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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

Building and analyzing metacells in single-cell genomics data.

Bilous M., Hérault L., Gabriel A.A., Teleman M., Gfeller D. Molecular systems biology. Peer-reviewed.

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

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][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]

2024

A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes.

Kuhl H., Tan W.H., Klopp C., Kleiner W., Koyun B., Ciorpac M., Feron R., Knytl M., Kloas W., Schartl M. et al., 2024/06/05. Nature communications, 15 (1) p. 4781. Peer-reviewed.

[DOI][Pmid][serval:BIB_F63BB3113A04]

preview resource BIB_5DF519357694.P001

Breaking down causes, consequences, and mediating effects of telomere length variation on human health.

Moix S., Sadler M.C., Kutalik Z., Auwerx C., 2024/05/17. Genome biology, 25 (1) p. 125. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_5DF519357694]

preview resource BIB_981E899095A4.P001

A resampling-based approach to share reference panels.

Cavinato T., Rubinacci S., Malaspinas A.S., Delaneau O., 2024/05. Nature computational science, 4 (5) pp. 360-366. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_981E899095A4]

Comparing various AI approaches to traditional quantitative assessment of the myocardial perfusion in [<sup>82</sup>Rb] PET for MACE prediction.

Bors S., Abler D., Dietz M., Andrearczyk V., Fageot J., Nicod-Lalonde M., Schaefer N., DeKemp R., Kamani C.H., Prior J.O. et al., 2024/04/26. Scientific reports, 14 (1) p. 9644. Peer-reviewed.

[DOI][Pmid][serval:BIB_6229F1E6792C]

preview resource BIB_5F1F27C4B8D4.P001

Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells.

Croce G., Bobisse S., Moreno D.L., Schmidt J., Guillame P., Harari A., Gfeller D., 2024/04/13. Nature communications, 15 (1) p. 3211. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_5F1F27C4B8D4]

preview resource BIB_4DBF20DED918.P001

Implication of polymerase recycling for nascent transcript quantification by live cell imaging.

Kindongo O., Lieb G., Skaggs B., Dusserre Y., Vincenzetti V., Pelet S., 2024/04. Yeast, 41 (4) pp. 279-294. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_4DBF20DED918]

preview resource BIB_65FA0943DC42.P001

SMYD3: a new regulator of adipocyte precursor proliferation at the early steps of differentiation.

Sajic T., Ferreira Gomes C.K., Gasser M., Caputo T., Bararpour N., Landaluce-Iturriria E., Augsburger M., Walter N., Hainard A., Lopez-Mejia I.C. et al., 2024/04. International journal of obesity, 48 (4) pp. 557-566. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_65FA0943DC42]

preview resource BIB_9C3A50F95C0E.P001

Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers.

Lizano AMD, Kim K.M., Juinio-Meñez M.A., Ravago-Gotanco R., 2024/02/28. Scientific reports, 14 (1) p. 4886. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_9C3A50F95C0E]

preview resource BIB_FC1B402F5F17.P001

An approach for integrating multimodal omics data into sparse and interpretable models.

Dong Y., Gottardo R., 2024/02/26. Cell reports methods, 4 (2) p. 100718. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_FC1B402F5F17]

PheWAS-based clustering of Mendelian Randomisation instruments reveals distinct mechanism-specific causal effects between obesity and educational attainment.

Darrous L., Hemani G., Davey Smith G., Kutalik Z., 2024/02/15. Nature communications, 15 (1) p. 1420. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_606B3CD78234]

Causality-enriched epigenetic age uncouples damage and adaptation.

Ying K., Liu H., Tarkhov A.E., Sadler M.C., Lu A.T., Moqri M., Horvath S., Kutalik Z., Shen X., Gladyshev V.N., 2024/02. Nature aging, 4 (2) pp. 231-246. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_18FB43C5A730]

preview resource BIB_95FE005765C9.P001

MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides.

Chang Y.T., Prompsy P., Kimeswenger S., Tsai Y.C., Ignatova D., Pavlova O., Iselin C., French L.E., Levesque M.P., Kuonen F. et al., 2024/01/25. Nature communications, 15 (1) p. 752. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_95FE005765C9]

Rare copy-number variants as modulators of common disease susceptibility.

Auwerx C., Jõeloo M., Sadler M.C., Tesio N., Ojavee S., Clark C.J., Mägi R., Estonian Biobank Research Team, Reymond A., Kutalik Z., 2024/01/08. Genome medicine, 16 (1) p. 5. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_91B2F5588645]

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

Altenhoff A.M., Warwick Vesztrocy A., Bernard C., Train C.M., Nicheperovich A., Prieto Baños S., Julca I., Moi D., Nevers Y., Majidian S. et al., 2024/01/05. Nucleic acids research, 52 (D1) pp. D513-D521. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_B96DA0D62CDE]

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity.

Varrone M., Tavernari D., Santamaria-Martínez A., Walsh L.A., Ciriello G., 2024/01. Nature genetics, 56 (1) pp. 74-84. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_27DAAEFFFB59]

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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 (19)

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]

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]

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]

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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