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Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection

S. Ciucci, C. Durán, A. Palladini, U. Ijaz, F. Sterbini, L. Masucci, G. Cammarota, G. Ianiro, P. Spuul, M. Schroeder, S. Grill, B. Parsons, D. Pritchard, B. Posteraro, M. Sanguinetti, G. Gasbarrini, A. Gasbarrini, and C. Cannistraci. (March 2020)

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Netrank: network-based approach for biomarker discoveryA. Al-Fatlawi, E. Rusadze, A. Shmelkin, N. Malekian, C. Ozen, C. Pilarsky, and M. Schroeder. BMC Bioinformatics, 24 (1): 304 (July 2023)The BOD1L subunit of the mammalian SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylationG. Ciotta, S. Singh, A. Gupta, D. Torres, J. Fu, R. Choudhury, W. Chu, C. Choudhary, L. Gahurova, A. Al-Fatlawi and 5 other author(s). (April 2023)A community effort in SARS‐CoV‐2 drug discoveryJ. Schimunek, P. Seidl, K. Elez, T. Hempel, T. Le, F. Noé, S. Olsson, L. Raich, R. Winter, H. Gokcan and 142 other author(s). Molecular Informatics, (November 2023)PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNAM. Adasme, K. Linnemann, S. Bolz, F. Kaiser, S. Salentin, V. Haupt, and M. Schroeder. Nucleic Acids Res., 49 (W1): W530--W534 (July 2021)A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistanceN. Malekian, A. Agrawal, T. Berendonk, A. Al-Fatlawi, and M. Schroeder. Scientific Reports, (May 2022)Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistanceN. Malekian, S. Sainath, A. Al-Fatlawi, and M. Schroeder. Frontiers in Microbiology, (December 2023)Explainable AI to improve acceptance of convolutional neural networks for automatic classification of dopamine transporter SPECT in the diagnosis of clinically uncertain parkinsonian syndromesM. Nazari, A. Kluge, I. Apostolova, S. Klutmann, S. Kimiaei, M. Schroeder, and R. Buchert. European Journal of Nuclear Medicine and Molecular Imaging, 49 (4): 1176–1186 (October 2021)Is protein BLAST a thing of the past?A. Al-Fatlawi, M. Menzel, and M. Schroeder. Nat. Commun., 14 (1): 8195 (December 2023)Deep learning improves pancreatic cancer diagnosis using RNA-based variantsA. Al-Fatlawi, N. Malekian, S. Garc\'ıa, A. Henschel, I. Kim, A. Dahl, B. Jahnke, P. Bailey, S. Bolz, A. Poetsch and 4 other author(s). Cancers (Basel), 13 (11): 2654 (May 2021)The Rad52 SSAP superfamily and new insight into homologous recombinationA. Al-Fatlawi, M. Schroeder, and A. Stewart. Commun. Biol., 6 (1): 87 (January 2023)

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