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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

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

Auwerx C., Moix S., Kutalik Z., Reymond A. American journal of human genetics. Peer-reviewed.

[DOI][Pmid][serval:BIB_CF9C4365E9CD]

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. Biological reviews of the Cambridge Philosophical Society. Peer-reviewed.

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

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. Nature genetics. Peer-reviewed.

[DOI][Pmid][serval:BIB_DE85673FF31D]

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. Heredity. Peer-reviewed.

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

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]

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. Cancer research. Peer-reviewed.

[DOI][Pmid][serval:BIB_94E89B6DCD10]

2024

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]

Importance of OCT-derived biomarkers for the recurrence of central serous chorioretinopathy using statistics and predictive modelling.

Seiler E., Delachaux L., Cattaneo J., Garjani A., Martin T., Duriez A., Baffou J., Mousavi S., Meloni I., Bergin C. et al., 2024/10/13. Scientific reports, 14 (1) p. 23940. Peer-reviewed.

[DOI][Pmid][serval:BIB_91EAFB429474]

Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study.

Friligkou E., Løkhammer S., Cabrera-Mendoza B., Shen J., He J., Deiana G., Zanoaga M.D., Asgel Z., Pilcher A., Di Lascio L. et al., 2024/10. Nature genetics, 56 (10) pp. 2036-2045. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_EDBAC44C578C]

Towards predicting the geographical origin of ancient samples with metagenomic data.

Bozzi D., Neuenschwander S., Cruz Dávalos D.I., Sousa da Mota B., Schroeder H., Moreno-Mayar J.V., Allentoft M.E., Malaspinas A.S., 2024/09/18. Scientific reports, 14 (1) p. 21794. Peer-reviewed.

[DOI][Pmid][serval:BIB_4C67F4828BA4]

A look beyond the QR code of SNARE proteins.

Yadav D., Hacisuleyman A., Dergai M., Khalifeh D., Abriata L.A., Peraro M.D., Fasshauer D., 2024/09. Protein science, 33 (9) pp. e5158. Peer-reviewed.

[DOI][Pmid][serval:BIB_1BE4B72B9C35]

preview resource BIB_A29B2514B933.P001

Association of pathogenic determinants of Fusobacterium necrophorum with bacteremia, and Lemierre's syndrome.

Carrara A., Bertelli C., Gardiol C., Marquis B., Andrey D.O., Schrenzel J., Pillonel T., Greub G., 2024/08/27. Scientific reports, 14 (1) p. 19804. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_A29B2514B933]

preview resource BIB_A21A8D0481BB.P001

Cohort Builder: A Software Pipeline for Generating Patient Cohorts with Predetermined Baseline Characteristics from Medical Records and Raw Ophthalmic Imaging Data

Mousavi Sepehr, Garjani Ali, Elwakil Adham, Brock Laurent Pierre, Dherse Alexandre, Forestier Edwige, Palaz Marine, Seiler Emilien, Duriez Alexia, Martin Thibaud et al., 2024/08/22. pp. 1151-1155 dans Digital Health and Informatics Innovations for Sustainable Health Care Systems, IOS Press.

[URN][DOI][Pmid][serval:BIB_A21A8D0481BB]

Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes.

Brunner M., Lopez-Rodriguez D., Estrada-Meza J., Dali R., Rohrbach A., Deglise T., Messina A., Thorens B., Santoni F., Langlet F., 2024/08/04. Nature communications, 15 (1) p. 6604. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_0B3E856627D3]

pyTWMR: transcriptome-wide Mendelian randomization in python.

Oreshkov S., Lepik K., Santoni F., 2024/08/02. Bioinformatics, 40 (8). Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_975C14D52EEC]

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

Piccardi Philippe, Ulrich Eric, Garcia-Garcerà Marc, Martino Rita Di, Testa Samuele E A, Mitri Sara, 2024/07/19. Evolution Letters.

[DOI][WoS][serval:BIB_C0328ED5D1E4]

Building and analyzing metacells in single-cell genomics data.

Bilous M., Hérault L., Gabriel A.A., Teleman M., Gfeller D., 2024/07. Molecular systems biology, 20 (7) pp. 744-766. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_D0B831889E85]

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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 (24)

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]

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]

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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