Attila Kertesz-Farkas

Publications³⁷

• Article Kertesz-Farkas A., Acquaye F. L., Stafford Noble W. Efficient indexing of peptides for database search using Tide // Journal of Proteome Research. 2023 (in press)
• Chapter Kertesz-Farkas A., Acquaye F. L., Latypov I. Hypernym Information and Sentiment Bias Probing in Distributed Data Representation, in: ICMLC 2023: 2023 15th International Conference on Machine Learning and Computing (ICMLC). NY : Association for Computing Machinery (ACM), 2023. (in press)
• Article Kertesz-Farkas A., Acquaye F. L., Kishankumar Bhimani, English J. K., Fondrie W. E., Grant C., Hoopmann M. R., Lin A., Lu Y. Y., Moritz R. L., MacCoss M. J., Noble W. S. The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data // Journal of Proteome Research. 2023. Vol. 22. No. 2. P. 561-569. doi
• Article Kudriavtseva P., Kashkinov M., Kertész-Farkas A. Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches // Journal of Proteome Research. 2021. Vol. 20. No. 10. P. 4708-4717. doi
• Article Sulimov P., Voronkova A. V., Kertész-Farkas A. Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics // Bioinformatics. 2020. Vol. 36. No. 12. P. 3781-3787. doi
• Article Sulimov P., Kertesz-Farkas A. Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics // Journal of Proteome Research. 2020. No. 19(4). P. 1481-1490. doi
• Article Moshkov N., Mathe B., Kertesz-Farkas A., Hollandi R., Horvath P. Test-time augmentation for deep learning-based cell segmentation on microscopy images // Scientific Reports. 2020. Vol. 10. Article 5068. doi
• Article Danilova Yulia, Voronkova Anastasia, Sulimov Pavel, Kertész-Farkas Attila. Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide Identification // Journal of Proteome Research. 2019. Vol. 18. No. 5. P. 2354-2358. doi
• Article Chereshnev R., Kertesz-Farkas A. GaIn: Human Gait Inference for Lower Limbic Prostheses for Patients Suffering From Double Trans-Femoral Amputation // Sensors. 2018. Vol. 18. No. 12. P. 1-20. doi
• Chapter Kertesz-Farkas A., Chereshnev Roman. HuGaDB: Human Gait Database for Activity Recognition from Wearable Inertial Sensor Networks, in: Analysis of Images, Social Networks and Texts. 6th International Conference, 2017, Revised Selected Papers / Ed. by W. M. van der Aalst, D. I. Ignatov, M. Khachay, S. Kuznetsov, V. Lempitsky, I. A. Lomazova, A. Napoli, A. Panchenko, P. M. Pardalos, A. V. Savchenko, S. Wasserman. Vol. 10716. Cham : Springer, 2018. doi P. 131-141.
• Article Kertesz-Farkas A., Bauwens B. F., Filatov G. LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification // Bioinformatics. 2018. Vol. 34. No. 19. P. 3281-3288. doi
• Chapter Shestakoff A., Kertesz-Farkas A., Shmelkin D., Doroshin D. Lookup Lateration: Mapping of Received Signal Strength to Position for Geo-Localization in Outdoor Urban Areas, in: Proceedings of Analysis of Images, Social Networks and Texts – 7th International Conference, AIST 2018, Moscow, Russia, July 5-7, 2018, Revised Selected Papers. Lecture Notes in Computer Science / Ed. by W. M. van der Aalst, V. Batagelj, G. Glavaš,, D. I. Ignatov, M. Khachay, O. Koltsova, S. Kuznetsov, I. A. Lomazova, N. Loukachevitch,, A. Napoli,, A. Savchenko, A. Panchenko,, P. M. Pardalos, M. Pelillo,. Vol. 11179. Berlin : Springer, 2018. doi P. 234-246. doi (in press)
• Article Kertesz-Farkas A., Nikitin D. New bifunctional restriction-modification enzyme AloI isoschizomer (PcoI): Bioinformatics analysis, purification and activity confirmation // Gene. 2018. Vol. 660. P. 8-12. doi
• Article Kertesz-Farkas A., Chereshnev R. RapidHARe: A computationally inexpensive method for real-time human activity recognition from wearable sensors // Journal of Ambient Intelligence and Smart Environments. 2018. Vol. 10. No. 5. P. 377-391. doi
• Article Kertesz-Farkas A., Keich U., Noble W. Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics // Journal of Proteome Research. 2015. Vol. 14. No. 8. P. 3148-3161.
• Article Kertesz-Farkas A., Ali H., Lisek K. Nuclear architecture dictates HIV-1 integration site selection // Nature. 2015. No. 521. P. 227-231.
• Article Kertesz-Farkas A., Noble W. Tandem mass spectrum identification via Cascaded search // Journal or Proteome Research. 2015. Vol. 14. No. 8. P. 3027-3038.
• Article Kertesz-Farkas A., Grant C. E., Howbert J. J., Hoopmann M. R., Eng J. K. Crux: rapid open source protein tandem mass spectrometry analysis // Journal of Proteome Research. 2014. Vol. 13. No. 10. P. 4488-4491.
• Article Kertesz-Farkas A., Juhász J., Szabó D., Pongor S. Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes. // Plos One. 2014. Vol. 9. No. 4
• Article Kertesz-Farkas A., Myers M. P. PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. // Bioinformatics. 2014. Vol. 30. No. 2. P. 234-241.
• Article Kertesz-Farkas A., Myers M. P. Precursor mass dependent filtering of mass spectra for proteomics analysis // Protein and peptide letters. 2014. Vol. 21. No. 8. P. 858-863.
• Article Kertesz-Farkas A., Myers M. P. Chemical rule-based filtering of MS/MS spectra. // Bioinformatics. 2013. Vol. 29. No. 7. P. 925-932.
• Article Vera R., Pérez-Riverol, Y., Pérez S., Ligeti B., Kertesz-Farkas A., Pongor S. JBioWH: an open-source Java framework for bioinformatics data integration // Database: the journal of biological databases and curation. 2013 doi
• Chapter Nikitin D. V., Kertesz-Farkas A., Solonin A. S., Mokrishcheva M. L. Bifunctional Prokaryotic DNA-Methyltransferases, in: Methylation - From DNA, RNA and Histones to Diseases and Treatment. InTech, 2012. doi doi
• Article Kertesz-Farkas A., Myers M. P. Data preprocessing and filtering in mass spectrometry based proteomics // Current Bioinformatics. 2012. Vol. 7. No. 2. P. 212-220.
• Article Kertesz-Farkas A., Myers M. P. Database searching in mass spectrometry based proteomics // Current Bioinformatics. 2012. Vol. 7. No. 2. P. 221-230.
• Article Kertesz-Farkas A., Bihary D., Kerenyi A., Gelencser Z., Netotea S., Venturi V., Pongor S. Simulation of communication and cooperation in multispecies bacterial communities with an agent based model // Scalable Computing: Practice and Experience. 2012. Vol. 13. No. 1
• Chapter Kertesz-Farkas A., Myers M. P. PTMSearch: A Greedy Tree Traversal Algorithm for Finding Protein Post-Translational Modifications in Tandem Mass Spectra, in: European Conference on Machine Learning and Principles and Practical Knowledge Discovery in Databases 2 Vol. 6912 . , 2011. P. 162-176. doi
• Article Kertesz-Farkas A., Adadey A., Peterson T. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature // Bioinformatics. 2011. Vol. 27. No. 3. P. 408-415.
• Article Kertesz-Farkas A., Pongor S. Detecting atypical examples of known domain types by sequence similarity searching: The SBASE domain library approach // Current Protein and Peptide Science. 2010 doi
• Article Kertesz-Farkas A., Dombi J. Applying Fuzzy Technologies to Equivalence Learning in Protein Classification // Journal of Computational Biology. 2009 doi
• Article Kertesz-Farkas A., Pongor S. Balanced ROC analysis (BAROC) protocol for the evaluation of protein similarities // Journal of Biochemical and Biophysical Methods. 2008 doi
• Article Kertesz-Farkas A., Pongor S. Benchmarking protein classification algorithms via supervised cross-validation // Journal of Biochemical and Biophysical Methods. 2008 doi
• Article Kertesz-Farkas A., Pongor S. A Protein Classification Benchmark collection for Machine Learning // Nucleic Acids Research. 2006 doi
• Article Kertesz-Farkas A., Kajan L., Pongor S. Application of a simple log likelihood ratio approximant to protein sequence classification // Bioinformatics. 2006 doi
• Article Kertesz-Farkas A., Pongor S. Application of compression-based distance measures to protein sequence-classification: a methodological study // Bioinformatics. 2006 doi
• Article Kertesz-Farkas A., Kelemen J., Kocsor A., Puskas L. Kalman Filtering for Disease-State Estimation from Microarray Data // Bioinformatics. 2006 doi