Sarah Daakour is a molecular biologist who earned her PhD in molecular biology from the University of Liege in Belgium. She has over 10 years of professional experience in protein signaling and interaction research. Her work has focused on identifying protein network perturbations in acute lymphoblastic leukemia and characterizing the tumor suppressor EXT-1 as a regulator of the Notch signaling pathway. She has published several journal articles and conference presentations on this topic.
National Resource for Networks Biology's TR&D Theme 3: Although networks have been very useful for representing molecular interactions and mechanisms, network diagrams do not visually resemble the contents of cells. Rather, the cell involves a multi-scale hierarchy of components – proteins are subunits of protein complexes which, in turn, are parts of pathways, biological processes, organelles, cells, tissues, and so on. In this technology research project, we will pursue methods that move Network Biology towards such hierarchical, multi-scale views of cell structure and function.
National Resource for Networks Biology's TR&D Theme 1: In this theme, we will develop a series of tools and methodologies for conducting differential analyses of biological networks perturbed under multiple conditions. The novel algorithmic methodologies enable us to make use of high-throughput proteomic level data to recover biological networks under specific biological perturbations. The software tools developed in this project enable researchers to further predict, analyze, and visualize the effects of these perturbations and alterations, while enabling researchers to aggregate additional information regarding the known roles of the involved interactions and their participants.
Whole Cell Volkswagen Summer School - a SEMS ProjectMarkusWolfien
"Combining standards for today's models"
A summary for a planned project for a summer school hosted by SEMS of University of Rostock in late 2014. We would like to transcribe the "Whole Cell - Mycoplasma genitalium Model" of Karr et al. (2012a) into standard formats to show its power and reusability.
For further information about the project and our group please visit:
>> https://sems.uni-rostock.de/workshops/volkwagen-summer-school-project/ <<
If you are interested in our project, please subscribe and get the latest news at:
>> https://groups.google.com/forum/#!forum/wholecell-symposium <<
Best regards,
Markus Wolfien
Agent-based and Chemical-inspired Approaches for Multicellular ModelsAndrea Omicini
The talk discusses the issue of finding suitable modelling approaches for capturing multicellular system dynamics. Computational models and tools envisioned by our group are presented. In particular the talk introduces (i) the Biochemical Tuple Spaces (BTS-SOC) coordination model adopted to simulate structured biochemical systems, (ii) MS-BioNET developed to efficiently simulate multi-compartment systems and (iii) ALCHEMIST developed for supporting chemical models of multi-compartment dynamic networks.
(Talk by Sara Montagna, CINI InfoLife, Pisa, Italy, 11/7/2014)
National Resource for Networks Biology's TR&D Theme 3: Although networks have been very useful for representing molecular interactions and mechanisms, network diagrams do not visually resemble the contents of cells. Rather, the cell involves a multi-scale hierarchy of components – proteins are subunits of protein complexes which, in turn, are parts of pathways, biological processes, organelles, cells, tissues, and so on. In this technology research project, we will pursue methods that move Network Biology towards such hierarchical, multi-scale views of cell structure and function.
National Resource for Networks Biology's TR&D Theme 1: In this theme, we will develop a series of tools and methodologies for conducting differential analyses of biological networks perturbed under multiple conditions. The novel algorithmic methodologies enable us to make use of high-throughput proteomic level data to recover biological networks under specific biological perturbations. The software tools developed in this project enable researchers to further predict, analyze, and visualize the effects of these perturbations and alterations, while enabling researchers to aggregate additional information regarding the known roles of the involved interactions and their participants.
Whole Cell Volkswagen Summer School - a SEMS ProjectMarkusWolfien
"Combining standards for today's models"
A summary for a planned project for a summer school hosted by SEMS of University of Rostock in late 2014. We would like to transcribe the "Whole Cell - Mycoplasma genitalium Model" of Karr et al. (2012a) into standard formats to show its power and reusability.
For further information about the project and our group please visit:
>> https://sems.uni-rostock.de/workshops/volkwagen-summer-school-project/ <<
If you are interested in our project, please subscribe and get the latest news at:
>> https://groups.google.com/forum/#!forum/wholecell-symposium <<
Best regards,
Markus Wolfien
Agent-based and Chemical-inspired Approaches for Multicellular ModelsAndrea Omicini
The talk discusses the issue of finding suitable modelling approaches for capturing multicellular system dynamics. Computational models and tools envisioned by our group are presented. In particular the talk introduces (i) the Biochemical Tuple Spaces (BTS-SOC) coordination model adopted to simulate structured biochemical systems, (ii) MS-BioNET developed to efficiently simulate multi-compartment systems and (iii) ALCHEMIST developed for supporting chemical models of multi-compartment dynamic networks.
(Talk by Sara Montagna, CINI InfoLife, Pisa, Italy, 11/7/2014)
Technology R&D Theme 2: From Descriptive to Predictive NetworksAlexander Pico
National Resource for Networks Biology's TR&D Theme 2: Genomics is mapping complex data about human biology and promises major medical advances. However, the routine use of genomics data in medical research is in its infancy, due mainly to the challenges of working with highly complex “big data”. In this theme, we will use network information to help organize, analyze and integrate these data into models that can be used to make clinically relevant diagnoses and predictions about an individual.
The NRNB has been funded as an NIGMS Biomedical Technology Research Resource since 2010. During the previous five-year period, NRNB investigators introduced a series of innovative methods for network biology including network-based biomarkers, network-based stratification of genomes, and automated inference of gene ontologies using network data. Over the next five years, we will seek to catalyze major phase transitions in how biological networks are represented and used, working across three broad themes: (1) From static to differential networks, (2) From descriptive to predictive networks, and (3) From flat to hierarchical networks bridging across scales. All of these efforts leverage and further support our growing stable of network technologies, including the popular Cytoscape network analysis infrastructure.
Summary: ENViz performs enrichment analysis for pathways and gene ontology (GO) terms in matched datasets of multiple data types (e.g. gene expression and metabolites or miRNA), then visualizes results as a Cytoscape network that can be navigated to show data overlaid on pathways and GO DAGs.
Background: Modern genomic, metabolomics, and proteomic assays produce multiplexed measurements that characterize molecular composition and biological activity from complimentary angles. Integrative analysis of such measurements remains a challenge to life science and biomedical researchers. We present an enrichment network approach to jointly analyzing two types of sample matched datasets and systematic annotations, implemented as a plugin to the Cytoscape [1] network biology software platform.
Approach: ENViz analyses a primary dataset (e.g. gene expression) with respect to a ‘pivot’ dataset (e.g. miRNA expression, metabolomics or proteomics measurements) and primary data annotation (e.g. pathway or GO). For each pivot entity, we rank elements of the primary data based on the correlation to the pivot across all samples, and compute statistical enrichment of annotation sets in the top of this ranked list based on minimum hypergeometric statistics [2]. Significant results are represented as an enrichment network - a bipartite graph with nodes corresponding to pivot and annotation entities, and edges corresponding to pivot-annotation pairs with statistical enrichmentscores above the user defined threshold. Correlations of primary data and pivot data are visually overlaid on biological pathways for significant pivot-annotation pairs using the WikiPathways resource [3], and on gene ontology terms. Edges of the enrichment network may point to functionally relevant mechanisms. In [4], a significant association between miR-19a and the cell-cycle module was substantiated as an association to proliferation, validated using a high-throughput transfection assay. The figures below show a pathway enrichment network, with pathway nodes green and miRNAs gray (left), network view of the edge between Inflammatory Response Pathway and mir-337-5p (center), and GO enrichment network with red areas indicating high enrichment for immune response and metabolic processes (right).
Predicting peptide interactions using protein building blocksPeter Vanhee
PhD thesis submitted in partial fulfilment of the requirements for the degree of Doctor in Bio-engineering Sciences. Peter Vanhee, 4th March 2011. Free University of Brussels.
Presentation for Network Biology SIG 2013 by Gang Su, University of Michigan, USA. “CoolMap Cytoscape App: Flexible Multi-scale Heatmap-Driven Molecular Network Exploration”
We offer complete interior design solution, customized products, and services to suit all needs of a customer. Our services include residential, corporate and commercial interior designing. We also handle architectural services, contracts and turnkey projects.
SRE Design renders a stunning look and positive environment to your home and office with it's innovative design and creative ideas. We offer complete interior designing solution and create a signature look that suits your needs and reflects your personality.
Technology R&D Theme 2: From Descriptive to Predictive NetworksAlexander Pico
National Resource for Networks Biology's TR&D Theme 2: Genomics is mapping complex data about human biology and promises major medical advances. However, the routine use of genomics data in medical research is in its infancy, due mainly to the challenges of working with highly complex “big data”. In this theme, we will use network information to help organize, analyze and integrate these data into models that can be used to make clinically relevant diagnoses and predictions about an individual.
The NRNB has been funded as an NIGMS Biomedical Technology Research Resource since 2010. During the previous five-year period, NRNB investigators introduced a series of innovative methods for network biology including network-based biomarkers, network-based stratification of genomes, and automated inference of gene ontologies using network data. Over the next five years, we will seek to catalyze major phase transitions in how biological networks are represented and used, working across three broad themes: (1) From static to differential networks, (2) From descriptive to predictive networks, and (3) From flat to hierarchical networks bridging across scales. All of these efforts leverage and further support our growing stable of network technologies, including the popular Cytoscape network analysis infrastructure.
Summary: ENViz performs enrichment analysis for pathways and gene ontology (GO) terms in matched datasets of multiple data types (e.g. gene expression and metabolites or miRNA), then visualizes results as a Cytoscape network that can be navigated to show data overlaid on pathways and GO DAGs.
Background: Modern genomic, metabolomics, and proteomic assays produce multiplexed measurements that characterize molecular composition and biological activity from complimentary angles. Integrative analysis of such measurements remains a challenge to life science and biomedical researchers. We present an enrichment network approach to jointly analyzing two types of sample matched datasets and systematic annotations, implemented as a plugin to the Cytoscape [1] network biology software platform.
Approach: ENViz analyses a primary dataset (e.g. gene expression) with respect to a ‘pivot’ dataset (e.g. miRNA expression, metabolomics or proteomics measurements) and primary data annotation (e.g. pathway or GO). For each pivot entity, we rank elements of the primary data based on the correlation to the pivot across all samples, and compute statistical enrichment of annotation sets in the top of this ranked list based on minimum hypergeometric statistics [2]. Significant results are represented as an enrichment network - a bipartite graph with nodes corresponding to pivot and annotation entities, and edges corresponding to pivot-annotation pairs with statistical enrichmentscores above the user defined threshold. Correlations of primary data and pivot data are visually overlaid on biological pathways for significant pivot-annotation pairs using the WikiPathways resource [3], and on gene ontology terms. Edges of the enrichment network may point to functionally relevant mechanisms. In [4], a significant association between miR-19a and the cell-cycle module was substantiated as an association to proliferation, validated using a high-throughput transfection assay. The figures below show a pathway enrichment network, with pathway nodes green and miRNAs gray (left), network view of the edge between Inflammatory Response Pathway and mir-337-5p (center), and GO enrichment network with red areas indicating high enrichment for immune response and metabolic processes (right).
Predicting peptide interactions using protein building blocksPeter Vanhee
PhD thesis submitted in partial fulfilment of the requirements for the degree of Doctor in Bio-engineering Sciences. Peter Vanhee, 4th March 2011. Free University of Brussels.
Presentation for Network Biology SIG 2013 by Gang Su, University of Michigan, USA. “CoolMap Cytoscape App: Flexible Multi-scale Heatmap-Driven Molecular Network Exploration”
We offer complete interior design solution, customized products, and services to suit all needs of a customer. Our services include residential, corporate and commercial interior designing. We also handle architectural services, contracts and turnkey projects.
SRE Design renders a stunning look and positive environment to your home and office with it's innovative design and creative ideas. We offer complete interior designing solution and create a signature look that suits your needs and reflects your personality.
گستردگی جغرافیایی کشورها از یکسو، کمبود نیروی انسانی متخصص در علوم مختلف و افزایش هزینههای کاری از سوی دیگر، منجر به عدم دسترسی سازمانها و شرکتها به همة منابع مورد نیاز شده است.
ویدئوکنفرانس یک فناوری منحصر به فرد است که برقراری ارتباط صوتی و تصویری (به صورت زنده) افراد را در مکانهای مختلف با فواصل مختلف امکانپذیر مینماید.
هزینههای سرسامآور جابجایی اساتید، متخصصین و مدیران مجموعهها برای برگزاری نشستهای گوناگون به صورت هزینههای آشکار و نیز از دستدادن بخش قابل توجهی از زمان، نیرو و بازده کاری و فکری این افراد، به عنوان هزینههای پنهان، نیاز بسیاری را برای به کارگیری از فناوریهای مدرن ارتباطی به خصوص ویدئوکنفرانس ایجاد کرده است.
در کنار امکانات ارتباطی ویدئوکنفرانس، با بهرهگیری از این سیستم میتوانید در یک زمان واحد در چندین مکان حضور داشته باشید. امکانی که تنها با استفاده از این تکنولوژی میسر خواهد بود.
Pathology is being disrupted by Data Integration, AI & Blockchain
curriculum vitae-Sarah daakour
1. Sarah Daakour
PhD in molecular biology
Brussels, Belgium
Mobile: +32.485.22.75.99
Email: sarah.daakour@gmail.com
Education
2010 - 2016: Ph. D. in Biochemistry, Molecular and cellular biology,
Bioinformatics and Modelling, University of Liege, Liege,
Belgium
2008 - 2009: MS in “Structure - Interaction of Macromolecules
and Functional Genomics”, faculty of science - Saint Joseph
university , Beirut, Lebanon
2004 - 2008: Maitrise in Biochemistry, Lebanese University, Beirut, Lebanon
Professional experience
2010 - 2015: Ph. D. Candidate, Laboratory of Protein Signaling and Interaction
- GIGA, Liège, Belgium
Topic: Perturbations of interactome networks in acute lymphoblastic
leukemia: identification of EXT-1 tumor suppressor as a Notch pathway
regulator
Dec. ’08 – Jun. ’09: MS Intern, Institut de Génétique Humaine
(IGH – CNRS UPR1142), Montpellier, France
Topic: Characterization of retrotransposon LINE-1
Ribonucleoprotein Particles.
Mar. - Jul. ’08: Maitrise final project, Lebanese University, Beirut, Lebanon
Topic: Molecular mechanisms of cardiac arrhythmias.
Honors
2010 – 2015: Ph. D. fellowship (Télévie) from National Funds for Scientific
Research
(FRS-FNRS)
Ph. D. fellowship: Winner of the Léon Frédéricq Fund– 2014 projects
2. Services
Conference Organization
o 15th International Conference on Human Retrovirology : HTLV and Related
Retroviruses; June 2011; Leuven and Gembloux; Belgium.
Training Master graduates
o Training and guiding Master I student, for Master thesis project - Laboratory
of Protein Signaling and Interaction - GIGA, Liège, Belgium.
Technical skills
Ø Laboratory skills: High throughput yeast two-hybrid screening, western
blot analyses, immunofluorescence and confocal microscopy, PCR and
quantitative PCR, cloning, cell culture, protein network analyses.
Ø Software and tools: Microsoft, Cytoscape, Endnote, Photoshop,
ImagJ, Graphpad.
Ø Publishing: Office Suite
Ø Languages: Arabic, English, French.
Publications
Journal Publications
o Simonis N, Rual JF, Lemmens I, Boxus M, Hirozane-Kishikawa T, Gatot
JS, Dricot A, Hao T, Vertommen D, Legros S, Daakour S, Klitgord N, Martin
M, Willaert JF, Dequiedt F, Navratil V, Cusick ME, Burny A, Van Lint C, Hill
DE, Tavernier J, Kettmann R, Vidal M, Twizere JC; Host-pathogen
interactome mapping for HTLV-1 and -2 retroviruses. Retrovirology.
2012 Mar.
o Bergiers I, Lambert B, Daakour S, Twizere JC, Rezsohazy R; Hox protein
interactions: screening and network building, Methods Mol Biol. 2014.
o Hajingabo LJ, Daakour S, Martin M, Grausenburger R, Panzer-Grümayer R,
Dequiedt F, Simonis N, Twizere JC; Predicting interactome networks
perturbations in human cancer: application to gene fusions in acute
lymphoblastic leukemia. Mol Biol Cell. 2014 Dec.
o Mansour MR, Reed C, Eisenberg AR, Tseng JC, Twizere JC, Daakour S,
Yoda A, Rodig SJ, Tal N, Shochat C, Berezovskaya A, DeAngelo DJ, Sallan SE,
4. o Sarah Daakour, Léon Hajingabo, Franck Dequiedt, Nicolas Simonis, and Jean-
Claude Twizere; Systematic interactome mapping of acute lymphoblastic
leukemia cancer gene products reveals EXT-1 tumor suppressor as a
Notch1 and FBWX7 common interactor; Signal transduction seminar; Liège;
Belgium; May 2011.
o Sarah Daakour, Léon Hajingabo, Franck Dequiedt, Nicolas Simonis, and Jean-
Claude Twizere; Systematic interactome mapping of acute lymphoblastic
leukemia cancer gene products reveals EXT-1 tumor suppressor as a
Notch1 and FBWX7 common interactor; «Séminaire de jeunes chercheurs -
Télévie 2012»; December 2011.
o Sarah Daakour, Léon Hajingabo, Franck Dequiedt, Nicolas Simonis, and Jean-
Claude Twizere; Systematic interactome mapping of acute lymphoblastic
leukemia cancer gene products reveals EXT-1 tumor suppressor as a
Notch1 and FBWX7 common interactor; Proteomics and Interactomics in
Signaling Networks; Gent University ; may 2012.
o Sarah Daakour, Léon Hajingabo, Franck Dequiedt, Nicolas Simonis, and Jean-
Claude Twizere; Systematic interactome mapping of acute lymphoblastic
leukemia cancer gene products reveals EXT-1 tumor suppressor as a
Notch1 and FBWX7 common interactor; «Signal Transduction Seminar»;
February 2013; Liège; Belgium.
o Sarah Daakour, Léon Hajingabo, Franck Dequiedt, Nicolas Simonis, and Jean-
Claude Twizere; Systematic interactome mapping of acute lymphoblastic
leukemia cancer gene products reveals EXT-1 tumor suppressor as a
Notch1 and FBWX7 common interactor; au “Séminaire de jeunes chercheurs
– Télévie”; 2013; Brussels, Belgium.
References
• Prof. Jean-Claude Twizere, Molecular Biology professor at Université de Liège;
Belgium.
Email: jean-claude.twizere@ulg.ac.be
• Prof. Frank Dequiedt, Molecular Biology professor at Université de Liège;
Belgium.
Email: fdequiedt@ulg.ac.be
• Dr. Nicolas Simonis, Bioinformatics scientist at Institut de Pathologie et de
Génétique, Brussels, Belgium.
Email: nicolassimonis@gmail.com