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
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.
After terminating a full laboratory technician training, Romain obtained a bachelor in biology. Interested by the field of bioinformatics and computational biology, Romain then completed a master in molecular life science with a bioinformatics specialization at UNIL during which he learnt the basics of high throughput sequencing data analysis. Eager to dig deeper in the computational field, he eventually joined the laboratory of Computational Cancer Genomics of Philipp Bucher at EPFL, first for an internship, then as PhD student. In order to better understand the mechanisms underlying transcriptional regulation, both at the chromatin organization level and at the transcription factor binding level, Romain is now interested in genomic data and sequences classification and develops efficient softwares and methods to mine these data.
Rocio Rama Ballesteros
Rocío studied Computer Science at University of Granada in Spain. She moved to Switzerland to work at CERN (European Organisation for Nuclear Research) in Geneva during 3 years as Software Developer.
Her passion for science moved her to apply and get a PhD student position at University of Lausanne. Currently her research is focused on investigating the use of machine learning to better understand the signature of selection and co-evolution on genomic data.
Tugce Bilgin Sonay
Tugce is a molecular biologist and bioengineer by training. Since her undergrad times though she only worked on bioinformatics with an emphasis on evolutionary biology. She was born and raised in Istanbul and this is also where she studied. She obtained her PhD in Andreas Wagner’s lab in University of Zurich on short tandem repeats and their gene regulatory role in evolution and cancer. Later, she worked on orangutan genomes in the Anthropology Department of the University of Zurich. Recently, she moved to UNIL to work with Christophe Dessimoz, Ana Marques and Sven Bergmann on long non-coding RNAs and their gene regulatory role.
She values being active in a society, and that’s why she is happy to be part of ISCB RSG. As an undergrad, she founded the society of her department so that students could interact more and the flow of information across years was maintained. Now she is an active member of evolutionary biology society in Turkey. She organizes and teaches various workshops in different countries. Besides work, she loves writing short stories, painting and yoga. She plans to become a yoga teacher as a side job ;). You can check out her website here: tugcebilgin.net.
The operational team – Zurich and Basel
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 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 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 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 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.