Alpha Tom Kodamullil

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 17

Top Topics

Causal Relations

Gene Expression Patterns

Neurodegenerative Diseases

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

Publications

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, Vanessa Lage-Rupprecht, Saulius Archipovas, Geltrude Mingrone, Marc Jacobs, Carsten Claussen, Martin Hofmann-Apitius, Alpha Tom Kodamullil
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk. Data 9 (2) (2024)
Bide Zhang, Vanessa Lage-Rupprecht, Philipp Wegner, Astghik Sargsyan, Stephan Gebel, Marc Jacobs, Jürgen Klein, Martin Hofmann-Apitius, Alpha Tom Kodamullil
Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining. Database J. Biol. Databases Curation 2023 (2023)
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
On the influence of several factors on pathway enrichment analysis. Briefings Bioinform. 23 (3) (2022)
Tim Adams, Marcin Namysl, Alpha Tom Kodamullil, Sven Behnke, Marc Jacobs
Benchmarking table recognition performance on biomedical literature on neurological disorders. Bioinform. 38 (6) (2022)
Philipp Wegner, Geena Mariya Jose, Vanessa Lage-Rupprecht, Sepehr Golriz Khatami, Bide Zhang, Stephan Springstubbe, Marc Jacobs, Thomas Linden, Cindy Ku, Bruce Schultz, Martin Hofmann-Apitius, Alpha Tom Kodamullil
Common data model for COVID-19 datasets. Bioinform. 38 (24) (2022)
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, Alpha Tom Kodamullil
Integrative data semantics through a model-enabled data stewardship. Bioinform. 38 (15) (2022)
Helena Balabin, Charles Tapley Hoyt, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. SWAT4HCLS (2022)
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
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38 (6) (2022)
Rebeca Queiroz Figueiredo, Sara Díaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, Daniel Domingo-Fernández
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. BMC Bioinform. 23 (1) (2022)
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, Martin Hofmann-Apitius
The COVID-19 Ontology. Bioinform. 36 (24) (2021)
Daniel Domingo-Fernández, Shounak Baksi, Bruce Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann-Apitius, Alpha Tom Kodamullil
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology. Bioinform. 37 (9) (2021)
Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He, Alpha Tom Kodamullil
CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView. ICBO/ODLS (2020)
Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. BMC Bioinform. 20 (1) (2019)
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
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools. Database J. Biol. Databases Curation 2019 (2019)
Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, Martin Hofmann-Apitius
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment. Bioinform. 33 (22) (2017)
Mufassra Naz, Alpha Tom Kodamullil, Martin Hofmann-Apitius
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Briefings Bioinform. 17 (3) (2016)
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
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). Database J. Biol. Databases Curation 2016 (2016)