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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 | 2023 | ...

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

Chromosome-level organization of the regulatory genome in the Drosophila nervous system.

Mohana G., Dorier J., Li X., Mouginot M., Smith R.C., Malek H., Leleu M., Rodriguez D., Khadka J., Rosa P. et al. Cell. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_314CD51C5560]

Significant Reduction of Radiation Exposure Using Specific Settings of the O-Arm for Percutaneous Cementoplasty in Accordance With the ALARA Principle.

Prod'homme M., Grasset D., Akiki A., Helfer L., Dietrich G., Müller J.P., Tomasoni M., Sellami M., Boscherini D. International journal of spine surgery. Peer-reviewed.

[DOI][Pmid][serval:BIB_0B026171EC4C]

Boost of innate immunity cytokines as biomarkers of response to extracorporeal photopheresis in leukaemic cutaneous T-cell lymphoma patients.

Tsai Y.C., Schlaepfer T., Ignatova D., Chang Y.T., Valaperti A., Amarov B., Blanchard G., Pehr K., Vonow-Eisenring M., Urosevic-Maiwald M. et al. The British journal of dermatology. Peer-reviewed.

[DOI][Pmid][serval:BIB_ACBD06166FA1]

2023

Genetic insights into the age-specific biological mechanisms governing human ovarian aging.

Ojavee S.E., Darrous L., Patxot M., Läll K., Fischer K., Mägi R., Kutalik Z., Robinson M.R., 2023/09/07. American journal of human genetics, 110 (9) pp. 1549-1563. Peer-reviewed.

[DOI][Pmid][serval:BIB_278672D79D5D]

preview resource BIB_E95C7A7DDD8F.P002

Genome-wide Association Studies of Retinal Vessel Tortuosity Identify Numerous Novel Loci Revealing Genes and Pathways Associated With Ocular and Cardiometabolic Diseases.

Tomasoni M., Beyeler M.J., Vela S.O., Mounier N., Porcu E., Corre T., Krefl D., Button A.L., Abouzeid H., Lazaros K. et al., 2023/09. Ophthalmology science, 3 (3) p. 100288. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E95C7A7DDD8F]

Chromosomal deletions on 16p11.2 encompassing SH2B1 are associated with accelerated metabolic disease.

Hanssen R., Auwerx C., Jõeloo M., Sadler M.C., Estonian Biobank Research Team, Henning E., Keogh J., Bounds R., Smith M., Firth H.V. et al., 2023/08/15. Cell reports. Medicine, 4 (8) p. 101155. Peer-reviewed.

[DOI][Pmid][serval:BIB_67978CA3D37E]

Response to Bassett et al.

Zamariolli M., Auwerx C., Sadler M.C., van der Graaf A., Lepik K., Schoeler T., Moysés-Oliveira M., Dantas A.G., Melaragno M.I., Kutalik Z., 2023/07/06. American journal of human genetics, 110 (7) pp. 1219-1220. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_01B60F44C10B]

CD38 Targeting Holds Potential for the Treatment of Aggressive Refractory Cutaneous T-Cell Lymphomas.

Pavlova O., Tsai Y.C., Chang Y.T., Vonow Eisenring M., Guenova E., 2023/07. The Journal of investigative dermatology, 143 (7) pp. 1122-1126. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_589F94F08AFD]

preview resource BIB_08B78C732656.P001

Multi-layered genetic approaches to identify approved drug targets

Sadler Marie C., Auwerx Chiara, Deelen Patrick, Kutalik Zoltán, 2023/07. Cell Genomics, 3 (7) p. 100341. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_08B78C732656]

Bias correction for inverse variance weighting Mendelian randomization.

Mounier N., Kutalik Z., 2023/06. Genetic epidemiology, 47 (4) pp. 314-331. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_F65931571130]

PascalX: a Python library for GWAS gene and pathway enrichment tests.

Krefl D., Brandulas Cammarata A., Bergmann S., 2023/05/04. Bioinformatics, 39 (5) pp. btad296. Peer-reviewed.

[DOI][Pmid][serval:BIB_D8824EBDC2F5]

Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition.

Hansen S.B., Bozzi D., Mak SST, Clausen C.G., Nielsen T.K., Kodama M., Hansen L.H., Gilbert MTP, Limborg M.T., 2023/05. Genomics, 115 (3) p. 110629. Peer-reviewed.

[DOI][Pmid][serval:BIB_5BEFC9E5466B]

Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization.

Lavanchy E., Goudet J., 2023/05. Molecular ecology resources, 23 (4) pp. 787-802. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_B16DA1524CF8]

preview resource BIB_3C3B7E71A649.P001

A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.

Ghannoum S., Fantini D., Zahoor M., Reiterer V., Phuyal S., Leoncio Netto W., Sørensen Ø., Iyer A., Sengupta D., Prasmickaite L. et al., 2023/04. PLoS computational biology, 19 (4) pp. e1010995. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_3C3B7E71A649]

preview resource BIB_EBB87EC8BBD4.P001

QuantImage v2: a comprehensive and integrated physician-centered cloud platform for radiomics and machine learning research.

Abler D., Schaer R., Oreiller V., Verma H., Reichenbach J., Aidonopoulos O., Evéquoz F., Jreige M., Prior J.O., Depeursinge A., 2023/03/22. European radiology experimental, 7 (1) p. 16. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_EBB87EC8BBD4]

preview resource BIB_33296666D7F5.P001

Exploiting the mediating role of the metabolome to unravel transcript-to-phenotype associations.

Auwerx C., Sadler M.C., Woh T., Reymond A., Kutalik Z., Porcu E., 2023/03/09. eLife, 12 pp. e81097. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_33296666D7F5]

preview resource BIB_4691B7A968A0.P001

Whole-genome doubling drives oncogenic loss of chromatin segregation.

Lambuta R.A., Nanni L., Liu Y., Diaz-Miyar J., Iyer A., Tavernari D., Katanayeva N., Ciriello G., Oricchio E., 2023/03. Nature, 615 (7954) pp. 925-933. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_4691B7A968A0]

preview resource BIB_7F288BABFB22.P001

Genome structures resolve the early diversification of teleost fishes.

Parey E., Louis A., Montfort J., Bouchez O., Roques C., Iampietro C., Lluch J., Castinel A., Donnadieu C., Desvignes T. et al., 2023/02/10. Science, 379 (6632) pp. 572-575. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_7F288BABFB22]

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Masters thesis

Publications (4)

preview resource BIB_8C9AFDB32534.P001

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]

preview resource BIB_62F3B9F51435.P001

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]

preview resource BIB_A82A763E0837.P001

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

Publications (15)

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_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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