JColorGrid: software for the visualization of biological measurements. - Marcin P. Joachimiak; Jennifer L. Weissman; Barnaby C. H. May (BMC Bioinform., 2006)

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; et al. (Nucleic Acids Res., 2010)

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; et al. (npj Digit. Medicine, 2019)

How to Teach a Computer to Learn About Microbes: KG-COVID-19 and Microbial Graph Learning - Abstract. - Marcin P. Joachimiak (XI-ML@KI, 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; et al. (Nucleic Acids Res., 2020)

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 (ICBO, 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-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; et al. (Patterns, 2021)

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)

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)

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 (IWBBIO (2), 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 Cortes; et al. (CoRR, 2023)

Gene Set Summarization using Large Language Models. - Marcin P. Joachimiak; J. Harry Caufield; Nomi L. Harris; Hyeongsik Kim 001; 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; et al. (CoRR, 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; et al. (CoRR, 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)

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, 2023)

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)

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)

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; et al. (CoRR, 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 001; Sierra A. T. Moxon; Justin T. Reese; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (Bioinform., 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; et al. (J. Biomed. Semant., 2024)