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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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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

Synergy and anti-cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS-RGL1.

Hacisuleyman A., Erman B. Proteins. Peer-reviewed.

[DOI][Pmid][serval:BIB_87CA828A4D75]

Bridging Time Scales in Evolutionary Biology

Hartasánchez Diego A., Latrille Thibault, Brasó-Vives Marina, Navarro Arcadi dans Mathematics Online First Collections, Springer International Publishing.

[URN][DOI][serval:BIB_715001A031E0]

E2F transcription factor-1 modulates expression of glutamine metabolic genes in mouse embryonic fibroblasts and uterine sarcoma cells.

Huber K., Giralt A., Dreos R., Michenthaler H., Geller S., Barquissau V., Ziegler D.V., Tavernari D., Gallart-Ayala H., Krajina K. et al. Biochimica et biophysica acta. Molecular cell research. Peer-reviewed.

[DOI][Pmid][serval:BIB_5EAE29F4CAA9]

An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains.

Lerra L., Panatta M., Bär D., Zanini I., Tan J.Y., Pisano A., Mungo C., Baroux C., Panse V.G., Marques A.C. et al. Molecular cell. Peer-reviewed.

[DOI][Pmid][serval:BIB_7E94B9835811]

Frequent jumps from human hosts.

Moi D., Dessimoz C. Nature ecology & evolution. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_EFCEB8CFF30F]

Quality assessment of gene repertoire annotations with OMArk.

Nevers Y., Warwick Vesztrocy A., Rossier V., Train C.M., Altenhoff A., Dessimoz C., Glover N.M. Nature biotechnology. Peer-reviewed.

[DOI][Pmid][serval:BIB_85062152E9B8]

The neurobiology of life course socioeconomic conditions and associated cognitive performance in middle to late adulthood.

Schrempft S., Trofimova O., Künzi M., Ramponi C., Lutti A., Kherif F., Latypova A., Vollenweider P., Marques-Vidal P., Preisig M. et al. The Journal of neuroscience. Peer-reviewed.

[DOI][Pmid][serval:BIB_8A36291FEC74]

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers.

Singh A.K., Walavalkar K., Tavernari D., Ciriello G., Notani D., Sabarinathan R. Molecular oncology. Peer-reviewed.

[DOI][Pmid][serval:BIB_C481A745E22C]

Exploring the conformational changes of the Munc18-1/syntaxin 1a complex.

Stefani I., Iwaszkiewicz J., Fasshauer D. Protein science. Peer-reviewed.

[DOI][Pmid][serval:BIB_46EE05B7E159]

2024

Functional hypoxia reduces mitochondrial calcium uptake.

Donnelly C., Komlódi T., Cecatto C., Cardoso LHD, Compagnion A.C., Matera A., Tavernari D., Campiche O., Paolicelli R.C., Zanou N. et al., 2024/05. Redox biology, 71 p. 103037. Peer-reviewed.

[DOI][Pmid][serval:BIB_2E8283116312]

Genetic determinants of plasma protein levels in the Estonian population.

Kalnapenkis A., Jõeloo M., Lepik K., Kukuškina V., Kals M., Alasoo K., Estonian Biobank Research Team, Mägi R., Esko T., Võsa U., 2024/04/02. Scientific reports, 14 (1) p. 7694. Peer-reviewed.

[DOI][Pmid][serval:BIB_2ED69D7E6C4B]

Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.

Garrido Marques A., Rubinacci S., Malaspinas A.S., Delaneau O., Sousa da Mota B., 2024/03/14. Scientific reports, 14 (1) p. 6227. Peer-reviewed.

[DOI][Pmid][serval:BIB_6950F9B87B01]

AI and the democratization of knowledge.

Dessimoz C., Thomas P.D., 2024/03/05. Scientific data, 11 (1) p. 268. Peer-reviewed.

[DOI][Pmid][serval:BIB_68521EFB4037]

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]

ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation.

Mazzeo L., Ghosh S., Di Cicco E., Isma J., Tavernari D., Samarkina A., Ostano P., Youssef M.K., Simon C., Dotto G.P., 2024/02/03. Nature communications, 15 (1) p. 1038. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_2999AA526D89]

preview resource BIB_DAEDB9D9F04F.P001

Publisher Correction: Population genomics of post-glacial western Eurasia.

Allentoft M.E., Sikora M., Refoyo-Martínez A., Irving-Pease E.K., Fischer A., Barrie W., Ingason A., Stenderup J., Sjögren K.G., Pearson A. et al., 2024/02. Nature, 626 (7997) pp. E3. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_DAEDB9D9F04F]

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_43F23549D204.P001

Cancer Evolution: A Multifaceted Affair.

Ciriello G., Magnani L., Aitken S.J., Akkari L., Behjati S., Hanahan D., Landau D.A., Lopez-Bigas N., Lupiáñez D.G., Marine J.C. et al., 2024/01/12. Cancer discovery, 14 (1) pp. 36-48. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_43F23549D204]

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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

Publications (22)

preview resource BIB_354C8834608C.P004

The non-breeding period of the Western barn owl (Tyto alba): Habitat selection, activity patterns and fitness

Bühler Roman, 2023., Université de Lausanne, Faculté de biologie et médecine, Roulin Alexandre (dir.).

[URN][serval:BIB_354C8834608C]

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_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]

The use of high throughput wildlife tracking technology to study multiple aspects of barn owl movement ecology

Schalcher Kim, 2023., Université de Lausanne, Faculté de biologie et médecine, Roulin Alexandre (dir.).

[serval:BIB_03E958E852F8]

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_26D5A182653A.P001

Evolutionary-functional genomics for an enhanced resolution of arthropod gene function

RUZZANTE Livio, 2022., Université de Lausanne, Faculté de biologie et médecine, Waterhouse Robert (dir.).

[URN][serval:BIB_26D5A182653A]

preview resource BIB_EB509CF38FFB.P001

How hybridisation and gene flow shaped the clownfishes’ evolutionary history

SCHMID Sarah, 2022., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_EB509CF38FFB]

preview resource BIB_447E0040C32C.P001

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]

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_FD58D0995E23.P002

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

Machado Ana Paula, 2021., Université de Lausanne, Faculté de biologie et médecine, Roulin Alexandre (dir.).

[URN][serval:BIB_FD58D0995E23]

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]

Assembly of SNARE protein complexes

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

[serval:BIB_5A81332FF00C]

Computer-based OMICS in human genetics disorders

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

[serval:BIB_A87430E7A180]

preview resource BIB_3CACAB6F72EA.P002

Integrative Analysis of Gene Expression data from a human cohort

Sönmez Flitman Reyhan, 2020., Université de Lausanne, Faculté de biologie et médecine, Bergmann Sven (dir.).

[URN][serval:BIB_3CACAB6F72EA]

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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