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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 | 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

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. Bioinformatics. Peer-reviewed.

[DOI][Pmid][serval:BIB_B6D821D0E6BE]

Dendritic cells direct circadian anti-tumor immune responses.

Wang C., Barnoud C., Cenerenti M., Sun M., Caffa I., Kizil B., Bill R., Liu Y., Pick R., Garnier L. et al. Nature. Peer-reviewed.

[DOI][Pmid][serval:BIB_33489F389D05]

2022

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]

Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion.

Zeng Q., Saghafinia S., Chryplewicz A., Fournier N., Christe L., Xie Y.Q., Guillot J., Yucel S., Li P., Galván J.A. et al., 2022/11/18. Science, 378 (6621) pp. eabl7207. Peer-reviewed.

[DOI][Pmid][serval:BIB_324086550512]

Parent-of-Origin inference for biobanks.

Hofmeister R.J., Rubinacci S., Ribeiro D.M., Buil A., Kutalik Z., Delaneau O., 2022/11/05. Nature communications, 13 (1) p. 6668. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_3678C632F528]

Liability-scale heritability estimation for biobank studies of low-prevalence disease.

Ojavee S.E., Kutalik Z., Robinson M.R., 2022/11/03. American journal of human genetics, 109 (11) pp. 2009-2017. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_9B059FA24681]

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.

Lepamets M., Auwerx C., Nõukas M., Claringbould A., Porcu E., Kals M., Jürgenson T., Estonian Biobank Research Team, Morris A.P., Võsa U. et al., 2022/10/13. HGG advances, 3 (4) p. 100133. Peer-reviewed.

[DOI][Pmid][serval:BIB_ACC82F5026CE]

Sex- and age-dependent genetics of longevity in a heterogeneous mouse population.

Bou Sleiman M., Roy S., Gao A.W., Sadler M.C., von Alvensleben GVG, Li H., Sen S., Harrison D.E., Nelson J.F., Strong R. et al., 2022/09/30. Science, 377 (6614) pp. eabo3191. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_5D922C3D5603]

Epistasis and evolutionary dependencies in human cancers.

Mina M., Iyer A., Ciriello G., 2022/09/28. Current opinion in genetics & development, 77 p. 101989. Peer-reviewed.

[DOI][Pmid][serval:BIB_87AEECFCDB0B]

preview resource BIB_9841656E1979.P001

Estimating roe deer density using motion‐sensitive cameras in Switzerland

Hinojo Amael, Christe Philippe, Moreno Inès, Hofmeister Robin J., Dandliker Gottlieb, Zimmermann Fridolin, 2022/09/02. The Journal of Wildlife Management. Peer-reviewed.

[URN][DOI][WoS][serval:BIB_9841656E1979]

Cross-GWAS coherence test at the gene and pathway level.

Krefl D., Bergmann S., 2022/09. PLoS computational biology, 18 (9) pp. e1010517. Peer-reviewed.

[DOI][Pmid][serval:BIB_347C6E9AAD44]

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation

Sima Ana Claudia, Mendes de Farias Tarcisio, Anisimova Maria, Dessimoz Christophe, Robinson-Rechavi Marc, Zbinden Erich, Stockinger Kurt, 2022/09. Distributed and Parallel Databases, 40 (2-3) pp. 409-440. Peer-reviewed.

[DOI][WoS][serval:BIB_EE90AD3795B0]

preview resource BIB_B7AD437C6019.P001

Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.

Wang Z., Emmerich A., Pillon N.J., Moore T., Hemerich D., Cornelis M.C., Mazzaferro E., Broos S., Ahluwalia T.S., Bartz T.M. et al., 2022/09. Nature genetics, 54 (9) pp. 1332-1344. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_B7AD437C6019]

preview resource BIB_4AC82BE10423.P001

Limited evidence for blood eQTLs in human sexual dimorphism.

Porcu E., Claringbould A., Weihs A., Lepik K., BIOS Consortium, Richardson T.G., Völker U., Santoni F.A., Teumer A., Franke L. et al., 2022/08/11. Genome medicine, 14 (1) p. 89. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_4AC82BE10423]

preview resource BIB_9696FED34BD7.P001

CYP2C19 expression modulates affective functioning and hippocampal subiculum volume-a large single-center community-dwelling cohort study.

Grosu C., Trofimova O., Gholam-Rezaee M., Strippoli M.F., Kherif F., Lutti A., Preisig M., Draganski B., Eap C.B., 2022/08/05. Translational psychiatry, 12 (1) p. 316. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_9696FED34BD7]

preview resource BIB_6A2C0BEAD983.P001

Federating and querying heterogeneous and distributed Web APIs and triple stores

Mendes de Farias Tarcisio, Dessimoz Christophe, Ayllon Benitez Aaron, Yang Chen, Long Jiao, Sima Ana-Claudia, 2022/08/02. dans 2022 ISMB Bio-Ontologies Community of Special Interest. Peer-reviewed.

[URN][DOI][serval:BIB_6A2C0BEAD983]

Megaviruses contain various genes encoding for eukaryotic vesicle trafficking factors.

Khalifeh D., Neveu E., Fasshauer D., 2022/08. Traffic, 23 (8) pp. 414-425. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_060706490373]

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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)

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]

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_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.).

[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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