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

Male reproductive genes experience rapid evolution and turnover across corbiculate bees.

Slater G*, Pereira Costa C, Gloag R, Irimia M, Ramirez S, Waterhouse RM, Ruzzante L, Dapper A,

Harpur B, IN REVIEW, 2026.

Climatic drivers of Plasmopara viticola oospore germination: Integrating long-term monitoring

into predictive modeling.

Leoni S, Ruzzante L, Fabre AL, Kasparian J, Wolf JP, Dubuis PH*, OENO One, 2026.

https://doi.org/10.20870/oeno-one.2026.60.3.9963 

Dysphagia in surgical critically ill patients: a post-hoc analysis of the DYnAMICS study.

Bertschi D*, Rotondo F, Ruzzante L, Waskowski J, Pfortmueller CA, Schefold JC, IN REVIEW, 2026.

Smart Agriculture using Digital Holography and Artificial Intelligence.

Basso T, Leoni S, Kartiyasa A, Berti N, Ruzzante L, Schnée S, Fabre AL, Hewison S, Kasparian J,

Dubuis PH, Wolf JP*, Frontiers in Plant Science, 2026.

https://doi.org/10.3389/fpls.2026.1871510 

Quadruplex real-time PCR targeting airborne spores of grapevine pathogens.

Leoni S, Carisse O, Ruzzante L, Fabre AL, Schnée S, Dubuis PH*, IN PRESS, 2025.

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5956303 

Entomopathogenic nematodes as an effective and sustainable alternative to control the fall

armyworm in Africa.

Fallet P, Bazagwira D, Ruzzante L, Ingabire G, Levivier S, Bustos-Segura C, Kajuga J, Toepfer S,

Turlings TCG*, PNAS Nexus, 2024.

https://doi.org/10.1093/pnasnexus/pgae122p1 

Influence of fluid accumulation on major adverse kidney events in critically ill patients — an

observational cohort study.

Hofer DM*, Ruzzante L, Waskowski J, Messmer AS, Pfortmueller CA, Annals of Intensive Care, 2024.

https://doi.org/10.1186/s13613-024-01281-7 

The impact of religion on changes in end-of-life practices in European intensive care units: a

comparative analysis over 16 years.

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, Intensive Care Medicine, 2023.

https://doi.org/10.1007/s00134-023-07228-z 

Anopheles mosquitoes reveal new principles of 3D genome organization in insects.

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*, Nature Communications, 2022.

https://doi.org/10.1038/s41467-022-29599-5 

Evolutionary-functional genomics for an enhanced resolution of arthropod gene function.

Ruzzante L*, Doctoral Thesis, SERVAL - UNIL IRIS, 2022.

https://iris.unil.ch/entities/publication/33c69b34-095c-4a34-a922-b3655362cb22 

Varying invertebrate biodiversity patterns among biodynamic, organic, and conventional viti-

culture.

Bosco L*, Siegenthaler D, Ruzzante L, Jacot A, Arlettaz R, Frontiers in conservation science, 2022.

https://doi.org/10.3389/fcosc.2022.837551 

Functional constraints on insect immune system components govern their evolutionary trajec-

tories.

Ruzzante L, Feron R, Reijnders MJ, ThiÃľbaut A, Waterhouse RM*, Molecular biology and evolution,

2022.

https://doi.org/10.1093/molbev/msab352 

Genus-wide characterization of bumblebee genomes provides insights into their evolution and

variation in ecological and behavioral traits.

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., Molecular biology and evolution, 2021.

https://doi.org/10.1093/molbev/msaa240 

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome as-

semblies.

Waterhouse RM*, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJ, Feron R, BÃľrard S,

George P, Hahn MW, Howell PI, Sharakov IV* et al., BMC biology, 2020.

https://doi.org/10.1186/s12915-019-0728-3 

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary

Alkali Bee (Halictidae: Nomia melanderi).

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, G3: Genes|Genomes|Genetics, 2019.

https://doi.org/10.1534/g3.118.200865 

Of genes and genomes: mosquito evolution and diversity.

Ruzzante L, Reijnders MJ, Waterhouse RM*, Trends in parasitology, 2018.

https://doi.org/10.1016/j.pt.2018.10.003 

Genome sequence of the wheat stem sawfly, Cephus cinctus, representing an early-branching

lineage of the Hymenoptera, illuminates evolution of hymenopteran chemoreceptors.

Robertson HM*, Waterhouse RM*, Walden KK, Ruzzante L, Reijnders MJ, Coates BS, Legeai F, Gress

JC, Biyiklioglu S, Weaver DK, Wanner KW, Genome biology and evolution, 2018.

https://doi.org/10.1093/gbe/evy2322 

The effects of management regime on arthropod communities in Argentinian vineyards.

Ruzzante L*, Master Thesis, UNIBE, 2022.

https://www.cb.iee.unibe.ch/unibe/portal/fak_naturwis/d_dbio/b_ioekev/abt_cb/content/e58879/e480453/e1268914/Ruzzante_MSc2016_2017_eng.pdf 

Peer Reviews

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

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

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

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

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

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.