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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 | ...

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

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

Altenhoff A.M., Warwick Vesztrocy A., Bernard C., Train C.M., Nicheperovich A., Prieto Baños S., Julca I., Moi D., Nevers Y., Majidian S. et al. Nucleic acids research. Peer-reviewed.

[DOI][Pmid][serval:BIB_B96DA0D62CDE]

From microbiome composition to functional engineering, one step at a time.

Burz S.D., Causevic S., Dal Co A., Dmitrijeva M., Engel P., Garrido-Sanz D., Greub G., Hapfelmeier S., Hardt W-D, Hatzimanikatis V. et al. Microbiology and molecular biology reviews. Peer-reviewed.

[DOI][Pmid][serval:BIB_422DE1C48246]

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]

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]

2023

Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life.

Himmel N.J., Moi D., Benton R., 2023/10/31. Current Biology, 33 (22) pp. 5023-5033. Peer-reviewed.

[DOI][Pmid][serval:BIB_3B786407249F]

Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia.

Cao L., Ruiz Buendía G.A., Fournier N., Liu Y., Armand F., Hamelin R., Pavlou M., Radtke F., 2023/10/24. Blood advances, 7 (20) pp. 6240-6252. Peer-reviewed.

[DOI][Pmid][serval:BIB_E01F5C4F58A0]

Genomic variant benchmark: if you cannot measure it, you cannot improve it.

Majidian S., Agustinho D.P., Chin C.S., Sedlazeck F.J., Mahmoud M., 2023/10/05. Genome biology, 24 (1) p. 221. Peer-reviewed.

[DOI][Pmid][serval:BIB_BFFAA42506DB]

Fine tuning rigid body docking results using the Dreiding force field: A computational study of 36 known nanobody-protein complexes.

Hacisuleyman A., Erman B., 2023/10. Proteins, 91 (10) pp. 1417-1426. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AD4A1D2EC8A3]

preview resource BIB_5B2668E2D1B4.P001

Expression of cell-wall related genes is highly variable and correlates with sepal morphology

Hartasánchez Diego A., Kiss Annamaria, Battu Virginie, Soraru Charline, Delgado-Vaquera Abigail, Massinon Florian, Brasó-Vives Marina, Mollier Corentin, Martin-Magniette Marie-Laure, Boudaoud Arezki et al., 2023/09/28. Peer Community Journal, 3. Peer-reviewed.

[URN][DOI][serval:BIB_5B2668E2D1B4]

Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma.

Gentien D., Saberi-Ansari E., Servant N., Jolly A., de la Grange P., Némati F., Liot G., Saule S., Teissandier A., Bourc'his D. et al., 2023/09/26. Cell reports, 42 (9) p. 113132. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_16A831564906]

The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes.

Aggarwal S., Huang E., Do H., Makthal N., Li Y., Bapteste E., Lopez P., Bernard C., Kumaraswami M., 2023/09/23. Nature communications, 14 (1) p. 5947. Peer-reviewed.

[DOI][Pmid][serval:BIB_DC405EC6F879]

Genetic insights into the age-specific biological mechanisms governing human ovarian aging.

Ojavee S.E., Darrous L., Patxot M., Läll K., Fischer K., Mägi R., Kutalik Z., Robinson M.R., 2023/09/07. American journal of human genetics, 110 (9) pp. 1549-1563. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_278672D79D5D]

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Cozzi D., Rossi M., Rubinacci S., Gagie T., Köppl D., Boucher C., Bonizzoni P., 2023/09/02. Bioinformatics, 39 (9). Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_A05A8B57A5AB]

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions.

Mészáros B., Hatos A., Palopoli N., Quaglia F., Salladini E., Van Roey K., Arthanari H., Dosztányi Z., Felli I.C., Fischer P.D. et al., 2023/09. Nature methods, 20 (9) pp. 1291-1303. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_ABFD74A3E19E]

preview resource BIB_E95C7A7DDD8F.P002

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., Konstantinidis Lazaros et al., 2023/09. Ophthalmology science, 3 (3) p. 100288. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E95C7A7DDD8F]

preview resource BIB_67978CA3D37E.P001

Chromosomal deletions on 16p11.2 encompassing SH2B1 are associated with accelerated metabolic disease.

Hanssen R., Auwerx C., Jõeloo M., Sadler M.C., Estonian Biobank Research Team, Henning E., Keogh J., Bounds R., Smith M., Firth H.V. et al., 2023/08/15. Cell reports. Medicine, 4 (8) p. 101155. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_67978CA3D37E]

CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers.

Bill R., Wirapati P., Messemaker M., Roh W., Zitti B., Duval F., Kiss M., Park J.C., Saal T.M., Hoelzl J. et al., 2023/08/04. Science, 381 (6657) pp. 515-524. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_17A3A9510B2F]

Response to Bassett et al.

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., 2023/07/06. American journal of human genetics, 110 (7) pp. 1219-1220. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_01B60F44C10B]

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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 (21)

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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