Vital-IT – Computational biology

Ducrest AL, San-Jose LM, Neuenschwander S, Schmid-Siegert E, Simon C, Pagni M, Iseli C, Richter H, Guex N, Cumer T, Beaudoing E, Dupasquier M, Charruau P, Ducouret P, Xenarios I, Goudet J, Roulin A. Melanin and Neurotransmitter Signalling Genes Are Differentially Co-Expressed in Growing Feathers of White and Rufous Barn Owls. Pigment Cell Melanoma Res 2025;38(2):e70001

1. Bozzi D, Neuenschwander S, Cruz Dávalos DI, Sousa da Mota B, Schroeder H, Moreno-Mayar JV, Allentoft ME, Malaspinas AS. Towards predicting the geographical origin of ancient samples with metagenomic data. Sci Rep 2024;14(1):21794
2. Cailleau G, Junier T, Paul C, Fatton M, Corona-Ramirez A, Gning O, Beck K, Vidal J, Bürgmann H, Junier P. Temporal and spatial changes in the abundance of antibiotic resistance gene markers in a wastewater treatment plant. Water Environ Res 2024;96(8):e11104
3. Castillo-Armengol J, Marzetta F, Sanchez-Archidona AR, Fledelius C, Evans M, McNeilly A, McCrimmon RJ, Ibberson M, Thorens B. Correction to: Disrupted hypothalamic transcriptomics and proteomics in a mouse model of type 2 diabetes exposed to recurrent hypoglycaemia. Diabetologia 2024;67(2):403
4. Decken Ivd, Gutiérrez DR, Sproll P, Opitz L, Stevenson B, Azimi H, Lang-Muritano M, Konrad D, Lenherr-Taube N, Kennedy U, L’Allemand D, Livshits L, Raafat S, Nef S, Biason-Lauber A. Maximizing the Benefits of WES Data for Clinical Diagnosis of individuals with Differences/Variations of Sex Development 2024
5. Delfin C, Dragan I, Kuznetsov D, Tajes JF, Smit F, Coral DE, Farzaneh A, Haugg A, Hungele A, Niknejad A, Hall C, Jacobs D, Marek D, Fraser DP, Thuillier D, Ahmadizar F, Mehl F, Pattou F, Burdet F, Hawkes G, Arts ICW, Blanch J, Van Soest J, Fernández-Real JM, Boehl J, Fink K, van Greevenbroek MMJ, Kavousi M, Minten M, Prinz N, Ipsen N, Franks PW, Ramos R, Holl RW, Horban S, Duarte-Salles T, Tran VDT, Raverdy V, Leal Y, Lenart A, Pearson E, Sparsø T, Giordano GN, Ioannidis V, Soh K, Frayling TM, Le Roux CW, Ibberson M. A Federated Database for Obesity Research: An IMI-SOPHIA Study. Life (Basel) 2024;14(2):262
6. Gaudry A, Pagni M, Mehl F, Moretti S, Quiros-Guerrero LM, Cappelletti L, Rutz A, Kaiser M, Marcourt L, Queiroz EF, Ioset JR, Grondin A, David B, Wolfender JL, Allard PM. A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery. ACS Cent Sci 2024;10(3):494-510
7. Gloyn AL, Ibberson M, Marchetti P, Powers AC, Rorsman P, Sander M, Solimena M. Author Correction: Every islet matters: improving the impact of human islet research. Nat Metab 2024;6(7):1415
8. Gouy A, Wang X, Kapopoulou A, Neuenschwander S, Schmid E, Excoffier L, Heckel G. Genomes of Microtus Rodents Highlight the Importance of Olfactory and Immune Systems in Their Fast Radiation. Genome Biol Evol 2024;16(11):evae233
9. Hurcombe JA, Dayalan L, Barrington F, Burdet F, Ni L, Coward JT, Brinkkoetter PT, Holzenberger M, Jeffries A, Oltean S, Welsh GI, Coward RJ. The insulin / IGF axis is critically important controlling gene transcription in the podocyte 2024
10. Keller F, Denicolò S, Leierer J, Kruus M, Heinzel A, Kammer M, Ju W, Nair V, Burdet F, Ibberson M, Menon R, Otto E, Choi YJ, Pyle L, Ladd P, Bjornstad PM, Eder S, Rosivall L, Mark PB, Wiecek A, Heerspink HJL, Kretzler M, Oberbauer R, Mayer G, Perco P. Association of Urinary Epidermal Growth Factor, Fatty Acid-Binding Protein 3, and Vascular Cell Adhesion Molecule 1 Levels with the Progression of Early Diabetic Kidney Disease. Kidney Blood Press Res 2024;49(1):1013-1025
11. Lay AC, Tran VDT, Nair V, Betin V, Hurcombe JA, Barrington AF, Pope RJ, Burdet F, Mehl F, Kryvokhyzha D, Ahmad A, Sinton MC, Lewis P, Wilson MC, Menon R, Otto E, Heesom KJ, Ibberson M, Looker HC, Nelson RG, Ju W, Kretzler M, Satchell SC, Gomez MF, Coward RJM, BEAt-DKD consortium. Profiling of insulin-resistant kidney models and human biopsies reveals common and cell-type-specific mechanisms underpinning Diabetic Kidney Disease. Nat Commun 2024;15(1):10018
12. Li S, Dragan I, Tran VDT, Fung CH, Kuznetsov D, Hansen MK, Beulens JWJ, Hart LM', Slieker RC, Donnelly LA, Gerl MJ, Klose C, Mehl F, Simons K, Elders PJM, Pearson ER, Rutter GA, Ibberson M. Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study. Front Endocrinol (Lausanne) 2024;15:1350796
13. Mehl F, Sánchez-Archidona AR, Meitil I, Gerl M, Cruciani-Guglielmacci C, Wigger L, Le Stunff H, Meneyrol K, Lallement J, Denom J, Klose C, Simons K, Pagni M, Magnan C, Ibberson M, Thorens B. A multiorgan map of metabolic, signaling, and inflammatory pathways that coordinately control fasting glycemia in mice. iScience 2024;27(11):111134
14. Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, Montagud A, Noël V, Marku M, Tsirvouli E, Torres MM, Harris LA, Sego TJ, Cockrell C, Shick AE, Balci H, Salazar A, Rian K, Hemedan AA, Esteban-Medina M, Staumont B, Hernandez-Vargas E, Martis B S, Madrid-Valiente A, Karampelesis P, Sordo Vieira L, Harlapur P, Kulesza A, Nikaein N, Garira W, Malik Sheriff RS, Thakar J, Tran VDT, Carbonell-Caballero J, Safaei S, Valencia A, Zinovyev A, Glazier JA. Immune digital twins for complex human pathologies: applications, limitations, and challenges. NPJ Syst Biol Appl 2024;10(1):141
15. Palmieri F, Diserens J, Gresse M, Magnin M, Helle J, Salamin B, Bisanti L, Bernasconi E, Pernot J, Shanmuganathan A, Trompette A, von Garnier C, Junier T, Neuenschwander S, Bindschedler S, Pagni M, Koutsokera A, Ubags N, Junier P. One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia. Microorganisms 2024;12(10):2025
16. Sempach L, Doll JPK, Limbach V, Marzetta F, Schaub AC, Schneider E, Kettelhack C, Mählmann L, Schweinfurth-Keck N, Ibberson M, Lang UE, Schmidt A. Examining immune-inflammatory mechanisms of probiotic supplementation in depression: secondary findings from a randomized clinical trial. Transl Psychiatry 2024;14(1):305
17. Slieker RC, Münch M, Donnelly LA, Bouland GA, Dragan I, Kuznetsov D, Elders PJM, Rutter GA, Ibberson M, Pearson ER, 't Hart LM, van de Wiel MA, Beulens JWJ. An omics-based machine learning approach to predict diabetes progression: a RHAPSODY study. Diabetologia 2024;67(5):885-894

• Arnaud Dance, Justine Fernandes, Bénédicte Toussaint, Emmanuel Vaillant, Raphaël Boutry, Morgane Baron, Hélène Loiselle, Beverley Balkau, Guillaume Charpentier, Sylvia Franc, Mark Ibberson, Michel Marre, Marie Gernay, Marjorie Fadeur, Nicolas Paquot, Martine Vaxillaire, Mathilde Boissel, Souhila Amanzougarene, Mehdi Derhourhi, Amna Khamis, Philippe Froguel, Amélie Bonnefond Exploring the Role of Purinergic Receptor P2RY1 in Type 2 Diabetes Risk and Pathophysiology: Insights from Human Functional Genomics. Molecular metabolism (2023) doi: 10.1016/j.molmet.2023.101867
• Caroline S Meier, Marco Pagni, Sophie Richard, Konrad Mühlethaler, João M G C F Almeida, Gilles Nevez, Melanie T Cushion, Enrique J Calderón, Philippe M Hauser Publisher Correction: Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires. Nature communications, 14 (2023) doi: 10.1038/s41467-023-43993-7
• Judit Castillo-Armengol, Flavia Marzetta, Ana Rodriguez Sanchez-Archidona, Christian Fledelius, Mark Evans, Alison McNeilly, Rory J McCrimmon, Mark Ibberson, Bernard Thorens Disrupted hypothalamic transcriptomics and proteomics in a mouse model of type 2 diabetes exposed to recurrent hypoglycaemia. Diabetologia (2023) doi: 10.1007/s00125-023-06043-x
• Caroline S Meier, Marco Pagni, Sophie Richard, Konrad Mühlethaler, João M G C F Almeida, Gilles Nevez, Melanie T Cushion, Enrique J Calderón, Philippe M Hauser Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires. Nature communications, 14 (2023) doi: 10.1038/s41467-023-42685-6
• Oliver FitzGerald, Frank Behrens, Anne Barton, Heidi Bertheussen, Bruno Boutouyrie-Dumont, Laura Coates, Owen Davies, Maarten de Wit, Filippo Fagni, Carl S Goodyear, Robert Gurke, Lisa Hahnefeld, Christine Huppertz, Vassilios Ioannidis, Mark Ibberson, Arnon Katz, Maximilian Klippstein, Michaela Koehm, Shimon Korish, Sina Mackay, David A Martin, Denis O'Sullivan, Khadijah Patel, Stefan Rueping, Georg Schett, Klaus Scholich, Jochen M Schwenk, Stefan Siebert, David Simon, Arani Vivekanantham, Stephen R Pennington Application of clinical and molecular profiling data to improve patient outcomes in psoriatic arthritis. Therapeutic advances in musculoskeletal disease, 15 (2023) doi: 10.1177/1759720X231192315
• Agnete T Lundgaard, Frédéric Burdet, Troels Siggaard, David Westergaard, Danai Vagiaki, Lisa Cantwell, Timo Röder, Dorte Vistisen, Thomas Sparsø, Giuseppe N Giordano, Mark Ibberson, Karina Banasik, Søren Brunak BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus. PLoS computational biology, 19 (2023) doi: 10.1371/journal.pcbi.1011403
• Sameer M Padhye, Mihir R Kulkarni, Marco Pagni, Nicolas Rabet New leptestherid clam shrimps (Pancrustacea: Branchiopoda: Spinicaudata: Leptestheriidae) from peninsular India. Zootaxa, 5264 (2023) doi: 10.11646/zootaxa.5264.2.3
• Danielle Welter, Nick Juty, Philippe Rocca-Serra, Fuqi Xu, David Henderson, Wei Gu, Jolanda Strubel, Robert T Giessmann, Ibrahim Emam, Yojana Gadiya, Tooba Abbassi-Daloii, Ebtisam Alharbi, Alasdair J G Gray, Melanie Courtot, Philip Gribbon, Vassilios Ioannidis, Dorothy S Reilly, Nick Lynch, Jan-Willem Boiten, Venkata Satagopam, Carole Goble, Susanna-Assunta Sansone, Tony Burdett FAIR in action - a flexible framework to guide FAIRification. Scientific data, 10 (2023) doi: 10.1038/s41597-023-02167-2
• Philippe Rocca-Serra, Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, Ishwar Chandramouliswaran, Andrea Splendiani, Tony Burdett, Robert T Giessmann, David Henderson, Dominique Batista, Ibrahim Emam, Yojana Gadiya, Lucas Giovanni, Egon Willighagen, Chris Evelo, Alasdair J G Gray, Philip Gribbon, Nick Juty, Danielle Welter, Karsten Quast, Paul Peeters, Tom Plasterer, Colin Wood, Eelke van der Horst, Dorothy Reilly, Herman van Vlijmen, Serena Scollen, Allyson Lister, Milo Thurston, Ramon Granell, , Susanna-Assunta Sansone The FAIR Cookbook - the essential resource for and by FAIR doers. Scientific data, 10 (2023) doi: 10.1038/s41597-023-02166-3
• Roderick C Slieker, Louise A Donnelly, Elina Akalestou, Livia Lopez-Noriega, Rana Melhem, Ayşim Güneş, Frederic Abou Azar, Alexander Efanov, Eleni Georgiadou, Hermine Muniangi-Muhitu, Mahsa Sheikh, Giuseppe N Giordano, Mikael Åkerlund, Emma Ahlqvist, Ashfaq Ali, Karina Banasik, Søren Brunak, Marko Barovic, Gerard A Bouland, Frédéric Burdet, Mickaël Canouil, Iulian Dragan, Petra J M Elders, Celine Fernandez, Andreas Festa, Hugo Fitipaldi, Phillippe Froguel, Valborg Gudmundsdottir, Vilmundur Gudnason, Mathias J Gerl, Amber A van der Heijden, Lori L Jennings, Michael K Hansen, Min Kim, Isabelle Leclerc, Christian Klose, Dmitry Kuznetsov, Dina Mansour Aly, Florence Mehl, Diana Marek, Olle Melander, Anne Niknejad, Filip Ottosson, Imre Pavo, Kevin Duffin, Samreen K Syed, Janice L Shaw, Over Cabrera, Timothy J Pullen, Kai Simons, Michele Solimena, Tommi Suvitaival, Asger Wretlind, Peter Rossing, Valeriya Lyssenko, Cristina Legido Quigley, Leif Groop, Bernard Thorens, Paul W Franks, Gareth E Lim, Jennifer Estall, Mark Ibberson, Joline W J Beulens, Leen M 't Hart, Ewan R Pearson, Guy A Rutter Identification of biomarkers for glycaemic deterioration in type 2 diabetes. Nature communications, 14 (2023) doi: 10.1038/s41467-023-38148-7
• Andrea Corona Ramirez, Danaé Bregnard, Thomas Junier, Guillaume Cailleau, Cristina Dorador, Saskia Bindschedler, Pilar Junier Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC microbiology, 23 (2023) doi: 10.1186/s12866-023-02809-w
• Yohan Bignon, Leonore Wigger, Camille Ansermet, Benjamin D Weger, Sylviane Lagarrigue, Gabriel Centeno, Fanny Durussel, Lou Götz, Mark Ibberson, Sylvain Pradervand, Manfredo Quadroni, Meltem Weger, Francesca Amati, Frédéric Gachon, Dmitri Firsov Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. The Journal of clinical investigation (2023) doi: 10.1172/JCI167133
• Karina Barreiro, Abigail C Lay, German Leparc, Van Du T Tran, Marcel Rosler, Lusyan Dayalan, Frederic Burdet, Mark Ibberson, Richard J M Coward, Tobias B Huber, Bernhard K Krämer, Denis Delic, Harry Holthofer An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. Journal of extracellular vesicles, 12 (2023) doi: 10.1002/jev2.12304
• Samuel Neuenschwander, Diana I Cruz Dávalos, Lucas Anchieri, Bárbara Sousa da Mota, Davide Bozzi, Simone Rubinacci, Olivier Delaneau, Simon Rasmussen, Anna-Sapfo Malaspinas Mapache: a flexible pipeline to map ancient DNA. Bioinformatics (Oxford, England) (2023) doi: 10.1093/bioinformatics/btad028

• Ewa Izabela Podobas, Danuta Gutowska-Owsiak, Sébastien Moretti, Jarosław Poznański, Mariusz Kulińczak, Marcin Grynberg, Aleksandra Gruca, Arkadiusz Bonna, Dawid Płonka, Tomasz Frączyk, Graham Ogg, Wojciech Bal Corrigendum: Ni-assisted hydrolysis may affect the human proteome; filaggrin degradation as an example of possible consequences. Frontiers in molecular biosciences, 9 (2022) doi: 10.3389/fmolb.2022.1101224
• Mathilda Fatton, Sevasti Filippidou, Thomas Junier, Guillaume Cailleau, Matthieu Berge, Daniel Poppleton, Thorsten B Blum, Marek Kaminek, Adolfo Odriozola, Jochen Blom, Shannon L Johnson, Jan Pieter Abrahams, Patrick S Chain, Simonetta Gribaldo, Elitza I Tocheva, Benoît Zuber, Patrick H Viollier, Pilar Junier Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. Environmental microbiology, 24 (2022) doi: 10.1111/1462-2920.16145
• Alysha S Taylor, Dinis Barros, Nastassia Gobet, Thierry Schuepbach, Branduff McAllister, Lorene Aeschbach, Emma L Randall, Evgeniya Trofimenko, Eleanor R Heuchan, Paula Barszcz, Marc Ciosi, Joanne Morgan, Nathaniel J Hafford-Tear, Alice E Davidson, Thomas H Massey, Darren G Monckton, Lesley Jones, Registry Investigators Of The European Huntington's Disease Network, Ioannis Xenarios, Vincent Dion Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing. NAR genomics and bioinformatics, 4 (2022) doi: 10.1093/nargab/lqac089
• Jonviea D Chamberlain, Sébastien Nusslé, Laurence Chapatte, Cassandre Kinnaer, Dusan Petrovic, Sylvain Pradervand, Murielle Bochud, Sarah E Harris, Janie Corley, Simon R Cox, Semira Gonseth Nusslé Blood DNA methylation signatures of lifestyle exposures: tobacco and alcohol consumption. Clinical epigenetics, 14 (2022) doi: 10.1186/s13148-022-01376-7
• Dylan Lawless, Christopher G McKennan, Suman R Das, Thomas Junier, Zhi Ming Xu, Larry J Anderson, Tebeb Gebretsadik, Meghan H Shilts, Emma Larkin, Christian Rosas-Salazar, James D Chappell, Jacques Fellay, Tina V Hartert Viral genetic determinants of prolonged respiratory syncytial virus infection among infants in a healthy term birth cohort. The Journal of infectious diseases (2022) doi: 10.1093/infdis/jiac442
• Robert Gurke, Annika Bendes, John Bowes, Michaela Koehm, Richard M Twyman, Anne Barton, Dirk Elewaut, Carl Goodyear, Lisa Hahnefeld, Rainer Hillenbrand, Ewan Hunter, Mark Ibberson, Vassilios Ioannidis, Sabine Kugler, Rik J Lories, Eduard Resch, Stefan Rüping, Klaus Scholich, Jochen M Schwenk, James C Waddington, Phil Whitfield, Gerd Geisslinger, Oliver FitzGerald, Frank Behrens, Stephen R Pennington, Omics and Multi-Omics Analysis for the Early Identification and Improved Outcome of Patients with Psoriatic Arthritis. Biomedicines, 10 (2022) doi: 10.3390/biomedicines10102387
• Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios Towards mouse genetic-specific RNA-sequencing read mapping. PLoS computational biology, 18 (2022) doi: 10.1371/journal.pcbi.1010552
• Anna L Gloyn, Mark Ibberson, Piero Marchetti, Alvin C Powers, Patrik Rorsman, Maike Sander, Michele Solimena Every islet matters: improving the impact of human islet research. Nature metabolism (2022) doi: 10.1038/s42255-022-00607-8
• Olof Asplund, Petter Storm, Vikash Chandra, Gad Hatem, Emilia Ottosson-Laakso, Dina Mansour-Aly, Ulrika Krus, Hazem Ibrahim, Emma Ahlqvist, Tiinamaija Tuomi, Erik Renström, Olle Korsgren, Nils Wierup, Mark Ibberson, Michele Solimena, Piero Marchetti, Claes Wollheim, Isabella Artner, Hindrik Mulder, Ola Hansson, Timo Otonkoski, Leif Groop, Rashmi B Prasad Islet Gene View-a tool to facilitate islet research. Life science alliance, 5 (2022) doi: 10.26508/lsa.202201376
• Aurélie Le Lay, Erwann Philippe, Fanny Roth, Ana Rodriguez Sanchez-Archidona, Florence Mehl, Jessica Denom, Rashmi Prasad, Olof Asplund, Ola Hansson, Mark Ibberson, Fabrizio Andreelli, Lyse Santoro, Paul Amouyal, Gilles Amouyal, Christian Brechot, Laure Jamot, Céline Cruciani-Guglielmacci, Christophe Magnan Regenerating islet-derived protein 3α: A promising therapy for diabetes. Preliminary data in rodents and in humans. Heliyon, 8 (2022) doi: 10.1016/j.heliyon.2022.e09944
• Sanne Schrevens, Eric Durandau, Van Du T Tran, Dominique Sanglard Using transcriptomics and RNA enrichment to identify genes involved in virulence of . Virulence (2022) doi: 10.1080/21505594.2022.2095716
• Eleni Georgiadou, Charanya Muralidharan, Michelle Martinez, Pauline Chabosseau, Elina Akalestou, Alejandra Tomas, Fiona Yong Su Wern, Theodoros Stylianides, Asger Wretlind, Cristina Legido-Quigley, Ben Jones, Livia Lopez Noriega, Yanwen Xu, Guoqiang Gu, Nour Alsabeeh, Céline Cruciani-Guglielmacci, Christophe Magnan, Mark Ibberson, Isabelle Leclerc, Yusuf Ali, Scott A Soleimanpour, Amelia K Linnemann, Tristan A Rodriguez, Guy A Rutter Mitofusins Mfn1 and Mfn2 are Required to Preserve Glucose- But Not Incretin-Stimulated Beta Cell Connectivity and Insulin Secretion. Diabetes (2022) doi: 10.2337/db21-0800
• Christina Lemberg, Kontxi Martinez de San Vicente, Ricardo Fróis-Martins, Simon Altmeier, Van Du T Tran, Sarah Mertens, Sara Amorim-Vaz, Laxmi Shanker Rai, Christophe d'Enfert, Marco Pagni, Dominique Sanglard, Salomé LeibundGut-Landmann Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation. PLoS pathogens, 18 (2022) doi: 10.1371/journal.ppat.1010012
• Ewa Izabela Podobas, Danuta Gutowska-Owsiak, Sébastien Moretti, Jarosław Poznański, Mariusz Kulińczak, Marcin Grynberg, Aleksandra Gruca, Arkadiusz Bonna, Dawid Płonka, Graham Ogg, Wojciech Bal Ni-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation as an Example of Possible Consequences. Frontiers in molecular biosciences, 9 (2022) doi: 10.3389/fmolb.2022.828674
• Yami Ommar Arizmendi Cárdenas, Samuel Neuenschwander, Anna-Sapfo Malaspinas Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ, 10 (2022) doi: 10.7717/peerj.12784
• Ewa Izabela Podobas, Danuta Gutowska-Owsiak, Sébastien Moretti, Jarosław Poznański, Mariusz Kulińczak, Marcin Grynberg, Aleksandra Gruca, Arkadiusz Bonna, Dawid Płonka, Graham Ogg and Wojciech Bal Ni2+-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation Ex Vivo as an Example of Possible Consequences Frontiers in Molecular Biosciences (2022) url: https://www.frontiersin.org/articles/10.3389/fmolb.2022.828674/full
• Aline Adler, Simon Poirier, Marco Pagni, Julien Maillard, Christof Holliger Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environmental microbiology (2022) doi: 10.1111/1462-2920.15947

• Ana Rodríguez Sánchez-Archidona, Céline Cruciani-Guglielmacci, Clara Roujeau, Leonore Wigger, Justine Lallement, Jessica Denom, Marko Barovic, Nadim Kassis, Florence Mehl, Jurgen Weitz, Marius Distler, Christian Klose, Kai Simons, Mark Ibberson, Michele Solimena, Christophe Magnan, Bernard Thorens Plasma triacylglycerols are biomarkers of ß-cell function in mice and humans. Molecular metabolism (2021) doi: 10.1016/j.molmet.2021.101355
• Roderick C Slieker, Louise A Donnelly, Hugo Fitipaldi, Gerard A Bouland, Giuseppe N Giordano, Mikael Åkerlund, Mathias J Gerl, Emma Ahlqvist, Ashfaq Ali, Iulian Dragan, Petra Elders, Andreas Festa, Michael K Hansen, Amber A van der Heijden, Dina Mansour Aly, Min Kim, Dmitry Kuznetsov, Florence Mehl, Christian Klose, Kai Simons, Imre Pavo, Timothy J Pullen, Tommi Suvitaival, Asger Wretlind, Peter Rossing, Valeriya Lyssenko, Cristina Legido Quigley, Leif Groop, Bernard Thorens, Paul W Franks, Mark Ibberson, Guy A Rutter, Joline Wj Beulens, Leen M 't Hart, Ewan R Pearson Distinct Molecular Signatures of Clinical Clusters in People with Type 2 Diabetes: an IMIRHAPSODY Study. Diabetes (2021) doi: 10.2337/db20-1281
• Kaan Mika, Steeve Cruchet, Phing Chian Chai, Lucia L Prieto-Godino, Thomas O Auer, Sylvain Pradervand, Richard Benton Olfactory receptor-dependent receptor repression in . Science advances, 7 (2021) doi: 10.1126/sciadv.abe3745
• Leonore Wigger, Marko Barovic, Andreas-David Brunner, Flavia Marzetta, Eyke Schöniger, Florence Mehl, Nicole Kipke, Daniela Friedland, Frederic Burdet, Camille Kessler, Mathias Lesche, Bernard Thorens, Ezio Bonifacio, Cristina Legido-Quigley, Pierre Barbier Saint Hilaire, Philippe Delerive, Andreas Dahl, Christian Klose, Mathias J Gerl, Kai Simons, Daniela Aust, Jürgen Weitz, Marius Distler, Anke M Schulte, Matthias Mann, Mark Ibberson, Michele Solimena Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories towards type 2 diabetes. Nature metabolism (2021) doi: 10.1038/s42255-021-00420-9
• Roderick C Slieker, Louise A Donnelly, Hugo Fitipaldi, Gerard A Bouland, Giuseppe N Giordano, Mikael Åkerlund, Mathias J Gerl, Emma Ahlqvist, Ashfaq Ali, Iulian Dragan, Andreas Festa, Michael K Hansen, Dina Mansour Aly, Min Kim, Dmitry Kuznetsov, Florence Mehl, Christian Klose, Kai Simons, Imre Pavo, Timothy J Pullen, Tommi Suvitaival, Asger Wretlind, Peter Rossing, Valeriya Lyssenko, Cristina Legido-Quigley, Leif Groop, Bernard Thorens, Paul W Franks, Mark Ibberson, Guy A Rutter, Joline W J Beulens, Leen M 't Hart, Ewan R Pearson Replication and cross-validation of type 2 diabetes subtypes based on clinical variables: an IMI-RHAPSODY study. Diabetologia (2021) doi: 10.1007/s00125-021-05490-8
• Emanuele Bosi, Lorella Marselli, Carmela De Luca, Mara Suleiman, Marta Tesi, Mark Ibberson, Decio L Eizirik, Miriam Cnop, Piero Marchetti Correction to 'Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes'. NAR genomics and bioinformatics, 3 (2021) doi: 10.1093/nargab/lqab053
• Petra Baumgaertner, Martial Sankar, Fernanda Herrera, Fabrizio Benedetti, David Barras, Anne-Christine Thierry, Denarda Dangaj, Lana E Kandalaft, George Coukos, Ioannis Xenarios, Nicolas Guex, Alexandre Harari Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery. Frontiers in immunology, 12 (2021) doi: 10.3389/fimmu.2021.633910
• Florian Clemente, Martina Unterländer, Olga Dolgova, Carlos Eduardo G Amorim, Francisco Coroado-Santos, Samuel Neuenschwander, Elissavet Ganiatsou, Diana I Cruz Dávalos, Lucas Anchieri, Frédéric Michaud, Laura Winkelbach, Jens Blöcher, Yami Ommar Arizmendi Cárdenas, Bárbara Sousa da Mota, Eleni Kalliga, Angelos Souleles, Ioannis Kontopoulos, Georgia Karamitrou-Mentessidi, Olga Philaniotou, Adamantios Sampson, Dimitra Theodorou, Metaxia Tsipopoulou, Ioannis Akamatis, Paul Halstead, Kostas Kotsakis, Dushka Urem-Kotsou, Diamantis Panagiotopoulos, Christina Ziota, Sevasti Triantaphyllou, Olivier Delaneau, Jeffrey D Jensen, J Víctor Moreno-Mayar, Joachim Burger, Vitor C Sousa, Oscar Lao, Anna-Sapfo Malaspinas, Christina Papageorgopoulou The genomic history of the Aegean palatial civilizations. Cell (2021) doi: 10.1016/j.cell.2021.03.039
• Heidi K Mod, Aline Buri, Erika Yashiro, Nicolas Guex, Lucie Malard, Eric Pinto-Figueroa, Marco Pagni, Hélène Niculita-Hirzel, Jan Roelof van der Meer, Antoine Guisan Predicting spatial patterns of soil bacteria under current and future environmental conditions. The ISME journal (2021) doi: 10.1038/s41396-021-00947-5
• Robertas Ursache, Cristovāo De Jesus Vieira Teixeira, Valérie Dénervaud Tendon, Kay Gully, Damien De Bellis, Emanuel Schmid-Siegert, Tonni Grube Andersen, Vinay Shekhar, Sandra Calderon, Sylvain Pradervand, Christiane Nawrath, Niko Geldner, Joop E M Vermeer GDSL-domain proteins have key roles in suberin polymerization and degradation. Nature plants (2021) doi: 10.1038/s41477-021-00862-9
• Anjali Kaushal, Giriram Mohana, Julien Dorier, Isa Özdemir, Arina Omer, Pascal Cousin, Anastasiia Semenova, Michael Taschner, Oleksandr Dergai, Flavia Marzetta, Christian Iseli, Yossi Eliaz, David Weisz, Muhammad Saad Shamim, Nicolas Guex, Erez Lieberman Aiden, Maria Cristina Gambetta CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions. Nature communications, 12 (2021) doi: 10.1038/s41467-021-21366-2
• Ming Hu, Inês Cebola, Gaelle Carrat, Shuying Jiang, Sameena Nawaz, Amna Khamis, Mickaël Canouil, Philippe Froguel, Anke Schulte, Michele Solimena, Mark Ibberson, Piero Marchetti, Fabian L Cardenas-Diaz, Paul J Gadue, Benoit Hastoy, Leonardo Alemeida-Souza, Harvey McMahon, Guy A Rutter Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion. Cell reports, 34 (2021) doi: 10.1016/j.celrep.2021.108703
• S Neda Mousavy Gharavy, Bryn M Owen, Steven J Millership, Pauline Chabosseau, Grazia Pizza, Aida Martinez-Sanchez, Emirhan Tasoez, Eleni Georgiadou, Ming Hu, Nicholas H F Fine, David A Jacobson, Matthew T Dickerson, Olof Idevall-Hagren, Alex Montoya, Holger Kramer, Zenobia Mehta, Dominic J Withers, Nikolay Ninov, Paul J Gadue, Fabian L Cardenas-Diaz, Céline Cruciani-Guglielmacci, Christophe Magnan, Mark Ibberson, Isabelle Leclerc, Marianne Voz, Guy A Rutter Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis. Diabetologia (2021) doi: 10.1007/s00125-020-05350-x
• Pilar Junier, Guillaume Cailleau, Ilona Palmieri, Celine Valloton, Olivia C Trautschold, Thomas Junier, Christophe Paul, Danae Bregnard, Fabio Palmieri, Aislinn Estoppey, Matteo Buffi, Andrea Lohberger, Aaron Robinson, Julia M Kelliher, Karen Davenport, Geoffrey L House, Demosthenes Morales, La Verne Gallegos-Graves, Armand E K Dichosa, Simone Lupini, Hang N Nguyen, Jamey D Young, Debora F Rodrigues, A Nicholas G Parra-Vasquez, Saskia Bindschedler, Patrick S G Chain Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS microbiology ecology (2021) doi: 10.1093/femsec/fiab003

• Cristina Bosmani, Florence Leuba, Nabil Hanna, Frauke Bach, Frédéric Burdet, Marco Pagni, Monica Hagedorn, Thierry Soldati Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum. Journal of cell science (2020) doi: 10.1242/jcs.242974
• Emanuele Bosi, Lorella Marselli, Carmela De Luca, Mara Suleiman, Marta Tesi, Mark Ibberson, Decio L Eizirik, Miriam Cnop, Piero Marchetti Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. NAR genomics and bioinformatics, 2 (2020) doi: 10.1093/nargab/lqaa097
• Kathryn J Burton-Pimentel, Grégory Pimentel, Maria Hughes, Charlotte Cjr Michielsen, Attia Fatima, Nathalie Vionnet, Lydia A Afman, Helen M Roche, Lorraine Brennan, Mark Ibberson, Guy Vergères Discriminating dietary responses by combining transcriptomics and metabolomics data in nutrition intervention studies. Molecular nutrition & food research (2020) doi: 10.1002/mnfr.202000647
• Lorella Marselli, Anthony Piron, Mara Suleiman, Maikel L Colli, Xiaoyan Yi, Amna Khamis, Gaelle R Carrat, Guy A Rutter, Marco Bugliani, Laura Giusti, Maurizio Ronci, Mark Ibberson, Jean-Valery Turatsinze, Ugo Boggi, Paolo De Simone, Vincenzo De Tata, Miguel Lopes, Daniela Nasteska, Carmela De Luca, Marta Tesi, Emanuele Bosi, Pratibha Singh, Daniela Campani, Anke M Schulte, Michele Solimena, Peter Hecht, Brian Rady, Ivona Bakaj, Alessandro Pocai, Lisa Norquay, Bernard Thorens, Mickaël Canouil, Philippe Froguel, Decio L Eizirik, Miriam Cnop, Piero Marchetti Persistent or Transient Human β Cell Dysfunction Induced by Metabolic Stress: Specific Signatures and Shared Gene Expression with Type 2 Diabetes. Cell reports, 33 (2020) doi: 10.1016/j.celrep.2020.108466
• Emma Ricart, Maude Pupin, Markus Müller, Frédérique Lisacek Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products. Analytical chemistry (2020) doi: 10.1021/acs.analchem.0c03208
• F Zanatta, R Engler, F Collart, O Broennimann, R G Mateo, B Papp, J Muñoz, D Baurain, A Guisan, A Vanderpoorten Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities. Nature communications, 11 (2020) doi: 10.1038/s41467-020-19410-8
• Sébastien Moretti, Van Du T Tran, Florence Mehl, Mark Ibberson, Marco Pagni MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Nucleic acids research (2020) doi: 10.1093/nar/gkaa992
• Anne Gleizes, Florian Laubscher, Nicolas Guex, Christian Iseli, Thomas Junier, Samuel Cordey, Jacques Fellay, Ioannis Xenarios, Laurent Kaiser, Philippe Le Mercier Virosaurus A Reference to Explore and Capture Virus Genetic Diversity. Viruses, 12 (2020) doi: 10.3390/v12111248
• Fabio Marino, Aikaterini Semilietof, Justine Michaux, Hui-Song Pak, George Coukos, Markus Müller, Michal Bassani-Sternberg Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference. Frontiers in immunology, 11 (2020) doi: 10.3389/fimmu.2020.01981
• Dionysios V Chartoumpekis, Panos G Ziros, Ilias Georgakopoulos-Soares, Adam A T Smith, Ana Claudia Marques, Mark Ibberson, Peter A Kopp, Ioannis Habeos, Ioannis P Trougakos, Nicholas K H Khoo, Gerasimos P Sykiotis The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System. Antioxidants (Basel, Switzerland), 9 (2020) doi: 10.3390/antiox9090884
• Rita Ahmed, Isaac Crespo, Sandra Tuyaerts, Amel Bekkar, Michele Graciotti, Ioannis Xenarios, Lana E Kandalaft Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform. Computational and structural biotechnology journal, 18 (2020) doi: 10.1016/j.csbj.2020.08.001
• Gustavo A Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y Tan, Victor Ythier, Emma L Randall, Ana C Marques, Tuncay Baubec, Rabih Murr, Ioannis Xenarios, Vincent Dion Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. Science advances, 6 (2020) doi: 10.1126/sciadv.aaz4012
• Heidi K Mod, Daniel Scherrer, Valeria Di Cola, Olivier Broennimann, Quentin Blandenier, Frank T Breiner, Aline Buri, Jérôme Goudet, Nicolas Guex, Enrique Lara, Edward A D Mitchell, Hélène Niculita-Hirzel, Marco Pagni, Loïc Pellissier, Eric Pinto-Figueroa, Ian R Sanders, Benedikt R Schmidt, Christophe V W Seppey, David Singer, Sylvain Ursenbacher, Erika Yashiro, Jan R van, der Meer, Antoine Guisan Greater topoclimatic control of above- Versus belowground communities. Global change biology (2020) doi: 10.1111/gcb.15330
• Gustavo A Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y Tan, Victor Ythier, Emma L Randall, Ana C Marques, Tuncay Baubec, Rabih Murr, Ioannis Xenarios, Vincent Dion Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. Science advances, 6 (2020) doi: 10.1126/sciadv.aaz4012
• Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi Del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D Thomas, Dénes Türei, Martin Kuiper The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics (Oxford, England) (2020) doi: 10.1093/bioinformatics/btaa622
• I Castanon, J T Hannich, L Abrami, F Huber, M Dubois, M Müller, F G van der Goot, M Gonzalez-Gaitan Wnt-controlled sphingolipids modulate Anthrax Toxin Receptor palmitoylation to regulate oriented mitosis in zebrafish. Nature communications, 11 (2020) doi: 10.1038/s41467-020-17196-3
• Emanuel Schmid-Siegert, Sophie Richard, Amanda Luraschi, Konrad Mühlethaler, Marco Pagni, Philippe M Hauser Expression pattern of the Pneumocystis jirovecii major surface glycoprotein superfamily in patients with pneumonia. The Journal of infectious diseases (2020) doi: 10.1093/infdis/jiaa342
• Cristina Bosmani, Florence Leuba, Nabil Hanna, Frauke Bach, Frédéric Burdet, Marco Pagni, Monica Hagedorn, Thierry Soldati Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in . Journal of cell science (2020) doi: 10.1242/jcs.242974
• Jérémy Gauthier, Mila Pajkovic, Samuel Neuenschwander, Lauri Kaila, Sarah Schmid, Ludovic Orlando, Nadir Alvarez Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Molecular ecology resources (2020) doi: 10.1111/1755-0998.13167
• Dassine Berdous, Xavier Berney, Ana Rodriguez Sanchez-Archidona, Maxime Jan, Clara Roujeau, Isabel Lopez Mejia, Randall Mynatt, Bernard Thorens A Genetic Screen Identifies Crat As A Regulator Of Pancreatic Beta-Cell Insulin Secretion. Molecular metabolism (2020) doi: 10.1016/j.molmet.2020.100993
• Christopher Dumayne, David Tarussio, Ana Rodriguez Sanchez-Archidona, Alexandre Picard, Davide Basco, Xavier Pascal Berney, Mark Ibberson, Bernard Thorens Klf6 protects β-cells against insulin resistance-induced dedifferentiation. Molecular metabolism, 35 (2020) doi: 10.1016/j.molmet.2020.02.001
• Otmane Lamrabet, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Thierry Soldati, Pierre Cosson Transcriptional Responses of Exposed to Different Classes of Bacteria. Frontiers in microbiology, 11 (2020) doi: 10.3389/fmicb.2020.00410
• Lucia L Prieto-Godino, Ana F Silbering, Mohammed A Khallaf, Steeve Cruchet, Karolina Bojkowska, Sylvain Pradervand, Bill S Hansson, Markus Knaden, Richard Benton Functional integration of "undead" neurons in the olfactory system. Science advances, 6 (2020) doi: 10.1126/sciadv.aaz7238
• Anne-Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid-Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M San-Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xenarios, Alexandre Roulin, Jérôme Goudet New genome assembly of the barn owl (). Ecology and evolution, 10 (2020) doi: 10.1002/ece3.5991
• Satoshi Fujita, Damien De Bellis, Kai H Edel, Philipp Köster, Tonni Grube Andersen, Emanuel Schmid-Siegert, Valérie Dénervaud Tendon, Alexandre Pfister, Peter Marhavý, Robertas Ursache, Verónica G Doblas, Marie Barberon, Jean Daraspe, Audrey Creff, Gwyneth Ingram, Jörg Kudla, Niko Geldner SCHENGEN receptor module drives localized ROS production and lignification in plant roots. The EMBO journal (2020) doi: 10.15252/embj.2019103894
• Chloe Chong, Markus Müller, HuiSong Pak, Dermot Harnett, Florian Huber, Delphine Grun, Marion Leleu, Aymeric Auger, Marion Arnaud, Brian J Stevenson, Justine Michaux, Ilija Bilic, Antje Hirsekorn, Lorenzo Calviello, Laia Simó-Riudalbas, Evarist Planet, Jan Lubiński, Marta Bryśkiewicz, Maciej Wiznerowicz, Ioannis Xenarios, Lin Zhang, Didier Trono, Alexandre Harari, Uwe Ohler, George Coukos, Michal Bassani-Sternberg Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nature communications, 11 (2020) doi: 10.1038/s41467-020-14968-9
• Tiziana Caputo, Van Du T Tran, Nasim Bararpour, Carine Winkler, Gabriela Aguileta, Khanh Bao Trang, Greta M P Giordano Attianese, Anne Wilson, Aurelien Thomas, Marco Pagni, Nicolas Guex, Béatrice Desvergne, Federica Gilardi Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue. Cellular and molecular life sciences : CMLS (2020) doi: 10.1007/s00018-020-03485-z
• Sophie Rodius, Niek de Klein, Céline Jeanty, Héctor Sánchez-Iranzo, Isaac Crespo, Mark Ibberson, Ioannis Xenarios, Gunnar Dittmar, Nadia Mercader, Simone P Niclou, Francisco Azuaje Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity. Scientific reports, 10 (2020) doi: 10.1038/s41598-020-59894-4
• Pierre Fontana, Mark Ibberson, Brian Stevenson, Leonore Wigger, Youssef Daali, Anne Niknejad, François Mach, Mylène Docquier, Ioannis Xenarios, Thomas Cuisset, Marie-Christine Alessi, Jean-Luc Reny Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients. Journal of thrombosis and haemostasis : JTH (2020) doi: 10.1111/jth.14776
• Romain Savary, Cindy Dupuis, Frédéric G Masclaux, Ivan D Mateus, Edward C Rojas, Ian R Sanders Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava. The ISME journal (2020) doi: 10.1038/s41396-020-0606-6
• Amel Bekkar, Anita Nasrallah, Nicolas Guex, Lluis Fajas, Ioannis Xenarios, Isabel C Lopez-Mejia PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinformatics (Oxford, England) (2020) doi: 10.1093/bioinformatics/btz858
• Harmonie Dehaene, Viviane Praz, Philippe Lhôte, Maykel Lopes, Winship Herr THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PloS one, 15 (2020) doi: 10.1371/journal.pone.0224646

• Pénélope A Andreux, William Blanco-Bose, Dongryeol Ryu, Frédéric Burdet, Mark Ibberson, Patrick Aebischer, Johan Auwerx, Anurag Singh, Chris Rinsch The mitophagy activator urolithin A is safe and induces a molecular signature of improved mitochondrial and cellular health in humans. Nature metabolism, 1 (2019) doi: 10.1038/s42255-019-0073-4
• Frédéric G Masclaux, Tania Wyss, Marco Pagni, Pawel Rosikiewicz, Ian R Sanders Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data. PloS one, 14 (2019) doi: 10.1371/journal.pone.0226497
• Charlotte N Hor, Jake Yeung, Maxime Jan, Yann Emmenegger, Jeffrey Hubbard, Ioannis Xenarios, Felix Naef, Paul Franken Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex. Proceedings of the National Academy of Sciences of the United States of America (2019) doi: 10.1073/pnas.1910590116
• Alice Newey, Beatrice Griffiths, Justine Michaux, Hui Song Pak, Brian J Stevenson, Andrew Woolston, Maria Semiannikova, Georgia Spain, Louise J Barber, Nik Matthews, Sheela Rao, David Watkins, Ian Chau, George Coukos, Julien Racle, David Gfeller, Naureen Starling, David Cunningham, Michal Bassani-Sternberg, Marco Gerlinger Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment. Journal for immunotherapy of cancer, 7 (2019) doi: 10.1186/s40425-019-0769-8
• Lionel O Mavoungou, Samuel Neuenschwander, Uyen Pham, Pavithra S Iyer, Nicolas Mermod Characterization of mesoangioblast cell fate and improved promyogenic potential of a satellite cell-like subpopulation upon transplantation in dystrophic murine muscles. Stem cell research, 41 (2019) doi: 10.1016/j.scr.2019.101619
• Maxime Jan, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xenarios A multi-omics digital research object for the genetics of sleep regulation. Scientific data, 6 (2019) doi: 10.1038/s41597-019-0171-x
• Pierre-Olivier Duroy, Sandra Bosshard, Emanuel Schmid-Siegert, Samuel Neuenschwander, Ghislaine Arib, Philippe Lemercier, Jacqueline Masternak, Lucien Roesch, Flavien Buron, Pierre-Alain Girod, Ioannis Xenarios, Nicolas Mermod Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. Biotechnology and bioengineering (2019) doi: 10.1002/bit.27200
• Isha Hashmi, Christophe Paul, Andrej Al-Dourobi, Frederic Sandoz, Priscilla Deschamps, Thomas Junier, Pilar Junier, Saskia Bindschedler Comparison of the plant growth-promotion performance of a consortium of Bacilli inoculated as endospores or as vegetative cells. FEMS microbiology ecology, 95 (2019) doi: 10.1093/femsec/fiz147
• Marko Barovic, Marius Distler, Eyke Schöniger, Nicole Radisch, Daniela Aust, Jürgen Weitz, Mark Ibberson, Anke M Schulte, Michele Solimena Metabolically phenotyped pancreatectomized patients as living donors for the study of islets in health and diabetes. Molecular metabolism, 27 (2019) doi: 10.1016/j.molmet.2019.06.006
• Bernard Thorens, Ana Rodriguez, Céline Cruciani-Guglielmacci, Leonore Wigger, Mark Ibberson, Christophe Magnan Use of preclinical models to identify markers of type 2 diabetes susceptibility and novel regulators of insulin secretion - A step towards precision medicine. Molecular metabolism, 27 (2019) doi: 10.1016/j.molmet.2019.06.008
• Noémie Matthey, Sandrine Stutzmann, Candice Stoudmann, Nicolas Guex, Christian Iseli, Melanie Blokesch Neighbor predation linked to natural competence fosters the transfer of large genomic regions in . eLife, 8 (2019) doi: 10.7554/eLife.48212
• Tony Teav, Héctor Gallart-Ayala, Vera van der Velpen, Florence Mehl, Hugues Henry, Julijana Ivanisevic Merged Targeted Quantification and Untargeted Profiling for Comprehensive Assessment of Acylcarnitine and Amino Acid Metabolism. Analytical chemistry (2019) doi: 10.1021/acs.analchem.9b02373
• Leonore Wigger, Cristina Casals-Casas, Michaël Baruchet, Khanh B Trang, Sylvain Pradervand, Aurélien Naldi, Béatrice Desvergne System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells. PloS one, 14 (2019) doi: 10.1371/journal.pone.0220894
• Elena Sügis, Jerome Dauvillier, Anna Leontjeva, Priit Adler, Valerie Hindie, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Herault, Jean-Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xenarios, Jaak Vilo, Michel Simonneau, Hedi Peterson HENA, heterogeneous network-based data set for Alzheimer's disease. Scientific data, 6 (2019) doi: 10.1038/s41597-019-0152-0
• A Luraschi, S Richard, J M G C F Almeida, M Pagni, M T Cushion, P M Hauser Expression and Immunostaining Analyses Suggest that Primary Homothallism Involves Trophic Cells Displaying Both Plus and Minus Pheromone Receptors. mBio, 10 (2019) doi: 10.1128/mBio.01145-19
• Frédéric Fumeron, Anthony Nicolas, Jean-Philippe Bastard, Soraya Fellahi, Léonore Wigger, Mark Ibberson, Céline Cruciani-Guglielmacci, Hervé Le Stunff, Gilberto Velho, Christophe Magnan, Michel Marre, Beverley Balkau, Ronan Roussel Dairy consumption is associated with lower plasma dihydroceramides in women from the D.E.S.I.R. cohort. Diabetes & metabolism (2019) doi: 10.1016/j.diabet.2019.06.002
• Piero Marchetti, Anke M Schulte, Lorella Marselli, Eyke Schoniger, Marco Bugliani, Werner Kramer, Lut Overbergh, Susanne Ullrich, Anna L Gloyn, Mark Ibberson, Guy Rutter, Philippe Froguel, Leif Groop, Mark I McCarthy, Francesco Dotta, Raphael Scharfmann, Christophe Magnan, Decio L Eizirik, Chantal Mathieu, Miriam Cnop, Bernard Thorens, Michele Solimena Fostering improved human islet research: a European perspective. Diabetologia (2019) doi: 10.1007/s00125-019-4911-4
• Sten Ilmjärv, Fiona Augsburger, Jerven Tjalling Bolleman, Robin Liechti, Alan James Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause Navigating in vitro bioactivity data by investigating available resources using model compounds. Scientific data, 6 (2019) doi: 10.1038/s41597-019-0046-1
• Paul A Saunders, Samuel Neuenschwander, Nicolas Perrin Impact of deleterious mutations, sexually antagonistic selection, and mode of recombination suppression on transitions between male and female heterogamety. Heredity (2019) doi: 10.1038/s41437-019-0225-z
• Amna Khamis, Mickaël Canouil, Afshan Siddiq, Hutokshi Crouch, Mario Falchi, Manon von Bulow, Florian Ehehalt, Lorella Marselli, Marius Distler, Daniela Richter, Jürgen Weitz, Krister Bokvist, Ioannis Xenarios, Bernard Thorens, Anke M Schulte, Mark Ibberson, Amelie Bonnefond, Piero Marchetti, Michele Solimena, Philippe Froguel Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. Molecular metabolism (2019) doi: 10.1016/j.molmet.2019.03.004
• Florian R Kirchner, Katharina Littringer, Simon Altmeier, Van Du T Tran, Franziska Schönherr, Christina Lemberg, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut-Landmann Persistence of in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression. Frontiers in immunology, 10 (2019) doi: 10.3389/fimmu.2019.00330
• Samuel Neuenschwander, Frédéric Michaud, Jérôme Goudet QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time. Bioinformatics (Oxford, England), 35 (2019) doi: 10.1093/bioinformatics/bty737
• Christophe Paul, Sevasti Filippidou, Isha Jamil, Wafa Kooli, Geoffrey L House, Aislinn Estoppey, Mathilda Hayoz, Thomas Junier, Fabio Palmieri, Tina Wunderlin, Anael Lehmann, Saskia Bindschedler, Torsten Vennemann, Patrick S G Chain, Pilar Junier Bacterial spores, from ecology to biotechnology. Advances in applied microbiology, 106 (2019) doi: 10.1016/bs.aambs.2018.10.002
• Sevasti Filippidou, Thomas Junier, Tina Wunderlin, Wafa M Kooli, Ilona Palmieri, Andrej Al-Dourobi, Veronica Molina, Reto Lienhard, Jorge E Spangenberg, Shannon L Johnson, Patrick S G Chain, Cristina Dorador, Pilar Junier Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in and Resistance to Extreme Conditions. Frontiers in microbiology, 10 (2019) doi: 10.3389/fmicb.2019.00102
• Emma Ricart, Valérie Leclère, Areski Flissi, Markus Mueller, Maude Pupin, Frédérique Lisacek rBAN: retro-biosynthetic analysis of nonribosomal peptides. Journal of cheminformatics, 11 (2019) doi: 10.1186/s13321-019-0335-x
• Phing Chian Chai, Steeve Cruchet, Leonore Wigger, Richard Benton Sensory neuron lineage mapping and manipulation in the Drosophila olfactory system. Nature communications, 10 (2019) doi: 10.1038/s41467-019-08345-4
• Ivan D Mateus, Frédéric G Masclaux, Consolée Aletti, Edward C Rojas, Romain Savary, Cindy Dupuis, Ian R Sanders Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis. The ISME journal (2019) doi: 10.1038/s41396-018-0342-3

• Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sulkowski, Kenneth C Millett, Eric J Rawdon, Andrzej Stasiak, Joanna I Sulkowska KnotProt 2.0: a database of proteins with knots and other entangled structures. Nucleic acids research (2018) doi: 10.1093/nar/gky1140
• Van Du T Tran, Sébastien Moretti, Alix T Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. Bioinformatics (Oxford, England) (2018) doi: 10.1093/bioinformatics/bty929
• Dusan Racko, Fabrizio Benedetti, Julien Dorier, Andrzej Stasiak Are TADs supercoiled? Nucleic acids research (2018) doi: 10.1093/nar/gky1091
• Sarah Schmid, Samuel Neuenschwander, Camille Pitteloud, Gerald Heckel, Mila Pajkovic, Raphaël Arlettaz, Nadir Alvarez Spatial and temporal genetic dynamics of the grasshopper revealed by museum genomics. Ecology and evolution, 8 (2018) doi: 10.1002/ece3.3699
• Thierry Lombardot, Anne Morgat, Kristian B Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alex Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan Bridge Updates in Rhea: SPARQLing biochemical reaction data. Nucleic acids research (2018) doi: 10.1093/nar/gky876
• Thibault Robin, Amos Bairoch, Markus Müller, Frédérique Lisacek, Lydie Lane Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project. Journal of proteome research (2018) doi: 10.1021/acs.jproteome.8b00392
• Felicia Gerst, Benjamin A Jaghutriz, Harald Staiger, Anke M Schulte, Estela Lorza-Gil, Gabriele Kaiser, Madhura Panse, Sieglinde Haug, Martin Heni, Monika Schütz, Mandy Stadion, Annette Schürmann, Flavia Marzetta, Mark Ibberson, Bence Sipos, Falko Fend, Thomas Fleming, Peter P Nawroth, Alfred Königsrainer, Silvio Nadalin, Silvia Wagner, Andreas Peter, Andreas Fritsche, Daniela Richter, Michele Solimena, Hans-Ulrich Häring, Susanne Ullrich, Robert Wagner TRThe Expression of Aldolase B in Islets is Negatively Associated with Insulin Secretion in Humans. The Journal of clinical endocrinology and metabolism (2018) doi: 10.1210/jc.2018-00791
• Roman Mylonas, Ilan Beer, Christian Iseli, Chloe Chong, Hui-Song Pak, David Gfeller, George Coukos, Ioannis Xenarios, Markus Müller, Michal Bassani-Sternberg Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome. Molecular & cellular proteomics : MCP (2018) doi: 10.1074/mcp.RA118.000877
• Shanaz Diessler, Maxime Jan, Yann Emmenegger, Nicolas Guex, Benita Middleton, Debra J Skene, Mark Ibberson, Frederic Burdet, Lou Götz, Marco Pagni, Martial Sankar, Robin Liechti, Charlotte N Hor, Ioannis Xenarios, Paul Franken A systems genetics resource and analysis of sleep regulation in the mouse. PLoS biology, 16 (2018) doi: 10.1371/journal.pbio.2005750
• Christophe Paul, Zhanna Bayrychenko, Thomas Junier, Sevasti Filippidou, Karin Beck, Matthieu Bueche, Gilbert Greub, Helmut Bürgmann, Pilar Junier Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PeerJ, 6 (2018) doi: 10.7717/peerj.4989
• Paul A Saunders, Samuel Neuenschwander, Nicolas Perrin Sex chromosome turnovers and genetic drift: A simulation study. Journal of evolutionary biology (2018) doi: 10.1111/jeb.13336
• Jennie R Lill, Peter A van Veelen, Stefan Tenzer, Arie Admon, Etienne Caron, Josh Elias, Albert J R Heck, Miguel Marcilla, Fabio Marino, Markus Müller, Bjoern Peters, Anthony Purcell, Alessandro Sette, Theo Sturm, Nicola Ternette, Juan Antonio Vizcaíno, Michal Bassani-Sternberg Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics (2018) doi: 10.1002/pmic.201800110
• Lara Bellini, Mélanie Campana, Claude Rouch, Marta Chacinska, Marco Bugliani, Kelly Meneyrol, Isabelle Hainault, Véronique Lenoir, Jessica Denom, Julien Véret, Nadim Kassis, Bernard Thorens, Mark Ibberson, Piero Marchetti, Agnieszka Blachnio-Zabielska, Céline Cruciani-Guglielmacci, Carina Prip-Buus, Christophe Magnan, Hervé Le Stunff Protective role of the ELOVL2/docosahexaenoic acid axis in glucolipotoxicity-induced apoptosis in rodent beta cells and human islets. Diabetologia (2018) doi: 10.1007/s00125-018-4629-8
• Ousmane H Cissé, Liang Ma, Da Wei Huang, Pavel P Khil, John P Dekker, Geetha Kutty, Lisa Bishop, Yueqin Liu, Xilong Deng, Philippe M Hauser, Marco Pagni, Vanessa Hirsch, Richard A Lempicki, Jason E Stajich, Christina A Cuomo, Joseph A Kovacs Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen . mBio, 9 (2018) doi: 10.1128/mBio.00381-18
• Julien Dorier, Dimos Goundaroulis, Fabrizio Benedetti, Andrzej Stasiak Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids. Bioinformatics (Oxford, England) (2018) doi: 10.1093/bioinformatics/bty365
• Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan Bridge, Ioannis Xenarios, Julien Dorier, Isaac Crespo Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. Database : the journal of biological databases and curation, 2018 (2018) doi: 10.1093/database/bay031
• Frédéric G Masclaux, Tania Wyss, Ivan D Mateus-Gonzalez, Consolée Aletti, Ian R Sanders Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis. Mycorrhiza (2018) doi: 10.1007/s00572-018-0834-z
• Wencke Walter, Laura Alonso-Herranz, Verdiana Trappetti, Isaac Crespo, Mark Ibberson, Marta Cedenilla, Anna Karaszewska, Vanessa Núñez, Ioannis Xenarios, Alicia G Arroyo, Fátima Sánchez-Cabo, Mercedes Ricote Deciphering the Dynamic Transcriptional and Post-transcriptional Networks of Macrophages in the Healthy Heart and after Myocardial Injury. Cell reports, 23 (2018) doi: 10.1016/j.celrep.2018.03.029
• S Richard, J M G C F Almeida, O H Cissé, A Luraschi, O Nielsen, M Pagni, P M Hauser Functional and Expression Analyses of theGenes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs. mBio, 9 (2018) doi: 10.1128/mBio.02201-17
• Ricardo Kanitz, Elsa G Guillot, Sylvain Antoniazza, Samuel Neuenschwander, Jérôme Goudet Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses. PloS one, 13 (2018) doi: 10.1371/journal.pone.0192460
• Laura Madueño, Christophe Paul, Thomas Junier, Zhanna Bayrychenko, Sevasti Filippidou, Karin Beck, Gilbert Greub, Helmut Bürgmann, Pilar Junier A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PeerJ, 6 (2018) doi: 10.7717/peerj.4197

• Dimos Goundaroulis, Neslihan Gügümcü, Sofia Lambropoulou, Julien Dorier, Andrzej Stasiak, Louis Kauffman Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. Polymers, 9 (2017) doi: 10.3390/polym9090444
• Shilpi Minocha, Dominic Villeneuve, Leonor Rib, Catherine Moret, Nicolas Guex, Winship Herr Segregated hepatocyte proliferation and metabolic states within the regenerating mouse liver. Hepatology communications, 1 (2017) doi: 10.1002/hep4.1102
• Sarah Schmid, Samuel Neuenschwander, Camille Pitteloud, Gerald Heckel, Mila Pajkovic, Raphaël Arlettaz, Nadir Alvarez Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics Authors Ecol Evol., 00:1–16 (2017) doi: https://doi.org/10.1002/ece3.3699
• Elisa Cavoto, Samuel Neuenschwander, Jérôme Goudet, Nicolas Perrin Sex-antagonistic genes, XY recombination, and feminized Y chromosomes. Journal of evolutionary biology (2017) doi: 10.1111/jeb.13235
• Julien Faget, Svenja Groeneveld, Gael Boivin, Martial Sankar, Nadine Zangger, Miguel Garcia, Nicolas Guex, Inti Zlobec, Loïc Steiner, Alessandra Piersigilli, Ioannis Xenarios, Etienne Meylan Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer. Cell reports, 21 (2017) doi: 10.1016/j.celrep.2017.11.052
• Emanuel Schmid-Siegert, Namrata Sarkar, Christian Iseli, Sandra Calderon, Caroline Gouhier-Darimont, Jacqueline Chrast, Pietro Cattaneo, Frédéric Schütz, Laurent Farinelli, Marco Pagni, Michel Schneider, Jérémie Voumard, Michel Jaboyedoff, Christian Fankhauser, Christian S Hardtke, Laurent Keller, John R Pannell, Alexandre Reymond, Marc Robinson-Rechavi, Ioannis Xenarios, Philippe Reymond Low number of fixed somatic mutations in a long-lived oak tree. Nature plants, 3 (2017) doi: 10.1038/s41477-017-0066-9
• Érika Cosset, Sten Ilmjärv, Valérie Dutoit, Kathryn Elliott, Tami von Schalscha, Maria F Camargo, Alexander Reiss, Toshiro Moroishi, Laetitia Seguin, German Gomez, Jung-Soon Moo, Olivier Preynat-Seauve, Karl-Heinz Krause, Hervé Chneiweiss, Jann N Sarkaria, Kun-Liang Guan, Pierre-Yves Dietrich, Sara M Weis, Paul S Mischel, David A Cheresh Glut3 Addiction Is a Druggable Vulnerability for a Molecularly Defined Subpopulation of Glioblastoma. Cancer cell (2017) doi: 10.1016/j.ccell.2017.10.016
• Michele Solimena, Anke M Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno-Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B Wollheim, Gustavo B Baretton, Raphael Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer-Puttlitz, Ugo Boggi, Hans-Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xenarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes. Diabetologia (2017) doi: 10.1007/s00125-017-4500-3
• Dusan Racko, Fabrizio Benedetti, Julien Dorier, Andrzej Stasiak Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes. Nucleic acids research (2017) doi: 10.1093/nar/gkx1123
• Emanuel Schmid-Siegert, Sophie Richard, Amanda Luraschi, Konrad Mühlethaler, Marco Pagni, Philippe M Hauser Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii. mBio, 8 (2017) doi: 10.1128/mBio.01470-17
• Markus Müller, David Gfeller, George Coukos, Michal Bassani-Sternberg 'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization. Frontiers in immunology, 8 (2017) doi: 10.3389/fimmu.2017.01367
• Anna Motterle, Sonia Gattesco, Marie-Line Peyot, Jonathan Lou S Esguerra, Ana Gomez-Ruiz, D Ross Laybutt, Patrick Gilon, Frédéric Burdet, Mark Ibberson, Lena Eliasson, Marc Prentki, Romano Regazzi Identification of islet-enriched long non-coding RNAs contributing to β-cell failure in type 2 diabetes. Molecular metabolism, 6 (2017) doi: 10.1016/j.molmet.2017.08.005
• Michael E Hughes, Katherine C Abruzzi, Ravi Allada, Ron Anafi, Alaaddin Bulak Arpat, Gad Asher, Pierre Baldi, Charissa de Bekker, Deborah Bell-Pedersen, Justin Blau, Steve Brown, M Fernanda Ceriani, Zheng Chen, Joanna C Chiu, Juergen Cox, Alexander M Crowell, Jason P DeBruyne, Derk-Jan Dijk, Luciano DiTacchio, Francis J Doyle, Giles E Duffield, Jay C Dunlap, Kristin Eckel-Mahan, Karyn A Esser, Garret A FitzGerald, Daniel B Forger, Lauren J Francey, Ying-Hui Fu, Frédéric Gachon, David Gatfield, Paul de Goede, Susan S Golden, Carla Green, John Harer, Stacey Harmer, Jeff Haspel, Michael H Hastings, Hanspeter Herzel, Erik D Herzog, Christy Hoffmann, Christian Hong, Jacob J Hughey, Jennifer M Hurley, Horacio O de la Iglesia, Carl Johnson, Steve A Kay, Nobuya Koike, Karl Kornacker, Achim Kramer, Katja Lamia, Tanya Leise, Scott A Lewis, Jiajia Li, Xiaodong Li, Andrew C Liu, Jennifer J Loros, Tami A Martino, Jerome S Menet, Martha Merrow, Andrew J Millar, Todd Mockler, Felix Naef, Emi Nagoshi, Michael N Nitabach, Maria Olmedo, Dmitri A Nusinow, Louis J Ptáček, David Rand, Akhilesh B Reddy, Maria S Robles, Till Roenneberg, Michael Rosbash, Marc D Ruben, Samuel S C Rund, Aziz Sancar, Paolo Sassone-Corsi, Amita Sehgal, Scott Sherrill-Mix, Debra J Skene, Kai-Florian Storch, Joseph S Takahashi, Hiroki R Ueda, Han Wang, Charles Weitz, Pål O Westermark, Herman Wijnen, Ying Xu, Gang Wu, Seung-Hee Yoo, Michael Young, Eric Erquan Zhang, Tomasz Zielinski, John B Hogenesch Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of biological rhythms (2017) doi: 10.1177/0748730417728663
• Robin Liechti, Nancy George, Lou Götz, Sara El-Gebali, Anastasia Chasapi, Isaac Crespo, Ioannis Xenarios, Thomas Lemberger SourceData: a semantic platform for curating and searching figures. Nature methods, 14 (2017) doi: 10.1038/nmeth.4471
• Romain Savary, Frédéric G Masclaux, Tania Wyss, Germain Droh, Joaquim Cruz Corella, Ana Paula Machado, Joseph B Morton, Ian R Sanders A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. The ISME journal (2017) doi: 10.1038/ismej.2017.153
• Fabrizio Benedetti, Dusan Racko, Julien Dorier, Yannis Burnier, Andrzej Stasiak Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic acids research, 45 (2017) doi: 10.1093/nar/gkx716
• Dusan Racko, Fabrizio Benedetti, Julien Dorier, Yannis Burnier, Andrzej Stasiak Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase. Methods in molecular biology (Clifton, N.J.), 1624 (2017) doi: 10.1007/978-1-4939-7098-8_24
• Luis Vale-Silva, Emmanuel Beaudoing, Van Du T Tran, Dominique Sanglard Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates. G3 (Bethesda, Md.), 7 (2017) doi: 10.1534/g3.117.042887
• Dimos Goundaroulis, Julien Dorier, Fabrizio Benedetti, Andrzej Stasiak Studies of global and local entanglements of individual protein chains using the concept of knotoids. Scientific reports, 7 (2017) doi: 10.1038/s41598-017-06649-3
• Trinidad Martín-Campos, Roman Mylonas, Alexandre Masselot, Patrice Waridel, Tanja Petricevic, Ioannis Xenarios, Manfredo Quadroni MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications. Journal of proteome research (2017) doi: 10.1021/acs.jproteome.7b00194
• Christian Linke, Anastasia Chasapi, Alberto González-Novo, Istabrak Al Sawad, Silvia Tognetti, Edda Klipp, Mart Loog, Sylvia Krobitsch, Francesc Posas, Ioannis Xenarios, Matteo Barberis A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. NPJ systems biology and applications, 3 (2017) doi: 10.1038/s41540-017-0008-1
• Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome biology, 18 (2017) doi: 10.1186/s13059-017-1222-2
• Riccardo Turrini, Angélique Pabois, Ioannis Xenarios, George Coukos, Jean-François Delaloye, Marie-Agnès Doucey TIE-2 expressing monocytes in human cancers. Oncoimmunology, 6 (2017) doi: 10.1080/2162402X.2017.1303585
• Giuseppe Marco Randazzo, David Tonoli, Petra Strajhar, Ioannis Xenarios, Alex Odermatt, Julien Boccard, Serge Rudaz Enhanced metabolite annotation via dynamic retention time prediction: Steroidogenesis alterations as a case study. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences (2017) doi: 10.1016/j.jchromb.2017.04.032
• François Mange, Viviane Praz, Eugenia Migliavacca, Ian M Willis, Frédéric Schütz, Nouria Hernandez, , Nouria Hernandez, Mauro Delorenzi, Bart Deplancke, Béatrice Desvergne, Nicolas Guex, Winship Herr, Felix Naef, Jacques Rougemont, Ueli Schibler, Teemu Andersin, Pascal Cousin, Federica Gilardi, Fabienne Lammers, François Mange, Dominic Villeneuve, Fabrice David, Roberto Fabbretti, Philippe Jacquet, Irina Krier, Dmitry Kuznetsov, Marion Leleu, Robin Liechti, Olivier Martin, Eugenia Migliavacca, Aurélien Naldi, Viviane Praz, Leonor Rib, Jonathan Sobel, Volker Vlegel, Ioannis Xenarios Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock. Genome research (2017) doi: 10.1101/gr.217521.116
• Céline Cruciani-Guglielmacci, Lara Bellini, Jessica Denom, Masaya Oshima, Neïké Fernandez, Priscilla Normandie-Levi, Xavier P Berney, Nadim Kassis, Claude Rouch, Julien Dairou, Tracy Gorman, David M Smith, Anna Marley, Robin Liechti, Dmitry Kuznetsov, Leonore Wigger, Frédéric Burdet, Anne-Laure Lefèvre, Isabelle Wehrle, Ingo Uphues, Tobias Hildebrandt, Werner Rust, Catherine Bernard, Alain Ktorza, Guy A Rutter, Raphael Scharfmann, Ioannis Xenarios, Hervé Le Stunff, Bernard Thorens, Christophe Magnan, Mark Ibberson Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion. Molecular metabolism, 6 (2017) doi: 10.1016/j.molmet.2017.01.009
• Fariza Tahi, Van Du T Tran, Anouar Boucheham In Silico Prediction of RNA Secondary Structure. Methods in molecular biology (Clifton, N.J.), 1543 (2017) doi: 10.1007/978-1-4939-6716-2_7
• Cedric Simillion, Robin Liechti, Heidi E L Lischer, Vassilios Ioannidis, Rémy Bruggmann Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics, 18 (2017) doi: 10.1186/s12859-017-1571-6
• Leonore Wigger, Céline Cruciani-Guglielmacci, Anthony Nicolas, Jessica Denom, Neïké Fernandez, Frédéric Fumeron, Pedro Marques-Vidal, Alain Ktorza, Werner Kramer, Anke Schulte, Hervé Le Stunff, Robin Liechti, Ioannis Xenarios, Peter Vollenweider, Gérard Waeber, Ingo Uphues, Ronan Roussel, Christophe Magnan, Mark Ibberson, Bernard Thorens Plasma Dihydroceramides Are Diabetes Susceptibility Biomarker Candidates in Mice and Humans. Cell reports, 18 (2017) doi: 10.1016/j.celrep.2017.02.019
• Aleksandre Japaridze, Georgi Muskhelishvili, Fabrizio Benedetti, Agni F M Gavriilidou, Renato Zenobi, Paolo De Los Rios, Giovanni Longo, Giovanni Dietler Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization. Nano letters (2017) doi: 10.1021/acs.nanolett.6b05294
• Gaelle R Carrat, Ming Hu, Marie-Sophie Nguyen-Tu, Pauline Chabosseau, Kyle J Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, Francois Pattou, Isabelle Leclerc, Timothy J Pullen, Matthew C Cane, Priyanka Prabhala, William Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E MacDonald, Jocelyn E Manning Fox, Anna L Gloyn, Philippe Froguel, Michele Solimena, Mark I McCarthy, Guy A Rutter Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. American journal of human genetics (2017) doi: 10.1016/j.ajhg.2017.01.011
• Jade Leiba, Ayman Sabra, Romain Bodinier, Anna Marchetti, Wanessa C Lima, Astrid Melotti, Jackie Perrin, Frederic Burdet, Marco Pagni, Thierry Soldati, Emmanuelle Lelong, Pierre Cosson Vps13F links bacterial recognition and intracellular killing in Dictyostelium. Cellular microbiology (2017) doi: 10.1111/cmi.12722

• Isaac Crespo, Lou Götz, Robin Liechti, George Coukos, Marie-Agnès Doucey, Ioannis Xenarios Identifying biological mechanisms for favorable cancer prognosis using non-hypothesis-driven iterative survival analysis. NPJ systems biology and applications, 2 (2016) doi: 10.1038/npjsba.2016.37
• Anne Morgat, Thierry Lombardot, Kristian B Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic acids research (2016) doi: 10.1093/nar/gkw1299
• Madhur S Dhingra, Jean Artois, Timothy P Robinson, Catherine Linard, Celia Chaiban, Ioannis Xenarios, Robin Engler, Robin Liechti, Dimitry Kuznetsov, Xiangming Xiao, Sophie Von Dobschuetz, Filip Claes, Scott H Newman, Gwenaëlle Dauphin, Marius Gilbert Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation. eLife, 5 (2016) doi: 10.7554/eLife.19571
• Sevasti Filippidou, Tina Wunderlin, Thomas Junier, Nicole Jeanneret, Cristina Dorador, Veronica Molina, David R Johnson, Pilar Junier A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. Frontiers in microbiology, 7 (2016) pmid: 27857706
• Amanda Luraschi, Ousmane H Cissé, Marco Pagni, Philippe M Hauser Identification and Functional Ascertainment of the Pneumocystis jirovecii Potential Drug Targets Gsc1 and Kre6 Involved in Glucan Synthesis. The Journal of eukaryotic microbiology (2016) doi: 10.1111/jeu.12385
• Harsha D Devalla, Roselle Gélinas, Elhadi H Aburawi, Abdelaziz Beqqali, Philippe Goyette, Christian Freund, Marie-A Chaix, Rafik Tadros, Hui Jiang, Antony Le Béchec, Jantine J Monshouwer-Kloots, Tom Zwetsloot, Georgios Kosmidis, Frédéric Latour, Azadeh Alikashani, Maaike Hoekstra, Jurg Schlaepfer, Christine L Mummery, Brian Stevenson, Zoltan Kutalik, Antoine Af de Vries, Léna Rivard, Arthur Am Wilde, Mario Talajic, Arie O Verkerk, Lihadh Al-Gazali, John D Rioux, Zahurul A Bhuiyan, Robert Passier TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT. EMBO molecular medicine (2016) doi: 10.15252/emmm.201505719
• Alexandre Picard, Josselin Soyer, Xavier Berney, David Tarussio, Simon Quenneville, Maxime Jan, Eric Grouzmann, Frédéric Burdet, Mark Ibberson, Bernard Thorens A Genetic Screen Identifies Hypothalamic Fgf15 as a Regulator of Glucagon Secretion. Cell reports, 17 (2016) doi: 10.1016/j.celrep.2016.10.041
• Van Du T Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid-Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection. mSystems, 1 (2016) pmid: 27822542
• Paula Vazquez-Pianzola, Bogdan Schaller, Martino Colombo, Dirk Beuchle, Samuel Neuenschwander, Anne Marcil, Rémy Bruggmann, Beat Suter The mRNA transportome of the BicD/Egl transport machinery. RNA biology (2016) doi: 10.1080/15476286.2016.1251542
• Anne Morgat, Thierry Lombardot, Kristian B Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge Updates in rhea-an expert curated resource of biochemical reactions. Nucleic acids research (2016) doi: 10.1093/nar/gkw990
• Julien Dorier, Isaac Crespo, Anne Niknejad, Robin Liechti, Martin Ebeling, Ioannis Xenarios Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. BMC bioinformatics, 17 (2016) pmid: 27716031
• Mihai Miclaus, Ovidiu Balacescu, Ioan Has, Loredana Balacescu, Voichita Has, Dana Suteu, Samuel Neuenschwander, Irene Keller, Rémy Bruggmann Maize cytolines unmask key nuclear genes that are under the control of retrograde signaling pathways in plants. Genome biology and evolution (2016) pmid: 27702813
• Kostyrko K, Neuenschwander S, Junier T, Regamey A, Iseli C, Schmid-Siegert E, Bosshard S, Majocchi S, Le Fourn V, Girod PA, Xenarios I, Mermod N. MAR-mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering Biotechnol Bioeng. (2016) doi: 10.1002/bit.26086
• Jean Artois, Scott H Newman, Madhur S Dhingra, Celia Chaiban, Catherine Linard, Giovanni Cattoli, Isabella Monne, Alice Fusaro, Ioannis Xenarios, Robin Engler, Robin Liechti, Dmitri Kuznetsov, Thanh Long Pham, Tung Nguyen, Van Dong Pham, David Castellan, Sophie Von Dobschuetz, Filip Claes, Gwenaëlle Dauphin, Ken Inui, Marius Gilbert Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors. Scientific reports, 6 (2016) doi: 10.1038/srep30316
• Graziano Pescia, Nicolas Guex, Christian Iseli, Liam Brennan, Magne Osteras, Ioannis Xenarios, Laurent Farinelli, Bernard Conrad Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6,388 consecutive cases. Genetics in medicine : official journal of the American College of Medical Genetics (2016) doi: 10.1038/gim.2016.72
• Pelin O Simsek Kiper, Hiroaki Saito, Francesca Gori, Sheila Unger, Eric Hesse, Kei Yamana, Riku Kiviranta, Nicolas Solban, Jeff Liu, Robert Brommage, Koray Boduroglu, Luisa Bonafé, Belinda Campos-Xavier, Esra Dikoglu, Richard Eastell, Fatma Gossiel, Keith Harshman, Gen Nishimura, Katta M Girisha, Brian J Stevenson, Hiroyuki Takita, Carlo Rivolta, Andrea Superti-Furga, Roland Baron Cortical-Bone Fragility--Insights from sFRP4 Deficiency in Pyle's Disease. The New England journal of medicine, 374 (2016) doi: 10.1056/NEJMoa1509342
• Ludovic Telley, Subashika Govindan, Julien Prados, Isabelle Stevant, Serge Nef, Emmanouil Dermitzakis, Alexandre Dayer, Denis Jabaudon Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex. Science (New York, N.Y.), 351 (2016) doi: 10.1126/science.aad8361
• Svetlana Nikolaeva, Camille Ansermet, Gabriel Centeno, Sylvain Pradervand, Vincent Bize, David Mordasini, Hugues Henry, Robert Koesters, Marc Maillard, Olivier Bonny, Natsuko Tokonami, Dmitri Firsov Nephron-Specific Deletion of Circadian Clock Gene Bmal1 Alters the Plasma and Renal Metabolome and Impairs Drug Disposition. Journal of the American Society of Nephrology : JASN (2016) pmid: 27056296
• Leonardo Murgiano, Vera Shirokova, Monika Maria Welle, Vidhya Jagannathan, Philippe Plattet, Anna Oevermann, Aldona Pienkowska-Schelling, Daniele Gallo, Arcangelo Gentile, Marja L Mikkola, Cord Drögemüller Correction: Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation. PLoS genetics, 12 (2016) doi: 10.1371/journal.pgen.1005688
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