Evaluating the effect of annotation size on measures of semantic similarity. - Maxat Kulmanov; Robert Hoehndorf (J. Biomed. Semant., 2017)

Semantic prioritization of novel causative genomic variants. - Imane Boudellioua; Rozaimi B. Mahamad Razali; Maxat Kulmanov; Yasmeen Hashish; Vladimir B. Bajic; Eva Goncalves-Serra; Nadia Schoenmakers; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (PLoS Comput. Biol., 2017)

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. - Maxat Kulmanov; Senay Kafkas; Andreas Karwath; Alexander Malic; Georgios V. Gkoutos; Michel Dumontier; Robert Hoehndorf (SWAT4LS, 2018)

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. - Maxat Kulmanov; Mohammad Asif Khan 001; Robert Hoehndorf (Bioinform., 2018)

Ontology-based validation and identification of regulatory phenotypes. - Maxat Kulmanov; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (Bioinform., 2018)

EL Embeddings: Geometric Construction of Models for the Description Logic EL++. - Maxat Kulmanov; Wang Liu-Wei; Yuan Yan; Robert Hoehndorf (IJCAI, 2019)

DeepPVP: phenotype-based prioritization of causative variants using deep learning. - Imane Boudellioua; Maxat Kulmanov; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (BMC Bioinform., 2019)

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. - Maxat Kulmanov; Robert Hoehndorf (PLoS Comput. Biol., 2020)

Semantic similarity and machine learning with ontologies. - Maxat Kulmanov; Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Briefings Bioinform., 2021)

DeepGOPlus: improved protein function prediction from sequence. - Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2021)

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. - Maxat Kulmanov; Fernando Zhapa-Camacho; Robert Hoehndorf (Nucleic Acids Res., 2021)

Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase. - Ali Syed; Senay Kafkas; Maxat Kulmanov; Robert Hoehndorf (SWAT4HCLS, 2022)

DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. - Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2022)

Description Logic EL++ Embeddings with Intersectional Closure. - Xi Peng; Zhenwei Tang; Maxat Kulmanov; Kexin Niu; Robert Hoehndorf (CoRR, 2022)

mOWL: Python library for machine learning with biomedical ontologies. - Fernando Zhapa-Camacho; Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2023)

Predicting protein functions using positive-unlabeled ranking with ontology-based priors. - Fernando Zhapa-Camacho; Zhenwei Tang; Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2024)

Protein function prediction as approximate semantic entailment. - Maxat Kulmanov; Francisco J. Guzmán-Vega; Paula Duek Roggli; Lydie Lane; Stefan T. Arold; Robert Hoehndorf (Nat. Mac. Intell., 2024)