Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. - Mufassra Naz; Alpha Tom Kodamullil; Martin Hofmann-Apitius (Briefings Bioinform., 2016)

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). - Juliane Fluck; Sumit Madan; Sam Ansari; Alpha Tom Kodamullil; Reagon Karki; Majid Rastegar-Mojarad; Natalie L. Catlett; William Hayes; Justyna Szostak; Julia Hoeng; Manuel C. Peitsch (Database J. Biol. Databases Curation, 2016)

Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment. - Daniel Domingo-Fernández; Alpha Tom Kodamullil; Anandhi Iyappan; Mufassra Naz; Mohammad Asif Emon; Tamara Raschka; Reagon Karki; Stephan Springstubbe; Christian Ebeling; Martin Hofmann-Apitius (Bioinform., 2017)

Building multiscale computable model of Alzheimer's disease and identification of novel mechanisms for new therapeutic interventions - Alpha Tom Kodamullil (2018)

PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools. - Daniel Domingo-Fernández; Allison Provost; Alpha Tom Kodamullil; Josep Marín-Llaó; Heather Lasseter; Kristophe Diaz; Nikolaos P. Daskalakis; Lee Lancashire; Martin Hofmann-Apitius; Magali Haas (Database J. Biol. Databases Curation, 2019)

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. - Reagon Karki; Alpha Tom Kodamullil; Charles Tapley Hoyt; Martin Hofmann-Apitius (BMC Bioinform., 2019)

CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView. - Asiyah Yu Lin; Stephan Gebel; Qingliang Leon Li; Sumit Madan; Johannes Darms; Evan Bolton; Barry Smith 001; Martin Hofmann-Apitius; Yongqun Oliver He; Alpha Tom Kodamullil (ICBO/ODLS, 2020)

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology. - Daniel Domingo-Fernández; Shounak Baksi; Bruce Schultz; Yojana Gadiya; Reagon Karki; Tamara Raschka; Christian Ebeling; Martin Hofmann-Apitius; Alpha Tom Kodamullil (Bioinform., 2021)

The COVID-19 Ontology. - Astghik Sargsyan; Alpha Tom Kodamullil; Shounak Baksi; Johannes Darms; Sumit Madan; Stephan Gebel; Oliver Keminer; Geena Mariya Jose; Helena Balabin; Lauren Nicole Delong; Manfred Kohler; Marc Jacobs 001; et al. (Bioinform., 2021)

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. - Helena Balabin; Charles Tapley Hoyt; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Martin Hofmann-Apitius; Daniel Domingo-Fernández (SWAT4HCLS, 2022)

On the influence of several factors on pathway enrichment analysis. - Sarah Mubeen; Alpha Tom Kodamullil; Martin Hofmann-Apitius; Daniel Domingo-Fernández (Briefings Bioinform., 2022)

Benchmarking table recognition performance on biomedical literature on neurological disorders. - Tim Adams; Marcin Namysl; Alpha Tom Kodamullil; Sven Behnke; Marc Jacobs 001 (Bioinform., 2022)

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. - Helena Balabin; Charles Tapley Hoyt; Colin Birkenbihl; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Paul G. Plöger; Martin Hofmann-Apitius; Daniel Domingo-Fernández (Bioinform., 2022)

Integrative data semantics through a model-enabled data stewardship. - Philipp Wegner; Sebastian Schaaf; Mischa Uebachs; Daniel Domingo-Fernández; Yasamin Salimi; Stephan Gebel; Astghik Sargsyan; Colin Birkenbihl; Stephan Springstubbe; Thomas Klockgether; Juliane Fluck; Martin Hofmann-Apitius; et al. (Bioinform., 2022)

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. - Rebeca Queiroz Figueiredo; Sara Díaz del Ser; Tamara Raschka; Martin Hofmann-Apitius; Alpha Tom Kodamullil; Sarah Mubeen; Daniel Domingo-Fernández (BMC Bioinform., 2022)

Common data model for COVID-19 datasets. - Philipp Wegner; Geena Mariya Jose; Vanessa Lage-Rupprecht; Sepehr Golriz Khatami; Bide Zhang; Stephan Springstubbe; Marc Jacobs 001; Thomas Linden; Cindy Ku; Bruce Schultz; Martin Hofmann-Apitius; Alpha Tom Kodamullil (Bioinform., 2022)

Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining. - Bide Zhang; Vanessa Lage-Rupprecht; Philipp Wegner; Astghik Sargsyan; Stephan Gebel; Marc Jacobs 001; Jürgen Klein; Martin Hofmann-Apitius; Alpha Tom Kodamullil (Database J. Biol. Databases Curation, 2023)

Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk. - Sepehr Golriz Khatami; Astghik Sargsyan; Maria Francesca Russo; Daniel Domingo-Fernández; Andrea Zaliani; Abish Kaladharan; Priya Sethumadhavan; Sarah Mubeen; Yojana Gadiya; Reagon Karki; Stephan Gebel; Ram Kumar Ruppa Surulinathan; et al. (Data, 2024)