Marcin P. Joachimiak

According to our database, Marcin P. Joachimiak authored at least 24 papers between 2006 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology.

William D. Duncan, Amarpreet Sabharwal, Alexander D. Diehl, Nivedita Dutta, Matthew Diller, Marcin P. Joachimiak, Gopikrishnan Mannamparambil Chandrasekharan

J. Biomed. Semant., December, 2026

2025

Explaining word embeddings with perfect fidelity: a case study in predicting research impact.

Lucie Dvorackova, Marcin P. Joachimiak, Michal Cerny, Adriana Kubecova, Vilém Sklenák, Tomás Kliegr

Mach. Learn., December, 2025

2024

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

Sabrina Toro, Anna V. Anagnostopoulos, Susan M. Bello, Kai Lewis Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig-Barbe, Justin T. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

J. Biomed. Semant., December, 2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall

Bioinform., March, 2024

CurateGPT: A flexible language-model assisted biocuration tool.

J. Harry Caufield, Carlo Kroll, Shawn T. O'Neil, Justin T. Reese, Marcin P. Joachimiak, Harshad Hegde, Nomi L. Harris, Madan Krishnamurthy, James A. McLaughlin, Damian Smedley, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall

CoRR, 2024

Explaining word embeddings with perfect fidelity: Case study in research impact prediction.

Lucie Dvorackova, Marcin P. Joachimiak, Michal Cerny, Adriana Kubecova, Vilém Sklenák, Tomás Kliegr

CoRR, 2024

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies.

Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield, Ryan Ly, Nomi L. Harris, Andrew J. Tritt, Christopher J. Mungall, Kristofer E. Bouchard

Appl. Ontology, 2024

2023

Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.

Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce

J. Biomed. Informatics, April, 2023

GRAPE for fast and scalable graph processing and random-walk-based embedding.

Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Carlos Cano, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin T. Reese, Giorgio Valentini

Nat. Comput. Sci., 2023

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

Sabrina Toro, Anna V. Anagnostopoulos, Sue Bello, Kai Lewis Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig, Justin P. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

CoRR, 2023

An Open-Source Knowledge Graph Ecosystem for the Life Sciences.

Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter

CoRR, 2023

Gene Set Summarization using Large Language Models.

Marcin P. Joachimiak, J. Harry Caufield, Nomi L. Harris, Hyeongsik Kim, Christopher J. Mungall

CoRR, 2023

KG-Hub - building and exchanging biological knowledge graphs.

J. Harry Caufield, Tim E. Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany J. Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina G. Cortes, Kent A. Shefchek, Glass Elsarboukh, James P. Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall, Justin T. Reese

Bioinform., 2023

Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs.

Luca Cappelletti, Stefano Taverni, Tommaso Fontana, Marcin P. Joachimiak, Justin T. Reese, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini

Proceedings of the Bioinformatics and Biomedical Engineering, 2023

2022

Why was this cited? Explainable machine learning applied to COVID-19 research literature.

Lucie Beranová, Marcin P. Joachimiak, Tomás Kliegr, Gollam Rabby, Vilém Sklenák

Scientometrics, 2022

Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions.

Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce

CoRR, 2022

2021

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

Justin T. Reese, Deepak R. Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A. Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall

Patterns, 2021

GraPE: fast and scalable Graph Processing and Embedding.

Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin T. Reese, Giorgio Valentini

CoRR, 2021

KG-Microbe: A Reference Knowledge-Graph and Platform for Harmonized Microbial Information.

Marcin P. Joachimiak, Harshad Hegde, William D. Duncan, Justin T. Reese, Luca Cappelletti, Anne E. Thessen, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

2020

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland

Nucleic Acids Res., 2020

How to Teach a Computer to Learn About Microbes: KG-COVID-19 and Microbial Graph Learning - Abstract.

Marcin P. Joachimiak

Proceedings of the First International Workshop on Explainable and Interpretable Machine Learning (XI-ML 2020) co-located with the 43rd German Conference on Artificial Intelligence (KI 2020), 2020

2019

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.

Xingmin Aaron Zhang, Amy Yates, Nicole A. Vasilevsky, Jean-Philippe F. Gourdine, Tiffany J. Callahan, Leigh C. Carmody, Daniel Danis, Marcin P. Joachimiak, Vida Ravanmehr, Emily R. Pfaff, James Champion, Kimberly Robasky, Hao Xu, Karamarie Fecho, Nephi A. Walton, Richard L. Zhu, Justin Ramsdill, Christopher J. Mungall, Sebastian Köhler, Melissa A. Haendel, Clement J. McDonald, Daniel J. Vreeman, David B. Peden, Tellen D. Bennett, James A. Feinstein, Blake Martin, Adrianne L. Stefanski, Lawrence E. Hunter, Christopher G. Chute, Peter N. Robinson

npj Digit. Medicine, 2019

2010

MicrobesOnline: an integrated portal for comparative and functional genomics.

Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna Dubchak, Eric J. Alm, Adam P. Arkin

Nucleic Acids Res., 2010

2006

JColorGrid: software for the visualization of biological measurements.

Marcin P. Joachimiak, Jennifer L. Weissman, Barnaby C. H. May

BMC Bioinform., 2006