Who are we?

The Leaders

2013-12-09 13.38.07

The founders (Namrata, Cynthia & Jonathan)

Amel Bekkar, President

Amel studied Biology at the university of Lausanne. She obtained a master degree in Molecular Life Sciences with a distinction in Bioinformatics at the university of Lausanne in 2015. For her Master’s degree project, she joined Vital-IT department at the SIB and worked on modeling and simulation of the underlying regulatory network of epithelial-to-mesenchymal transition in cancer. She  then joined Vital-IT as PhD student to develop and apply Boolean methodologies for regulatory networks modeling in disease in particular cardiovascular diseases. Amel is also passionate about cooking and pastries,  she likes to discovers different cultures and world cuisines.

Anna Marcionetti, Treasurer 

Anna obtained a Bachelor degree in Biology at the university of Lausanne, where she continued her studies and in 2015 obtained a Master degree in Molecular Life Sciences with a distinction in Bioinformatics. For her Master project, she joined the the Computational Phylogenetics group, which is part of the Departement of Ecology and Evolution from the University of Lausanne as well as the SIB. Her work focused on the investigation of the genetic basis of floral color differentiation occurring during pollination shifts. She started then a PhD in the same group, and she is currently investigating the genetic basis of clownfishes adaptive radiation.

David Dylus, General Secretary

Leonardo de Oliveira Martins, Webmaster 

Leo Martins is a postdoc at the Dessimoz Group of the University of Lausanne working with phylogenomics. He has a B.Sc. in Molecular Sciences and an M.Sc. in Biotechnology by the University of Sao Paulo (Brazil), where he studied the population genetics of viruses. He did his PhD at the University of Tokyo (Japan) working with prof. Hirohisa Kishino, where he developed phylogenetic models for detection of recombination in viral sequences. At that time he also learned how to build and administrate an HPC cluster. He then moved to the University of Vigo (Spain), to work with prof. David Posada on Bayesian models for phylogenomic reconstruction. Together they also created simulations and tests for deep phylogenies, which can be applied in the search for the Trees of Life. Leo later worked as a Data Scientist at the Molly Stevens Group of the Imperial College London (UK), developing tools to analyse hyperspectral images (Raman, SIMS) and for microscope image processing and classification.
He currently works in the Department of Ecology and Evolution of UNIL, designing and implementing fast algorithms for large-scale phylogenomics – specially species tree inference and proper consideration of estimation uncertainty. When he is not in the computer, he is watching movies, learning to cook or hitting the gym.

The operational team – Lausanne

Jonathan Sobel

After accomplishing his Master degree in ‘Proteomics and Bioinformatics’ at the University of Geneva in 2011 on endometriosis biomarkers, Jonathan decided to go in the field of computational biology. His PhD project is part of the CycliX project founded by the SystemsX initiative. He is working in the Computational Systems biology lab at EPFL under the supervision of Prof. Felix Naef. He is working on chromatin accessibility in the circadian context in mouse liver, using next generation sequencing approaches. Enjoying teamwork he is president of the Swiss group of students of the international society of computational biology (ISCB-RSG Switzerland) and he intends to increase the accessibility of potential career opportunities in the domain of life science with Bioscience network lausanne (BSNL). He likes martial arts, guitar playing and beers.

Namrata Sarkar

Namrata Sarkar is the Vice-President of the Swiss group of students of the International society of computational biology (ISCB-RSG Switzerland). She is enthusiastic about building a strong foundation for the Regional Group of Switzerland.

She completed her Masters in Bioinformatics from King’s College London, United Kingdom in January, 2012. During her Masters she has developed a Software tool that allows filtering disease gene candidates identified by Exome Sequencing approaches for Cluster Headache Patients across the world. She has a background of Engineering and Bioinformatics through her Bachelors and Masters. Currently, she is working on Next Generation Sequencing Data Analysis at University of Lausanne and Swiss Institute of Bioinformatics, Switzerland. She is interested in the looking into, how the change in Copy Number Variation (CNVs) and Single nucleotide polymorphism (SNPs) affect phenotype(s). Other than research, she loves Painting, Photography, Swimming and playing Chess.

Elsa Guillot

Dr Elsa Guillot is a Post-doctoral fellow at the University of Lausanne in Switzerland where she investigates selection signals in humans. She received her PhD in statistical genetics at Massey University (New Zealand)  working on modeling the link between marriage rules and population genetics in humans. Her research interests are human statistical genetics, Bayesian inference for complex system modeling, human societies.

Madeleine Suffiotti

Madeleine had a Bachelor in Biology at the University of Lausanne, then she get a Master degree in Molecular Life Sciences with specialisation in Bioinformatics in 2016. During the Master project she worked with the Bioinformatics Core Facility group and SIB. She mainly worked on penalized-generalized linear models for colorectal cancer classification in subtypes according to the specific gene expression patterns of tumors.
She recently joined as PhD student the department of Immunology and Allergy at the CHUV, with collaboration of the Computational group of Vaccine and Infectious Disease Division at the Fred Hutchinson Cancer Research Center in Seattle.  She’s currently working on immunodeficiency diseases by analysing CyTOF data.

Julia Kraemer

Julia Kraemer is a PhD student at the Institute for Work and Health (Lausanne, Switzerland) and the Institute for Infectious Diseases (Bern, Switzerland). Her work focuses on the characterization of microbial communities in Swiss pig farms, using high throughput sequencing. She majored in Microbiology at Ulm University, Germany and chose Bioinformatics as one of her minor subjects. She was later introduced to next generation sequencing while working at the Luxembourg Institute of Health. In her free time she likes to take part in an English theatre group.

The operational team – Zurich and Basel

Nottania Campbell

Nottania Campbell is currently a PhD candidate in Professor Karin Metzner’s research group at the University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology. As a computational scientist the focus of her PhD thesis is to characterize the evolution of transmitted HIV viruses for individuals enrolled in the Zurich HIV Infection Study. This is achieved by employing Illumina Next Generation Sequencing, haplotype reconstruction, as well as phylogenetic and statistical methods to determine patterns that are inherent to the virus that results in the initial acute clinical infection in contrast to those necessary to maintain a persistent/chronic infection. Her academic history includes a Master’s Degree in Bioinformatics for the Analysis of Biological Data from a joint degree program by the University of Geneva and the Swiss Institute of Bioinformatics. The aim was to profile epitopes of metalloproteinase, MMP2 and MMP9, which are involved in pathways leading to hematopoietic aberrations using mass spectra, proteomic algorithms and databases. A social butterfly, she enjoys traveling, dancing – more or less anything that involves movement, the company of friends, and a good laugh.

Patrizia Spoerri

Patrizia is currently doing her PhD in the biophysics group at the department for biosystems science and engineering (D-BSSE) of ETH Zurich (located in Basel). She is enrolled in the systems biology PhD program of Life Science Zurich and enjoys participating in the student community via activities such as the organization of the 2014 PhD retreat. Prior to coming to Basel, Patrizia obtained her master’s degree in bioengineering from EPFL. She spent one year in Boston for her master’s thesis on tunable hydrogels; there she also contributed to the organization of the 2013 European Career Fair at MIT. Patrizia gathered some industry experience during internships with Lundbeck and Accenture. Her most recent endeavor is to bring more industry exposure to the people studying and working at the D-BSSE.

Denis Schapiro

Denis Schapiro studied Technical Biology at the University of Stuttgart and Harvard University. He did his research thesis in the laboratory of Prof. Alfred Goldberg at the Harvard Medical School, working on protein degradation and proteome dynamics. Moving from wet lab to dry lab, he joined the Complex Systems Modeling group as an intern at Bayer where he was working on mechanistic computer models describing the physiology-based distribution of substances in the body (PBPK modeling). This classical engineering approach in biology fascinated him so much that he continued working in the field of Systems Biology by joining the laboratory of Prof. Peter Sorger at the Harvard Medical School for his diploma thesis where he focused on Rheumatoid Arthritis. Afterwards, he joined the Systems Biology PhD program which is run jointly by the ETH Zurich and the University of Zurich. Currently he works in the laboratory of Prof. Bernd Bodenmiller in the area of single cell proteomics using Imaging Mass Cytometry.
Besides he  is Vice President Industry Relations position in the ISCB-RSG Switzerland, he is an active member of the Life Science Zurich Young Scientist Network as well as an organizer of an academic talk series at the Systems Biology PhD program.

Athos Fiori 

Athos obtained a BsC in Physics at EPFL in  2012, he then moved to ETHZ where he obtained a MsC with focus on Theoretical Particle Physics. After his master thesis, done with Prof. C. Anastasiou, he decided to leave physics and joined the Computational System Biology group of Prof. E. Van Nimwegen at Biozentrum. The aim of his project concerns the study of stochastic aspect of gene regulation at the single-cells level. He is currently developing Bayesian model to analyze the stochastic response of single cells to changes in growth conditions and theoretical models attempting to understand such behavior. During his free time Athos enjoys hiking and skiing and he certainly doesn’t dislike watching a nice Ice Hockey match.

Adithi Varadarajan 

Adithi is currently a PhD student with Dr.Christian Ahrens at Agroscope, Wädenswil in collaboration with Dr.Bernd Wollscheid from D-HEST, ETH Zurich. Her primary area of expertise is Bioinformatics and systems biology and is focusing on developing proteogenomics approaches to identify the full coding potential in prokaryotic genomes. After completing her Bachelors in Bioinformatics from India, she worked as Bioinformatics research fellow for 2 years in a Molecular Biology Laboratory at International Rice Research Institute (IRRI) working towards protein sequence & structural analysis for better yield and stress tolerance in Rice plans. She then obtained her Masters degree in Bioinformatics from Wageningen University and Research Centre- Netherlands. Her thesis topic was focused on constructing gene regulatory network (GRNs) architecture across different plant species in an evolutionary context. She then joined as an intern with Dr.Christian Ahrens at Agroscope, Wädenswil focusing on high-throughput genomics and transcriptomics methods. Thereafter, she continued her PhD since October 2015. Currently, for her PhD she is working on enhancing and curating a robust pipeline for proteogenomics which provides protein level evidence for unannotated short ORFs potentially in prokaryotic genomes. Thereby, she is trying to improve the current level of genome annotations which would also help to identify novel compounds for therapeutics, agriculture and other fields. Apart from bioinformatics and research she takes interest in cooking, socializing, badminton to mention a few and is the newly joined member of ISCB, RSG.

Former Members

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