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Kai Zhao, Zhuocheng Ji, Linlin Zhang, Na Quan, Yuheng Li, Guanglei Yu, Xuehua Bi

Xuehua Bi, Zhuocheng Ji, Linlin Zhang, Guanglei Yu, Zhipeng Gao, Kai Zhao

Brandon T. Garcia, Lauren Westerfield, Priya Yelemali, Nikhita Gogate, E. Andres Rivera-Munoz, Haowei Du, Moez Dawood, Angad Jolly, James R. Lupski, Jennifer E. Posey

Erva Ulusoy, Tunca Doğan

Jorge Novoa, Javier López-Ibáñez, Mónica Chagoyen, Juan A G Ranea, Florencio Pazos

Heval Atas Guvenilir, Tunca Doğan

Fatma Cankara, Tunca Doğan

Atakan Yüksel, Erva Ulusoy, Atabey Ünlü, Tunca Doğan

Fulya Ciray, Tunca Doğan

Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu

Katy Börner, Andreas Bueckle, Bruce W. Herr, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, N. Heath Patterson, Griffin M. Weber

Florencio Pazos, Mónica Chagoyen, Pedro Seoane, Juan A.G. Ranea

Isabella Herman, Angad Jolly, Haowei Du, Moez Dawood, Ghada M. H. Abdel‐Salam, Dana Marafi, Tadahiro Mitani, Daniel G. Calame, Zeynep Coban‐Akdemir, Jawid M. Fatih, Ibrahim Hegazy, Shalini N. Jhangiani, Richard A. Gibbs, Davut Pehlivan, Jennifer E. Posey, James R. Lupski

Rushabh Patel, Yanhui Guo, Adi Alhudhaif, Fayadh Alenezi, Sara A Althubiti, Kemal Polat

Sarah Okashah, Dhanya Vasudeva, Aya El Jerbi, Houssein Khodjet-El-khil, Mashael Al-Shafai, Najeeb Syed, Marios Kambouris, Sharda Udassi, Luis R. Saraiva, Hesham Al-Saloos, Jai Udassi, Kholoud N. Al-Shafai

Tunca Doğan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Martin, Rengul Cetin-Atalay

Morteza Pourreza Shahri, Indika Kahanda

F. M. Jabato, Pedro Seoane, James R. Perkins, Elena Rojano, Adrián García Moreno, M. Chagoyen, Florencio Pazos, Juan A. G. Ranea

Lizhi Liu, Shanfeng Zhu

Maxat Kulmanov, Robert Hoehndorf

Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu

Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu

Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry, David Osumi-Sutherland, Valentina Cipriani, James P Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh Dawkins, Michael Segal, Anna C Jansen, Ahmed Muaz, Willie H Chang, Jenna Bergerson, Stanley J F Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F Freeman, Panagiotis I Sergouniotis, Daniel Durkin, Andrea L Storm, Marc Hanauer, Michael Brudno, Susan M Bello, Murat Sincan, Kayli Rageth, Matthew T Wheeler, Renske Oegema, Halima Lourghi, Maria G Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin A Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia Smith, Joshua D Milner, Dorothée Leroux, Cornelius F Boerkoel, Amy Klion, Melody C Carter, Tudor Groza, Damian Smedley, Melissa A Haendel, Chris Mungall, Peter N Robinson

Pietro Cinaglia, Pietro H Guzzi, Pierangelo Veltri

2025	HPOseq: a deep ensemble model for predicting the protein-phenotype relationships based on protein sequences BMC Bioinformatics Kai Zhao, Zhuocheng Ji, Linlin Zhang, Na Quan, Yuheng Li, Guanglei Yu, Xuehua Bi
2025	MFF-HPO: Protein–Phenotype Associations Prediction Based on Sequence Using Multi-Feature Fusion Journal of Computational Biology Xuehua Bi, Zhuocheng Ji, Linlin Zhang, Guanglei Yu, Zhipeng Gao, Kai Zhao
2025	Improving automated deep phenotyping through large language models using retrieval-augmented generation Genome Medicine Brandon T. Garcia, Lauren Westerfield, Priya Yelemali, Nikhita Gogate, E. Andres Rivera-Munoz, Haowei Du, Moez Dawood, Angad Jolly, James R. Lupski, Jennifer E. Posey
2024	Mutual annotation‐based prediction of protein domain functions with Domain2GO Protein Science Erva Ulusoy, Tunca Doğan
2024	CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature Database Jorge Novoa, Javier López-Ibáñez, Mónica Chagoyen, Juan A G Ranea, Florencio Pazos
2023	How to approach machine learning-based prediction of drug/compound–target interactions Journal of Cheminformatics Heval Atas Guvenilir, Tunca Doğan
2023	ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations Computational and Structural Biotechnology Journal Fatma Cankara, Tunca Doğan
2023	SELFormer: molecular representation learning via SELFIES language models Machine Learning: Science and Technology Atakan Yüksel, Erva Ulusoy, Atabey Ünlü, Tunca Doğan
2022	Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features Expert Opinion on Drug Discovery Fulya Ciray, Tunca Doğan
2022	HPODNets: deep graph convolutional networks for predicting human protein–phenotype associations Bioinformatics Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2022	Tissue registration and exploration user interfaces in support of a human reference atlas Communications Biology Katy Börner, Andreas Bueckle, Bruce W. Herr, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, N. Heath Patterson, Griffin M. Weber
2022	CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature Journal of Molecular Biology Florencio Pazos, Mónica Chagoyen, Pedro Seoane, Juan A.G. Ranea
2022	Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses American Journal of Medical Genetics Part A Isabella Herman, Angad Jolly, Haowei Du, Moez Dawood, Ghada M. H. Abdel‐Salam, Dana Marafi, Tadahiro Mitani, Daniel G. Calame, Zeynep Coban‐Akdemir, Jawid M. Fatih, Ibrahim Hegazy, Shalini N. Jhangiani, Richard A. Gibbs, Davut Pehlivan, Jennifer E. Posey, James R. Lupski
2022	Graph-Based Link Prediction between Human Phenotypes and Genes Mathematical Problems in Engineering Rushabh Patel, Yanhui Guo, Adi Alhudhaif, Fayadh Alenezi, Sara A Althubiti, Kemal Polat
2022	Investigation of Genetic Causes in Patients with Congenital Heart Disease in Qatar: Findings from the Sidra Cardiac Registry Genes Sarah Okashah, Dhanya Vasudeva, Aya El Jerbi, Houssein Khodjet-El-khil, Mashael Al-Shafai, Najeeb Syed, Marios Kambouris, Sharda Udassi, Luis R. Saraiva, Hesham Al-Saloos, Jai Udassi, Kholoud N. Al-Shafai
2021	Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases PLOS Computational Biology Tunca Doğan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Martin, Rengul Cetin-Atalay
2021	Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes BMC Bioinformatics Morteza Pourreza Shahri, Indika Kahanda
2021	Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations Human Genetics F. M. Jabato, Pedro Seoane, James R. Perkins, Elena Rojano, Adrián García Moreno, M. Chagoyen, Florencio Pazos, Juan A. G. Ranea
2021	Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review Phenomics Lizhi Liu, Shanfeng Zhu
2020	DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology Maxat Kulmanov, Robert Hoehndorf
2020	Data mining powered by the gene ontology WIREs Data Mining and Knowledge Discovery Prashanti Manda
2020	HPOLabeler: improving prediction of human protein–phenotype associations by learning to rank Bioinformatics Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2019	HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology Journal of Biomedical Informatics Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu
2019	Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources Nucleic Acids Research Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry, David Osumi-Sutherland, Valentina Cipriani, James P Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh Dawkins, Michael Segal, Anna C Jansen, Ahmed Muaz, Willie H Chang, Jenna Bergerson, Stanley J F Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F Freeman, Panagiotis I Sergouniotis, Daniel Durkin, Andrea L Storm, Marc Hanauer, Michael Brudno, Susan M Bello, Murat Sincan, Kayli Rageth, Matthew T Wheeler, Renske Oegema, Halima Lourghi, Maria G Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin A Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia Smith, Joshua D Milner, Dorothée Leroux, Cornelius F Boerkoel, Amy Klion, Melody C Carter, Tudor Groza, Damian Smedley, Melissa A Haendel, Chris Mungall, Peter N Robinson
2018	2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pietro Cinaglia, Pietro H Guzzi, Pierangelo Veltri
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