On the influence of several factors on pathway enrichment analysis
Mubeen, Sarah, Tom Kodamullil, Alpha, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel
Published in Briefings in bioinformatics (13.05.2022)
Published in Briefings in bioinformatics (13.05.2022)
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Journal Article
Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis
Hofmann-Apitius, Martin, Gündel, Michaela, Tom Kodamullil, Alpha, Khanam Irin, Afroza
Published in Journal of Immunology Research (01.01.2015)
Published in Journal of Immunology Research (01.01.2015)
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Journal Article
Contribution of syndecans to cellular uptake and fibrillation of α-synuclein and tau
Hudák, Anett, Kusz, Erzsébet, Domonkos, Ildikó, Jósvay, Katalin, Kodamullil, Alpha Tom, Szilák, László, Hofmann-Apitius, Martin, Letoha, Tamás
Published in Scientific reports (12.11.2019)
Published in Scientific reports (12.11.2019)
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Journal Article
Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease
Karki, Reagon, Madan, Sumit, Gadiya, Yojana, Domingo-Fernández, Daniel, Kodamullil, Alpha Tom, Hofmann-Apitius, Martin
Published in Journal of Alzheimer's disease (01.01.2020)
Published in Journal of Alzheimer's disease (01.01.2020)
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Journal Article
Design of the formalized and integrated Alzheimer’s Disease Ontology and its application in retrieving textual data via text mining
Zhang, Bide, Lage-Rupprecht, Vanessa, Wegner, Philipp, Sargsyan, Astghik, Gebel, Stephan, Jacobs, Marc, Klein, Jürgen, Hofmann-Apitius, Martin, Tom Kodamullil, Alpha
Published in Database : the journal of biological databases and curation (02.12.2023)
Published in Database : the journal of biological databases and curation (02.12.2023)
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Journal Article
Of Mice and Men: Comparative Analysis of Neuro-Inflammatory Mechanisms in Human and Mouse Using Cause-and-Effect Models
Kodamullil, Alpha Tom, Iyappan, Anandhi, Karki, Reagon, Madan, Sumit, Younesi, Erfan, Hofmann-Apitius, Martin
Published in Journal of Alzheimer's disease (01.01.2017)
Published in Journal of Alzheimer's disease (01.01.2017)
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Journal Article
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets
Figueiredo, Rebeca Queiroz, Del Ser, Sara Díaz, Raschka, Tamara, Hofmann-Apitius, Martin, Kodamullil, Alpha Tom, Mubeen, Sarah, Domingo-Fernández, Daniel
Published in BMC bioinformatics (15.06.2022)
Published in BMC bioinformatics (15.06.2022)
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Journal Article
A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer's Disease
Golriz Khatami, Sepehr, Domingo-Fernández, Daniel, Mubeen, Sarah, Hoyt, Charles Tapley, Robinson, Christine, Karki, Reagon, Iyappan, Anandhi, Kodamullil, Alpha Tom, Hofmann-Apitius, Martin
Published in Journal of Alzheimer's disease (01.01.2021)
Published in Journal of Alzheimer's disease (01.01.2021)
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Journal Article
Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases
Emon, Mohammad Asif Emran Khan, Kodamullil, Alpha Tom, Karki, Reagon, Younesi, Erfan, Hofmann-Apitius, Martin
Published in Journal of Alzheimer's disease (01.01.2017)
Published in Journal of Alzheimer's disease (01.01.2017)
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Journal Article
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization
Schultz, Bruce, Zaliani, Andrea, Ebeling, Christian, Reinshagen, Jeanette, Bojkova, Denisa, Lage-Rupprecht, Vanessa, Karki, Reagon, Lukassen, Sören, Gadiya, Yojana, Ravindra, Neal G., Das, Sayoni, Baksi, Shounak, Domingo-Fernández, Daniel, Lentzen, Manuel, Strivens, Mark, Raschka, Tamara, Cinatl, Jindrich, DeLong, Lauren Nicole, Gribbon, Phil, Geisslinger, Gerd, Ciesek, Sandra, van Dijk, David, Gardner, Steve, Kodamullil, Alpha Tom, Fröhlich, Holger, Peitsch, Manuel, Jacobs, Marc, Hoeng, Julia, Eils, Roland, Claussen, Carsten, Hofmann-Apitius, Martin
Published in Scientific reports (26.05.2021)
Published in Scientific reports (26.05.2021)
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Journal Article
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders
Hofmann-Apitius, Martin, Ball, Gordon, Gebel, Stephan, Bagewadi, Shweta, de Bono, Bernard, Schneider, Reinhard, Page, Matt, Kodamullil, Alpha Tom, Younesi, Erfan, Ebeling, Christian, Tegnér, Jesper, Canard, Luc
Published in International journal of molecular sciences (07.12.2015)
Published in International journal of molecular sciences (07.12.2015)
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Journal Article
A natural language processing system for the efficient updating of highly curated pathophysiology mechanism knowledge graphs
Babaiha, Negin Sadat, Elsayed, Hassan, Zhang, Bide, Kaladharan, Abish, Sethumadhavan, Priya, Schultz, Bruce, Klein, Jürgen, Freudensprung, Bruno, Lage-Rupprecht, Vanessa, Kodamullil, Alpha Tom, Jacobs, Marc, Geissler, Stefan, Madan, Sumit, Hofmann-Apitius, Martin
Published in Artificial intelligence in the life sciences (15.12.2023)
Published in Artificial intelligence in the life sciences (15.12.2023)
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Journal Article
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk
Khatami, Sepehr Golriz, Sargsyan, Astghik, Russo, Maria Francesca, Domingo-Fernández, Daniel, Zaliani, Andrea, Kaladharan, Abish, Sethumadhavan, Priya, Mubeen, Sarah, Gadiya, Yojana, Karki, Reagon, Gebel, Stephan, Ruppa Surulinathan, Ram Kumar, Lage-Rupprecht, Vanessa, Archipovas, Saulius, Mingrone, Geltrude, Jacobs, Marc, Claussen, Carsten, Hofmann-Apitius, Martin, Kodamullil, Alpha Tom
Published in Data (Basel) (01.01.2024)
Published in Data (Basel) (01.01.2024)
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Journal Article
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures
Golriz Khatami, Sepehr, Mubeen, Sarah, Bharadhwaj, Vinay Srinivas, Kodamullil, Alpha Tom, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel
Published in NPJ systems biology and applications (27.10.2021)
Published in NPJ systems biology and applications (27.10.2021)
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Journal Article
Corrigendum to “Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases”[Artificial Intelligence in Life Sciences] 1(2021), 100020
Linden, Thomas, Hanses, Frank, Domingo-Fernández, Daniel, DeLong, Lauren Nicole, Kodamullil, Alpha Tom, Schneider, Jochen, Vehreschild, Maria J.G.T., Lanznaster, Julia, Ruethrich, Maria Madeleine, Borgmann, Stefan, Hower, Martin, Wille, Kai, Feldt, Torsten, Rieg, Siegbert, Hertenstein, Bernd, Wyen, Christoph, Roemmele, Christoph, Vehreschild, Jörg Janne, Jakob, Carolin E.M., Stecher, Melanie, Kuzikov, Maria, Zaliani, Andrea, Fröhlich, Holger
Published in Artificial intelligence in the life sciences (01.12.2022)
Published in Artificial intelligence in the life sciences (01.12.2022)
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Journal Article
Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases
Linden, Thomas, Hanses, Frank, Domingo-Fernández, Daniel, DeLong, Lauren Nicole, Kodamullil, Alpha Tom, Schneider, Jochen, Vehreschild, Maria J.G.T., Lanznaster, Julia, Ruethrich, Maria Madeleine, Borgmann, Stefan, Hower, Martin, Wille, Kai, Feldt, Torsten, Rieg, Siegbert, Hertenstein, Bernd, Wyen, Christoph, Roemmele, Christoph, Vehreschild, Jörg Janne, Jakob, Carolin E.M., Stecher, Melanie, Kuzikov, Maria, Zaliani, Andrea, Fröhlich, Holger
Published in Artificial intelligence in the life sciences (01.12.2021)
Published in Artificial intelligence in the life sciences (01.12.2021)
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Journal Article