| Year |
Citation |
Score |
| 2022 |
Balabin H, Hoyt CT, Birkenbihl C, Gyori BM, Bachman J, Kodamullil AT, Plöger PG, Hofmann-Apitius M, Domingo-Fernández D. STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs. Bioinformatics (Oxford, England). PMID 34986221 DOI: 10.1093/bioinformatics/btac001 |
0.694 |
|
| 2021 |
Khatami SG, Domingo-Fernández D, Mubeen S, Hoyt CT, Robinson C, Karki R, Iyappan A, Kodamullil AT, Hofmann-Apitius M. A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer's Disease. Journal of Alzheimer's Disease : Jad. PMID 33554913 DOI: 10.3233/JAD-201397 |
0.691 |
|
| 2020 |
Karki R, Madan S, Gadiya Y, Domingo-Fernández D, Kodamullil AT, Hofmann-Apitius M. Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease. Journal of Alzheimer's Disease : Jad. PMID 32925069 DOI: 10.3233/Jad-200752 |
0.312 |
|
| 2020 |
Birkenbihl C, Emon MA, Vrooman H, Westwood S, Lovestone S, Hofmann-Apitius M, Fröhlich H. Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice. The Epma Journal. 11: 367-376. PMID 32843907 DOI: 10.1007/S13167-020-00216-Z |
0.34 |
|
| 2020 |
Muslu O, Hoyt CT, De Lacerda MP, Hofmann-Apitius M, Froehlich H. GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750869 DOI: 10.1109/Tcbb.2020.3003830 |
0.691 |
|
| 2020 |
Sood M, Sahay A, Karki R, Emon MA, Vrooman H, Hofmann-Apitius M, Fröhlich H. Realistic simulation of virtual multi-scale, multi-modal patient trajectories using Bayesian networks and sparse auto-encoders. Scientific Reports. 10: 10971. PMID 32620927 DOI: 10.1038/S41598-020-67398-4 |
0.385 |
|
| 2020 |
Emon MA, Domingo-Fernández D, Hoyt CT, Hofmann-Apitius M. PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. Bmc Bioinformatics. 21: 231. PMID 32503412 DOI: 10.1186/S12859-020-03568-5 |
0.686 |
|
| 2020 |
Mubeen S, Hoyt CT, Gemünd A, Hofmann-Apitius M, Fröhlich H, Domingo-Fernández D. Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. Frontiers in Genetics. 11: 436. PMID 32411185 DOI: 10.3389/Fgene.2020.00436 |
0.68 |
|
| 2020 |
Humayun F, Domingo-Fernández D, Paul George AA, Hopp MT, Syllwasschy BF, Detzel MS, Hoyt CT, Hofmann-Apitius M, Imhof D. A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. Frontiers in Bioengineering and Biotechnology. 8: 74. PMID 32211383 DOI: 10.3389/Fbioe.2020.00074 |
0.708 |
|
| 2020 |
Golriz Khatami S, Mubeen S, Hofmann-Apitius M. Data science in neurodegenerative disease: its capabilities, limitations, and perspectives. Current Opinion in Neurology. PMID 32073441 DOI: 10.1097/Wco.0000000000000795 |
0.363 |
|
| 2019 |
Golriz Khatami S, Robinson C, Birkenbihl C, Domingo-Fernández D, Hoyt CT, Hofmann-Apitius M. Challenges of Integrative Disease Modeling in Alzheimer's Disease. Frontiers in Molecular Biosciences. 6: 158. PMID 31993440 DOI: 10.3389/Fmolb.2019.00158 |
0.71 |
|
| 2019 |
Mubeen S, Hoyt CT, Gemünd A, Hofmann-Apitius M, Fröhlich H, Domingo-Fernández D. The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. Frontiers in Genetics. 10: 1203. PMID 31824580 DOI: 10.3389/Fgene.2019.01203 |
0.704 |
|
| 2019 |
Karki R, Kodamullil AT, Hoyt CT, Hofmann-Apitius M. Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. Bmc Bioinformatics. 20: 494. PMID 31604427 DOI: 10.1186/S12859-019-3101-1 |
0.731 |
|
| 2019 |
Domingo-Fernández D, Provost A, Kodamullil AT, Marín-Llaó J, Lasseter H, Diaz K, Daskalakis NP, Lancashire L, Hofmann-Apitius M, Haas M. PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools. Database : the Journal of Biological Databases and Curation. 2019. PMID 31260040 DOI: 10.1093/Database/Baz081 |
0.304 |
|
| 2019 |
Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database : the Journal of Biological Databases and Curation. 2019. PMID 31225582 DOI: 10.1093/Database/Baz068 |
0.708 |
|
| 2019 |
Domingo-Fernández D, Mubeen S, Marín-Llaó J, Hoyt CT, Hofmann-Apitius M. PathMe: merging and exploring mechanistic pathway knowledge. Bmc Bioinformatics. 20: 243. PMID 31092193 DOI: 10.1186/S12859-019-2863-9 |
0.715 |
|
| 2019 |
Domingo-Fernández D, Hoyt CT, Bobis-Álvarez C, Marín-Llaó J, Hofmann-Apitius M. Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. Npj Systems Biology and Applications. 5: 10. PMID 30854225 DOI: 10.1038/s41540-019-0082-7 |
0.652 |
|
| 2019 |
Domingo-Fernández D, Hoyt CT, Bobis-Álvarez C, Marín-Llaó J, Hofmann-Apitius M.. ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. Npj Syst Biol Appl.. PMID 30564458 DOI: 10.1038/s41540-018-0078-8 |
0.688 |
|
| 2018 |
Hoyt CT, Domingo-Fernández D, Hofmann-Apitius M.. BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database. PMID 30576488 DOI: 10.1093/Database/Bay126 |
0.699 |
|
| 2018 |
Khanna S, Domingo-Fernández D, Iyappan A, Emon MA, Hofmann-Apitius M, Fröhlich H. Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms. Scientific Reports. 8: 11173. PMID 30042519 DOI: 10.1038/S41598-018-29433-3 |
0.354 |
|
| 2018 |
Gündel M, Hoyt CT, Hofmann-Apitius M.. BEL2ABM: agent-based simulation of static models in Biological Expression Language. Bioinformatics. 34: 2316-2318. PMID 29949955 DOI: 10.1093/Bioinformatics/Bty107 |
0.683 |
|
| 2018 |
Hoyt CT, Domingo-Fernández D, Balzer N, Güldenpfennig A, Hofmann-Apitius M.. A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. Database. PMID 29873705 DOI: 10.1093/Database/Bay050 |
0.706 |
|
| 2017 |
Geerts H, Hofmann-Apitius M, Anastasio TJ. Knowledge-driven computational modeling in Alzheimer's research: Current state and future trends. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. PMID 28917669 DOI: 10.1016/J.Jalz.2017.08.011 |
0.426 |
|
| 2017 |
Kawalia SB, Raschka T, Naz M, de Matos Simoes R, Senger P, Hofmann-Apitius M. Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. Journal of Alzheimer's Disease : Jad. 59: 1237-1254. PMID 28800327 DOI: 10.3233/Jad-170011 |
0.396 |
|
| 2017 |
Kodamullil AT, Iyappan A, Karki R, Madan S, Younesi E, Hofmann-Apitius M. Of Mice and Men: Comparative Analysis of Neuro-Inflammatory Mechanisms in Human and Mouse Using Cause-and-Effect Models. Journal of Alzheimer's Disease : Jad. 59: 1045-1055. PMID 28731442 DOI: 10.3233/Jad-170255 |
0.334 |
|
| 2017 |
Domingo-Fernández D, Kodamullil AT, Iyappan A, Naz M, Emon MA, Raschka T, Karki R, Springstubbe S, Ebeling C, Hofmann-Apitius M. Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment. Bioinformatics (Oxford, England). 33: 3679-3681. PMID 28651363 DOI: 10.1093/Bioinformatics/Btx399 |
0.344 |
|
| 2017 |
Talikka M, Bukharov N, Hayes WS, Hofmann-Apitius M, Alexopoulos L, Peitsch MC, Hoeng J. Novel approaches to develop community-built biological network models for potential drug discovery. Expert Opinion On Drug Discovery. 1-9. PMID 28585481 DOI: 10.1080/17460441.2017.1335302 |
0.416 |
|
| 2017 |
Emon MA, Kodamullil AT, Karki R, Younesi E, Hofmann-Apitius M. Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases. Journal of Alzheimer's Disease : Jad. 56: 677-686. PMID 28035920 DOI: 10.3233/Jad-160222 |
0.389 |
|
| 2017 |
Naz M, Younesi E, Hofmann-Apitius M. Systematic Analysis of GWAS Data Reveals Genomic Hotspots for Shared Mechanisms between Neurodegenerative Diseases Journal of Alzheimer’S Disease & Parkinsonism. 7. DOI: 10.4172/2161-0460.1000368 |
0.37 |
|
| 2016 |
Langley GR, Adcock IM, Busquet F, Crofton KM, Csernok E, Giese C, Heinonen T, Herrmann K, Hofmann-Apitius M, Landesmann B, Marshall LJ, McIvor E, Muotri AR, Noor F, Schutte K, et al. Towards a 21st-century roadmap for biomedical research and drug discovery: consensus report and recommendations. Drug Discovery Today. PMID 27989722 DOI: 10.1016/J.Drudis.2016.10.011 |
0.369 |
|
| 2016 |
Iyappan A, Kawalia SB, Raschka T, Hofmann-Apitius M, Senger P. NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. Journal of Biomedical Semantics. 7: 45. PMID 27392431 DOI: 10.1186/S13326-016-0079-8 |
0.393 |
|
| 2016 |
Iyappan A, Gündel M, Shahid M, Wang J, Li H, Mevissen HT, Müller B, Fluck J, Jirsa V, Domide L, Younesi E, Hofmann-Apitius M. Toward a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration. Journal of Alzheimer's Disease : Jad. PMID 27079715 DOI: 10.3233/Jad-151178 |
0.408 |
|
| 2016 |
Naz M, Kodamullil AT, Hofmann-Apitius M. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Briefings in Bioinformatics. 17: 505-16. PMID 26249223 DOI: 10.1093/Bib/Bbv063 |
0.414 |
|
| 2015 |
Hofmann-Apitius M, Ball G, Gebel S, Bagewadi S, de Bono B, Schneider R, Page M, Kodamullil AT, Younesi E, Ebeling C, Tegnér J, Canard L. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. International Journal of Molecular Sciences. 16: 29179-206. PMID 26690135 DOI: 10.3390/Ijms161226148 |
0.404 |
|
| 2015 |
Khanam Irin A, Kodamullil AT, Gündel M, Hofmann-Apitius M. Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis. Journal of Immunology Research. 2015: 737168. PMID 26636108 DOI: 10.1155/2015/737168 |
0.379 |
|
| 2015 |
Bagewadi S, Adhikari S, Dhrangadhariya A, Irin AK, Ebeling C, Namasivayam AA, Page M, Hofmann-Apitius M, Senger P. NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database : the Journal of Biological Databases and Curation. 2015. PMID 26475471 DOI: 10.1093/Database/Bav099 |
0.38 |
|
| 2015 |
Younesi E, Malhotra A, Gündel M, Scordis P, Kodamullil AT, Page M, Müller B, Springstubbe S, Wüllner U, Scheller D, Hofmann-Apitius M. PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain. Theoretical Biology & Medical Modelling. 12: 20. PMID 26395080 DOI: 10.1186/S12976-015-0017-Y |
0.367 |
|
| 2015 |
Malhotra A, Younesi E, Sahadevan S, Zimmermann J, Hofmann-Apitius M. Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. Scientific Reports. 5: 13634. PMID 26346705 DOI: 10.1038/Srep13634 |
0.397 |
|
| 2015 |
Szostak J, Ansari S, Madan S, Fluck J, Talikka M, Iskandar A, De Leon H, Hofmann-Apitius M, Peitsch MC, Hoeng J. Construction of biological networks from unstructured information based on a semi-automated curation workflow. Database : the Journal of Biological Databases and Curation. 2015: bav057. PMID 26200752 DOI: 10.1093/Database/Bav057 |
0.403 |
|
| 2015 |
Hofmann-Apitius M. Is dementia research ready for big data approaches? Bmc Medicine. 13: 145. PMID 26099627 DOI: 10.1186/S12916-015-0367-7 |
0.322 |
|
| 2015 |
Kodamullil AT, Younesi E, Naz M, Bagewadi S, Hofmann-Apitius M. Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. PMID 25849034 DOI: 10.1016/J.Jalz.2015.02.006 |
0.351 |
|
| 2015 |
Hofmann-Apitius M, Alarcón-Riquelme ME, Chamberlain C, McHale D. Towards the taxonomy of human disease. Nature Reviews. Drug Discovery. 14: 75-6. PMID 25633780 DOI: 10.1038/Nrd4537 |
0.31 |
|
| 2014 |
Bagewadi S, Bobić T, Hofmann-Apitius M, Fluck J, Klinger R. Detecting miRNA Mentions and Relations in Biomedical Literature. F1000research. 3: 205. PMID 26535109 DOI: 10.12688/F1000Research.4591.3 |
0.735 |
|
| 2014 |
Malhotra A, Younesi E, Bagewadi S, Hofmann-Apitius M. Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease. Genome Medicine. 6: 97. PMID 25484918 DOI: 10.1186/S13073-014-0097-Z |
0.409 |
|
| 2014 |
Sahadevan S, Gunawan A, Tholen E, Große-Brinkhaus C, Tesfaye D, Schellander K, Hofmann-Apitius M, Cinar MU, Uddin MJ. Pathway based analysis of genes and interactions influencing porcine testis samples from boars with divergent androstenone content in back fat. Plos One. 9: e91077. PMID 24614349 DOI: 10.1371/Journal.Pone.0091077 |
0.333 |
|
| 2014 |
Fluck J, Hofmann-Apitius M. Text mining for systems biology. Drug Discovery Today. 19: 140-4. PMID 24070668 DOI: 10.1016/J.Drudis.2013.09.012 |
0.316 |
|
| 2014 |
Malhotra A, Younesi E, Gündel M, Müller B, Heneka MT, Hofmann-Apitius M. ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. 10: 238-46. PMID 23830913 DOI: 10.1016/J.Jalz.2013.02.009 |
0.426 |
|
| 2013 |
Shahid M, Shahzad Cheema M, Klenner A, Younesi E, Hofmann-Apitius M. SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling. Molecular Informatics. 32: 241-9. PMID 27481519 DOI: 10.1002/Minf.201200116 |
0.3 |
|
| 2013 |
Younesi E, Hofmann-Apitius M. Biomarker-guided translation of brain imaging into disease pathway models. Scientific Reports. 3: 3375. PMID 24287435 DOI: 10.1038/Srep03375 |
0.338 |
|
| 2013 |
Younesi E, Hofmann-Apitius M. From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine. The Epma Journal. 4: 23. PMID 24195840 DOI: 10.1186/1878-5085-4-23 |
0.368 |
|
| 2013 |
Malhotra A, Younesi E, Gurulingappa H, Hofmann-Apitius M. 'HypothesisFinder:' a strategy for the detection of speculative statements in scientific text. Plos Computational Biology. 9: e1003117. PMID 23935466 DOI: 10.1371/Journal.Pcbi.1003117 |
0.384 |
|
| 2013 |
Deyati A, Younesi E, Hofmann-Apitius M, Novac N. Challenges and opportunities for oncology biomarker discovery. Drug Discovery Today. 18: 614-24. PMID 23280501 DOI: 10.1016/J.Drudis.2012.12.011 |
0.351 |
|
| 2013 |
Gurulingappa H, Mudi A, Toldo L, Hofmann-Apitius M, Bhate J. Challenges in mining the literature for chemical information Rsc Advances. 3: 16194-16211. DOI: 10.1039/C3Ra40787J |
0.326 |
|
| 2012 |
Younesi E, Toldo L, Müller B, Friedrich CM, Novac N, Scheer A, Hofmann-Apitius M, Fluck J. Mining biomarker information in biomedical literature. Bmc Medical Informatics and Decision Making. 12: 148. PMID 23249606 DOI: 10.1186/1472-6947-12-148 |
0.392 |
|
| 2012 |
Sahadevan S, Hofmann-Apitius M, Schellander K, Tesfaye D, Fluck J, Friedrich CM. Text mining in livestock animal science: introducing the potential of text mining to animal sciences. Journal of Animal Science. 90: 3666-76. PMID 22665627 DOI: 10.2527/Jas.2011-4841 |
0.371 |
|
| 2012 |
Gurulingappa H, Rajput AM, Roberts A, Fluck J, Hofmann-Apitius M, Toldo L. Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. Journal of Biomedical Informatics. 45: 885-92. PMID 22554702 DOI: 10.1016/J.Jbi.2012.04.008 |
0.339 |
|
| 2011 |
Thomas PE, Klinger R, Furlong LI, Hofmann-Apitius M, Friedrich CM. Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. Bmc Bioinformatics. 12: S4. PMID 21992066 DOI: 10.1186/1471-2105-12-S4-S4 |
0.765 |
|
| 2011 |
Ivchenko O, Younesi E, Shahid M, Wolf A, Müller B, Hofmann-Apitius M. PLIO: an ontology for formal description of protein-ligand interactions. Bioinformatics (Oxford, England). 27: 1684-90. PMID 21546398 DOI: 10.1093/Bioinformatics/Btr256 |
0.398 |
|
| 2010 |
Wolf A, Shahid M, Kasam V, Ziegler W, Hofmann-Apitius M. In silico drug discovery approaches on grid computing infrastructures. Current Clinical Pharmacology. 5: 37-46. PMID 19642967 DOI: 10.2174/157488410790410560 |
0.33 |
|
| 2009 |
Kasam V, Salzemann J, Botha M, Dacosta A, Degliesposti G, Isea R, Kim D, Maass A, Kenyon C, Rastelli G, Hofmann-Apitius M, Breton V. WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures. Malaria Journal. 8: 88. PMID 19409081 DOI: 10.1186/1475-2875-8-88 |
0.346 |
|
| 2009 |
Kolárik C, Klinger R, Hofmann-Apitius M. Identification of histone modifications in biomedical text for supporting epigenomic research. Bmc Bioinformatics. 10: S28. PMID 19208128 DOI: 10.1186/1471-2105-10-S1-S28 |
0.752 |
|
| 2008 |
Klinger R, Kolárik C, Fluck J, Hofmann-Apitius M, Friedrich CM. Detection of IUPAC and IUPAC-like chemical names. Bioinformatics (Oxford, England). 24: i268-76. PMID 18586724 DOI: 10.1093/bioinformatics/btn181 |
0.766 |
|
| 2008 |
Hofmann-Apitius M, Fluck J, Furlong L, Fornes O, Kolárik C, Hanser S, Boeker M, Schulz S, Sanz F, Klinger R, Mevissen T, Gattermayer T, Oliva B, Friedrich CM. Knowledge environments representing molecular entities for the virtual physiological human. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 366: 3091-110. PMID 18559317 DOI: 10.1098/Rsta.2008.0099 |
0.773 |
|
| 2008 |
Furlong LI, Dach H, Hofmann-Apitius M, Sanz F. OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature. Bmc Bioinformatics. 9: 84. PMID 18251998 DOI: 10.1186/1471-2105-9-84 |
0.39 |
|
| 2007 |
Klinger R, Friedrich CM, Mevissen HT, Fluck J, Hofmann-Apitius M, Furlong LI, Sanz F. Identifying gene-specific variations in biomedical text. Journal of Bioinformatics and Computational Biology. 5: 1277-96. PMID 18172929 DOI: 10.1142/S0219720007003156 |
0.773 |
|
| 2007 |
Wolf A, Zimmermann M, Hofmann-Apitius M. Alternative to consensus scoring--a new approach toward the qualitative combination of docking algorithms. Journal of Chemical Information and Modeling. 47: 1036-44. PMID 17492829 DOI: 10.1021/Ci6004965 |
0.301 |
|
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