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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 | 2025 | 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

Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation.

Gaboriau T., Tobias J.A., Silvestro D., Salamin N. Systematic biology. Peer-reviewed.

[DOI][Pmid][serval:BIB_04FF91A74ECB]

Role of Mutual Information Profile Shifts in Assessing the Pathogenicity of Mutations on Protein Functions: The Case of Pyrin Variants Associated With Familial Mediterranean Fever.

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

[DOI][WoS][Pmid][serval:BIB_D33C3339E284]

Associations between common genetic variants and income provide insights about the socio-economic health gradient.

Kweon H., Burik CAP, Ning Y., Ahlskog R., Xia C., Abner E., Bao Y., Bhatta L., Faquih T.O., de Feijter M. et al. Nature human behaviour. Peer-reviewed.

[DOI][Pmid][serval:BIB_1386C6C6562F]

Comprehensive evaluation of lifespan-extending molecules in C. elegans.

Phelps G.B., Morin J., Pinto C., Schoenfeldt L., Guilmot S., Ocampo A., Perez K. Aging cell. Peer-reviewed.

[DOI][Pmid][serval:BIB_4BE8BAA7C4CC]

The impact of self-report inaccuracy in the UK Biobank and its interplay with selective participation.

Schoeler T., Pingault J.B., Kutalik Z. Nature human behaviour. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_8ADA5F20BFC3]

Decoding the Clinical and Molecular Signatures of EGFR Common, Compound, and Uncommon Mutations in Non-Small Cell Lung Cancer.

Tavernari D., Borgeaud M., Liu X., Kaushal P., Le X., Ciriello G., Addeo A. Journal of thoracic oncology. Peer-reviewed.

[DOI][Pmid][serval:BIB_55E39726C98A]

2025

preview resource BIB_E59BAB5E6436.P001

Highly expressed cell wall genes contribute to robustness of sepal size.

Hartasánchez D.A., Dumond M., Dubrulle N., Monéger F., Boudaoud A., 2025/12. Plant signaling & behavior, 20 (1) p. 2446858. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E59BAB5E6436]

Melanin and Neurotransmitter Signalling Genes Are Differentially Co-Expressed in Growing Feathers of White and Rufous Barn Owls.

Ducrest A.L., San-Jose L.M., Neuenschwander S., Schmid-Siegert E., Simon C., Pagni M., Iseli C., Richter H., Guex N., Cumer T. et al., 2025/03. Pigment cell & melanoma research, 38 (2) pp. e70001. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_9F344E2BBD34]

Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.

Schreiber J.M., Boix C.A., Wook Lee J., Li H., Guan Y., Chang C.C., Chang J.C., Hawkins-Hooker A., Schölkopf B., Schweikert G. et al., 2025/02/13. Genome biology, 26 (1) p. 31. Peer-reviewed.

[DOI][Pmid][serval:BIB_64E010EFFA3C]

Orthology inference at scale with FastOMA.

Majidian S., Nevers Y., Yazdizadeh Kharrazi A., Warwick Vesztrocy A., Pascarelli S., Moi D., Glover N., Altenhoff A.M., Dessimoz C., 2025/02. Nature methods, 22 (2) pp. 269-272. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_16D2692F826F]

N-acetylated sugars in clownfish and damselfish skin mucus as messengers involved in chemical recognition by anemone host.

Heim S., Teav T., Cortesi F., Gallart-Ayala H., Ivanisevic J., Salamin N., 2025/01/15. Scientific reports, 15 (1) p. 2048. Peer-reviewed.

[DOI][Pmid][serval:BIB_9F210F2925EB]

Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.

Koptekin D., Yapar E., Vural K.B., Sağlıcan E., Altınışık N.E., Malaspinas A.S., Alkan C., Somel M., 2025/01/09. Genome biology, 26 (1) p. 6. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_6281E750B9DB]

Phylogenetic characterization of Bifidobacterium kimbladii sp. nov., a novel species from the honey stomach of the honeybee Apis mellifera.

Modesto M., Scarafile D., Vásquez A., Pukall R., Neumann-Schaal M., Pascarelli S., Sgorbati B., Ancora M., Cammà C., Mattarelli P. et al., 2025/01. Systematic and applied microbiology, 48 (1) p. 126579. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_1C5366735A3D]

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., 2025/01. Nature biotechnology, 43 (1) pp. 124-133. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_85062152E9B8]

2024

A Novel method for quantifying fluctuations in wearable derived daily cardiovascular parameters across the menstrual cycle.

Jasinski S.R., Presby D.M., Grosicki G.J., Capodilupo E.R., Lee V.H., 2024/12/23. NPJ digital medicine, 7 (1) p. 373. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_68F755CB46AA]

preview resource BIB_4335A47B02F4.P001

Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening.

Santamaria-Martínez A., Epiney J., Srivastava D., Tavernari D., Varrone M., Milowich D., Letovanec I., Krueger T., Duran R., Ciriello G. et al., 2024/12/09. Nature communications, 15 (1) p. 10650. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_4335A47B02F4]

An Unbiased Approach to Identifying Cellular Reprogramming-Inducible Enhancers.

Klagkou E., Valakos D., Foutadakis S., Polyzos A., Papadopoulou A., Vatsellas G., Thanos D., 2024/12/06. International journal of molecular sciences, 25 (23). Peer-reviewed.

[DOI][Pmid][serval:BIB_3AC9363F86AE]

preview resource BIB_48F1CCA92512.P001

Identification of rare disease genes as drivers of common diseases through tissue-specific gene regulatory networks.

Bakker O.B., Claringbould A., Westra H.J., Wiersma H., Boulogne F., Võsa U., Urzúa-Traslaviña C.G., Mulcahy Symmons S., Zidan MMM, Sadler M.C. et al., 2024/12/04. Scientific reports, 14 (1) p. 30206. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_48F1CCA92512]

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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 (28)

preview resource BIB_4378AC7E7774.P001

The impact of mutualistic interactions on the ecology and evolution of clownfishes

García Jiménez Alberto J., 2024., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_4378AC7E7774]

preview resource BIB_C6CA557B0DFA.P001

Tale of Cancer Evolution : Insights from Co-mutation Analysis

IYER Arvind Krishnamurthy, 2024., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[URN][serval:BIB_C6CA557B0DFA]

An evolutionary genomics and behavioural approach to investigate the evolution of temperature preference in drosophilids

KAFLE Tanuj, 2024., Université de Lausanne, Faculté de biologie et médecine, Arguello Roman (dir.).

[serval:BIB_3C8C7F143968]

preview resource BIB_3A2CCC38831D.P002

Interdisciplinary study into the association between farmer-scientist collaboration, farmers’ pro-environmental behaviors, and barn owl conservation in Switzerland

Milliet Estelle, 2024., Université de Lausanne, Faculté de biologie et médecine, Roulin Alexandre (dir.).

[URN][serval:BIB_3A2CCC38831D]

preview resource BIB_B03FDDD4ECB2.P001

Imputation of ancient genomes and the genomic history of the Rapanui

TEIXEIRA DE SOUSA COELHO DA MOTA Bárbara, 2024., Université de Lausanne, Faculté de biologie et médecine, Malaspinas Anna-Sapfo (dir.).

[URN][serval:BIB_B03FDDD4ECB2]

Computational models to characterize spatial intra-tumor heterogeneity

VARRONE Marco, 2024., Université de Lausanne, Faculté de biologie et médecine, Ciriello Giovanni (dir.).

[serval:BIB_B18CB8C81268]

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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