Call 2019

Selected projects

Advanced Research Network for Historic Photographs in Art History

Art History
Humanities

The Department of Art History of the University of Geneva and the Swiss Art Research Infrastructure (SARI) of the University of Zurich have successfully implemented the project National Research Network for Historic Photographs in Art History, starting 2018. The goal of the project was to make the department of Art History of the University of Geneva’s unique collection of historic photographs accessible to all Swiss Art History departments, by creating a national, multilingual network for the management, research, and retrieval of digitized historic photographs, slides, and other visual artefacts (along with the Institute of Art History at University of Zurich’s collection, amongst others).

As part of this initial project, a multilingual research environment for scholarly data curation has been implemented and made available to the University of Geneva. Next, a representative number of digital reproductions of the University of Geneva's historic photographic collection has been loaded and the related metadata then have been extracted, loaded, and curated using the tools developed within the project. The results are currently undergoing editorial verification and will be published to the scholarly community by the end of the project (8/2019).

In view of the next generation of this network and in close cooperation with the international Consortium for Open Research Data in the Humanities (CORDh), the University of Zurich’s SARI developed and published a standardised, peer-reviewed Reference Data Model for the semantic representation of all key entities that are required for describing visual artefacts, such as historic slides and photographs. Being entirely based on scholarly acknowledged, yet extendable standards for conceptual modelling in the cultural heritage domain (such as CIDOC-CRM) and the current de-facto standards for storage, access, and exchange of semantic data (such as OWL, RDF, RDF-S), the implementation of the new Reference Data Model significantly improves the visibility of the collection data in question and guarantees better re-usability for research, by providing standardised, machine-processable access across the world-wide Semantic Web. Thus, the content becomes interoperable and re-usable with comparable data from internationally leading actors, such as the PHAROS Consortium, the British Museum, and the Yale Center for British Art. However, this approach not only fosters visibility of the project and it’s collection data, but also significantly raised the potential for funding in the context of further research projects (see below).

This proposal aims at transforming the existing Research Network for Historic Photographs in Art History to become fully interoperable with the world-wide Semantic Web, allowing for both human-interpretable and machine-processable data access, exchange, and re-use (based on Linked Open Data technology). This requires further development, full implementation, and publication of an extended Semantic Reference Data Model, tailored to the specific needs of the Research Network for Historic Photographs in Art History. It also includes the development, implementation and publication of dedicated, multilingual Reference Entity Vocabularies for historic terms, places, persons and institutions, and alike, that will guarantee both machine-processability and -reusability within the data across the semantic web.

projects
Participants
Prof. Dr. Tristan Weddigen
University of Zurich
Prof. Frédéric Elsig
University of Geneva

CAsAnOMa: A computer-based tool for the assisted annotation of manuscripts

Digital Studies
Languages
Literature

Working with historical manuscripts requires skills in the area of Digital Humanities, for example annotation standards (TEI, XML) in order to construct, query and explore digital corpora for linguistic, historical, societal, literature and diversity studies. Creating and annotating conformant documents is often too demanding for the students themselves. In order to facilitate the task, we are developing a graphical tool which allows the students to perform all the necessary steps in a user-friendly fashion, from OCR corrections to adding annotation and querying the documents.

A prototype is currently being designed, based on Transkribus and in close collaboration with the Transkribus developers. Jean-Philippe Goldman is the main programmer. We are using the genres ‘letters’ and ‘diaries’ as a first application, constructing a corpus of the letters to/by and the diaries of Mary Hamilton (1736-1821). The challenges of hand-written text recognition (single hand) and TEI annotation (letters/diaries) offer a good starting set. In the proposed project we would like to extend to more and more open domains, several hands, different languages, and further applications, to test the versatility and portability of the tool.

In particular, a larger and different subset of TEI will be used, and extensions for researchers with partly different questions and needs will be added. For linguists and historians, e.g. the ability to aggregate and tabulate query results according to the metadata is important. For semantic analyses, we will add keyword detection.

Such a tool will allow linguists to perform a variationist analysis of the Mary Hamilton corpus, a domain in which Marianne Hundt, Eric Haeberli, and Gerold Schneider have ample experience. They will investigate syntactic variation (e.g. do-support, word order, PP complementation) morphosyntax (progressives, past tense), and development of vocabulary, in comparison to corpora of the period, like ARCHER and CLMET. Some of the texts exist in draft versions, which allow us to track the editing process from a cognitive perspective.

projects
Participants
Prof Eric Haeberli
University of Geneva
Dr Gerold Schneider
University of Zurich
M. Jean-philippe Goldman
University of Geneva
Prof Marianne Hundt
University of Zurich
Prof Martin Volk
University of Zurich
Prof Gilles Falquet
University of Geneva

Characterizing vascular smooth muscles in intimal hyperplasia during vascularized composite allotransplantation

Medicine

Vascularized composite allotransplantation (VCA) is the transplantation of composite tissue as a single unit. Both acute and chronic rejection is inevitable during VCA, albeit in the presence of immunosuppression. Rejection is associated with graft vasculopathy and typically identified with intimal hyperplasia (IH) in blood vessels.

The Plock laboratory at UZH has established an in vivo model of VCA with allogenic hind limb transplantation in rats. In this model, acute and chronic rejection was achieved by transplanting hind limbs from Brown Norway to Lewis rats (complete mismatch) and from Fischer to Lewis rats (partial mismatch), respectively. Histological analysis of the transplanted tissue at rejection revealed typical features of IH as observed in the clinics. The participating inflammatory pathway during this pathology is an ongoing study in the laboratory. Simultaneously, understanding the mechanism of IH is pivotal to develop strategies to attenuate IH in VCA.

During IH, vascular smooth muscle cells (SMCs) accumulate in the intima where they switch from a contractile to a synthetic phenotype, proliferating and producing extracellular matrix components. The Bochaton-Piallat laboratory at UniGE, extensively compares, at a molecular level, the characteristic features of SMCs during atherosclerosis, a pathology that also involves IH.

The main goal of this collaboration is to mitigate IH, lowering graft vasculopathy and thereby attenuating rejection in VCA. This will be achieved by bringing together the expertise of Bochaton-Piallat laboratory in characterizing SMCs during IH and that of Plock laboratory in VCA.

projects
Participants
Prof. Jan Plock MD
University of Zurich
Dr. Pranitha Jayadev Kamat PhD
University of Zurich
PD. Marie-Luce Bochaton-Piallat PhD
University of Geneva

Evaluation of discovery programs for refugees at University – The impact on students, peers and social integration

Psychology
Educational Sciences

The Department of Consultation-Liaison Psychiatry and Psychosomatic Medicine of the University of Zurich and the Abnormal Emotion and Trauma Lab of the University of Geneva, in close collaboration with the Immigration Policy Lab of the ETH Zurich and the Department of Economics of the University of Zurich, apply for Joint Seed Funding in order to establish a sustainable collaboration.

The number of refugees requesting asylum in Switzerland and Europe has sharply increased in 2015 and remains at high levels. Most, if not all, refugees have endured traumatic events, struggled through forceful relocation, and suffered an abrupt dissolution of their social ties, interruption of their scholastic carrier, and change in their daily lives. Not surprisingly, once settled in a new environment, many refugee children and teenagers suffer from behavioral problems and school deficits. Therefore, refugee arrivals present an opportunity, but also a challenge for host communities and schools. Several Swiss universities have started to address this challenge by planning specific integration programs for refugees wishing to pursue academic studies. The University of Zurich and the University of Geneva both offer a discovery program, intended to enable refugees to attend lectures and to experience student life. The program usually last one year and is open to refugees with previous study experience. Usually, each refugee can count on the support of another student as a mentor figure who accompanies him/her in the process of academic integration.

To the best of our knowledge, no empirical study has evaluated these programs. The impact of the discovery programs on refugee students’ well-being, integration into host society and their labor market outcomes remain open to date. Given the importance of a better understanding of these programs cost-effectiveness, their impact on refugee students, on regular students and stakeholders will be considered.

The current project aims to provide further understanding of these academic programs in a multi-center perspective. At the same time, the project will consolidate a joint Swiss research network fitting together knowledge and resources of Swiss research centers interested in refugees and migration. The project will be conducted in collaboration with academic partners responsible of the discovery programs in Zurich and Geneva.

The overall aim of this project is to evaluate the discovery programs. This will include an assessment of refugee students, mentors, local students, and integration stakeholders. As a first step, a joint workshop is planned, where the goals, methodology, and relevant partners of the study will be identified. On this basis, a joint pilot study and research proposal will be prepared to further strengthen the collaboration between the universities.

projects
Participants
Dr. Naser Morina
University of Zurich
Dr. Grazia Ceschi
University of Geneva
Prof. Dominik Hangartner
ETH Zürich
Prof. Pietro Biroli PhD
University of Zurich
Dr. Andreas Beerli PhD
ETH Zürich

Even more Language and Interpretation Skills for Geneva and Zurich Law Students

Languages
Law

French diplomat Charles-Maurice de Talleyrand-Périgord is reported to have said that “language was given to man to disguise his thoughts”. While this may be correct for diplomacy it could not be further from the truth for the field of law. For lawyers, language is not merely an important but the only tool to express their opinions, interpretations and arguments. Whether a judge is delivering a judgement, a defence lawyer is pleading for her client’s innocence or a corporate counsel is drawing up a contract, they all need strong active and passive linguistic skills to achieve optimal results.

The language requirements for Swiss lawyers are unique in the sense that all federal laws in Switzerland are published in French, German, and Italian. The three versions have equal standing and lawyers must be able to compare the different versions and to draw normative inferences from them. Furthermore, approximately 95% of the jurisprudence of the Federal Supreme Court is rendered either in French or German with no official translations. Although the leading cases are generally translated from one language into the other, this is often done with considerable delay, thus exposing attorneys to liability issues. Understanding German and French is therefore an indispensable prerequisite for any Swiss lawyer and being able to express oneself in both languages presents a distinct career advantage.

With that in mind professors Yvan Jeanneret (UniGE), André Kuhn (UniGE/UniNE) and Marc Thommen (UZH) created a project which from September 2018 until June 2019 invited professors from Geneva to Zurich to teach a course in French and professors from Zurich to Geneva to teach a course in German. The aims of the project are to enable law students to understand federal acts and case law in German and French and to make them comfortable with considering legal matters in their non-native tongue.

The project was kindly supported by UniGE-UZH Joint Seed Funding making it possible for Alexandre Flückiger (public law), Anne-Sylvie Dupont (social security law), Ursula Cassani, Yvan Jeanneret, and Bernhard Sträuli (all criminal law) from Geneva to hold lectures in Zurich. Their counterparts traveling from Zurich to Geneva were Thomas Gächter (social security law), Regina Kiener, Johannes Reich (both public law), and Marc Thommen (criminal law). These exchanges have not only enhanced the German-speaking students’ skills in the French legal language and vice versa but also provided excellent opportunities for professors of both universities to meet and discover shared research and teaching interests.

The fact that the project was not only very well received by students but also by faculty colleagues shows a strong demand for French-German language exchanges between Swiss law schools. As several professors from both universities have shown a keen interest in participating, we wish to continue and expand the project to more fields (foundations, civil law, commercial law) and other formats (tutorials, seminars, workshops). The long-term goal is to offer students from Geneva and Zurich a constant and permanent opportunity to develop language and interpretation skills in their non-native tongue as part of their studies.

projects
Participants
Prof. Dr. Marc Thommen
University of Zurich
Prof. Dr. Regina Kiener
University of Zurich
Prof. Dr. Thomas Gächter
University of Zurich
Prof. Dr. Johannes Reich
University of Zurich
Prof. Yvan Jeanneret
University of Geneva
Prof. André Kuhn
University of Geneva/Neuchâtel
Prof. Dr. Ursula Cassani
University of Geneva
Prof. Dr. Stéphanie Dagron
University of Geneva
Prof. Dr. Bernhard Sträuli
University of Geneva

Improving metabolic health by activation of futile adipose de novo lipogenesis

Medicine

Obesity is a major metabolic disease manifested with increased peripheral and central accumulation of subcutaneous and visceral white adipose tissue (WAT). During prolonged cold exposure the subcutaneous WAT undergoes major morphological and functional alterations, leading to appearance of mitochondria-rich, UCP1-expressing beige adipocytes that promote energy dissipation and heat generation, a process called fat browning. An under-appreciated function of WAT is its role in clearing glucose and amino-acid from plasma by converting them into lipids for storage. The synthesis of fatty acids from non-lipid precursors is called de novo lipogenesis (DNL). High fat diet or defective lipid metabolism often found in obese individuals suppresses DNL in the adipose tissue which renders the patients insulin resistant and diabetic. Against all expectations, it is becoming increasingly clear that activation of adipose DNL is beneficial for improved fat metabolism, glucose homeostasis, insulin sensitivity, and whole-body metabolism, especially when these pathways are active in visceral WAT. Most of the work to understand fat browning, has, however, been done in subcutaneous fat. Despite its critical importance in obesity-related metabolic disorders, the capacity of the visceral WAT to convert into beige-like adipose tissue, remains poorly investigated.

The Trajkovski group at the Unige recently made an unexpected discovery and showed that exposing microbiota-depleted mice to low temperatures promotes UCP1-independent browning of visceral WAT. This leads to a drastic metabolic activation of this tissue, and dramatic weight loss of the animals. Preliminary transcriptome analyses of the involved tissues show an unanticipated up-regulation of DNL and high glucose consumption specifically in visceral WAT. The gene expression data also indicate that under these conditions DNL might run in a futile cycle that is specific for the visceral WAT of microbiota-depleted cold-exposed mice. This raises the possibility that the visceral WAT is continuously degrading fat it has just synthesized; a situation which leads to a net loss of metabolic energy and might explain the drastic loss of fat mass in these animals.

The Klemm laboratory at UZH has recently discovered that adipocytes have specialized cellular machinery to control DNL in order to regulate healthy development of white adipocytes. The Klemm lab has established methods for the genetic perturbation of adipocytes by CRISPR-Cas9 gene knock outs and developed a set of approaches to trace incorporation of isotope labelled glucose and amino acids into fat to quantify DNL in these cells.

The central working hypothesis in our seed project is that futile DNL is the underlying reason for the drastic weight loss in the described mouse model.

To test this hypothesis we will carry out the following specific experiments, which will start the collaboration between UZH and UniGe:

1- Use the isotope based tracing experiments to test if microbiota-depleted, cold exposed mice prepared at UniGe run futile visceral DNL.
2- To identify factors involved in driving futile DNL we will analyze transcriptome changes in a differentiation time course of a CRISPR-Cas9 adipocyte K.O. model defective in futile DNL (already produced at UZH) and compare them to the transcriptome data obtained with the mouse model.

projects
Participants
Dr. Robin Klemm
University of Zurich
Prof. Mirko Trajkovski
University of Geneva

Língua-lugar, Digital journal of literature, history and cultural studies in Portuguese

Area Studies
Languages
Literature

Língua-lugar. Literatura, História, Estudos Culturais is an upcoming, academically challenging, digital, scientific journal, aiming to advance dialogue amongst scholars across various disciplines, academic traditions and geographical areas of Lusophone countries.

Associated with the Centre d'Études Lusophones (CEL), Língua-lugar. Literatura, História, Estudos Culturais’s mission will be to study Portuguese-speaking cultures from a postcolonial and interdisciplinary perspective. It will pool the experiences and academic visions of two university departments, namely, the Département de Langues et Littératures Romanes in the humanities faculty of the University of Geneva and the Romanisches Seminar of the University of Zürich. The journal will be jointly coordinated by Alexander Keese and Nazaré Torrão of the University of Geneva and by Eduardo Jorge de Oliveira of the University of Zurich, and will encourage academic collaboration between the two.

The journal aims to be a channel for reflection in Portuguese — a language that is enriched by a variety of aesthetic and literary phenomena and benefits from a wealth of epistemological and critical material. We propose, on one hand, to reflect upon the plurality of literature and culture in several different types of Portuguese, and on the other hand, to conduct our reflection in Portuguese. This will allow us an insider’s perspective of the language, with its hallmark flexible syntax, reversible punctuation and figures of rhetoric, as Fernando Santoro[1] insightfully noted.

It is crucial for us to engage in critical interdisciplinary reflection. Today’s world is marked by audio-visual culture, that interfere in the creation and reception of our imaginary worlds and distort scientific interpretation of the world. Only critical reflection can help us to detach ourselves, step back and deeply reflect upon this moment in history, when media manipulation has so greatly increased. The journal will seek to spur readers to deconstruct the discourses cross the cultural products of the Portuguese-speaking world. The notion of “discourses” will be addressed through the concept of "discursive formations", a notion first defined by Michel Foucault in L'Archéologie du Savoir, and further developed by other scholars, such as Deleuze and Guattari[2].

Thus, discourses’ common theme will be divided into subtopics that analyse different types of discourse in politically relevant contexts of the Lusophone world. Over the next four years, our areas of study will focus primarily on the construction of discourses based on the concepts of identity, memory, colonialism and post-colonialism, exile, migration and gender. Toward this end, workshops will be held with students and faculty members from both departments, with digital training provided.

[1] Santoro, Fernando (2004). “Portugais”. Cassin, Barbara. Vocabulaire européen des philosophies, Paris, Seuil, Le Robert, p. 967.

[2] Maingueneau, Dominique (2011) : « Pertinence de la notion de formation discursive en analyse du discours », CAIRN, 2011/1 n˚ 135, pp. 87-99.

projects
Participants
Dr. Nazaré Torrão
University of Geneva
Dr. Eduardo de Oliveira
University of Zurich
Dr. Alexander Keese
University of Geneva

Materials by design: Experimental and computational realization of artificial oxide materials

Physics

Search for novel strategies and materials is nowadays key to keep with the present race towards electronic device miniaturization. In this context, transition metal oxides arise as attractive candidates for next generation devices due to the variety of physical properties they display (i.e. magnetism, superconductivity, etc.). In addition to the many functionalities of bulk oxide crystals, very fascinating are also the phenomena occurring at the interface between two dissimilar oxides. That is, when an oxide layer (only a few atoms thick) grows on top of another one, the two compounds must accommodate to the new structural and electronic environment resulting into interfacial reconstructions. This approach allows the further tuning and control of the properties of oxides and, interestingly, also paves the way to the emergence of novel properties at interfaces that can be completely different from those exhibited by the parent compounds. Outstanding examples include the emergence of superconductivity between the insulators LaAlO3 and SrTiO3 or magnetism in a material a priori non-magnetic like LaNiO3 – both results reported by the PIs of this proposal. Therefore, atomic-scale understanding of the interfacial interactions is decisive for the design of oxide materials with the desired properties. This research field is known as oxide interface physics and constitutes the core of the present proposal.

In this project, we aim to intensify the research and share expertise in the novel properties of oxides by promoting the collaboration between the well-established UNIGE group of Prof. Jean-Marc Triscone and the recently developing group of SNF-Prof. Marta Gibert at UZH. We will also extend our collaboration with the computational group of Philippe Ghosez in Liège (Belgium) – the ab-initio computational support for these artificial materials being absolutely key.

projects
Participants
SNF Prof. Marta Gibert
University of Zurich
Prof. Jean-Marc Triscone
University of Geneva
Gabriele De Luca
University of Zurich
Claribel Dominguez
University of Geneva

Monitoring Land Surface Phenology over Switzerland using the Swiss Data Cube satellite Earth Observations time-series

Earth & Environment Science

Land Surface Phenology (LSP) is defined as the seasonal and inter-annual variation in land surface vegetation photosynthetic activity, as measured by satellite vegetation indices. LSP is a key indicator for understanding the dynamics (e.g., responses and feedbacks) of ecosystems to changing climate system and environmental stresses, as well as for representing these in terrestrial biosphere models. By allowing the quantification of vegetation phenological trends at various scales, LSP fills the gap between traditional phenological (field) observations and the large-scale view of global models.
The important role of LSP is recognized by its contribution to the Remote Sensing enabled Essential Biodiversity Variables (RS-EBVs) project initiated by the European Space Agency (ESA). RS-EBVs are defined as the measurements required to study, report, and manage biodiversity changes using satellite data. They provide information on the status and trends of biodiversity, and have the potential to act as brokers between monitoring initiatives and decision makers.
The Swiss Data Cube (SDC –
http://www.swissdatacube.ch) is an innovative analytical cloud-computing platform allowing users the access, analysis and visualizationof35 years of optical (e.g., Sentinel-2; Landsat 5, 7, 8) and radar (e.g., Sentinel-1) satellite Earth Observation (EO) Analysis Ready Data. Importantly, the SDC minimizes the time and scientific knowledge required for national-scale analyses of large volumes of consistently calibrated and spatially aligned satellite observations.
The objective of the SDC is to support the Swiss government for environmental monitoring and reporting, as well as enabling Swiss scientific institutions to benefit from EO data for research and innovation. Additionally, the SDC allows for high spatial and temporal resolution LSP monitoring, thereby facilitating the study of seasonal dynamics of vegetated land surfaces in response to climate and environmental change.
In the framework of the ESA-funded GlobDiversity project (https://www.globdiversity.net),UZH has developed a new algorithm for monitoring LSP. It has been tested and validated in the Laegern region (10 km2) and shows promising results. In order to provide national information on the biodiversity of terrestrial ecosystems and simultaneously generate a decision-ready product, the LSP monitoring algorithm now requires to be scaled up from the development stage to the operational level, encompassing entire Switzerland. Such a product could be readily used as a basis for the design, implementation and evaluation of policies, as well as developing policy advice, programs and regulation.

  • Consequently, the aims of the project are to use the SDC platform to:
  • Implement the LSP algorithm developed by UZH and consider improvements;
  • Generate an LSP product retrieval from EO data for the entire Switzerland to contribute to provide baseline data for monitoring biodiversity;
  • Demonstrate the use and capability of processing open and freely available Big EO data on a cloud-computing platform;
  • Review and evaluate the variability and evolution of satellite-derived growing season length (GSL) nationwide;
  • Test start- and end-of-season metrics (SOS and EOS, respectively) for linear trends as well as for significant trend shifts over the study period;
projects
Participants
Dr. Gregory Giuliani
University of Geneva
Dr. Claudia Röösli
University of Zurich
Dr. Vladimir Wingate
University of Zurich
Dr. David Small
University of Zurich
Prof. Michael Shaepman
University of Zurich
Mr Bruno Chatenoux
University of Geneva
Ms Charlotte Poussin
University of Geneva
Prof. Pascal Peduzzi
University of Geneva
Prof. Anthony Lehmann
University of Geneva

Practical lexicography for speakers and linguists: developing a usage-embedded dictionary of Albanian in multilingual Switzerland

Digital Studies
Languages

Being able to speak various languages is considered an increasingly valuable skill, not only in terms of practical aspects such as job and career perspectives, but also in terms of strengthening cultural awareness and intercultural competence. Both is of particular relevance for heritage speakers: they face the double challenge of developing language skills that enable them to successfully participate in the socio-economic life of their new home while at the same time keeping the language of their origin in order to maintain ties to the socio-cultural background they brought with them. The relation between both aspects changes over time: while for first generation speakers, acquiring the languages of their (new) social surrounding is most challenging, the later generations struggle with the language of their (grand)parents. Even though specific classes in school do a good job in teaching children their heritage language, there is a growing need of hands-on material supporting these speakers in a very practical way. One of the main needs consists in a dictionary covering and meeting the demands of actual language usage, i.e. reflecting contemporary language and being at hand whenever need arises.

This project aims at developing the technical infrastructure for such a usage-embedded dictionary of Albanian and German/French, thus taking into account the multilingual environment in Switzerland. The above-mentioned needs are meet by designing it as an interactive web application with the following functionalities: (a) text fields for adding lemmas and translations to existing lemmas, (b) multiple choice fields for judging translations (highly reliable – not reliable), (c) questionnaires asking for personal information (anonymised) such as age, gender, language competence etc. Functions (a) and (b) are contributed by and beneficial for users, functions (b) and (c) provide for linguistic insight into lexical contact, entrenchment and change. Within the project the basic technical infrastructure will be developed and tested on the basis of a prototype.

In 2018, an SNF-grant investigating Albanian as a heritage language in Switzerland was awarded to Barbara Sonnenhauser (PI) and Paul Widmer (cooperation partner; both U Zurich). A crucial component of this project, which aims at tracing mechanisms of language change, identifying processes of identity formation and developing teaching materials, consists in building-up a crowdsourcing platform to involve speakers in acquiring linguistic data. This platform is being developed with the help of Jean-Philippe Goldman (U Geneva). He provides his computational skills for the present project as well, which allows for synergies on the linguistic and technical level. The linguistic and technical expertise is complemented by Shpresa Jashari’s (U Zurich) ethnological approach. She will identify the precise needs to be covered by the dictionary, take care of the equal integration of speakers/informants and supply her networks among the Albanian community. At the University of Geneva, a precious technical help will be added by Luka Nerima (U Geneva) from the unit of Computational Linguistics (within the Department of Linguistics). He has a long experience on building, maintaining and capitalizing on syntactic bilingual lexicons for various NLP applications.

projects
Participants
Barbara Sonnenhauser
University of Zurich
Paul Widmer
University of Zurich
Luka Nerima
University of Geneva
M. Jean-philippe Goldman
University of Geneva
Sphresa Jashari
University of Zurich

The Cell Line Tool: Digital two-step verification of cancer cell lines

Digital Studies
Medicine

Cancer cell lines are important tools for understanding disease mechanisms the as well as for development and pre-testing of appropriate therapeutics. However, cancer cell lines are prone to contamination and misidentification, which devaluate observations with respect to the assumed original cancer type. The ICLAC (International Cell Line Authentication Committee) has confirmed more than 500 problematic cell lines, many of which are commonly used for research resulting, in ~32,000 publications with questionable results according to a recently published estimate.

Large-scale surveys of identification errors for cancer cell lines have been mostly limited to text-based analysis. Importantly, such analyses cannot estimate the concordance between cell line data and corresponding primary tumors of a given disease. Here, the use of genomic profiling data for the review of published cell line experiments provides a novel, highly promising approach to this problem.

We propose a strategic collaboration between the team behind the Cellosaurus reference cell line resource at the University of Geneva (lead: Prof. Amos Bairoch), and the group "Theoretical Oncogenomics" (lead: Prof. Michael Baudis) at the University of Zurich. Synergies will arise from resources and data curation of the Geneva team, combined with cancer profiling data and expertise in genome data analysis of the Zurich group.Recently, the Zurich group has developed a method to quantify similarities between cell lines as well as type-matched primary tumors. Initially, 3675 genomic profiling experiments of 1539 distinct cell lines were processed and data was mapped to corresponding Cellosaurus entries. Probe-level genome data was visualised and re-calibrated, using arrayMap data and software. Future refinements of the method will include linkage disequilibrium (LD) models for CL identity mapping, to make identification and contamination status of a cell line unambiguous.

The primary aim of the proposed project will be to provide a high quality tool for researchers to assess their cell lines, collaboratively developed by the groups at Zurich & Geneva. This tool will provide a two-step identification of the cell lines. First step is genomic cell line fingerprinting based on genomic variation profiles and - where available - LD block analysis. In a second step, cell line variation data is compared to the vast arrayMap & Progenetix cancer datasets, providing a similarity score for the genome of interest compared to primary tumor profiles. Our resource will provide researcher in the areas of cancer genomics, physiology and pharmacology with an important tool for optimising resource use and guaranteeing correct interpretation of expensive and time consuming experiments. Support of this Data Science proposal through the UNIGE - UZH collaborative framework would allow us to develop this proposal into a long-term strategy with appropriate funding support and increasing collaborative participation.

projects
Participants
Prof. Dr. Amos Bairoch
University of Geneva
Prof. Dr. Michael Baudis
University of Zurich
Rahel Paloots
University of Zurich