  | KLEE, M., AHO, V., MAY, P., Heintz-Buschart, A., LANDOULSI, Z., JONSDOTTIR, S., PAULY, C., PAVELKA, L., DELACOUR, L., KAYSEN, A., Krüger, R., WILMES, P., LEIST, A., Acharya, G., Aguayo, G., Alexandre, M., ALI, M., Ammerlann, W., ARENA, G., ... ZELIMKHANOV, G. (2024). Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome. Journal of Prevention of Alzheimer's Disease. doi:10.14283/jpad.2024.19  Peer reviewed |
 | ACENCIO, M. L., OSTASZEWSKI, M., MAZEIN, A., Rosenstiel, P., Aden, K., Mishra, N., Andersen, V., Sidiropoulos, P., Banos, A., Filia, A., Rahmouni, S., Finckh, A., GU, W., SCHNEIDER, R., & SATAGOPAM, V. (01 November 2023). The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease. Frontiers in Immunology, 14. doi:10.3389/fimmu.2023.1257321 Peer Reviewed verified by ORBi |
 | WELTER, D., Rocca-Serra, P., GROUES, V., SALLAM, N., Ancien, F., SHABANI, A., Asariardakani, S., ALPER, P., GHOSH, S., Burdett, T., Sansone, S.-A., GU, W., & SATAGOPAM, V. (20 July 2023). The Translational Data Catalog - discoverable biomedical datasets. Scientific Data, 10 (1), 470. doi:10.1038/s41597-023-02258-0 Peer Reviewed verified by ORBi |
 | MAZEIN, A., ACENCIO, M. L., BALAUR, I.-A., Rougny, A., WELTER, D., Niarakis, A., Ramirez Ardila, D., Dogrusoz, U., GAWRON, P., SATAGOPAM, V., GU, W., KREMER, A., SCHNEIDER, R., & OSTASZEWSKI, M. (2023). A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers in Bioinformatics, 3, 1197310. doi:10.3389/fbinf.2023.1197310 Peer reviewed |
 | Gu, W., Rong, P., Hofmann-Apitius, M., & Satagopam, V. (2022). Editorial: Digital Innovation and Data-Driven Research in Neurodegenerative Diseases. Frontiers in Neurology, 13. doi:10.3389/fneur.2022.961847 |
  | Alharbi, E., Gadiya, Y., Henderson, D., Zaliani, A., Delfin-Rossaro, A., Cambon-Thomsen, A., Kohler, M., Witt, G., Welter, D., Juty, N., Jay, C., Engkvist, O., Goble, C., Reilly, D. S., Satagopam, V., Ioannidis, V., Gu, W., & Gribbon, P. (2022). Selection of data sets for FAIRification in drug discovery and development: Which, why, and how? Drug Discovery Today. doi:10.1016/j.drudis.2022.05.010 Peer Reviewed verified by ORBi |
 | Wilken, S. E., Besançon, M., Kratochvil, M., Kuate, C. A. F., Trefois, C., Gu, W., & Ebenhöh, O. (2022). Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models. Metabolic Engineering. doi:10.1016/j.ymben.2022.09.002 Peer reviewed |
 | Bernhofer, M., Dallago, C., Karl, T., Satagopam, V., Heinzinger, M., Littmann, M., Olenyi, T., Qiu, J., Schütze, K., Yachdav, G., Ashkenazy, H., Ben-Tal, N., Bromberg, Y., Goldberg, T., Kajan, L., O’Donoghue, S., Sander, C., Schafferhans, A., Schlessinger, A., ... Rost, B. (2021). PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. doi:10.1093/nar/gkab354 Peer reviewed |
 | Badimon, L., Robinson, E. L., Jusic, A., Carpusca, I., deWindt, L. J., Emanueli, C., Ferdinandy, P., Gu, W., Gyöngyösi, M., Hackl, M., Karaduzovic-Hadziabdic, K., Lustrek, M., Martelli, F., Nham, E., Potočnjak, I., Satagopam, V., Schneider, R., Thum, T., Devaux, Y., & CA17129, O. B. O. E. U.-C. C. A. (2021). Cardiovascular RNA markers and artificial intelligence may improve COVID-19 outcome: a position paper from the EU-CardioRNA COST Action CA17129. Cardiovascular Research. doi:10.1093/cvr/cvab094 Peer Reviewed verified by ORBi |
 | Kratochvil, M.* , Heirendt, L.* , Wilken, S. E., Pusa, T., Arreckx, S., Noronha, A., van Aalst, M., Satagopam, V., Ebenhöh, O., Schneider, R., Trefois, C., & Gu, W. (2021). COBREXA.jl: constraint-based reconstruction and exascale analysis. Bioinformatics. doi:10.1093/bioinformatics/btab782 Peer reviewed* These authors have contributed equally to this work. |
 | Gu, W., Hasan, S., Rocca-Serra, P., & Satagopam, V. (2020). Road to effective data curation for translational research. Drug Discovery Today. doi:10.1016/j.drudis.2020.12.007 Peer Reviewed verified by ORBi |
 | Hartl, D.* , May, P.* , Gu, W.* , Mayhaus, M., Pichler, S., Spaniol, C., Glaab, E., Bobbili, D. R., Antony, P., Köglsberger, S., Kurz, A., Grimmer, T., Morgan, K., Vardarajan, B. N., Reitz, C., Hardy, J., Bras, J., Guerreiro, R., AESG, ... Riemenschneider, M. (09 July 2020). A rare loss-of function variant of ADAM17 is associated with late-onset familial Alzheimer disease. Molecular Psychiatry, 25 (3), 629-639. doi:10.1038/s41380-018-0091-8 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | Gu, W., Yildirimman, R., Van der Stuyft, E., Verbeeck, D., Herzinger, S., Satagopam, V., Barbosa-Silva, A., Schneider, R., Lange, B., Lehrach, H., Guo, Y., Henderson, D., Rowe, A., & on behalf of the IMI OncoTrack and the IMI eTRIKS consortia. (2019). Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium. BMC Bioinformatics, 20 (1), 164. doi:10.1186/s12859-019-2748-y Peer Reviewed verified by ORBi |
 | Kunkle, B. W., Grenier-Boley, B., Sims, R., Bis, J. C., Damotte, V., Naj, A. C., Boland, A., Vronskaya, M., van der Lee, S. J., Amlie-Wolf, A., Bellenguez, C., Frizatti, A., Chouraki, V., Martin, E. R., Sleegers, K., Badarinarayan, N., Jakobsdottir, J., Hamilton-Nelson, K. L., Moreno-Grau, S., ... Pericak-Vance, M. A. (2019). Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nature Genetics, 51 (3), 414. doi:10.1038/s41588-019-0358-2 Peer Reviewed verified by ORBi |
 | Herzinger, S., Groues, V., Gu, W., Satagopam, V., Banda, P., Trefois, C., & Schneider, R. (2018). Fractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data. GigaScience. doi:10.1093/gigascience/giy109 Peer reviewed |
 | Barbosa-Silva, A., Bratfalean, D., Gu, W., Satagopam, V., Houston, P., Becnel, L. B., Eifes, S., Richard, F., Tielmann, A., Herzinger, S., Rege, K., Balling, R., Peeters, P., & Schneider, R. (2018). Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART. Bioinformatics, 809. doi:10.1093/bioinformatics/bty809 Peer reviewed |
 | Herzinger, S., Gu, W., Satagopam, V., Eifes, S., Rege, K., Barbosa Da Silva, A., & Schneider, R. (2017). SmartR: An open-source platform for interactive visual analytics for translational research data. Bioinformatics. doi:10.1093/bioinformatics/btx137 Peer reviewed |
 | Sims, R., van der Lee, S. J., Naj, A. C., Bellenguez, C., Badarinarayan, N., Jakobsdottir, J., Kunkle, B. W., Boland, A., Raybould, R., Bis, J. C., Martin, E. R., Grenier-Boley, B., Heilmann-Heimbach, S., Chouraki, V., Kuzma, A. B., Sleegers, K., Vronskaya, M., Ruiz, A., Graham, R. R., ... Schellenberg, G. D. (2017). Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease. Nature Genetics, 49, 1373-1384. doi:10.1038/ng.3916 Peer Reviewed verified by ORBi |
 | Hartl, D., May, P., Gu, W., Mayhaus, M., Glaab, E., Antony, P., Bobbili, D. R., Köglsberger, S., Pichler, S., Spaniol, C., Kurz, A., Balling, R., Schneider, J., & Riemenschneider, M. (2017). IDENTIFICATION OF A RARE GENE VARIANT THAT IS ASSOCIATED WITH FAMILIAL ALZHEIMER DISEASE AND REGULATES APP EXPRESSION. Alzheimer's and Dementia: the Journal of the Alzheimer's Association, 13 (7, Supplement), 648. doi:10.1016/j.jalz.2017.06.758 Peer reviewed |
 | Pichler, S., Gu, W., Hartl, D., Gasparoni, G., Leidinger, P., Keller, A., Meese, E., Mayhaus, M., Hampel, H., & Riemenschneider, M. (2016). The miRNome of Alzheimer's disease: consistent downregulation of the miR-132/212 cluster. Neurobiology of Aging, 50, 167. doi:10.1016/j.neurobiolaging.2016.09.019 Peer Reviewed verified by ORBi |
 | Satagopam, V., Gu, W., Eifes, S., Gawron, P., Ostaszewski, M., Gebel, S., Barbosa-Silva, A., Balling, R., & Schneider, R. (2016). Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. Big Data, 4 (2), 97-108. doi:10.1089/big.2015.0057 Peer reviewed |
 | Hartl, D., Gu, W., Mayhaus, M., Pichler, S., Schöpe, J., Wagenpfeil, S., & Riemenschneider, M. (2015). Amyloid-β Protein Precursor Cleavage Products in Postmortem Ventricular Cerebrospinal Fluid of Alzheimer’s Disease Patients. Journal of Alzheimer's Disease, 47 (2), 365-372. doi:10.3233/JAD-150191 Peer reviewed |
 | Trefois, C., Jarosz, Y., Gu, W., Satagopam, V., Coronado, S., & Schneider, R. (December 2014). Reproducible Research Results R3 [Poster presentation]. 9th Benelux Bioinformatics Conference, Luxembourg, Luxembourg. |
 | Ferrari, R., Hernandez, D. G., Nalls, M. A., Rohrer, J. D., Ramasamy, A., Kwok, J. B. J., Dobson-Stone, C., Brooks, W. S., Schofield, P. R., Halliday, G. M., Hodges, J. R., Piguet, O., Bartley, L., Thompson, E., Haan, E., Hernandez, I., Ruiz, A., Boada, M., Borroni, B., ... Momeni, P. (2014). Frontotemporal dementia and its subtypes: a genome-wide association study. The Lancet Neurology, 13 (7), 686-99. doi:10.1016/S1474-4422(14)70065-1 Peer Reviewed verified by ORBi |
 | Escott-Price, V., Bellenguez, C., Wang, L.-S., Choi, S.-H., Harold, D., Jones, L., Holmans, P., Gerrish, A., Vedernikov, A., Richards, A., DeStefano, A. L., Lambert, J.-C., Ibrahim-Verbaas, C. A., Naj, A. C., Sims, R., Jun, G., Bis, J. C., Beecham, G. W., Grenier-Boley, B., ... Williams, J. (2014). Gene-wide analysis detects two new susceptibility genes for Alzheimer's disease. PLoS ONE, 9 (6), 94661. doi:10.1371/journal.pone.0094661 Peer Reviewed verified by ORBi |
| Lambert, J.-C., Ibrahim-Verbaas, C. A., Harold, D., Naj, A. C., Sims, R., Bellenguez, C., Jun, G., DeStefano, A. L., Bis, J. C., Beecham, G. W., Grenier-Boley, B., Russo, G., Thornton-Wells, T. A., Jones, N., Smith, A. V., Chouraki, V., Thomas, C., Ikram, M. A., Zelenika, D., ... Amouyel, P. (2013). Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nature Genetics, 45, 1452-1458. doi:10.1038/ng.2802 Peer Reviewed verified by ORBi |
 | Herzog, E.* , Gu, W.* , Juhnke, H. D., Haas, A. H., Maentele, W., Simon, J., Helms, V., & Lancaster, C. R. D. (2012). Hydrogen-Bonded Networks Along and Bifurcation of the E-Pathway in Quinol:Fumarate Reductase. Biophysical Journal, 103 (6), 1305-1314. doi:10.1016/j.bpj.2012.07.037 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | Gu, W., Zhou, B., Geyer, T., Hutter, M., Fang, H., & Helms, V. (2011). Design of a Gated Molecular Proton Channel. Angewandte Chemie International Edition, 50 (3), 768-771. doi:10.1002/anie.201002564 Peer Reviewed verified by ORBi |
 | Ahmad, M., Gu, W., Geyer, T., & Helms, V. (2011). Adhesive water networks facilitate binding of protein interfaces. Nature Communications, 2. doi:10.1038/ncomms1258 Peer Reviewed verified by ORBi |
 | Zuo, G., Gu, W., Fang, H., & Zhou, R. (2011). Carbon Nanotube Wins the Competitive Binding over Proline-Rich Motif Ligand on SH3 Domain. Journal of Physical Chemistry. C, Nanomaterials and interfaces, 115 (25), 12322-12328. doi:10.1021/jp2026303 Peer reviewed |
 | Devanathan, R., Venkatnathan, A., Rousseau, R., Dupuis, M., Frigato, T., Gu, W., & Helms, V. (2010). Atomistic Simulation of Water Percolation and Proton Hopping in Nation Fuel Cell Membrane. Journal of Physical Chemistry B, 114 (43), 13681-13690. doi:10.1021/jp103398b Peer Reviewed verified by ORBi |
 | Wang, L., Siu, S. W. I., Gu, W., & Helms, V. (2010). Downhill Binding Energy Surface of the Barnase-Barstar Complex. Biopolymers, 93 (11), 977-985. doi:10.1002/bip.21507 Peer Reviewed verified by ORBi |
 | Gu, W., & Helms, V. (2009). Tightly Connected Water Wires Facilitate Fast Proton Uptake at The Proton Entrance of Proton Pumping Proteins. Journal of the American Chemical Society, 131 (6), 2080. doi:10.1021/ja809301w Peer Reviewed verified by ORBi |
 | Ahmad, M., Gu, W., & Helms, V. (2008). Mechanism of fast peptide recognition by SH3 domains. Angewandte Chemie International Edition, 47 (40), 7626-7630. doi:10.1002/anie.200801856 Peer Reviewed verified by ORBi |
 | Gu, W., Frigato, T., Straatsma, T. P., & Helms, V. (2007). Dynamic protonation equilibrium of solvated acetic acid. Angewandte Chemie International Edition, 46 (16), 2939-2943. doi:10.1002/anie.200603583 Peer Reviewed verified by ORBi |
 | Gu, W., & Helms, V. (2007). Different protonation equilibria of 4-methylimidazole and acetic acid. Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 8 (17), 2445-2451. doi:10.1002/cphc.200700442 Peer Reviewed verified by ORBi |
 | Piotukh, K., Gu, W., Kofler, M., Labudde, D., Helms, V., & Freund, C. (2005). Cyclophilin a binds to linear peptide motifs containing a consensus that is present in many human proteins. Journal of Biological Chemistry, 280 (25), 23668-23674. doi:10.1074/jbc.M503405200 Peer Reviewed verified by ORBi |
 | Gu, W., Kofler, M., Antes, I., Freund, C., & Helms, V. (2005). Alternative binding modes of proline-rich peptides binding to the GYF domain. Biochemistry, 44 (17), 6404-6415. doi:10.1021/bi0479914 Peer Reviewed verified by ORBi |
 | Shakya, S. K., Gu, W., & Helms, V. (2005). Molecular dynamics simulation of truncated bovine adrenodoxin. Biopolymers, 78 (1), 9-20. doi:10.1002/bip.20242 Peer Reviewed verified by ORBi |
 | Staritzbichler, R., Gu, W., & Helms, V. (2005). Are solvation free energies of homogeneous helical peptides additive? Journal of Physical Chemistry B, 109 (40), 19000-19007. doi:10.1021/jp052403x Peer Reviewed verified by ORBi |
 | Gu, W., & Helms, V. (2005). Dynamical binding of proline-rich peptides to their recognition domains. Biochimica et Biophysica Acta - Proteins and Proteomics, 1754 (1-2), 232-238. doi:10.1016/j.bbapap.2005.07.033 Peer Reviewed verified by ORBi |
 | Gu, W., Rahi, S. J., & Helms, V. (2004). Solvation free energies and transfer free energies for amino acids from hydrophobic solution to water solution from a very simple residue model. Journal of Physical Chemistry B, 108 (18), 5806-5814. doi:10.1021/jp0376424 Peer Reviewed verified by ORBi |
 | Gu, W., Wang, T. T., Zhu, J., Shi, Y. Y., & Liu, H. Y. (2003). Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions. Biophysical Chemistry, 104 (1), 79-94. doi:10.1016/S0301-4622(02)00340-X Peer Reviewed verified by ORBi |
Gu, W., Zhu, J., & Liu, H. Y. (2002). DIFFERENT PROTONATION STATES OF THE BACILLUS CEREUS BINUCLEAR ZINC METALLO-β-LACTAMASE ACTIVE SITE STUDIED BY COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL SIMULATIONS. Journal of Theoretical and Computational Chemistry. doi:10.1142/S0219633602000038 Peer Reviewed verified by ORBi |