nano magnetic materials as well as genome-wide transcriptomic measurements. 

Ms. Sarah Al-Aqeel: PhD Student candidate (Biosciences) is interesting in studying the Biofouling organisms’ specifically the barnacle Balanus amphitrite of Red Sea Region. The barnacle is considered the most important biofouling model species due to its wide range of distribution worldwide as well as the comprehensive studies on its biology and chemistry.

Mr. Harris Mavromatis: PhD Student candidate (Biosciences) is using Ultra-high throughput RNA sequencing (RNA-seq) we simultaneously elucidate the gene expression and transcript diversity including non-coding regulatory RNA (e.g. microRNAs) of macrophages and their invading pathogen. These sequencing data are then integrated with other genome-wide datasets such as protein-protein and protein-DNA interactions to elucidate the regulatory networks underline the host/pathogen relationship.

Mr. (José) Efraín Pérez: PhD Student candidate (Biosciences) in his project, magnetic nanowires of different materials and aspect ratios are fabricated and then characterized using imaging techniques. As nanowires are currently being used for many biomedical applications, the main objective of the study is to look at their cytotoxicity on different cell tissues and to find the different effects they can have depending on concentration, cell type, or nanowire length or diameter. This could prove useful for future biomedical research in which magnetic nanowires are involved.

Mr. Michael Bogdan Margineanu: MS student (Biosciences) is currently contributing to an interdisciplinary project addressing the utilization of magnetic nanowires for cancer treatment. His goal is to understand the cellular mechanisms responsible for cell death upon treatment with the nanowires and the signaling pathways involved.
He’s also having an interest in population genetics and I am contributing in this regard to a collaborative project with University of Cambridge.

Ms. Marija Kupresanin: Laboratory Manager is responsible for the day-to-day operations of the Integrative Systems Biology Lab.  This includes maintaining a safe, organized, and functional environment for all researchers.


Selected Publications
FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70.

Cannistraci CV, Alanis-Lobato G, Ravasi T. Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. Bioinformatics. 2013 Jul 1;29(13):i199-209.

Cannistraci CV, Alanis-Lobato G, Ravasi T. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Sci Rep. 2013;3:1613.

Ravasi T, Cannistraci CV, Katayama K, Bajic VB, Tan K, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140-5, 744-752, 5 March 2010. (Faculty of 1000).

Carninci P, Kasukawa T, Katayama T, Gough J, Frith M, Maeda M, Oyama M, Ravasi T, et al. The Transcriptional Landscape ofthe Mammalian Genome. Science, 309:1559-1563, 2005. Faculty of 1000).