Centre de compétence bioinformatique

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Publications | Mémoires et thèses

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49 publications

En préparation
 
CDK4 deletion in mice prevents fat accumulation and increases endurance capacity through activation of estrogen-related receptor (ERR)-driven oxidative metabolism in skeletal muscle
Barquissau Valentin, Zanou Nadège, Geller Sarah, Castillo-Armengol Judit, Marzetta Flavia, Huber Katharina, Ziegler Dorian, Lopez-Mejia Isabel, Fernandez Joan Blanco, Roger Catherine et al..
[DOI][serval:BIB_2CA3F1A4A423]
Repairing a deleterious domestication variant in a floral regulator of tomato by base editing
Glaus Anna N., Brechet Marion, Lebeigle Ludivine, Iwaszkiewicz Justyna, Ambrosini Giovanna, Julca Irene, Zhang Jing, Roberts Robyn, Iseli Christian, Guex Nicolas et al..
[URN][DOI][serval:BIB_D6B8B598E8AC]
Sous presse
 
Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinants.
Tonelli A., Cousin P., Jankowski A., Wang B., Dorier J., Barraud J., Zunjarrao S., Gambetta M.C. Developmental cell. Peer-reviewed.
[DOI][Pmid][serval:BIB_2A951E5FC6A3]
 
Can we accurately predict the distribution of soil microorganism presence and relative abundance?
Verdon Valentin, Malard Lucie, Collart Flavien, Adde Antoine, Yashiro Erika, Lara Pandi Enrique, Mod Heidi, Singer David, Niculita-Hirzel Hélène, Guex Nicolas et al. Ecography. Peer-reviewed.
[DOI][WoS][serval:BIB_9607C43737E4]
2024
Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex.
Lorin C., Guiet R., Chiaruttini N., Ambrosini G., Boci E., Abdellah M., Markram H., Keller D., 2024/11. Glia, 72 (11) pp. 2001-2021. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7C608FE96D05]
 
DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen.
Martin S., Fournes F., Ambrosini G., Iseli C., Bojkowska K., Marquis J., Guex N., Collier J., 2024/10/28. Nucleic acids research, 52 (19) pp. 11519-11535. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0C3DF5C03B52]
Phosphate deficiency alters transcript isoforms via alternative transcription start sites.
Reis R.S., Clúa J., Jaskolowski A., Deforges J., Jacques-Vuarambon D., Guex N., Poirier Y., 2024/10. The Plant journal, 120 (1) pp. 218-233. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DFA16258AAE3]
 
tRNA-derived fragments in T lymphocyte-beta cell crosstalk and in type 1 diabetes pathogenesis in NOD mice.
Brozzi F., Jacovetti C., Cosentino C., Menoud V., Wu K., Bayazit M.B., Abdulkarim B., Iseli C., Guex N., Guay C. et al., 2024/10. Diabetologia, 67 (10) pp. 2260-2274. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BF3CD8D4736F]
Model integration of circadian- and sleep-wake-driven contributions to rhythmic gene expression reveals distinct regulatory principles.
Jan M., Jimenez S., Hor C.N., Dijk D.J., Skeldon A.C., Franken P., 2024/07/17. Cell systems, 15 (7) pp. 610-627.e8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_992D59CD8131]
Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs.
Brümmer A., Bergmann S., 2024/05/06. Nature communications, 15 (1) p. 3786. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D3A95CE7F2D1]
The hindbrain and cortico-reticular pathway in adolescent idiopathic scoliosis.
Soh RCC, Chen B.Z., Hartono S., Lee M.S., Lee W., Lim S.L., Gan J., Maréchal B., Chan L.L., Lo Y.L., 2024/05. Clinical radiology, 79 (5) pp. e759-e766. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DF4A2A986A1E]
Comparative assessment of cytometry by time-of-flight and full spectral flow cytometry based on a 33-color antibody panel.
Schäfer A., D'Almeida S.M., Dorier J., Guex N., Villard J., Garcia M., 2024/04. Journal of immunological methods, 527 p. 113641. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2897FE5D053E]
2023
Mechanopathology of biofilm-like Mycobacterium tuberculosis cords.
Mishra R., Hannebelle M., Patil V.P., Dubois A., Garcia-Mouton C., Kirsch G.M., Jan M., Sharma K., Guex N., Sordet-Dessimoz J. et al., 2023/11/09. Cell, 186 (23) pp. 5135-5150.e28. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A264D4C42F48]
Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder.
Mattioli F., Worpenberg L., Li C.T., Ibrahim N., Naz S., Sharif S., Firouzabadi S.G., Vosoogh S., Saraeva-Lamri R., Raymond L. et al., 2023/09. Genetics in medicine, 25 (9) p. 100900. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D38F5D2EC77B]
Chromosome-level organization of the regulatory genome in the Drosophila nervous system
Mohana Giriram, Dorier Julien, Li Xiao, Mouginot Marion, Smith Rebecca C., Malek Héléna, Leleu Marion, Rodriguez Daniel, Khadka Jenisha, Rosa Patrycja et al., 2023/08. Cell, 186 (18) pp. 3826-3844.e26. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_04C850D22DE3]
DNA modifications impact natural transformation of Acinetobacter baumannii.
Vesel N., Iseli C., Guex N., Lemopoulos A., Blokesch M., 2023/06/23. Nucleic acids research, 51 (11) pp. 5661-5677. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C242A3B7D937]
A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy.
Ibrahim N., Naz S., Mattioli F., Guex N., Sharif S., Iqbal A., Ansar M., Reymond A., 2023/03/13. Genes, 14 (3) p. 707. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_73E78E497318]
Molecular insights into sex-specific metabolic alterations in Alzheimer's mouse brain using multi-omics approach.
Strefeler A., Jan M., Quadroni M., Teav T., Rosenberg N., Chatton J.Y., Guex N., Gallart-Ayala H., Ivanisevic J., 2023/01/09. Alzheimer's research & therapy, 15 (1) p. 8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5426CE38C858]
Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles.
Conrad B., Iseli C., Pirovino M., 2023. PloS one, 18 (3) pp. e0281661. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D1DF15A14C6D]
Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING.
Pinjusic K., Ambrosini G., Lourenco J., Fournier N., Iseli C., Guex N., Egorova O., Nassiri S., Constam D.B., 2023. Frontiers in immunology, 14 p. 1335207. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_B5ECAE9D66D5]
2022
Revisiting the specificity and ability of phospho-S129 antibodies to capture alpha-synuclein biochemical and pathological diversity.
Lashuel H.A., Mahul-Mellier A.L., Novello S., Hegde R.N., Jasiqi Y., Altay M.F., Donzelli S., DeGuire S.M., Burai R., Magalhães P. et al., 2022/10/20. NPJ Parkinson's disease, 8 (1) p. 136. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_36AEA1313356]
The Transcriptional Regulator Prdm1 Is Essential for the Early Development of the Sensory Whisker Follicle and Is Linked to the Beta-Catenin First Dermal Signal.
Manti P.G., Darbellay F., Leleu M., Coughlan A.Y., Moret B., Cuennet J., Droux F., Stoudmann M., Mancini G.F., Hautier A. et al., 2022/10/20. Biomedicines, 10 (10) p. 2647. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D1168205EA84]
 
Lipid biosynthesis enzyme Agpat5 in AgRP-neurons is required for insulin-induced hypoglycemia sensing and glucagon secretion.
Strembitska A., Labouèbe G., Picard A., Berney X.P., Tarussio D., Jan M., Thorens B., 2022/09/30. Nature communications, 13 (1) p. 5761. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B0ED46C3DA7C]
Towards mouse genetic-specific RNA-sequencing read mapping.
Gobet N., Jan M., Franken P., Xenarios I., 2022/09. PLoS computational biology, 18 (9) pp. e1010552. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_5FBE8DE15F37]
Essential role of Cp190 in physical and regulatory boundary formation.
Kaushal A., Dorier J., Wang B., Mohana G., Taschner M., Cousin P., Waridel P., Iseli C., Semenova A., Restrepo S. et al., 2022/05/13. Science advances, 8 (19) pp. eabl8834. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EEEA9AFE8EED]
Soil protist function varies with elevation in the Swiss Alps.
Mazel F., Malard L., Niculita-Hirzel H., Yashiro E., Mod H.K., Mitchell EAD, Singer D., Buri A., Pinto E., Guex N. et al., 2022/04. Environmental microbiology, 24 (4) pp. 1689-1702. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4C32247201A1]
DNA methylation-based age acceleration observed in IDH wild-type glioblastoma is associated with better outcome-including in elderly patients.
Bady P., Marosi C., Weller M., Grønberg B.H., Schultz H., Taphoorn MJB, Gijtenbeek JMM, van den Bent M.J., von Deimling A., Stupp R. et al., 2022/03/24. Acta neuropathologica communications, 10 (1) p. 39. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3D6A92122001]
Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean.
Machado A.P., Topaloudis A., Cumer T., Lavanchy E., Bontzorlos V., Ceccherelli R., Charter M., Kassinis N., Lymberakis P., Manzia F. et al., 2022/03. Molecular ecology, 31 (5) pp. 1375-1388. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E06218648494]
Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.
Brümmer A., Dreos R., Marques A.C., Bergmann S., 2022/02/03. Molecular biology and evolution, 39 (2) pp. msab356. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_480A22B18475]
SPICA: Swiss portal for immune cell analysis.
Andreatta M., David FPA, Iseli C., Guex N., Carmona S.J., 2022/01/07. Nucleic acids research, 50 (D1) pp. D1109-D1114. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1425D341196A]
Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles.
Machado A.P., Cumer T., Iseli C., Beaudoing E., Ducrest A.L., Dupasquier M., Guex N., Dichmann K., Lourenço R., Lusby J. et al., 2022/01. Molecular ecology, 31 (2) pp. 482-497. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_59DDCB29C598]
2021
 
A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root.
Graeff M., Rana S., Wendrich J.R., Dorier J., Eekhout T., Aliaga Fandino A.C., Guex N., Bassel G.W., De Rybel B., Hardtke C.S., 2021/12/06. Molecular plant, 14 (12) pp. 1985-1999. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6A28C040E088]
Blood virosphere in febrile Tanzanian children.
Cordey S., Laubscher F., Hartley M.A., Junier T., Keitel K., Docquier M., Guex N., Iseli C., Vieille G., Le Mercier P. et al., 2021/12. Emerging microbes & infections, 10 (1) pp. 982-993. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B0B6B061E9F0]
Inhibition of G-protein signalling in cardiac dysfunction of intellectual developmental disorder with cardiac arrhythmia (IDDCA) syndrome.
De Nittis P., Efthymiou S., Sarre A., Guex N., Chrast J., Putoux A., Sultan T., Raza Alvi J., Ur Rahman Z., Zafar F. et al., 2021/12. Journal of medical genetics, 58 (12) pp. 815-831. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D9A4B043FC02]
Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss.
Bassani S., van Beelen E., Rossel M., Voisin N., Morgan A., Arribat Y., Chatron N., Chrast J., Cocca M., Delprat B. et al., 2021/09/15. Human molecular genetics, 30 (19) pp. 1785-1796. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1B6DF3F33981]
Predicting spatial patterns of soil bacteria under current and future environmental conditions.
Mod H.K., Buri A., Yashiro E., Guex N., Malard L., Pinto-Figueroa E., Pagni M., Niculita-Hirzel H., van der Meer J.R., Guisan A., 2021/09. The ISME journal, 15 (9) pp. 2547-2560. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_595C7D7FADB0]
Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING.
Bruand M., Barras D., Mina M., Ghisoni E., Morotti M., Lanitis E., Fahr N., Desbuisson M., Grimm A., Zhang H. et al., 2021/07/20. Cell reports, 36 (3) p. 109412. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_745449157CA6]
 
Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.
Voisin N., Schnur R.E., Douzgou S., Hiatt S.M., Rustad C.F., Brown N.J., Earl D.L., Keren B., Levchenko O., Geuer S. et al., 2021/05/06. American journal of human genetics, 108 (5) pp. 857-873. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A61CD673B3D6]
DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies.
Bararpour N., Gilardi F., Carmeli C., Sidibe J., Ivanisevic J., Caputo T., Augsburger M., Grabherr S., Desvergne B., Guex N. et al., 2021/03/11. Scientific reports, 11 (1) p. 5657. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C00E7D1EAE17]
CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions.
Kaushal A., Mohana G., Dorier J., Özdemir I., Omer A., Cousin P., Semenova A., Taschner M., Dergai O., Marzetta F. et al., 2021/02/12. Nature communications, 12 (1) p. 1011. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6E8BCA9FDAE9]
 
Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.
den Hoed J., de Boer E., Voisin N., Dingemans AJM, Guex N., Wiel L., Nellaker C., Amudhavalli S.M., Banka S., Bena F.S. et al., 2021/02/04. American journal of human genetics, 108 (2) pp. 346-356. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0EBEF17D8EA2]
Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue.
Caputo T., Tran VDT, Bararpour N., Winkler C., Aguileta G., Trang KB, Giordano Attianese GMP, Wilson A., Thomas A., Pagni M. et al., 2021/01. Cellular and molecular life sciences, 78 (1) pp. 227-247. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_713DAFDC1C95]
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients.
Bibert S., Guex N., Lourenco J., Brahier T., Papadimitriou-Olivgeris M., Damonti L., Manuel O., Liechti R., Götz L., Tschopp J. et al., 2021. Frontiers in immunology, 12 p. 666163. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_91CEC9119F7E]
Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery.
Baumgaertner P., Sankar M., Herrera F.G, Benedetti F., Barras D., Thierry A.C., Dangaj D., Kandalaft L.E., Coukos G., Xenarios I. et al., 2021. Frontiers in immunology, 12 p. 633910. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E707FFE34C52]
2020
Greater topoclimatic control of above- versus below-ground communities.
Mod H.K., Scherrer D., Di Cola V., Broennimann O., Blandenier Q., Breiner F.T., Buri A., Goudet J., Guex N., Lara E. et al., 2020/12. Global change biology, 26 (12) pp. 6715-6728. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_858D58CF6336]
Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.
Gleizes A., Laubscher F., Guex N., Iseli C., Junier T., Cordey S., Fellay J., Xenarios I., Kaiser L., Mercier P.L., 2020/11/01. Viruses, 12 (11) pp. E1248. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5E9093826570]
 
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Wells D.K., van Buuren M.M., Dang K.K., Hubbard-Lucey V.M., Sheehan KCF, Campbell K.M., Lamb A., Ward J.P., Sidney J., Blazquez A.B. et al., 2020/10/29. Cell, 183 (3) pp. 818-834.e13. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F6095670EC38]
Visualization and normalization of drift effect across batches in metabolome-wide association studies
Bararpour N., Gilardi F., Carmeli C., Sidibe J., Ivanisevic J., Caputo T., Augsburger M., Grabherr S., Desvergne B., Guex N. et al., 2020/01/22..
[URN][DOI][serval:BIB_45680B563CA2]
2019
 
1-Deoxydihydroceramide causes anoxic death by impairing chaperonin-mediated protein folding.
Hannich J.T., Haribowo A.G., Gentina S., Paillard M., Gomez L., Pillot B., Thibault H., Abegg D., Guex N., Zumbuehl A. et al., 2019/10. Nature metabolism, 1 (10) pp. 996-1008. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_62B2442C63AD]
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