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DBC News is a monthly publication that seeks to inform first and foremost faculty members, researchers and students. It also reaches out to a wider community - Department of Computational Biology partners, visiting faculty and friends.
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Alongside the Department's website it is a complementary means of keeping abreast of the Department's rich and diversified scientific activities - visiting faculty, exceptional conferences, publications, awards, appointments, calls for papers and research, ...
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DBC new Director
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We are pleased to announce that the direction of the department will be shared between Profs Giovanni Ciriello and Nicolas Salamin from January 1st. There will be a transition period during 2025 until Giovanni takes the full role of director in 2026.
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The whole DBC extends the warmest of welcomes to new members.
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I am excited to join Lehtinen Group as a PhD student to work on the evolution of antibiotic resistance in bacteria through mathematical modelling, and hopefully provide useful insight into this major health problem.
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Trained as a physicist, I have long been fascinated by modeling ecological systems and the evolution of populations. Currently, I am a postdoctoral researcher in Sonja Lehtinen's group, where I focus on studying microbiota assembly and the dynamics of antibiotic resistance.
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"Testing evolutionary hypothesis using a novel database of population genetic diversity and species ranges"
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January 30th - DBC Seminar
with Dr. Meike Ramon
Assistant Professor and Swiss National Science Foundation PRIMA (Promoting Women in Academia) Fellow - AFC Lab
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"Natural and synthetic face recognition research: fundament and societal benefits"
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January 14th - Mapping your path workshop
An opportunity for doctoral and postdoc researchers from all UNIL faculties to review their current situation and how they could imagine their next career steps.
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February 6th – February 7th - Lausanne (Gen)Omics Days 2025
The Lausanne Genomics Days is a 2-day international conference meant to share advances in (Gen)Omics and their impact on biological research, applied to a wide range of topics.
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February 12th - SDM-CH: Modelling species distributions in Switzerland for science and practice
Are you interested in modeling species distribution in Switzerland for science and applications? Join the SDM-CH symposium to learn more about existing tools and predictions in Switzerland, as well as ongoing projects and future needs.
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Biology25 conference -
February 13-14
Biology25 is the largest conference dedicated to organismal biology in Switzerland and serves as the annual joint meeting of the Swiss Zoological Society, the Swiss Botanical Society, and the Swiss Systematics Society. It offers a great opportunity for PhD students and early-career researchers to showcase their research.
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July 27-31st - Leena Peltonen School of Human Genetics summer school
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This prestigious summer school brings together 20 leaders in human genetics with 20 students close to their PhD completion. This isn't just a course; it's a science summer camp designed for in-depth exploration of the future of genomics through vibrant discussions and debates, with the participation of amazing researchers such as Prof. Zoltán Kutalik.
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📅 When? : July 27-31, 2025
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📍 Where? : Wellcome Genome Campus, Hinxton, UK
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📝 Application deadline : March 7, 2025
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How do scientists find genes using computers?
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Where to find your DNA in the Genes?
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All the events of the APNS here
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What follows is a small sampling of recently published research across the department — for a more complete list of publications, visit PubMed. If there is a paper you would like to see highlighted in the next issue of the newsletter, please email us.
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With Diego A Hartasánchez - The study explored the role of gene expression variability in the size and shape of Arabidopsis sepals. Researchers found that cell-wall related genes, which show high variability in expression, contribute to the robustness of sepal size. Interestingly, sepal size variability in mutants correlated with the mean gene expression of the corresponding gene in wild-type plants, rather than with gene expression variation. This suggests that cell-wall related genes help maintain consistent sepal size.
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Six novel Bifidobacterium strains were isolated from the honey stomach of Apis mellifera. These strains are Gram-positive, non-motile, non-sporulating, and facultatively anaerobic. Genetic analysis revealed that some strains are closely related to Bifidobacterium polysaccharolyticum, while others are related to Bifidobacterium apousia. Phenotypic and genotypic characterization confirmed that strain H1HS16NT represents a novel species, proposed as Bifidobacterium kimbladii sp. nov.
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Orthology inference at scale with FastOMA - With Sina Majidian, Yannis Nevers, Alex Warwick Vesztrocy , Stefano Pascarelli, David Moi, Natasha Glover, Christophe Dessimoz
The increasing volume of genome data, with a goal to sequence 1.5 million eukaryotes in a decade, poses challenges for traditional genomics methods. To address this, 'FastOMA' offers linear scalability for orthology inference, allowing the processing of thousands of eukaryotic genomes in a day. It maintains the accuracy and resolution of the established Orthologous Matrix (OMA) approach. FastOMA is available on GitHub.
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Role of Mutual Information Profile Shifts in Assessing the Pathogenicity of Mutations on Protein Functions: The Case of Pyrin Variants Associated With Familial Mediterranean Fever - With Aysima Hacisuleyman - This study introduces a method to assess the pathogenicity of pyrin protein mutations using mutual information (MI) to measure correlations between residue motions and phenotypic changes. The concept of MI profile shift quantifies changes in MI upon mutation, providing insights into critical residue interactions. Applied to pyrin variants associated with familial Mediterranean fever (FMF), the method highlights the impact of mutations on protein stability and function. Negative MI shifts indicate severe functional effects, while positive shifts suggest potential compensatory mechanisms. The study emphasizes the need for comprehensive analysis considering genetic, environmental, and stochastic factors.
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A Novel method for quantifying fluctuations in wearable derived daily cardiovascular parameters across the menstrual cycle - With David M Presby
This study developed a novel measure to quantify cardiovascular fluctuations (cardiovascular amplitude) using wrist-worn biometric data from 11,590 participants across 45,811 menstrual cycles. Resting heart rate (RHR) and heart rate variability (RMSSD) showed regular patterns, with RHRmin and RMSSDmax at cycle day 5, RHRmax at day 26, and RMSSDmin at day 27. Cardiovascular amplitude was lower in older participants and those using birth control, indicating it may reflect hormonal fluctuations. This metric could provide non-invasive monitoring of female physiology and health throughout the menstrual cycle.
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The impact of self-report inaccuracy in the UK Biobank and its interplay with selective participation - With Tabea Schoeler, Zoltán Kutalik
This study developed a novel measure to quantify cardiovascular fluctuations (cardiovascular amplitude) using wrist-worn biometric data from 11,590 participants across 45,811 menstrual cycles. Resting heart rate (RHR) and heart rate variability (RMSSD) showed regular patterns, with RHRmin and RMSSDmax at cycle day 5, RHRmax at day 26, and RMSSDmin at day 27. Cardiovascular amplitude was lower in older participants and those using birth control, indicating it may reflect hormonal fluctuations. This metric could provide non-invasive monitoring of female physiology and health throughout the menstrual cycle.
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Decoding the Clinical and Molecular Signatures of EGFR Common, Compound, and Uncommon Mutations in Non-Small Cell Lung Cancer - With Daniele Tavernari , Giovanni Ciriello - This study developed a novel measure to quantify cardiovascular fluctuations (cardiovascular amplitude) using wrist-worn biometric data from 11,590 participants across 45,811 menstrual cycles. Resting heart rate (RHR) and heart rate variability (RMSSD) showed regular patterns, with RHRmin and RMSSDmax at cycle day 5, RHRmax at day 26, and RMSSDmin at day 27. Cardiovascular amplitude was lower in older participants and those using birth control, indicating it may reflect hormonal fluctuations. This metric could provide non-invasive monitoring of female physiology and health throughout the menstrual cycle.
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Are you an alumnus or former employee of the department? Email us your news and updates to include in an upcoming newsletter!
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