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ORCIDAlpha Tom Kodamullil
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Books and Theses
- 2018
[b1]Alpha Tom Kodamullil:
Building multiscale computable model of Alzheimer's disease and identification of novel mechanisms for new therapeutic interventions. University of Bonn, Germany, 2018
Journal Articles
- 2025
- [j16]Sathvik Guru Rao
, Pranitha Rokkam, Bide Zhang, Astghik Sargsyan, Abish Kaladharan, Priya Sethumadhavan, Marc Jacobs, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
Three-layered semantic framework for public health intelligence. J. Biomed. Semant. 16(1): 17 (2025) - 2024
- [j15]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): 25 (2024) - 2023
- [j14]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) - 2022
- [j13]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) - [j12]Tim Adams, Marcin Namysl, Alpha Tom Kodamullil, Sven Behnke, Marc Jacobs:
Benchmarking table recognition performance on biomedical literature on neurological disorders. Bioinform. 38(6): 1624-1630 (2022) - [j11]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): 1648-1656 (2022) - [j10]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): 3850-3852 (2022) - [j9]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): 5466-5468 (2022) - [j8]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): 231 (2022) - 2021
- [j7]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): 5703-5705 (2021) - [j6]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): 1332-1334 (2021) - 2019
- [j5]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: baz081 (2019) - [j4]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): 494:1-494:8 (2019) - 2017
- [j3]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): 3679-3681 (2017) - 2016
- [j2]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): 505-516 (2016) - [j1]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)
Conference and Workshop Papers
- 2022
- [c2]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: 103-107 - 2020
- [c1]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: 1-12
Coauthor Index
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