Publications & Works

Publication Network
Published journal articles indexed by SCI, SSCI, and AHCI

Design, synthesis, and evaluation of novel Indole-Based small molecules as sirtuin inhibitors with anticancer activities

BINARCI B., Kilic E. K., DOĞAN T., ATALAY R., KAHRAMAN D. C., BAYTAŞ S.
DRUG DEVELOPMENT RESEARCH , vol.85, no.7, 2024 (SCI-Expanded) identifier identifier identifier

Mutual annotation-based prediction of protein domain functions with Domain2GO

Ulusoy E., DOĞAN T.
PROTEIN SCIENCE , vol.33, no.6, 2024 (SCI-Expanded) Sustainable Development identifier identifier identifier

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data

Shojaei M., Mohammadvand N., DOĞAN T., Alkan C., Çetin Atalay R., ACAR A.
Computers in Biology and Medicine , vol.169, 2024 (SCI-Expanded) identifier identifier

How to approach machine learning-based prediction of drug/compound–target interactions

Atas Guvenilir H., DOĞAN T.
Journal of Cheminformatics , vol.15, no.1, 2023 (SCI-Expanded) Creative Commons License identifier identifier identifier

Democratizing knowledge representation with BioCypher

Lobentanzer S., Aloy P., Baumbach J., Bohar B., Carey V. J., Charoentong P., et al.
Nature Biotechnology , vol.41, no.8, pp.1056-1059, 2023 (SCI-Expanded) identifier identifier

SELFormer: molecular representation learning via SELFIES language models

Yüksel A., Ulusoy E., Ünlü A., DOĞAN T.
Machine Learning: Science and Technology , vol.4, no.2, 2023 (SCI-Expanded) Creative Commons License identifier

ProFAB-open protein functional annotation benchmark

Özdilek A. S., ATAKAN A., ÖZSARI G., Acar A., ATALAY M. V., DOĞAN T., et al.
Briefings in bioinformatics , vol.24, no.2, 2023 (SCI-Expanded) identifier identifier identifier

UniProt: the Universal Protein Knowledgebase in 2023

Bateman A., Martin M., Orchard S., Magrane M., Ahmad S., Alpi E., et al.
Nucleic Acids Research , vol.51, no.D1, 2023 (SCI-Expanded) identifier identifier

ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations

Cankara F., DOĞAN T.
Computational and Structural Biotechnology Journal , vol.21, pp.4743-4758, 2023 (SCI-Expanded) identifier identifier

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins

ÖZSARI G., RİFAİOĞLU A. S., ATAKAN A., Tunca Dogan T., Martin M. J., ATALAY R., et al.
BIOINFORMATICS , vol.38, no.17, pp.4226-4229, 2022 (SCI-Expanded) identifier identifier identifier

Learning functional properties of proteins with language models

Unsal S., Atas H., Albayrak M., Turhan K., Acar A. C., Doğan T.
NATURE MACHINE INTELLIGENCE , vol.4, no.3, pp.227-245, 2022 (SCI-Expanded) identifier identifier

Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features

Ciray F., DOĞAN T.
Expert Opinion on Drug Discovery , vol.17, no.12, pp.1425-1441, 2022 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

Editorial: Machine Learning Methodologies to Study Molecular Interactions

Yakimovich A., oezguer A., DOĞAN T., Ozkirimli E.
FRONTIERS IN MOLECULAR BIOSCIENCES , vol.8, 2021 (SCI-Expanded) Creative Commons License identifier identifier identifier

A crowdsourcing open platform for literature curation in UniProt

Wang Y., Wang Q., Huang H., Huang W., Chen Y., McGarvey P. B., et al.
PLOS BIOLOGY , vol.19, no.12, 2021 (SCI-Expanded) Creative Commons License identifier identifier identifier

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases

Doğan T., Guzelcan E. A., Baumann M., Koyas A., Atas H., Baxendale I., et al.
PLOS COMPUTATIONAL BIOLOGY , vol.17, no.11, 2021 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Doğan T., Atas H., Joshi V., Atakan A., Rifaioğlu A. S., Nalbat E., et al.
NUCLEIC ACIDS RESEARCH , vol.49, no.16, 2021 (SCI-Expanded) identifier identifier identifier

Crowdsourced mapping of unexplored target space of kinase inhibitors

Cichonska A., Ravikumar B., Allaway R. J., Wan F., Park S., Isayev O., et al.
NATURE COMMUNICATIONS , vol.12, no.1, 2021 (SCI-Expanded) Creative Commons License identifier identifier identifier

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery

Rifaioglu A. S., Atalay R. C., KAHRAMAN D. C., DOĞAN T., Martin M., Atalay V.
BIOINFORMATICS , vol.37, no.5, pp.693-704, 2021 (SCI-Expanded) identifier identifier identifier

UniProt: the universal protein knowledgebase in 2021

Bateman A., Martin M., Orchard S., Magrane M., Agivetova R., Ahmad S., et al.
NUCLEIC ACIDS RESEARCH , vol.49, no.D1, 2021 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

iBioProVis: interactive visualization and analysis of compound bioactivity space

DÖNMEZ A., RİFAİOĞLU A. S., ACAR A. C., DOĞAN T., ATALAY R., ATALAY M. V.
BIOINFORMATICS , vol.36, no.14, pp.4227-4230, 2020 (SCI-Expanded) Sustainable Development identifier identifier identifier

DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

Rifaioğlu A. S., Nalbat E., Atalay V., Martin M. J., Cetin-Atalay R., Doğan T.
CHEMICAL SCIENCE , vol.11, no.9, pp.2531-2557, 2020 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou N., Jiang Y., Bergquist T. R., Lee A. J., Kacsoh B. Z., Crocker A. W., et al.
GENOME BIOLOGY , vol.20, no.1, 2019 (SCI-Expanded) identifier identifier identifier

FAIR adoption, assessment and challenges at UniProt

Garcia L., Bolleman J., Gehant S., Redaschi N., Martin M., Bateman A., et al.
SCIENTIFIC DATA , vol.6, 2019 (SCI-Expanded) Creative Commons License identifier identifier identifier

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Rifaioğlu A. S., Atas H., Martin M. J., Cetin-Atalay R., Atalay V., Dogan T.
BRIEFINGS IN BIOINFORMATICS , vol.20, no.5, pp.1878-1912, 2019 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

Rifaioğlu A. S., Doğan T., Martin M. J., Cetin-Atalay R., Atalay V.
SCIENTIFIC REPORTS , vol.9, 2019 (SCI-Expanded) Creative Commons License identifier identifier identifier

UniProt: a worldwide hub of protein knowledge

Bateman A., Martin M., Orchard S., Magrane M., Alpi E., Bely B., et al.
NUCLEIC ACIDS RESEARCH , vol.47, 2019 (SCI-Expanded) identifier identifier identifier

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

Dalkiran A., Rifaioğlu A. S., Martin M. J., Cetin-Atalay R., Atalay V., Dogan T.
BMC BIOINFORMATICS , vol.19, 2018 (SCI-Expanded) identifier identifier identifier

HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences

Doğan T.
PEERJ , vol.6, 2018 (SCI-Expanded) Sustainable Development identifier identifier identifier

Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants

Rifaioğlu A. S., Dogan T., Sarac O. S., Ersahin T., Saidi R., Atalay M. V., et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , vol.86, no.2, pp.135-151, 2018 (SCI-Expanded) identifier identifier identifier

A Structural Perspective on the Modulation of Protein-protein Interactions with Small Molecules

Demirel H. C., Dogan T., TUNÇBAĞ N.
CURRENT TOPICS IN MEDICINAL CHEMISTRY , vol.18, no.8, pp.700-713, 2018 (SCI-Expanded) Sustainable Development identifier identifier identifier

Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

Atas H., Tunçbağ N., Doğan T.
COMPUTATIONAL DRUG DISCOVERY AND DESIGN , vol.1762, pp.51-69, 2018 (SCI-Expanded) identifier identifier

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Poux S., Arighi C. N., Magrane M., Bateman A., Wei C., Lu Z., et al.
BIOINFORMATICS , vol.33, no.21, pp.3454-3460, 2017 (SCI-Expanded) Creative Commons License identifier identifier identifier

From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB

Zaru R., Magrane M., O'Donovan C., Bateman A., Martin M. J., Alpi E., et al.
BIOCHEMICAL JOURNAL , vol.474, pp.493-515, 2017 (SCI-Expanded) Creative Commons License identifier identifier identifier

UniProt: the universal protein knowledgebase

Bateman A., Martin M. J., O'Donovan C., Magrane M., Alpi E., Antunes R., et al.
NUCLEIC ACIDS RESEARCH , vol.45, 2017 (SCI-Expanded) Creative Commons License identifier identifier identifier

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang Y., Oron T. R., Clark W. T., Bankapur A. R., D'Andrea D., Lepore R., et al.
GENOME BIOLOGY , vol.17, 2016 (SCI-Expanded) identifier identifier identifier

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Doğan T., Macdougall A., Saidi R., Poggioli D., Bateman A., O'donovan C., et al.
BIOINFORMATICS , vol.32, no.15, pp.2264-2271, 2016 (SCI-Expanded) Creative Commons License identifier identifier identifier

The UniProtKB guide to the human proteome

Breuza L., Poux S., Estreicher A., Famiglietti M. L., Magrane M., Tognolli M., et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION , 2016 (SCI-Expanded) Creative Commons License identifier identifier identifier

Tools and data services registry: a community effort to document bioinformatics resources

Ison J., Rapacki K., Menager H., Kalas M., Rydza E., Chmura P., et al.
NUCLEIC ACIDS RESEARCH , vol.44, 2016 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

UniProt: a hub for protein information

Bateman A., Martin M. J., O'Donovan C., Magrane M., Apweiler R., Alpi E., et al.
NUCLEIC ACIDS RESEARCH , vol.43, 2015 (SCI-Expanded) Creative Commons License identifier identifier identifier

Activities at the Universal Protein Resource (UniProt)

Apweiler R., Bateman A., Martin M. J., O'Donovan C., Magrane M., Alam-Faruque Y., et al.
NUCLEIC ACIDS RESEARCH , vol.42, 2014 (SCI-Expanded) Creative Commons License identifier identifier identifier

Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences

Doğan T., Karacali B.
PLOS ONE , vol.8, no.9, 2013 (SCI-Expanded) Creative Commons License identifier identifier identifier
Articles Published in Other Journals

Transfer learning for drug-target interaction prediction

DALKIRAN A., ATAKAN A., Rifaioğlu A. S., Martin M. J., Atalay R. Ç., ACAR A., et al.
Bioinformatics (Oxford, England) , vol.39, no.39, 2023 (Scopus) Creative Commons License identifier identifier

Data Centric Molecular Analysis and Evaluation of Hepatocellular Carcinoma Therapeutics Using Machine Intelligence-Based Tools

Cetin-Atalay R., Kahraman D. C., Nalbat E., Rifaioğlu A. S., Atakan A., Dönmez A., et al.
JOURNAL OF GASTROINTESTINAL CANCER , vol.52, no.4, pp.1266-1276, 2021 (Peer-Reviewed Journal) identifier identifier identifier
Refereed Congress / Symposium Publications in Proceedings

In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC

NALBAT E., Rifaioglu A. S., DOĞAN T., Martin M. J., Cetin-Atalay R., ATALAY M. V.
AACR Annual Meeting, ELECTR NETWORK, 22 - 24 June 2020, vol.80 identifier

Unsupervised identification of redundant domain entries in InterPro database using clustering techniques

RİFAİOĞLU A. S., Doǧan T., CAN T.
6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2015, Georgia, United States Of America, 9 - 12 September 2015, pp.505-506 identifier

2-D thresholding of the connectivity map following the multiple sequence alignments of diverse datasets

Doǧan T., Karaçali B.
10th IASTED International Conference on Biomedical Engineering, BioMed 2013, Innsbruck, Austria, 13 - 15 February 2013, pp.1-8 Creative Commons License identifier

Evolutionary relationships between gene sequences via nonlinear embedding Doǧrusal olmayan gömme teknikleri altinda gen dizilerinin evrimsel i̇lişkileri

Doǧan T., Karaçcali B.
2010 15th National Biomedical Engineering Meeting, BIYOMUT2010, Antalya, Turkey, 21 - 24 April 2010 identifier
Metrics

Publication

48

Citation (WoS)

17299

H-Index (WoS)

21

Citation (Scopus)

22060

H-Index (Scopus)

21

Citation (Scholar)

30963

H-Index (Scholar)

25

Project

10

Open Access

23
UN Sustainable Development Goals