Early Stage Researcher
Senior Engineer and PhD student in the Immunobiology of Infections Group at Institut Pasteur de Tunis.
I am involved in the Laboratory management according to quality standards and application of biosecurity procedures, and in this frame, I attended different workshops and courses on the Management of Biological Risk, Biosafety and Biosecurity, Good Experimental and Ethical Practices on Laboratory Animals. During the last years, I have acquired experience in cell and parasite culture, molecular biology techniques and handling of laboratory animals.
Early Stage Researcher
I am currently a PhD student at the Laboratory of Transmission, Control and Immunobiology of Infections, Immunobiology of Leishmaniasis in Institut Pasteur de Tunis. I am involved in exploring human macrophage-Leishmania conflict through the analysis of host response modulation upon infection but also genomics and transcriptomics features of hyper-virulent and hypo-virulent isolates of Leishmania parasites using the high-throughput data generated from different experiments we are performing in our group. During the last years, I attended several courses and workshops on High-throughput Next Generation Sequencing where I acquired more knowledge and expertise on common tools and workflows used in analyzing NGS data including sequence alignment tools, visualization tools, genome browsers and comparison tools, python and R. On the other hand, I have acquired experience in cell and parasitic culture and molecular biology techniques.
Early Stage Researcher
PhD student in the Immunobiology of Infections Group at Institut Pasteur de Tunis.
I am currently focusing on the study of Leishmania major escape mechanisms from the innate immune response. I have been able to attend several courses such as innate immunity and infectious diseases course at the Institut Pasteur de Paris, the IUISYFAIS course Ethiopia 2017 witch is about neglected tropical diseases. I followed a training on biosecurity and good laboratory practices and flow cytometry workshop. Since joining the laboratory, I have gained experience in cell and parasite culture as well as some molecular biology techniques.
Oussama began to work at IPT in March 2011 as a Project Manager in technology transfer. His mission is to enhance the activities of the Institute and to promote commercial development of inventions and industrial partnering. Before joining Institut Pasteur de Tunis, Oussama has worked at the Technology Transfer Office, FIST (France Innovation Scientifique et Transfert), of the CNRS (National Center of Scientific Research) in Paris (France) for one year, where he was also a Project Manager in Transfer & Licensing (Life Sciences). Oussama holds a research Masters of Sciences and Technologies: Integrative Physiology, with a specialty in comparative physiology and marine adaptation and a professional Masters in Health Law Specialty: Industrial Property and Health Industries. Oussama is also a PhD candidate since 2013, and his focus area is knowledge and technology transfer from public health institutes (biotech related to infectious diseases). Oussama is also an AUTM member (Association of University Technology Managers) since 2015 and he participated to the last AUTM Annual Meeting in San Diego (Feb. 2016).
Having successfully completed different national and international studies in Epidemiology, Public Health, Environmental health impact assessment, biostatistics, and infectious diseases, I have gained a wealth of theoretical knowledge that I consolidated by the different practical works and researches I undertook as part of my job as Associate Professor of Epidemiology and Preventive Medicine, Faculty of Medicine of Tunis and Department of Epidemiology/ Laboratory of Transmission, Control and Immunobioogy of Infections at Institut Pasteur de Tunis. Indeed, during the past 8 years I contributed to the publication of around thirty articles. My first publications were about several public health issues such as evaluation of epidemiological surveillance systems and quantitative risk assessment of the short-term impact of climate change on health. Later on I concentrated on the study of Zoonotic Cutaneous Leishmaniasis (ZCL). I conducted collaborative research that address the epidemiology and temporal dynamics or the impact of climate factors on ZCL transmission risk and the molecular cell biology of Leishmania parasites isolated from different stages of the parasite life cycle: patients, reservoir hosts and sand fly vectors.
I am a clinical trial coordinator, working at Epidemiology Department IPT since 1993. I was involved in several research projects as a coordinator, especially in the area of CL clinical trial. As an early stage researcher, I am interested recently in Socio-psychological impact of CL. In 2016-2017, I was the Co-PI of the Tunisian part of an international multicentric research study intitled: “Disease experience of Cutaneous Leishmaniasis patients”, sponsored by WHO-TDR.
I am an Assistant Professor in the Laboratory of Transmission Control and Immunobiology of Infection (LTCII) at Pasteur Institute of Tunis. My research activities consist on analysis of the Human immune responses during infection by the parasite Leishmania, specifically the cytotoxic immune response and identification of its role in resistance to re-infection. This was done using large scale prospective longitudinal study of L. major transmission analyzing the effect of host factors (tested at the baseline of the cohort follow-up) on the resistance against ZCL. In addition to analysis of the immune correlates of protection I am involved in several study concerning the characterization and/or validation of new vaccine candidates of parasite origin. This was made in the context of collaborative projects aimed to develop a vaccine against leishmaniasis: the first one was the LeishDNAvax, consisting in the development of a DNA vaccine composed of five Leishmania antigens, which appears protective in rodent model of infection, the second one consist on vaccination with PEPCK which induced strong durable cross-species protection in both resistant and susceptible mice. All these studies in which I have been involved allowed me to gain an expertise in studying antigenicity and immunogenicity of several potential vaccine candidate antigens and analyzing the efficacy of vaccine.
Over twenty (20) years of significant and progressive veterinary scientific research activities. In current position, as Veterinary Senior at IPT, my research activities are focused on the development of bio-sensors as new gender tools for detection/diagnostic of infectious diseases that target rapidly, with simplicity and in field condition, the majority of pathogens biomarkers (proteomic, genomic, metabolomic and volatolomic). In this research area, I focused on developing electrochemical biosensors for diagnostic of zoonotic infectious diseases. We developed a label-free impedimetric method for immune-electrochemical detection of pathogens virus (avian influenza virus and rabies virus) and label free square wave method for immune-electrochemical detection of M. tuberculosis virulent factor for tuberculosis diagnostic. We developed a simple chrono-amperometric method for leishmania parasite detection and quantification, a promising tool for theranostic and diagnostic of leishmaniasis in field conditions. Actually, we work on a research program for the development of an electronic nose as a noninvasive breath test for early diagnosis of tropical diseases/leishmaniasis. My research activities included also eco-epidemiological studies of zoonotic infectious diseases focusing on animal's reservoirs. This expertise was used to undertake clinical trials of veterinary use rabies vaccines (Rabies DNA vaccine and cell culture vaccine) newly developed by our research team in order to improve the control of animal rabies, a disease still present in Tunisia.
I am Assistant Professor, working at IPT since 2013. My work focalizes on rodents and small mammals reservoir hosts of Leishmania parasites and the genetic of strains isolated from these reservoirs.
Experienced Researcher – WP leader (WP5)
The work I am involved in is essentially devoted to understand the role played by partners involved in the parasitic cycle of Leishmania (the human host and the parasite) and how they interact together to determine in) finae the clinical expression of the disease. As part of different projects that have been conducted in the laboratory, I was in charge of further identifying genes of human infected macrophages and of infecting parasites, whose differential modulations account for the spectrum of responses to Leishmania isolates infection. Moreover, we are screening for molecular signatures of field parasites showing a contrasted high/low profiles of severity of the cutaneous disease in patients. The studies that I conducted are mainly based on high-throughput genomics and transcriptomics. This allowed me to gain an expertise not only in performing large-scale genomic (DNA-seq) and transcriptomic (RNA-seq) experiments in terms of sample preparation, but also in parallel data analysis using bioinformatics tools and methods. Developing my expertise in performing high-throughput data analysis and in analysing them using bioinformatics tools, allowed me to be involved in different scientific projects as PI or collaborator, but also to be involved in several training activities in international courses and workshops.
A computer scientist by background, Amel Ghoulia earned a PhD in Bioinformatics from the LIRMM laboratory, Montpellier, France. During her PhD she worked on developing new tools to improve eukaryotic pathogens functional annotation. She is currently a bioinformatician at Institut Pasteur de Tunis, where she works on the frame of the pan-African bioinformatics network H3ABionet supporting researchers and their projects while developing bioinformatics capacity throughout Africa.
Najet Hadhri is in charge of fundraising and scouting. She is responsible for identifying funding opportunities, matching it with scientific interests, providing support for preparation and submission of project applications to national and international funding agencies. She also contributes to managing research information in order to facilitate data sharing, research monitoring and providing metrics and KPI on publications, projects, and collaborations. Recently, she was appointed as National Focal Point for the European Commission H2020-SWAFS (Sciences and with society) program.
I received my PhD degree in Parasitology from the URCA-University of Reims Champagne Ardenne France in 2013 (Contribution to the study of leishmaniasis in Tunisia: Phlebotomus, parasites, reservoirs and human). I am since 2015 a Postdoc of Parasitology and Medical Entomology at Medical Epidemiology Department/Laboratory of Transmission, Control and Immunobiology of Infections (LR11IPT02) under Prof. Afif Ben Salah supervision. My research interests are focused on Parasitology and Medical Entomology (Human cutaneous leishmaniasis, canine leishmaniasis, Molecular Biology, morphological identification of sandflies). I have published 21 research articles.
Dhafer is a group Leader at the Laboratory of Transmission, Control and Immunobiology of Infections (LR11IPT02) at Institut Pasteur de Tunis (IPT). After obtaining his PhD in Immunology and Molecular Biology, he held several postdoctoral positions: Institute Pasteur, Paris, France and Harvard Medical School, Boston, USA, specializing in Immunology. He is currently heading the Group Immunobiology of Infections that focuses on the use of several approaches to investigate host-pathogen interactions.
- PhD in Immunology (2014), Faculty of Sciences, Tunis El Manar University, Tunisia.
- MA in Microbiology (2014), Faculty of Sciences, Tunis El Manar University, Tunisia.
- University degree in “Proteins Biochemistry (2011), Paris-Diderot University, France.
- Postdoctoral researcher since 2013 in Laboratory of transmission control and immunobiology of Infections
- H index: 6
- Research Project: Combined Parasite and Vector-saliva Multiantigen Vaccine against Human Leishmaniasis
- Postdoctoral fellow for two months in 2014 at the laboratory of malaria and vector research NIAID/NIH (Washington, USA)
I have an academic background in management with the specialization in finances. This education was completed by diverse trainings and courses in related fields such as taxing, trading and commerce. Through my actual position at the Institut Pasteur de Tunis, my duties include, but are not restricted, to the administrative and financial management of Scientific Programs and Projects, Clinical Trials and Institutional Training Centers. Throughout these years I was focusing on gaining more through different trainings and workshops e.g., Leadership at Harvard University, USA, Project Management, Knowledge Academy, NY, USA, Professional Active Planning, Tunisia, Placement Responsibility of the Investigator in the Process of a Clinical Study, IFIS, France, Grant writing and Grants Policy and Management, NIH, USA.
Early Stage Researcher
I am a veterinary principal senior technician, working in Institut Pasteur de Tunis since 2014. My work focused on the different elements of Leishmaniasis life cycle including entomological aspects and reservoir hosts’ ecology.
Early Stage Researcher
I am a Senior Laboratory Technician in Biology, working in Institut Pasteur de Tunis since 2014. My work focuses on the different elements of Leishmaniasis life cycle including entomological aspects and reservoir hosts’s ecology.
I am an adjunct biologist working at IPT in the MEEP laboratory directed by Pr Ikram Guizani. I got my PhD in Biology (Genetics and molecular Biology) on June 2008, working on the Leishmania eukaryotic initiation factor LeIF, also considered as a natural Th1 adjuvant. Under the supervision of Pr. Ikram Guizani, I have characterized this antigen on phylogenetic, genetic, biochemical and immunological levels. These results were published as 3 articles in international journals (FEBS journal, and Parasite Immunology). Then I pursued a postdoctoral training at Hellenic Pasteur Institute, laboratory of cellular Immunology under supervision of Dr Eleni Dotsika, where I better characterized the adjuvant effect of LeIF. I also developed in vivo mice models of vaccination against leishmaniasis using LeIF-sensitized Dendritic cells (Barhoumi et al., in preparation) and I demonstrated the potential of LeIF as a novel anti-infective therapeutic molecule (Koutsoni & Barhoumi et al., 2014). I also pursued a postdoctoral training at the NIH in the laboratory of parasitic diseases under the supervision of Dr David Sacks and Michael Grigg, where I developed a new MLST scheme for Leishmania spp genetic typing (Barhoumi et al., in preparation). I collaborated on this project with IPA team. Currently, lab colleagues and myself are characterizing the mechanism of resistance gained by macrophage exposed to LieIF/IFNg by analyzing the gene expression using RNAseq approach.
I am an Engineer at Institut Pasteur de Tunis conducting research activities in the "Laboratory of Molecular Epidemiology and Experimental Pathology", directed by Dr. Ikram GUIZANI. I got my research Master Degree in "Genetics" in 2005, my engineering diploma in "Agronomy" in 2003 and my bachelor in "Experimental Sciences section" in 1998.
My research activities started as part of a collaborative international project supported by the Institut Pasteur PTR program entitled: "Structural and Experimental approaches to validate Leishmania LeIF antigen as drug target and immunotherapeutic molecule". In this context, I have established the Leishmania infantum model in PMA activated THP1 cells to screen and characterize the biological activities of a selection of small molecules that target the eukaryotic initiation factor eIF4A in Leishmania (LeIF) for their effect on viability of promastigote and amastigote forms, their infectivity and cytotoxicity on THP1 cells. I am first author with equal contribution on this work, published in January 2018 in PLoS-NTD journal where we describe novel small leishmanicial molecules (Harigua-Souiai et al., 2018); and first author on a second work in preparation where we describe the inhibitory effect of Leishmania LeIF antigen on the L. infantum macrophage infection in vitro (Bassoumi-Jamoussi et al., in preparation). We extend here the study to investigate the effect of LeIF in this model on the gene expression in infected cells.
I am a molecular biologist working as a permanent scientist researcher at Institut Pasteur of Tunis at the laboratory of Molecular Epidemiology and Experimental Pathology (MEEP) directed by Dr. Ikram Guizani. I joined the laboratory in June 2013 and since this date my research interest focuses on developing and implementing novel rapid point-of-care molecular diagnostic tests that detect and identify Leishmania parasites with high specificity and sensitivity to screen patients wherever they are. Currently, I am a Co-investigator of a project entitled " Diagnosis of Cutaneous Leishmaniasis: Development and Evaluation of Multiplex POC DNA Assays" financed by the National Academy of Sciences (USA), in the frame of Partnerships for Enhanced Engagement in Research (PEER cycle 5) program. The goal of this study is to develop rapid, simple and cost effective molecular tools for the diagnosis of cutaneous leishmaniasis in the Old World. I am also a key team member of the project entitled "Comparative evaluation of new generation molecular tools for the molecular diagnosis of the cutaneous leishmaniasis" implemented in the Clinical Investigation Center of Institut Pasteur de Tunis and financed by the Ministry of Higher Education of Tunisia. The aim of this project is to evaluate a new developed molecular diagnosis tool in Tunisian clinical samples.
In the framework of my master (2013-2014) as well as my PhD thesis (2004-2009), I worked on the identification of new loci (Bel Hadj Ali et al. 2007, 2008) and genetic markers responsible and/or associated to the otosclerosis (Bel Hadj Ali et al. 2012) which is a complex genetic disease causing non syndromic hearing loss. I performed genome wide linkage study, HLA typing and statistical analysis to identify genetic and environmental component leading to disease susceptibility.
In addition to a Bachelors degree in the Sciences, Mr. Bouattour earned his DVM in Veterinary Medicine from the Veterinary School of Tunis (1981), M.S. in Ecology Parasitological, PhD in Vector Entomology from the Faculty of Sciences Tunis, and HDR in Vector and Vector-Borne Diseases from Institut Pasteur. His research interest includes medical entomology, particularly mosquitoes, ticks, flea and sand flies and epidemiological studies of arthropods-borne diseases. He is involved in national research programs run at the Institute Pasteur of Tunis and international and regional consortia on ticks, mosquitoes and arboviroses. His professional activities and services include coordination of training mission of IPT. He is also Senior Lecturer in Arthropod Vectors and Vector-Borne Diseases at Faculty of Science, Tunis. He is the author of more 50 publications in peer reviewed journals and he supervised more than 40 Msc and PhD students.
I’m a researcher in the Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis with expertise in cellular and molecular Biology. I am leading a group working on identification and characterization of natural bioactive substances from either snake venom or plant extracts that have anti-tumor effect. My scientific interest is basically getting more insights into the cell-bioactive molecules interaction field and understanding the molecular and cellular interactions in several infectious and non-infectious diseases. I did my PhD work (1999-2004) in the laboratory of venoms and toxins, Institut Pasteur de Tunis on genetic engineering of scorpion toxins. I then performed a three year post doctorate (2004-2007) at the Institute of Developmental Biology and Cancer Research UMR CNRS 6543, University of Nice-Sophia Antipolis, Nice, France on “The role of ERK signalling pathway in tumour angiogenesis”. I was financed by the Association for International Cancer Research (AICR). In 2008, I got a permanent position at the "Institut Pasteur de Tunis". I obtained a degree of ‘Habilitation à Diriger des Recherches’ in cell Biology in 2010.
I have collaborated with teams of the IPIN in the frame of the PTR426 project (Harigua-Souiai, Abdelkrim, Bassoumi & al., 2018) to investigate the potential of LeIF protein as an immunomodulatory molecule or a drug target
I’m a geneticist and a molecular biologist researcher working at the laboratory of Molecular Epidemiology and Experimental Pathology (MEEP) directed by Pr. I. Guizani. I did my PhD work (1998-2003) in this laboratory in collaboration with the Institute of Tropical Medicine, in Antwerp, Belgium, under the supervision of Pr. J.C. Dujardin. My work concerned analysis of chromosomal size variability by Pulsed Field Gel Electrophoresis in correlation with clinical pleomorphism of Leishmania (L.) infantum parasites from Tunisia and Southern France (Guerbouj et al., 2001a). I also implemented PCR-RFLP based strategy using gp63 genes for the identification of Old World Leishmania species and analysis of L. infantum intra-specific polymorphism (Guerbouj et al., 2000; 2001b; Dujardin et al., 2002). Since 2005, I have a position at the Faculty of Sciences of Tunis as an Assistant Professor and joined the lab as an associated researcher, then progressed to be a Lecturer in 2015. Since then, I contributed as co-investigator in different national and international collaborations interested in molecular epidemiological studies, which allowed me to gain expertise using molecular techniques for the study and identification of Leishmania species in Tunisia (BenSaid et al., 2006) and Sudan (Elamin et al., 2005; 2008), application of specific PCR tools for canine leishmaniasis investigation in Tunisia (Guerbouj et al., 2014a and b) and parasite identification from Giemsa-stained slides, in Algeria (contribution as PI; Beldi et al., 2017). In the context of elucidating the transmission cycle of CL due to L. infantum, I also contributed to the investigation of phlebotomine sandfly species in northern Tunisia and evaluation of infection rates using molecular tools (Guerbouj et al., 2007). Within this frame, I also contributed showing the involvement of hedgehogs as reservoir hosts of leishmaniasis in Tunisia with specific PCR, PCR-RFLP and sequencing methods (Chemkhi et al., 2015; Souguir-Omrani et al., under review). Actually, I’m a co-PI in a collaborative project with Dr. Y. Mghirbi (PCI support from IPT)) in which we are studying infections and agents, including parasites, in a wide variety of domestic and wild reservoir hosts, for a one health perspective, using HRM strategy and other molecular tools. Also, in the frame of an AUF grant in collaboration with the Centre de Recherche en Infectiologie, Québec, Canada, I’m involved in NGS sequencing and analysis of several genomes of L. infantum responsible of VL and CL in Tunisia and Algeria, for which I am conducting bioinformatics analyses of NGS data for CNV investigation in correlation with clinical pleomorphism.
Position: Senior investigator (Biologiste Principal) at IPT and head of laboratory of Molecular Epidemiology and Experimental Pathology (MEEP) at the Institut Pasteur de Tunis. I joined IPT in 1989 to develop and conduct research lines on Leishmaniasis.
Education: After graduation in Tunisia in 1982, I studied in France as postgraduate to obtain a DEA in Molecular and Cell Genetics in 1983, and a PhD in Microbiology/ Virology in 1986. Then I graduated in Tunisia in 2002 to obtain a Doctorat d’Etat.
Expertise: I am molecular biologist and geneticist. My area of expertise is in the fields of Genetics and molecular analysis of Leishmania parasites and its applications to epidemiology and disease control. It encompasses genome analyses, biomarkers identification and characterization, bioinformatics selection and experimental characterization of diagnostic or drug targets, biochemical and biological validation of small molecules, development & validation of DNA diagnostics. Current projects deal with the development and/ or validation of novel POC DNA assays/ prototype kits for CL diagnosis (PEER & CIC); the comparative genome analyses of North African L. infantum parasites (AUF). We also work on dissecting the effect of LeIF as an immune-modulatory/ prophylactic protein and also as a potential drug target (previous PTR and current support from the Ministry of Higher Education and research).
I am a bioinformatician specialized in computer-aided drug discovery. I hold a bachelor in "Mathematics & Physics", an engineer degree in "Analytical Chemistry & Instrumentation" and a master degree in "Information Processing & Complexity of the Alive". In March 2011, I started my PhD in the "Structural Bioinformatics Unit" at Institute Pasteur (Paris) under the co-supervision of Pr. M. Nilges and Dr. I. Guizani. My internships at IP were funded by the international fellowship of the Unesco-L’Oreal "For Women In Science" programme (2012-2014) and "Yersin & Calmette" fellowhips of the RIIP. I was awarded the American Society of Tropical Medecine & Hygiene ACMCIP trainee award for LMIC in 2016.
My PhD project had two outcomes: (i) I am the principal contributor to a new computational method that proved very efficient in identifying binding sites on proteins (Harigua-Souiai et al., 2015, BMC Bioinformatics), and (ii) first author with equal contribution on a drug discovery project that yielded to the identification of novel anti-Leishmania molecules (Harigua-Souiai et al., 2018, PloS NTD).
Since April 2016, I am a post-doctoral fellow at IPT in the group of Dr. Ikram Guizani. I am currently working on multiple projects: (i) Structural genomics projects applied to Leishmania, (ii) Cheminformatics & chemogenomics in silico approches for anti-Leishmania drug discovery and (iii) Molecular epidemiology studies of leishmaniases in the MENA region using biostatistics and bioinformatics including genome analyses. Current projects involve IPA & IPM.
I also have expertise as Lecturer/Trainer in bioinformatics: Linux, R, Python, Databases, Data visualisation, Statistics, Molecular modeling, Docking simulation, Machine learning, either at courses at IPT or within the frame of teaching curricula as faculty.
I am an assistant professor, since 2009, working as a permanent scientist researcher at Institute Pasteur of Tunis at the Laboratory of Medical Entomology directed by Dr. Ali BOUATTOUR. I am the leader of the research group that is interested to the molecular epidemiology of vector-borne diseases, pathogen biodiversity and biomolecules. Within this group, I am in charge of development of molecular tools for the diagnosis of pathogens transmitted by arthropods (ticks, fleas, mosquitoes, sandflies) such as bacteria (Anaplasma, Ehrlichia, Bartonella, Rickettsia), protozoa (Theileria, Babesia, Leishmania) and arboviruses (phleboviruses, …) (M’ghirbi et al., 2009, 2010, 2012, 2013, 2016). In addition, my research field focuses on the characterization of biomolecules in tick salivary glands (M’ghirbi, 2016; Bensaoud et al., 2017, Bensaoud et al., 2018). Actually, I’m principal investigator of a project entitled “Bionomics of zoonotic vector-borne pathogens in wild and domestic mammals in northern west of Tunisia, an endemic area for leishmaniasis: A one health perspective.” financed by the institute Pasteur of Tunis in the frame of internal collaborative projects. The goal of this study is to contribute to the knowledge of the epidemiology of emerging zoonotic pathogens and to further characterize patterns of natural co-endemicity of Leishmania parasites with Anaplasma, Ehrlichia, Rickettsia, Bartonella and Babesia applying DNA diagnostics based on PCR-HRM. I am also a key team member of a regional project entitled “Environmental changes and mosquito-borne diseases: the example of West Nile”, financed by the Instituts Pasteur of the MATI region.
During my master degree (2004) and my PhD (2009) I was involved in several national and international projects in the same laboratory. I did my PhD work (2005-2009) in collaboration with the Reference National Center of Borrelia, Institut Pasteur, under the supervision of Pr. Danièle POSTIC and in the Neiker-Tecnalia Basque Institute for Agricultural Research and Development, under the supervision of Pr. Ana HURTADO.
I’m a Post-Doc researcher working at the laboratory of Molecular Epidemiology and Experimental Pathology (MEEP) directed by Pr. Ikram Guizani. I did my PhD work (2007-2016) in this laboratory. Through my PhD project I developed expertise in molecular epidemiology of Leishmania parasites, and in the development of novel biomarkers and their molecular and bioinformatic characterization. I also have experience with conduction of national (Tunisia) and international (Sudan, Brazil) collaborative projects. My research interest is focused on the molecular genetics and genomics of Leishmania sp, protozoan parasites that are the causative agents of Leishmaniases, widely distributed in Africa and MENA including my country, Tunisia. During my thesis project, we developed a strategy to select relevant genetic markers for the differentiation of parasites according to traits relevant to epidemiology. We exploited the knowledge on Leishmania genome to develop biomarkers and PCR assays useful for identification and characterization of the Leishmania parasites according to their taxonomy and geographical origin in the African region (Mkada et al., 2014; in preparation).
Actually, I work in two interrelated projects (national and international), which involve close collaborations with clinicians to establish quality assured molecular diagnosis in a hospital unit in Central Tunisia, in order to alleviate their burden of increasing demands for diagnosis of cutaneous and visceral Leishmaniases. I am involved in collaborative projects with the teams in IPA and IPM.
Since 2008, I am a Senior Engineer in the Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis. My research activities consist on the development of novel diagnostic tools that allows the detection and the identification of Leishmania species encountered in Tunisia and the Mediterranean region. In a previous study I have developed a sensitive, simple and rapid molecular diagnostic tool based on DNA arrays for Cutaneous Leishmaniasis diagnosis. This innovative tool allows the concomitant detection and identification of Leishmania parasites in less than 5 hours. Currently, I’m working on the evaluation and the validation of my DNA tools (DNA arrays & PCR-HRM) using clinical samples from Tunisian patients. This project is a key project of the consortium of the Clinical Investigation Center of Institut Pasteur de Tunis. I am also a member of a project aiming at developing and evaluating an isothermal multiplex POC DNA Assays which was selected to be financed by the National Academy of Sciences (NAS) in the frame of the Partnerships for Enhanced Engagement in Research (PEER cycle 5) program. In my current work I am also in charge of establishing Standard operating procedures and other documents to assure consistency, accuracy, and quality of the results in the lab. I have obtained my master degree in 2007 and my Engineer National Diploma in 2006; my projects were in the molecular tools development and so I have developed my expertise since then.
I collaborate with ACOBIOM on the miniarrays and HRM project, and with the team in IPA and IPM in POC DNA diagnostics using isothermal amplification.
I am a bioinformatician specialized in host-pathogen molecular interactions. I conducted my PhD research under the co-supervision of Dr Alia Benkahla and Christine Brun in respectively the Institut Pasteur de Tunis and the TAGC, an Inserm laboratory in France. During my thesis I worked successfully on the prediction, inference and analysis of host and pathogen interaction networks. After my thesis defense, I was engaged in 2 years contract as post-doc fellow in the INRA, Versailles. During these 2 years, I focused on the annotation of phage proteins using hidden Markov models. During my second post-doc, in the CNRS- France, I worked on analysis of RNAseq data and more specifically on the Detection of generic differential RNA processing events from RNA-seq data. The last post-doc position was at the Pasteur Institute of Tunis as RNA-seq analyst. I was particularly focusing on transcriptomic changes for public health issue diseases such as (Leishmaniosis, TB, Crohn disease). I have a position as assistant professor at the Université de Tunis El Manar teaching bioinformatics. I have also experience as Lecturer/Trainer in bioinformatics courses.
Experienced Researcher – WP leader (WP1)
- MD, Professor in Parasitology
- Head of the Lab of Epidemiology & Ecology of Parasites
- Expert in Leishmaniasis (visceral and cutaneous forms): Epidemiology, Diagnosis, Treatment and control
2010 - 2012 - Master Degree in Microbiology: Faculty of Sciences of Tunis
2007 - 2010 - The Engineer National Degree: Biological Engineering: Université Libre de Tunis
2004- 2007 - The Undergraduate Degree of Technology: Applied Biology Higher Institute of Tunis
2017: Participation in Bioniformatics and Genome Analyses Course (Institut Pasteur de Tunis)
2017: Participation in H3ABioNet IBT
2017: Introduction to bioinformatics course
2017: Engineer in technological platform (Institut Pasteur de Tunis)
2015: A training workshop on Biological Risk Management in the laboratory
2014: Training in laboratory of Structural Mass Spectrometry and Proteomics (Institut Pasteur Paris)
Dr Alia Benkahla is a bioinformaticist she did her PhD studies at the IGS-CNRS in Marseille. Her initial training was in Mathematics. She worked as Post-Doctoral fellow at the Max-Planck Institute in Berlin, and moved to the Institut Pasteur de Tunis in January 2005. She initiated the Group of Bioinformatics and Mathematical Modeling and invested her initial period at IPT in capacity building in the field of Bioinformatics by: training students; co-organizing international events in Africa; developing her network; and looking for funds in Bioinformatics for Tunisia’s and Africa’s health issues. She is the President of the African Society of Bioinformatics and Computational Biology since September 2015. She was the chair of the third ISCB Africa ASBCB Conference on Bioinformatics 2013. She is head of the Laboratory BioInformatics, bioMathematics and biostatistics (BIMS). She was the PI of 6 research projects and is the PI of the actual H3ABioNet Tunisian node. She is member of the Scientific and Training Advisory Board of the Wellcome Trust DELTAS project: "Developing Excellence in Leadership and Genetic Training for Malaria Elimination in Sub-Saharan Africa (DELGEME)". She is member of the Technical Advisory Committee of the "NIH Global Health Bioinformatics Research Training for West-Africa –WASLITBRe". She is co-coordinating the H3Africa Phenotype Harmonization WG. Her research is mainly in the area of systems biology aimed at understanding processes of regulation, interaction, signaling mechanisms activated in response to diseases (i.e., leishmaniasis and/or tuberculosis, cancer).
Early Stage Researcher
Haifa Bichiou is a PhD student working on the identification if transcription factors playing a key role in shaping the Leishmania-infected macrophage response.
Cell/parasite culture; infection; SDS-PAGE; western-blot, NO/ROS measurement; ELISA; PCR; RT-PCR; SiRNA…
During the present mission she plan to Investigate the expression and activation of different TFs that we suspect to play a key role in shaping the cell response to Leishmania parasite using cells from resistant and sensitive to drug patients.
Early Stage Researcher
Cyrine Bouabid is a PhD student working on the identification of mechanism of acquired resistance of Leishmania to drug.
Cell/parasite culture; cell infection; RNA /DNA extraction; PCR and RT-PCR; SDS-PAGE; Western blot; SiRNA; ELISA….
She aim to compare cytokines/chemokine production and to screen for differences in T cell population using cells isolated from drug resistant/sensitive patients blood.
- MD, Professor in Parasitology
- Head of the Lab of Parasitology and Mycology
- Head of the Research Lab of Medical Parasitology, Biotechnology and Biomolecules
- Expert in Leishmaniasis (Molecular epidemiology)
Researcher at IPT. Also an associate professor at Higher School of Sciences and Techniques of Health of Tunis. My research focuses on genetic susceptibility of complexes diseases (cancer, inflamtory and infection diseases) and their interaction with micro-environmental factors. Development of molecular methods focus on Hig resolution melting (HRM) and its application (mutations discovery (gene scaning), SNP genotying, spices identification).
Early stage researcher
PhD student in biological sciences at the Faculty of Sciences of Bizerte-Tunisia.
Member of the research laboratory “Medical Parasitology, Biotechnology and Biomolecules” of Pasteur Institute of Tunis under the direction of Professor Pr. Aida Bouratbine.
Research theme and mission: Developing molecular technics of detection and identification of protozoa. We plan to test different strategies of molecular technologies such as quantitative Real time PCR, PCRs/Sequencing and new generation sequencing 18S rDNA in order to conduct field investigations on the prevalence and genetic polymorphism of protozoa. We are also interested in developing novel diagnosis molecular technologies.
- PhD in Entomology
- Assistant-Professor at Higher Institute of Environmental Sciences and Technologies, Borj-Cedria Tunisia
- Member of Research Laboratory "Medical Parasitology, Biotechnology and Biomolecules", IPT
- Major research interests in medical entomology specially in taxonomy and bionomics of Phlebotomine sandflies, leishmaniasis vectors, vectoral capacity and in eco-epidemiology of leishmaniasis
Current involvement in projects: CRDI 104270-015 and ACIP 02-2014
Early stage researcher
PhD student at the Faculty of Sciences of Bizerte (biological sciences).
Member of the research laboratory “Medical Parasitology, Biotechnology and Biomolecules” of Pasteur Institute of Tunis under the direction of Professor Karim AOUN.
Research theme and mission: Developing experience in the techniques of biology of parasitic systems mainly molecular identification of pathogens using molecular tools particularly real time PCR followed by high resolution melting analysis (qPCR-HRM). This new technique is rapid and sensitive for protozoa detection while allowing identification of the involved species simultaneously.
Early Stage Researcher
PhD student at university of Tunis EL Manar. Member team of the Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR11IPT06, under the direction of Pr. Aida BOURATBINE.
Research interest: developing new tools for leishmaniasis diagnosis and understanding better the mechanisms of immune response in CL.
Early Stage Researcher
PhD student at the Faculty of Science of Tunis (biological sciences).
Member of the research laboratory "Medical Parasitology, Biotechnology and Biomolecules" of Pasteur Institute of Tunis under the direction of Professor Aida BOURATBINE.
Research theme: study of both ecological and epidemiological populations of sandflies of the household of Leishmaniasis in Tunisia.
Developing experience in the techniques of capture of sandflies, morphological and molecular identification of sandflies species, as well as the identification and detection of pathogens.
Early Stage Researcher
PhD student at university of Tunis EL Manar. Team member of the Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR11IPT06 (PMBB), directed by Pr. Aida BOURATBINE
Research interest in the frame of the project: Molecular biology tools (RT-PCR), genetic, gene expression, Immunology.
- Doctoral degree in Human Genetics and Molecular Biology
- Assistant Biologistat the Pasteur Institute of Tunis
- Responsible of the Technological Platform of the Pasteur Institute of Tunis
- Teaching of metabolic and clinical biochemistry
- Member Organizer of several congresses and workshop
- Involving in research projects