Livio Ruzzante, Ph.D.

February 9, 2025

ORCID: https://orcid.org/0000-0002-8693-8678

Completed Degrees

• Ph.D. in Life Sciences (Unil), doctoral schools:

Integrative and Experimental Computational Biology (now Quantitative Biology):
https://www.unil.ch/quantitative-biology/en/home/menuinst/about.html

StarOmics: https://biologie.cuso.ch/staromics/welcome

Ecology and Evolutionary Biology: https://biologie.cuso.ch/ecology-evolution/welcome 

• Master of Science in Biology (Unine), specialisations:

Conservation Biology, Biodiversity & Evolution, Sustainable Agriculture

Program details: https://www.unine.ch/formation/master-of-science-in-biology 

• Bachelor of Science in Life Sciences Engineering (EPFL)

Program details: https://www.epfl.ch/education/bachelor/programs/life-sciences-engineering/ 

Publications

•  Fallet P, Bazagwira D, Ruzzante L, Ingabire G, Levivier S, Bustos-Segura C, Kajuga J, Toepfer S, Turlings TCG*, Entomopathogenic nematodes as an effective and sustainable alternative to control the fall armyworm in Africa.

PNAS Nexus, 2024, https://doi.org/10.1093/pnasnexus/pgae122.

•  Hofer DM*, Ruzzante L, Waskowski J, Messmer AS, Pfortmueller CA, Influence of fluid accumulation on major adverse kidney events in critically ill patients — an observational cohort study.

Annals of Intensive Care, 2024, https://doi.org/10.1186/s13613-024-01281-7.

•  Schefold JC*, Ruzzante L*, Sprung CL, Gruber A, Soreide E, Cosgrove J, Mullick S, Papathanakos G, Koulouras V, Azevedo Maia P, Ricou B, Posch M, Metnitz P, Bülow HH, Avidan A on behalf of the ETHICUS II Study Group, The impact of religion on changes in end-of-life practices in European intensive care units: a comparative analysis over 16 years.

Intensive Care Medicine, 2023, https://doi.org/10.1007/s00134-023-07228-z.

•  Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina P, Liang J, Reijnders MJ, Ruzzante L, Feron R, Waterhouse RM, Wu Y, Mao C, Tu Z, Sharakhov IV*, Fishman V*, Anopheles mosquitoes reveal new principles of 3D genome organization in insects.

Nature Communications, 2022, https://doi.org/10.1038/s41467-022-29599-5.

•  Bosco L*, Siegenthaler D, Ruzzante L, Jacot A, Arlettaz R, Varying invertebrate biodiversity patterns among biodynamic, organic, and conventional viticulture. Frontiers in conservation science, 2022, https://doi.org/10.3389/fcosc.2022.837551.

•  Ruzzante L, Feron R, Reijnders MJ, Thibaut A, Waterhouse RM*, Functional constraints on insect immune system components govern their evolutionary trajectories.

Molecular biology and evolution, 2021, https://doi.org/10.1093/molbev/msab352.

•  Sun C*, Huang J, Wang Y, Zhao X, Su L, Thomas GW, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Ruzzante L, Waterhouse RM* et al., Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits.

Molecular biology and evolution, 2021, https://doi.org/10.1093/molbev/msaa240.

•   Waterhouse RM*, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJ, Feron R, Brard S, George P, Hahn MW, Howell PI, Sharakov IV* et al., Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.

BMC biology, 2020, https://doi.org/10.1186/s12915-019-0728-3.

•  Kapheim KM*, Pan H, Li C, Blatti C, Harpur BA, Ioannidis P, Jones BM, Kent CF, Ruzzante L, Sloofman L, Stolle E, Waterhouse RM, Zayed A, Zhang G, Wcislo WT, Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi).

G3: Genes|Genomes|Genetics, 2019, https://doi.org/10.1534/g3.118.200865.

•   Ruzzante L, Reijnders MJ, Waterhouse RM*, Of genes and genomes: mosquito evolution and diversity.

Trends in parasitology, 2018, https://doi.org/10.1016/j.pt.2018.10.003

•  Robertson HM*, Waterhouse RM*, Walden KK, Ruzzante L, Reijnders MJ, Coates BS, Legeai F, Gress JC, Biyiklioglu S, Weaver DK, Wanner KW, Genome sequence of the wheat stem sawfly, Cephus cinctus, representing an early-branching lineage of the Hymenoptera, illuminates evolution of hymenopteran chemoreceptors.

Genome biology and evolution, 2018, https://doi.org/10.1093/gbe/evy232.

Peer Reviews

•    Mantica Federica, et al., Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects. Nature, 2022.

•    Richter Daniel J., et al., EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. PCI Genomics, 2022.

•    Mathers Thomas C, Improved genome assembly and annotation of the soybean aphid (Aphis glycines Matsumura). G3: Genes, Genomes, Genetics, 2020.

•    Almudi Isabel, et al., Genomic adaptations to aquatic and aerial life in mayflies and the origin of wings in insects. Nature Communications, 2019.

•    Li Sheng, et al., The genomic and functional landscapes of developmental plasticity in the American cockroach. Nature Communications, 2018.

Conferences & Workshops

•    1-5 Jul 2024, World Aerobiology, Vilnius (LT): talk

•    25-27 Jan 2024, Agrovina, Martigny (CH): exhibition stand, outreach

•    14-15 Jun 2022, Swiss Institute of Bioinformatics Days, Biel (CH): talk

•    5-9 Sep 2020, European Conference of Computational Biology, Sitges (SP, virtual)

•   21-23 Jul 2020, Arthropod Genomics Symposium, (International, virtual): poster

•    16-17 Jun 2020, Phylogenomics & Comparative Genomics, IBE Barcelona (SP, virtual): poster

•    26-27 Jun 2020, Swiss Institute of Bioinformatics Days, Lausanne (CH, virtual): poster

•    13 Feb 2020, Imperial College London, Christophides Lab internal seminar, London (UK): talk

•    23 Jul 2019, Molecular and population biology of mosquitoes and other disease vectors, Kolymbari, Chania (GR): poster

•    13 Jun 2019, Arthropod Genomics Symposium, Manhattan KS (US): talk, poster

•    15 Nov 2018, Symposium of Ecology and Evolution Doctoral Students 2018, Neuchˆatel (CH): talk

•    2-6 Jul 2018, XI European Congress of Entomology, Naples (IT): talk, poster

•    28-29 Jun 2018, Swiss Institute of Bioinformatics PhD Training Network Retreat, Biel (CH): talk

•    26-27 Jun 2018, Swiss Institute of Bioinformatics Days, Biel (CH): lightning talk, poster, workshop assistance

•    7-9 Jun 2018, 11th Arthropod Genomics Symposium, Urbana-Champaign IL (US): poster, workshop assistance

•    Spring 2018, Les Mystères de l’UNIL, Lausanne (CH): university open-day for primary school classes, co-organisation and teaching

Teaching Assistance

•    Spring 2021, Introduction to Bioinformatics, Prof. Marc Robinson-Rechavi, University of Lausanne (CH): 2nd year Bachelor students

•   17 Sep 2020, Comparative Genomics - lectures and practicals, Prof. Robert Waterhouse, Swiss Institute of Bioinformatics (CH): aimed at PhD students, postdocs, and other researchers

•    Spring 2020, Introduction to Bioinformatics, Prof. Marc Robinson-Rechavi, University of Lausanne (CH): 2nd year Bachelor students

•    13 Jan 2020, Bioinformatics tools for Comparative Genomics, Prof. Robert Waterhouse, invited at the Imperial College London, London (UK): Master students

•    Autumn 2019, Introduction to Programming, Prof. Nicolas Salamin, University of Lausanne (CH): 2nd year Bachelor students

•    Spring 2019, Introduction to Bioinformatics Prof. Marc Robinson-Rechavi, University of Lausanne (CH): 2nd year Bachelor students

•    Autumn 2018, Introduction to Programming Prof. Nicolas Salamin, University of Lausanne (CH): 2nd year Bachelor students

•    Autumn 2018, Scientific Writing, Prof. Robert M. Waterhouse, University of Lausanne (CH): 1st year Master students

•    Spring 2018, Zoology Practicals, Prof. Tadeusz J. Kawecki, University of Lausanne (CH): 1st year Bachelor students

•    Autumn 2017, Scientific Writing, Prof. Robert M. Waterhouse, University of Lausanne (CH): 2nd year Bachelor students

•    Autumn 2013, General Physics I, Prof. Rolf Gruetter, Ecole Polytechnique F´ed´erale´ de Lausanne, EPFL (CH): 1st year Bachelor students

•    Autumn 2012, General Physics I, Prof. Rolf Gruetter, Ecole Polytechnique F´ed´erale´ de Lausanne, EPFL (CH): 1st year Bachelor students

Completed Doctoral School Courses

•    2021, Phylogenetics and Phylogenomics

•    2021, Introduction to Bayesian Inference in Practice

•    2020, Introduction to Adobe Illustrator

•    2020, Introduction to Machine Learning

•    2020, First steps with Python in Life Sciences

•    2020, Enrichment Analysis

•    2019, Lausanne Genomics Days

•    2019, Introduction to R Shiny

•    2019, Reasoning and Logic in Experimental and Computational Biology

•    2019, Reviews in Quantitative Biology

•    2018, Better coding practices (with Damian Conway)

•    2018, Intermediate stats: data analysis in practice

•    2018, High Performance Computing (HPC) in Life Science

•    2018, Winter school — Whole genome sequence assembly and annotation: the long and the short of it

Student Supervisions

•    2021, Eastern Africa Network for Bioinformatics Training, Master (MSc) project: Evolutionary features of the Glossina genes.

•    2020, University of Lausanne (CH), Internship: Quantification of gene losses across Arthropoda.

•    2019, University of Lausanne (CH), First Step Master (MSc) Project: Comparative genomics of adaptive evolution in invertebrates.

•    2019, University of Lausanne (CH), Internship: Arthropod phylogenies: a systematic exploration of the available phylogenomics software.

Education

•    Ph.D. in Integrative and Experimental Computational Biology — Teaching assistant, 10/2017 - 03/2022, Dpt. of Ecology and Evolution - Faculty of Biology and Medicine - University of Lausanne (CH) Doctoral degree in evolution, bioinformatics, and comparative functional genomics. Modeling the evolutionary histories and generating automated putative function predictions of millions of arthropod genes by developing bioinformatics pipelines using phylogenomics approaches, gene orthology delineations, and novel evolutionary features through unsupervised clustering algorithms. The doctoral thesis work was entitled ”Evolutionary-functional genomics for an enhanced resolution of arthropod gene function” and led by Prof. Robert Waterhouse.

•    M.Sc. Biology, 09/2015 - 08/2017, Faculty of Biology - University of Neuchâtel (CH) Master of Science in Biology, with a focus on Biodiversity, Evolution and Sustainable Agriculture. The master thesis project was entitled ”The effects of management regime on arthropod communities in Argentinian vineyards” and led by Prof. Rapha¨el Arlettaz from the University of Bern in collaboration with the Universidad Nacional de Cuyo, Argentina.

•    B.Sc. Life Sciences Engineering, 09/2010 - 07/2014, Faculty of Life Sciences - Ecole Polytechnique Fédérale de Lausanne, EPFL (CH) Bachelor in Life Sciences and Bio-Engineering, the thesis project was entitled ”3-D mapping of motoneuron pools from different rat hindlimb muscles” and led by Prof. Grégoire Courtine.

•    European Baccalaureat, 07/2010, Scuola Europea, Varese (IT) Baccalaureat obtained with a special focus on philosophy, biology, mathematics, and Italian literature.

Internships

•  Spring 2016, Epidemiological modelling intern, Institute of Biology (Prof. Koella), University of Neuchâtel (CH). Modelling life history traits, senescence and virulence dynamics in the laboratory of ecology, and epidemiology of parasites. Development of differential equation systems and parametric searches in R.

•  Spring 2015, Brain activity modelling intern, Medical Image Processing Lab (Prof. Van de Ville), EPFL (CH). Simulating BOLD activity in focal epilepsy using TheVirtualBrain simulator.

•  Summer 2014, MATLAB scientist and lab technician, Translational Neural Engineering Lab (Prof. Micera), EPFL (CH). Assembly of electrodes, data recording, processing, and analysis. Programming MATLAB visualisations of electrical stimulation and locomotion tracking.

•  Summer 2012, Neuroprostethics lab intern, Center for Neuroprosthetics (Prof. Courtine), EPFL (CH). Exploring the recovery of locomotion after severe spinal cord injury. Benchwork included rat surgery, histology, staining, confocal microscopy, image processing, and 3D reconstructions.