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Faculty of Biology and Medicine

Department of Computational Biology

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Publications | Masters and Phd thesis

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Publications

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2022 | 2021 | ...

2022

Improving polygenic prediction with genetically inferred ancestry.

Naret O., Kutalik Z., Hodel F., Xu Z.M., Marques-Vidal P., Fellay J., 2022/07/14. HGG advances, 3 (3) p. 100109. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_DFFCB5547228]

Pretrained Knowledge Base Embeddings for improved Sentential Relation Extraction

Papaluca Andrea, Krefl Daniel, Suominen Hanna, Lenskiy Artem, 2022/05. Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics: Student Research Workshop pp. 373–382. Peer-reviewed.

[serval:BIB_7CBA92AF9878]

The individual and global impact of copy-number variants on complex human traits.

Auwerx C., Lepamets M., Sadler M.C., Patxot M., Stojanov M., Baud D., Mägi R., Estonian Biobank Research Team, Porcu E., Reymond A. et al., 2022/04/07. American journal of human genetics, 109 (4) pp. 647-668. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_A48E696D6EA7]

OMAMO: orthology-based alternative model organism selection.

Nicheperovich A., Altenhoff A.M., Dessimoz C., Majidian S., 2022/03/18. Bioinformatics, 38 (10) pp. 2965-2966. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E49811D00537]

Meta-GWAS Reveals Novel Genetic Variants Associated with Urinary Excretion of Uromodulin.

Joseph C.B., Mariniello M., Yoshifuji A., Schiano G., Lake J., Marten J., Richmond A., Huffman J.E., Campbell A., Harris S.E. et al., 2022/03. Journal of the American Society of Nephrology, 33 (3) pp. 511-529. Peer-reviewed.

[DOI][Pmid][serval:BIB_74BD331CF8E5]

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean.

Machado A.P., Topaloudis A., Cumer T., Lavanchy E., Bontzorlos V., Ceccherelli R., Charter M., Kassinis N., Lymberakis P., Manzia F. et al., 2022/03. Molecular ecology, 31 (5) pp. 1375-1388. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E06218648494]

2021

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae).

Zhang Q., Ree R.H., Salamin N., Xing Y., Silvestro D., 2021/12/16. Systematic biology, 71 (1) pp. 242-258. Peer-reviewed.

[DOI][Pmid][serval:BIB_C1BA117F09FD]

Simultaneous estimation of bi-directional causal effects and heritable confounding from GWAS summary statistics.

Darrous L., Mounier N., Kutalik Z., 2021/12/14. Nature communications, 12 (1) p. 7274. Peer-reviewed.

[DOI][Pmid][serval:BIB_E3BA5FA37823]

Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits.

Patxot M., Banos D.T., Kousathanas A., Orliac E.J., Ojavee S.E., Moser G., Holloway A., Sidorenko J., Kutalik Z., Mägi R. et al., 2021/11/30. Nature communications, 12 (1) p. 6972. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_9710808BCDCD]

Untargeted Metabolome- and Transcriptome-Wide Association Study Suggests Causal Genes Modulating Metabolite Concentrations in Urine.

Sönmez Flitman R., Khalili B., Kutalik Z., Rueedi R., Brümmer A., Bergmann S., 2021/11/05. Journal of proteome research, 20 (11) pp. 5103-5114. Peer-reviewed.

[DOI][Pmid][serval:BIB_83A8DE848FD3]

Enteral nutrition and dynamics of citrulline and intestinal fatty acid-binding protein in adult ICU patients.

Padar M., Starkopf J., Starkopf L., Forbes A., Hiesmayr M., Jakob S.M., Rooijackers O., Wernerman J., Ojavee S.E., Reintam Blaser A., 2021/10. Clinical nutrition ESPEN, 45 pp. 322-332. Peer-reviewed.

[DOI][Pmid][serval:BIB_84240EF05272]

Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression.

Saghafinia S., Homicsko K., Di Domenico A., Wullschleger S., Perren A., Marinoni I., Ciriello G., Michael I.P., Hanahan D., 2021/10. Cancer discovery, 11 (10) pp. 2638-2657. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E3BABADE6621]

preview resource BIB_BA8FC21210D4.P001

Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy.

Robinson M.R., Patxot M., Stojanov M., Blum S., Baud D., 2021/09/28. Scientific reports, 11 (1) p. 19238. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_BA8FC21210D4]

preview resource BIB_253FEBED3C3F.P001

Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

Porcu E., Sadler M.C., Lepik K., Auwerx C., Wood A.R., Weihs A., Sleiman MSB, Ribeiro D.M., Bandinelli S., Tanaka T. et al., 2021/09/24. Nature communications, 12 (1) p. 5647. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_253FEBED3C3F]

Heritability and association with distinct genetic loci of erythropoietin levels in the general population.

Corre T., Ponte B., Pivin E., Pruijm M., Ackermann D., Ehret G., Spanaus K., Bochud M., Wenger R.H., 2021/09/01. Haematologica, 106 (9) pp. 2499-2501. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_A24F2D13A3DD]

Hidden cell diversity in Placozoa: ultrastructural insights from Hoilungia hongkongensis.

Romanova D.Y., Varoqueaux F., Daraspe J., Nikitin M.A., Eitel M., Fasshauer D., Moroz L.L., 2021/09. Cell and tissue research, 385 (3) pp. 623-637. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_C466BC2969FF]

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.

Võsa U., Claringbould A., Westra H.J., Bonder M.J., Deelen P., Zeng B., Kirsten H., Saha A., Kreuzhuber R., Yazar S. et al., 2021/09. Nature genetics, 53 (9) pp. 1300-1310. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_9462F2AB5F22]

preview resource BIB_5AA3BA80411A.P001

The molecular basis, genetic control and pleiotropic effects of local gene co-expression.

Ribeiro D.M., Rubinacci S., Ramisch A., Hofmeister R.J., Dermitzakis E.T., Delaneau O., 2021/08/10. Nature communications, 12 (1) p. 4842. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_5AA3BA80411A]

Genetic insights into biological mechanisms governing human ovarian ageing.

Ruth K.S., Day F.R., Hussain J., Martínez-Marchal A., Aiken C.E., Azad A., Thompson D.J., Knoblochova L., Abe H., Tarry-Adkins J.L. et al., 2021/08. Nature, 596 (7872) pp. 393-397. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AEC34ED6E894]

preview resource BIB_745449157CA6.P001

Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING.

Bruand M., Barras D., Mina M., Ghisoni E., Morotti M., Lanitis E., Fahr N., Desbuisson M., Grimm A., Zhang H. et al., 2021/07/20. Cell reports, 36 (3) p. 109412. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_745449157CA6]

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Masters thesis

Publications (1)

preview resource BIB_02FF794E29C7.P001

Is sex specific phenotypic robustness reflected In gene expression data?

MAKOWKA S., 2017. 21, Université de Lausanne, Faculté de biologie et médecine, BERGMANN S. (dir.).

[URN][serval:BIB_02FF794E29C7]

Phd thesis

In preparation (2)

preview resource BIB_FD58D0995E23.P002

Impact of landscape barriers and isolation on the genetic and phenotypic evolution of the barn owl

Machado Ana Paula, Université de Lausanne, Faculté de biologie et médecine, Roulin Alexandre (dir.).

[URN][serval:BIB_FD58D0995E23]

preview resource BIB_3CACAB6F72EA.P002

Integrative Analysis of Gene Expression data from a human cohort

Sönmez Flitman Reyhan, Université de Lausanne, Faculté de biologie et médecine, Bergmann Sven (dir.).

[URN][serval:BIB_3CACAB6F72EA]

Publications (13)

Probing the conformational flexibility of the Munc18-1/Syntaxin-1a complex

Stefani Ioanna, 2022., Université de Lausanne, Faculté de biologie et médecine, Fasshauer Dirk (dir.).

[URN][serval:BIB_447E0040C32C]

Probing the conformational flexibility of the Munc18-1/Syntaxin-1a complex.

STEFANI Ioanna, 2022., Université de Lausanne, Faculté de biologie et médecine, Fasshauer Dirk (dir.).

[URN][serval:BIB_3D9533FB5B3A]

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_7360DFA238AF.P001

Genomics of clownfish adaptive radiation

MARCIONETTI Anna, 2021., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_7360DFA238AF]

Non-genetic mechanisms of tumor progression in B-cell lymphoma and lung adenocarcinoma

TAVERNARI Daniele, 2021., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[serval:BIB_1F64C05D0B27]

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]

Exploring differential activation of topologically associating domains in cancer

ZUFFEREY Marie, 2021., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[serval:BIB_B37292166FA1]

preview resource BIB_D64CBC923F3D.P002

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

Sima Ana Claudia, 2020/10/26., Université de Lausanne, Faculté de biologie et médecine, Dessimoz Christophe (dir.).

[URN][serval:BIB_D64CBC923F3D]

Bioinformatic Analysis of Ocular Diseases

Cisárová Katarina Vizár, 2020., Université de Lausanne, Faculté de biologie et médecine, Bergmann Sven (dir.).

[serval:BIB_7FF91597EFAC]

preview resource BIB_2B6A348B7E00.P001

Assembly of SNARE protein complexes

Khalifeh Dany, 2020., Université de Lausanne, Faculté de biologie et médecine, Fasshauer Dirk (dir.).

[URN][serval:BIB_2B6A348B7E00]

Computer-based OMICS in human genetics disorders

QUINODOZ Mathieu, 2020., Université de Lausanne, Faculté de biologie et médecine, Bergmann Sven (dir.).

[serval:BIB_A87430E7A180]

Plant diversification in Neotropical rainforests

Loiseau Oriane, 2019/04/12., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[serval:BIB_17938308CDAE]

preview resource BIB_DDEAE5AD2D66.P001

Inferring Hierarchical Orthologous Groups

Train Clément, 2019., Université de Lausanne, Faculté de biologie et médecine, Dessimoz Christophe (dir.).

[URN][serval:BIB_DDEAE5AD2D66]

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