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Faculty of Biology and Medicine

Doctoral Program in Quantitative Biology

Publications

Publications authored by QB PhD students

Publications | Masters and Phd thesis

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Publications

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In Press | 2024 | ...

Indigenous peoples in eastern Brazil: insights from 19<sup>th</sup> century genomes and metagenomes

Cruz Dávalos Diana Ivette, Arizmendi Cárdenas Yami Ommar, Bravo-Lopez Miriam Jetzabel, Neuenschwander Samuel, Reis Silvia, Bastos Murilo Q. R., Stenderup Jesper, Yediay Fulya Eylem, Villa-Islas Viridiana, Reyna-Blanco Carlos S. et al..

[DOI][serval:BIB_47F5B2CAEC7C]

Imputation of ancient genomes

Sousa da Mota Bárbara, Rubinacci Simone, Cruz Dávalos Diana Ivette, Amorim Carlos Eduardo G., Sikora Martin, Johannsen Niels N., Szmyt Marzena, Włodarczak Piotr, Szczepanek Anita, Przybyła Marcin M. et al..

[DOI][serval:BIB_AC8F25835B20]

In Press

Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.

Bastian F.B., Cammarata A.B., Carsanaro S., Detering H., Huang W.T., Joye S., Niknejad A., Nyamari M., Mendes de Farias T., Moretti S. et al. Nucleic acids research. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_3F567BF2FDA6]

A novel homozygous missense variant in POC1B causes cone dystrophy in a consanguineous Pakistani family.

Munir A., Khan I.U., Rashid A., Anwar I., Shah S., Oreshkov S., Ullah M., Khan H.A., Ullah U., Ahmad A. et al. Ophthalmic genetics. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_CC276CE83205]

Author Correction: Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

Pétremand R., Chiffelle J., Bobisse S., Perez MAS, Schmidt J., Arnaud M., Barras D., Lozano-Rabella M., Genolet R., Sauvage C. et al. Nature biotechnology. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_88A45E78E09C]

Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

Pétremand R., Chiffelle J., Bobisse S., Perez MAS, Schmidt J., Arnaud M., Barras D., Lozano-Rabella M., Genolet R., Sauvage C. et al. Nature biotechnology. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AF334A302D27]

SuperSpot: Coarse Graining Spatial Transcriptomics Data into Metaspots.

Teleman M., Ag Gabriel A., Hérault L., Gfeller D. Bioinformatics. Peer-reviewed.

[DOI][Pmid][serval:BIB_8C770A03F8F3]

Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinants.

Tonelli A., Cousin P., Jankowski A., Wang B., Dorier J., Barraud J., Zunjarrao S., Gambetta M.C. Developmental cell. Peer-reviewed.

[DOI][Pmid][serval:BIB_2A951E5FC6A3]

2024

Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening.

Santamaria-Martínez A., Epiney J., Srivastava D., Tavernari D., Varrone M., Milowich D., Letovanec I., Krueger T., Duran R., Ciriello G. et al., 2024/12/09. Nature communications, 15 (1) p. 10650. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_4335A47B02F4]

preview resource BIB_21A381994DAC.P001

The moulting arthropod: a complete genetic toolkit review.

Campli G., Volovych O., Kim K., Veldsman W.P., Drage H.B., Sheizaf I., Lynch S., Chipman A.D., Daley A.C., Robinson-Rechavi M. et al., 2024/12. Biological reviews of the Cambridge Philosophical Society, 99 (6) pp. 2338-2375. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_21A381994DAC]

preview resource BIB_8F26100816A9.P001

Too big to purge: persistence of deleterious Mutations in Island populations of the European Barn Owl (Tyto alba).

Lavanchy E., Cumer T., Topaloudis A., Ducrest A.L., Simon C., Roulin A., Goudet J., 2024/12. Heredity, 133 (6) pp. 437-449. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_8F26100816A9]

The evolution of reduced facilitation in a four-species bacterial community.

Piccardi P., Ulrich E., Garcia-Garcerà M., Martino R.D., Testa SEA, Mitri S., 2024/12. Evolution letters, 8 (6) pp. 828-840. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_C0328ED5D1E4]

PupilMetrics: a support system for preprocessing of pupillometric data and extraction of outcome measures.

Amiot V., Tomasoni M., Minier A., Gisselbaek S., Kawasaki A., Kostic C., 2024/11/20. Scientific reports, 14 (1) p. 28775. Peer-reviewed.

[DOI][Pmid][serval:BIB_9D8B03EDFF40]

Resistance Management for Cancer: Lessons from Farmers.

Seyedi S., Harris V.K., Kapsetaki S.E., Narayanan S., Saha D., Compton Z., Yousefi R., May A., Fakir E., Boddy A.M. et al., 2024/11/15. Cancer research, 84 (22) pp. 3715-3727. Peer-reviewed.

[DOI][Pmid][serval:BIB_94E89B6DCD10]

The recombination landscape of the barn owl, from families to populations.

Topaloudis A., Cumer T., Lavanchy E., Ducrest A.L., Simon C., Machado A.P., Paposhvili N., Roulin A., Goudet J., 2024/11/15. Genetics. Peer-reviewed.

[DOI][Pmid][serval:BIB_0FD5E043D8EA]

NOODAI: A webserver for network-oriented multi-omics data analysis and integration pipeline

Totu Tiberiu, Tomasoni Mattia, Bolck Hella Anna, Buljan Marija, 2024/11/11..

[DOI][serval:BIB_08FABBB47B5F]

preview resource BIB_CF9C4365E9CD.P001

Disentangling mechanisms behind the pleiotropic effects of proximal 16p11.2 BP4-5 CNVs.

Auwerx C., Moix S., Kutalik Z., Reymond A., 2024/11/07. American journal of human genetics, 111 (11) pp. 2347-2361. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_CF9C4365E9CD]

preview resource BIB_08552644537E.P001

Phenotypic and genetic characteristics of retinal vascular parameters and their association with diseases.

Ortín Vela S., Beyeler M.J., Trofimova O., Iuliani I., Vargas Quiros J.D., de Vries V.A., Meloni I., Elwakil A., Hoogewoud F., Liefers B. et al., 2024/11/06. Nature communications, 15 (1) p. 9593. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_08552644537E]

Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank.

Gaynor S.M., Joseph T., Bai X., Zou Y., Boutkov B., Maxwell E.K., Delaneau O., Hofmeister R.J., Krasheninina O., Balasubramanian S. et al., 2024/11. Nature genetics, 56 (11) pp. 2345-2351. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_DE85673FF31D]

When less is more: sketching with minimizers in genomics.

Ndiaye M., Prieto-Baños S., Fitzgerald L.M., Yazdizadeh Kharrazi A., Oreshkov S., Dessimoz C., Sedlazeck F.J., Glover N., Majidian S., 2024/10/14. Genome biology, 25 (1) p. 270. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E86014EEAF89]

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Masters thesis

Publications (4)

Automatic Grading of Vasculitis Inflammation in Fluorescein Angiography Images

Amiot Victor, Anjos Andre, 2023/02/21., EPFL, Odobez Jean-Marc (dir.).

[URN][serval:BIB_8C9AFDB32534]

Automatic Retinal Blood Velocity Estimation in the Living Human Retina, using AOSLO

Tsaritsyn Mikhail, Dubis Adam, 2022/09/05., EPFL, Salzmann Mathieu (dir.).

[serval:BIB_62F3B9F51435]

Computer Vision to investigate Choriocapillaris-like pattern in Transscleral Optical Images

Canton Diego, Mantel Irmela, Kowalczuk Laura Emmanuelle, 2022/09/02., EPFL, Moser Christophe (dir.).

[serval:BIB_A82A763E0837]

Computer Vision for in-vivo Analysis of Photoreceptors in Diabetic Patients

James Bardet, Adam Dubis, Chiara Eandi, Ferenc Sallo, 2022/07/18., EPFL, Alexander Mathis (dir.).

[serval:BIB_9BF46939AF4A]

Phd thesis

In preparation (1)

preview resource BIB_E419FABDF5B9.P003

Integrating the genetics of omics and diseases for drug-target and drug-response predictions

Sadler Marie Teresa Cathérine, Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[URN][serval:BIB_E419FABDF5B9]

Publications (27)

preview resource BIB_FD973D0CD126.P002

Investigating relationships between sequence conservation and function using multispecies whole genome alignments

Feron Romain, 2024/11/01., Université de Lausanne, Faculté de biologie et médecine, Waterhouse Robert (dir.).

[URN][serval:BIB_FD973D0CD126]

preview resource BIB_1BFE79774F1F.P002

Where rare meets common: Leveraging population cohorts to study rare copy-number variants

Auwerx Chiara Maria Paula, 2024/07/02., Université de Lausanne, Faculté de biologie et médecine, Reymond Alexandre (dir.).

[URN][serval:BIB_1BFE79774F1F]

preview resource BIB_7447169ECAA8.P003

Using genomics to measure the extent and consequences of inbreeding

Lavanchy Eléonore, 2024/04/12., Université de Lausanne, Faculté de biologie et médecine, Goudet Jérôme (dir.).

[URN][serval:BIB_7447169ECAA8]

Dissecting the functional consequences of missense mutations across contexts

Ho Uyen Linh, 2024., Université de Lausanne, Faculté de biologie et médecine, Van Leeuwen Jolanda (dir.).

[serval:BIB_8EC01CEE9E50]

Tale of Cancer Evolution : Insights from Co-mutation Analysis

IYER Arvind Krishnamurthy, 2024., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[URN][serval:BIB_C6CA557B0DFA]

An evolutionary genomics and behavioural approach to investigate the evolution of temperature preference in drosophilids

KAFLE Tanuj, 2024., Université de Lausanne, Faculté de biologie et médecine, Arguello Roman (dir.).

[serval:BIB_3C8C7F143968]

Imputation of ancient genomes and the genomic history of the Rapanui

TEIXEIRA DE SOUSA COELHO DA MOTA Bárbara, 2024., Université de Lausanne, Faculté de biologie et médecine, Malaspinas Anna-Sapfo (dir.).

[URN][serval:BIB_B03FDDD4ECB2]

Unbiased screening of DNA factors important for gene insulation

Tonelli Anastasiia, 2024., Université de Lausanne, Faculté de biologie et médecine, Gambetta Maria Cristina (dir.).

[serval:BIB_ADA90B6A9C8D]

Role of immune regulators in skin disorders

Tsai Yi-Chien, 2024., Université de Lausanne, Faculté de biologie et médecine, Guenova Emmanuella (dir.).

[URN][serval:BIB_B89F691DF7F1]

Computational models to characterize spatial intra-tumor heterogeneity

VARRONE Marco, 2024., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[serval:BIB_B18CB8C81268]

Genomic differences in gut microbiota composition between nurses and foragers of the honeybee Apis mellifera

Baud Gilles, 2023/06/26., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[serval:BIB_364E28990D8D]

preview resource BIB_27A1E9610087.P002

Quantitative genetic variation in symbiotic fungi and its effect on fungal gene expression

Cruz Corella Joaquim, 2023/06/23., Université de Lausanne, Faculté de biologie et médecine, Sanders Ian (dir.).

[URN][serval:BIB_27A1E9610087]

Taxonomic and functional diversity of Swiss cheese starter cultures

Somerville Vincent, 2023/01/10., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[serval:BIB_014DCD5701D2]

Genomic history of ancient populations in the Americas

CRUZ DÁVALOS Diana Ivette, 2023., Université de Lausanne, Faculté de biologie et médecine, Malaspinas Anna-Sapfo (dir.).

[serval:BIB_410DF8130F27]

preview resource BIB_9670460764B5.P002

Robust Causal Inference Methods to Assess Risk Factors for Common Diseases

Darrous Liza, 2023., Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[URN][serval:BIB_9670460764B5]

preview resource BIB_2032C8B1B0F0.P003

A systems genetics approach for sleep regulation

Gobet Nastassia, 2023., Université de Lausanne, Faculté de biologie et médecine, Xenarios Ioannis (dir.).

[URN][serval:BIB_2032C8B1B0F0]

preview resource BIB_49346D79C118.P001

Haplotypes in complex traits genetics

Hofmeister Robin, 2023., Université de Lausanne, Faculté de biologie et médecine, Delaneau Olivier (dir.).

[URN][serval:BIB_49346D79C118]

Rendering the Epigenetic Cloud: Developing Novel Anti-Aging Approaches Based on Chemical Reprogramming

PAINE Patrick Treat, 2023., Université de Lausanne, Faculté de biologie et médecine, Ocampo Mendez Alejandro (dir.).

[serval:BIB_B02EFAC07CF8]

Age-at-onset informed analysis of complex trait genetics

Ojavee Sven Erik, 2022., Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[serval:BIB_091781AA069B]

preview resource BIB_53C85E2623EE.P001

Validating and optimizing the specificity of imaging biomarkers for personalized medicine

Oreiller Valentin, 2022., Université de Lausanne, Faculté de biologie et médecine, Prior John O. (dir.).

[URN][serval:BIB_53C85E2623EE]

preview resource BIB_4C2394C34F24.P001

Genetic basis of common complex traits

Patxot Bertran Marion, 2022., Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[URN][serval:BIB_4C2394C34F24]

preview resource BIB_247B252C9293.P001

Machine learning to infer the process of coevolution under the light of evolution

RAMA BALLESTEROS Rocío, 2022., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_247B252C9293]

preview resource BIB_07B22E00B8C7.P001

Towards Big data comparative genomics

Rossier Victor, 2022., Université de Lausanne, Faculté de biologie et médecine, Dessimoz Christophe (dir.).

[URN][serval:BIB_07B22E00B8C7]

preview resource BIB_0FA20CE34775.P003

Characterizing obesity and its consequences on health

Sulc Jonathan, 2021/11/12., Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[URN][serval:BIB_0FA20CE34775]

preview resource BIB_698632559905.P001

Defining the mechanism of action in a novel class of anti-PD-1 antibodies

Joo Victor, Fenwick Craig, 2021., Université de Lausanne, Faculté de biologie et médecine, Pantaleo Giuseppe (dir.).

[URN][serval:BIB_698632559905]

preview resource BIB_03589C92E22E.P001

Mendelian randomization and its application to genome-wide association studies

MOUNIER Ninon, 2021., Université de Lausanne, Faculté de biologie et médecine, Kutalik Zoltán (dir.).

[URN][serval:BIB_03589C92E22E]

Large-scale biomedical data analysis: from molecules to organs

Tomasoni Mattia, 2021., Université de Lausanne, Faculté de biologie et médecine, Bergmann Sven (dir.).

[serval:BIB_8C04C58B3709]

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