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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 | 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

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.

Dylus D., Altenhoff A., Majidian S., Sedlazeck F.J., Dessimoz C. Nature biotechnology. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AB990544B7BE]

Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE.

Lopez Vazquez A., Allenbach Petrolati L., Legris M., Dessimoz C., Lampugnani E.R., Glover N., Fankhauser C. The Plant cell. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_58EBDD8BFA7C]

2023

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.

[DOI][Pmid][serval:BIB_E95C7A7DDD8F]

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]

Topography of associations between cardiovascular risk factors and myelin loss in the ageing human brain.

Trofimova O., Latypova A., DiDomenicantonio G., Lutti A., de Lange A.G., Kliegel M., Stringhini S., Marques-Vidal P., Vaucher J., Vollenweider P. et al., 2023/04/10. Communications biology, 6 (1) p. 392. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_611EAA504585]

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.

[DOI][Pmid][serval:BIB_3C3B7E71A649]

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_5376D39C0896.P001

The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis.

Peter V.G., Kaminska K., Santos C., Quinodoz M., Cancellieri F., Cisarova K., Pescini Gobert R., Rodrigues R., Custódio S., Paris L.P. et al., 2023/03. PNAS nexus, 2 (3) pp. pgad043. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_5376D39C0896]

Novel Biological Insights Into the Common Heritable Liability to Substance Involvement: A Multivariate Genome-wide Association Study

Schoeler Tabea, Baldwin Jessie, Allegrini Andrea, Barkhuizen Wikus, McQuillin Andrew, Pirastu Nicola, Kutalik Zoltán, Pingault Jean-Baptiste, 2023/03. Biological Psychiatry, 93 (6) pp. 524-535. Peer-reviewed.

[DOI][WoS][serval:BIB_CB17FE6B148D]

preview resource BIB_6E38BFCA1196.P001

Divergence in metabolomic profile in clownfish and damselfish skin mucus

Heim S., Teav T., Gallart-Ayala H., Ivanisevic J., Salamin N., 2023/02/07. Frontiers in Ecology and Evolution, 11.

[URN][DOI][WoS][serval:BIB_6E38BFCA1196]

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]

Dendritic cells direct circadian anti-tumour immune responses.

Wang C., Barnoud C., Cenerenti M., Sun M., Caffa I., Kizil B., Bill R., Liu Y., Pick R., Garnier L. et al., 2023/02. Nature, 614 (7946) pp. 136-143. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_33489F389D05]

2022

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]

Gene set enrichment analysis of pathophysiological pathways highlights oxidative stress in psychosis.

Pistis G., Vázquez-Bourgon J., Fournier M., Jenni R., Cleusix M., Papiol S., Smart S.E., Pardiñas A.F., Walters JTR, MacCabe J.H. et al., 2022/12. Molecular psychiatry, 27 (12) pp. 5135-5143. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_42876FD4E721]

Parallel evolution of amphioxus and vertebrate small-scale gene duplications.

Brasó-Vives M., Marlétaz F., Echchiki A., Mantica F., Acemel R.D., Gómez-Skarmeta J.L., Hartasánchez D.A., Le Targa L., Pontarotti P., Tena J.J. et al., 2022/11/18. Genome biology, 23 (1) p. 243. Peer-reviewed.

[DOI][Pmid][serval:BIB_B6794F5FB6F2]

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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 (17)

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]

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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