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Liens UNIL

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 | 2022 | ...

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

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. Nature. Peer-reviewed.

[DOI][Pmid][serval:BIB_4691B7A968A0]

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

Lavanchy E., Goudet J. Molecular ecology resources. Peer-reviewed.

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

2023

preview resource BIB_A5198D931AE8.P001

Cancer vaccines based on whole-tumor lysate or neoepitopes with validated HLA binding outperform those with predicted HLA-binding affinity.

Fritah H., Graciotti M., Lai-Lai Chiang C., Huguenin-Bergenat A.L., Petremand R., Ahmed R., Guillaume P., Schmidt J., Stevenson B.J., Gfeller D. et al., 2023/04/21. iScience, 26 (4) p. 106288. Peer-reviewed.

[DOI][Pmid][serval:BIB_A5198D931AE8]

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][Pmid][serval:BIB_33296666D7F5]

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]

Mapache: a flexible pipeline to map ancient DNA.

Neuenschwander S., Cruz Dávalos D.I., Anchieri L., Sousa da Mota B., Bozzi D., Rubinacci S., Delaneau O., Rasmussen S., Malaspinas A.S., 2023/02/03. Bioinformatics, 39 (2) pp. btad028. Peer-reviewed.

[DOI][Pmid][serval:BIB_B6D821D0E6BE]

The impact of 22q11.2 copy-number variants on human traits in the general population.

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., 2023/02/02. American journal of human genetics, 110 (2) pp. 300-313. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_CD61220861A1]

The MHC Motif Atlas: a database of MHC binding specificities and ligands.

Tadros D.M., Eggenschwiler S., Racle J., Gfeller D., 2023/01/06. Nucleic acids research, 51 (D1) pp. D428-D437. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_3F10404EDD7E]

2022

preview resource BIB_7E0928230246.P001

Global analysis of suppressor mutations that rescue human genetic defects

Ünlü B., Pons C., Ho U.L., Aloy P., van Leeuwen J., 2022/12/22..

[URN][DOI][serval:BIB_7E0928230246]

Quantifying the role of transcript levels in mediating DNA methylation effects on complex traits and diseases.

Sadler M.C., Auwerx C., Lepik K., Porcu E., Kutalik Z., 2022/12/07. Nature communications, 13 (1) p. 7559. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_8C3AFBD3E3D3]

Epistasis and evolutionary dependencies in human cancers.

Mina M., Iyer A., Ciriello G., 2022/12. Current opinion in genetics & development, 77 p. 101989. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_87AEECFCDB0B]

Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing.

Taylor A.S., Barros D., Gobet N., Schuepbach T., McAllister B., Aeschbach L., Randall E.L., Trofimenko E., Heuchan E.R., Barszcz P. et al., 2022/12. NAR genomics and bioinformatics, 4 (4) pp. lqac089. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_16ADA4432905]

Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion.

Zeng Q., Saghafinia S., Chryplewicz A., Fournier N., Christe L., Xie Y.Q., Guillot J., Yucel S., Li P., Galván J.A. et al., 2022/11/18. Science, 378 (6621) pp. eabl7207. Peer-reviewed.

[DOI][Pmid][serval:BIB_324086550512]

Parent-of-Origin inference for biobanks.

Hofmeister R.J., Rubinacci S., Ribeiro D.M., Buil A., Kutalik Z., Delaneau O., 2022/11/05. Nature communications, 13 (1) p. 6668. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_3678C632F528]

Reproducibility of lung cancer radiomics features extracted from data-driven respiratory gating and free-breathing flow imaging in [<sup>18</sup>F]-FDG PET/CT.

Faist D., Jreige M., Oreiller V., Nicod Lalonde M., Schaefer N., Depeursinge A., Prior J.O., 2022/10/30. European journal of hybrid imaging, 6 (1) p. 33. Peer-reviewed.

[DOI][Pmid][serval:BIB_B5DE6B69D4AD]

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.

Lepamets M., Auwerx C., Nõukas M., Claringbould A., Porcu E., Kals M., Jürgenson T., Estonian Biobank Research Team, Morris A.P., Võsa U. et al., 2022/10/13. HGG advances, 3 (4) p. 100133. Peer-reviewed.

[DOI][Pmid][serval:BIB_ACC82F5026CE]

Sex- and age-dependent genetics of longevity in a heterogeneous mouse population.

Bou Sleiman M., Roy S., Gao A.W., Sadler M.C., von Alvensleben GVG, Li H., Sen S., Harrison D.E., Nelson J.F., Strong R. et al., 2022/09/30. Science, 377 (6614) pp. eabo3191. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_5D922C3D5603]

preview resource BIB_9841656E1979.P001

Estimating roe deer density using motion‐sensitive cameras in Switzerland

Hinojo Amael, Christe Philippe, Moreno Inès, Hofmeister Robin J., Dandliker Gottlieb, Zimmermann Fridolin, 2022/09/02. The Journal of Wildlife Management. Peer-reviewed.

[URN][DOI][WoS][serval:BIB_9841656E1979]

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Phd thesis

In preparation (1)

preview resource BIB_4C2394C34F24.P001

Genetic basis of common complex traits

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

[URN][serval:BIB_4C2394C34F24]

Publications (6)

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_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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