ideaconsult.net

2025 

• Filipovska, J. et al. P18-65 Advancing the Grouping and Harmonization of Similar Key Events in the AOP Wiki: Ontology-Based Key Event Component Combinations as Catalysts for Integration. Toxicol. Lett. 411, S214–S215 (2025).
• Coca-Lopez, N. et al. Open and FAIR Raman spectroscopy. Paving the way for artificial intelligence. Preprint (2025) DOI: 10.26434/chemrxiv-2025-0q2mt.
• Lellinger, D. et al. An Interlaboratory Study to Minimize Wavelength Calibration Uncertainty Due to Peak Fitting of Reference Material Spectra in Raman Spectroscopy. Appl. Spectrosc. (2025) DOI: 10.1177/00037028251330654.
• Georgiev, G. et al. Open Source for Raman Spectroscopy Data Harmonization. J. Raman Spectrosc. (2025) DOI: 10.1002/jrs.6789.
• Tancheva, G. et al. High-throughput screening data generation, scoring and FAIRification: a case study on nanomaterials. J. Cheminform. 17, 59 (2025).

2024 

• Di Battista, V. et al. Similarity of multicomponent nanomaterials in a safer-by-design context: the case of core–shell quantum dots. Environ. Sci. Nano 11, 924–941 (2024).
• Groenewold, M. et al. Governance of advanced materials: Shaping a safe and sustainable future. NanoImpact 35, 100513 (2024).
• Jeliazkova, N. et al. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nat. Protoc. (2024) DOI: 10.1038/s41596-024-00993-1.

2023 

• Martens, M. et al. ELIXIR and Toxicology: a community in development. F1000Research 10, 1129 (2023).
• Mancardi, G. et al. A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability. Mater. Today 67, 344–370 (2023).
• Furuhama, A. et al. Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project. SAR QSAR Environ. Res. 34, 983–1001 (2023).
• Jeliazkova, N., Kochev, N. & Tancheva, G. FAIR data model for chemical substances. Development challenges, management strategies and applications. in Data Integrity and Data Governance (2023) DOI: 10.5772/intechopen.110248.

2022 

• Jeliazkova, N., Ma-Hock, L., Janer, G., Stratmann, H. & Wohlleben, W. Possibilities to group nanomaterials across different substances – A case study on organic pigments. NanoImpact 26, 100391 (2022).
• Wyrzykowska, E. et al. Representing and describing nanomaterials in predictive nanoinformatics. Nat. Nanotechnol. 17, 924–932 (2022).
• van Rijn, J. et al. European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials. J. Cheminform. 14, 57 (2022).
• Basei, G., Rauscher, H., Jeliazkova, N. & Hristozov, D. A methodology for the automatic evaluation of data quality and completeness of nanomaterials for risk assessment purposes. Nanotoxicology 1–22 (2022) DOI: 10.1080/17435390.2022.2065222.

2021 

• Kochev, N., Jeliazkova, N. & Tancheva, G. Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation. Mol. Inform. 40, 2100027 (2021).
• Jeliazkova, N. et al. How can we justify grouping of nanoforms for hazard assessment? Concepts and tools to quantify similarity. NanoImpact 100366 (2021) DOI: 10.1016/j.impact.2021.100366.
• Jeliazkova, N. et al. Towards FAIR nanosafety data. Nat. Nanotechnol. 16, 644–654 (2021).

2020 

• Kochev, N. et al. Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database. Nanomaterials 10, 1908 (2020).
• Sturm, N. et al. Industry-scale application and evaluation of deep learning for drug target prediction. J. Cheminform. 12, 26 (2020).
• Stone, V. et al. A framework for grouping and read-across of nanomaterials- supporting innovation and risk assessment. Nano Today 35, 100941 (2020).
• Terziyski, A., Tenev, S., Jeliazkov, V., Jeliazkova, N. & Kochev, N. METER.AC: Live Open Access Atmospheric Monitoring Data for Bulgaria with High Spatiotemporal Resolution. Data 5, 36 (2020).
• Mansouri, K. et al. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Environ. Health Perspect. 128, 027002 (2020).

2019 

• Kochev, N. T., Paskaleva, V. H. & Jeliazkova, N. Automatic generation of molecular zwitterionic forms with Ambit-Zwitterion. Bulg. Chem. Commun. 51, (2019).
• Terziyski, A. et al. Balloon-borne measurements in the upper troposphere and lower stratosphere above Bulgaria (N41-43° E24-26°). Bulg. Chem. Commun. 51, (2019).
• Willighagen, E., Jeliazkova, N. & Guha, R. Journal of Cheminformatics, ORCID, and GitHub. J. Cheminform. 11, (2019).
• de Bruyn Kops, C. et al. GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism. Front. Chem. 7, (2019).
• Kochev, N., Paskaleva, V., Pukalov, O. & Jeliazkova, N. Ambit-GCM: An Open-source Software Tool for Group Contribution Modelling. Mol. Inform. (2019) DOI: 10.1002/minf.201800138.
• Basei, G. et al. Making use of available and emerging data to predict the hazards of engineered nanomaterials by means of in silico tools: A critical review. NanoImpact 13, 76–99 (2019).
• Jeliazkova, N. & Jeliazkov, V. CHAPTER 5. Making Big Data Available: Integrating Technologies for Toxicology Applications. in Big Data in Predictive Toxicology (Issues in Toxicology) (eds. Neagu, D. & Richarz, A.-N.) 166–184 (Royal Society of Chemistry, 2019) DOI: 10.1039/9781782623656-00166.
• Kochev, N., Jeliazkova, N. & Tsakovska, I. CHAPTER 3. Chemoinformatics Representation of Chemical Structures – A Milestone for Successful Big Data Modelling in Predictive Toxicology. in Big Data in Predictive Toxicology (eds. Neagu, D. & Richarz, A.-N.) 69–107 (RSC Publishing, 2019) DOI: 10.1039/9781782623656-00069.

2018 

• Karcher, S. et al. Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. NanoImpact 9, 85–101 (2018).
• Honma, M. et al. Improvement of quantitative structure–activity relationship (QSAR) tools for predicting Ames mutagenicity: outcomes of the Ames/QSAR International Challenge Project. Mutagenesis (2018) DOI: 10.1093/mutage/gey031.
• Mech, A. et al. Insights into possibilities for grouping and read-across for nanomaterials in EU chemicals legislation. Nanotoxicology 1–23 (2018) DOI: 10.1080/17435390.2018.1513092.
• Kochev, N., Avramova, S. & Jeliazkova, N. Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation. J. Cheminform. 10, 42 (2018).
• Kochev N, Avramova S, Jeliazkova N: Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation. J Cheminform 2018, 10:42. 

 

2017

• Karcher, S.; Willighagen, E. L.; Rumble, J.; Ehrhart, F.; Evelo, C. T.; Fritts, M.; Gaheen, S.; Harper, S. L.; Hoover, M. D.; Jeliazkova, N.; et al. Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. NanoImpact 2017 DOI:10.1016/j.impact.2017.11.002.
• Nymark, P.; Rieswijk, L.; Ehrhart, F.; Jeliazkova, N.; Tsiliki, G.; Sarimveis, H.; Evelo, C. T.; Hongisto, V.; Kohonen, P.; Willighagen, E.; et al. A data fusion pipeline for generating and enriching Adverse Outcome Pathway descriptions. Toxicol. Sci. 2017 DOI: 10.1093/toxsci/kfx252.
• Puzyn, T.; Jeliazkova, N.; Sarimveis, H.; Marchese Robinson, R. L.; Lobaskin, V.; Rallo, R.; Richarz, A.-N.; Gajewicz, A.; Papadopulos, M. G.; Hastings, J.; et al. Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology. Food Chem. Toxicol. 2017 , DOI:10.1016/j.fct.2017.09.037.
• Willighagen, E. L.; Mayfield, J. W.; Alvarsson, J.; Berg, A.; Carlsson, L.; Jeliazkova, N.; Kuhn, S.; Pluskal, T.; Rojas-Cherto, M.; Spjuth, O.; et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminform. 2017, 9, 33 DOI: 10.1186/s13321-017-0220-4.
• J. Sun, N. Jeliazkova, V. Chupakin, J.-F. Golib-Dzib, O. Engkvist, L. Carlsson, J. Wegner, H. Ceulemans, I. Georgiev, V. Jeliazkov, N. Kochev, T. J. Ashby, and H. Chen, ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics, J. Cheminform., vol. 9, no. 1, p. 17, Mar. 2017. 10.1186/s13321-017-0203-5
• N. Jeliazkova and V. Jeliazkov, Making Big Data Available: Integrating Technologies for Toxicology Applications, in Big Data in Predictive Toxicology, D. Neagu and A. Richarz, Eds. RSC Publishing, 1 edition 2017 .
• N. Kochev, I. Tsakovska, and N. Jeliazkova, Cheminformatics representation of chemical structures - a milestone for successful big data modelling, in Big Data in Predictive Toxicology, D. Neagu and A. Richarz, Eds. RSC Publishing, 1 edition 2017.

 

2016

• O. Spjuth, P. Rydberg, E. L. Willighagen, C. T. Evelo, and N. Jeliazkova, XMetDB: an open access database for xenobiotic metabolism, J. Cheminform., vol. 8, no. 1, p. 47, Dec. 2016.
• N. Jeliazkova, V. Koch, Q. Li, U. Jensch, J. S. Reigl, R. Kreiling, I. Georgiev, and B. Hubesch, Linking LRI AMBIT chemoinformatic system with the IUCLID substance database to support read-across of substance endpoint data and category formation, Toxicol. Lett., vol. 258, pp. S114-S115, Sep. 2016. 10.1016/j.toxlet.2016.06.1469
   

2015

• N. Jeliazkova, C. Chomenidis, P. Doganis, B. Fadeel, R. Grafström, B. Hardy, J. Hastings, M. Hegi, V. Jeliazkov, N. Kochev, P. Kohonen, C. R. Munteanu, H. Sarimveis, B. Smeets, P. Sopasakis, G. Tsiliki, D. Vorgrimmler, and E. Willighagen, The eNanoMapper database for nanomaterial safety information, Beilstein J. Nanotechnol., vol. 6, pp. 1609-1634, Jul. 2015. doi:10.3762/bjnano.6.165
• Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C. R., Steinbeck, C., & Willighagen, E., eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment, Journal of Biomedical Semantics, 2015, 6(10). doi:10.1186/s13326-015-0005-5

2014

• Jeliazkova, N., Doganis, P., Fadeel, B., Grafstrom, R., Hastings, J., Jeliazkov, V., Kohonen, P., Munteanu, C.R., Sarimveis, H., Smeets, B., Tsiliki, G., Vorgrimmler, D., Willighagen. E., The first eNanoMapper prototype: a substance database to support safe-by-design, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 1–9). doi:10.1109/BIBM.2014.6999367
• Sahlin, U., Jeliazkova, N., Oberg, T., Applicability Domain Dependent Predictive Uncertainty in QSAR Regressions, Molecular Informatics, 2014, 33(1);26-35

2013

• Kohonen P., Benfenati E., Bower D., Ceder R., Crump M., Cross K., Grafström R., Healy L., Helma C., Jeliazkova N., Jeliazkov V., Maggioni S., Miller S., Myatt G., Rautenberg M., Stacey G., Willighagen E., Wiseman J., Hardy B.,  The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing, Molecular Informatics, 2013, 32(1);47-63
• Kochev N., Paskaleva V., Jeliazkova N., Ambit-Tautomer: An Open Source Tool for Tautomer Generation, Molecular Informatics, 2013, 32(5-6):481-504. doi:10.1002/minf.201200133
• Cassani S., Kovarich S., Papa E., Roy PP., Rahmberg M., Nilsson S., Sahlin U., Jeliazkova N., Kochev N., Pukalov O., Tetko I., Brandmaier S., Durjava MK., Kolar B., Peijnenburg W., Gramatica P. Evaluation of CADASTER QSAR models for the aquatic toxicity of (benzo)triazoles and prioritisation by consensus prediction, Altern Lab Anim., 2013, 41(1):49-64.

2012

• Jeliazkova, N., Jeliazkov V., Chemical Landscape Analysis with the Opentox Framework, Current Topics in Medicinal Chemistry, 2012, 12(18);1987-2001(15).
• Willighagen E., Affentranger A., Grafström R., Hardy B., Jeliazkova N., Spjuth O., Chapter 2. Interactive predictive toxicology with Bioclipse and OpenTox, In Lee Harland, & Mark Forster (Eds.), Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond (Woodhead Publishing Series in Biomedicine) (pp. 35-61), Woodhead Publishing, 2012
• Jeliazkova, N., Web tools for predictive toxicology model building, Expert Opinion on Drug Metabolism & Toxicology, 2012, 8(5);1-11 doi: 10.1517/17425255.2012.685158
• Hardy B., Apic G., Carthew P, Clark D., Cook D., Dix I., Escher S., Hastings J., Heard D.J., Jeliazkova N., Judson P., Matis-Mitchell S., Mitic D., Myatt G., Shah I., Spjuth O., Tcheremenskaia O., Toldo L., Watson D., White A., Yang C., Toxicology Ontology Perspectives, ALTEX-Alternatives to Animal Experimentation, 2012, 29(2);139- 156.
• Hardy B., Apic G., Carthew P, Clark D., Cook D., Dix I., Escher S., Hastings J., Heard D.J., Jeliazkova N., Judson P., Matis-Mitchell S., Mitic D., Myatt G., Shah I., Spjuth O., Tcheremenskaia O., Toldo L., Watson D., White A., Yang C., A Toxicology Ontology Roadmap, ALTEX-Alternatives to Animal Experimentation, 2012, 29(2);129-137.
• Tcheremenskaia O., Benigni R., Nikolova I., Jeliazkova N., Escher S., Batke M., Baier T., Poroikov V., Lagunin A., Rautenberg M., Hardy B., OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia, J Biomed Semantics, 2012; 3(Suppl 1): S7.

2011

• Jeliazkova N., Jeliazkov V., AMBIT RESTful web services: an implementation of the OpenTox application programming interface, 2011, Journal of Cheminformatics, doi:10.1186/1758-2946-3-18
• Jeliazkova N., Kochev N. Ambit-SMARTS: Efficient Searching Of Chemical Structures And Fragments, Molecular Informatics, 2011; 30(8):707-720. doi:10.1002/minf.201100028
• Willighagen E., Jeliazkova N., Hardy B., Grafstrom R., Spjuth O., Computational toxicology using the OpenTox application programming interface and Bioclipse, BMC Research Notes 2011 4 (1), 487
• Noel M O'Boyle , Rajarshi Guha , Egon L Willighagen , Samuel E Adams , Jonathan Alvarsson , Jean-Claude Bradley , Igor V Filippov , Robert M Hanson , Marcus D Hanwell , Geoffrey R Hutchison , Craig A James , Nina Jeliazkova , Andrew SID Lang , Karol M Langner , David C Lonie , Daniel M Lowe , Jerome Pansanel , Dmitry Pavlov , Ola Spjuth , Christoph Steinbeck , Adam L Tenderholt , Kevin J Theisen and Peter Murray-Rust, Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on Journal of Cheminformatics 2011, 3:37, doi:10.1186/1758-2946-3-37
• Bhhatarai B., Teetz W., Liu T., Oberg T., Jeliazkova N., Kochev N., Pukalov O., Tetko I., Kovarich S., Papa E., Gramatica P., CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals, Molecular Informatics 2011; 30(2-3):189–204

2010

• Jeliazkova N., Jaworska J., Worth A. (2010) Chapter 17. Open Source Tools for Read-Across and Category Formation, In M. Cronin, & Madden J. (Eds.), In Silico Toxicology : Principles and Applications (pp. 408-445). Cambridge, UK: RSC Publishing
• B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. Gütlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky , S. Chawla, I. Ghosh, S. Ray, H. Patel, S. Escher, Collaborative Development of Predictive Toxicology Applications, Journal of Cheminformatics 2010, 2:7doi:10.1186/1758-2946-2-7.

2009

• Nina Jeliazkova, Computer tools for Threshold of Toxicological Concern elucidation, Toxicology Letters, Abstracts of the 46th Congress of the European Societies of Toxicology, Volume 189, Supplement 1, 13 September 2009, Page S10
• R. Benigni, A. Worth, T. Netzeva, N. Jeliazkova, C. Bossa, A. Gruska, R. Franke, Structural motifs modulating the carcinogenic risk of aromatic amines, Environmental and Molecular Mutagenesis, 2009, 50:152161

2008

• Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR QSAR Environ Res. 2008;19(5-6):495-524.
• G. Patlewicz, N. Jeliazkova, A. Gallegos Saliner, A. P. Worth, Toxmatch-a new software tool to aid in the development and evaluation of chemically similar groups,SAR and QSAR in Environmental Research, 19:3, 397 — 412(2008)
• Ana Gallegos-Saliner, Albert Poater, Nina Jeliazkova, Grace Patlewicz, Andrew P. Worth, Toxmatch—A chemical classification and activity prediction tool based on similarity measures ,Regulatory Toxicology and Pharmacology,Volume 52, Issue 2, November 2008, Pages 77-84
• N. Kochev, O. Pukalov, G. Andreev, N. Jeliazkova; Software Module For Prediction Of Molar Refractivity; Scientific Researches of The Union of Scientists in Bulgaria - Plovdiv, Series B, "Natural Sciences and the Humanities" 2008, Vol X, 225-228.

2007

• Joanna Jaworska, Nina Nikolova-Jeliazkova, How can structural similarity analysis help in category formation, SAR and QSAR in Environmental Research, vol 18, 3-4 (2007)

2005

• Joanna Jaworska, Nina Nikolova-Jeliazkova, Tom Aldenberg QSAR Applicability Domain Estimation by Projection of the Training Set in Descriptor Space: A Review, ATLA, 33, 445–459 (2005)
• Nina Nikolova-Jeliazkova, Joanna Jaworska An Approach to Determining Applicability Domains for QSAR Group Contribution Models: An Analysis of SRC KOWWIN, ATLA, 33, 461–470 (2005)
• T.I. Netzeva, A.P. Worth,T. Aldenberg, R. Benigni, M.T.D. Cronin, P. Gramatica, J.S. Jaworska, S. Kahn, G. Klopman, C.A. Marchant, G. Myatt, N. Nikolova-Jeliazkova, G.Y. Patlewicz, R. Perkins, D.W. Roberts, T.W. Schultz, D.T. Stanton, J.J.M. van de Sandt, W. Tong, G. Veith & C. Yang ECVAM WORKSHOP REPORT Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships , ATLA, 33, 155-173 (2005)
• Aynur O. Aptula, Nina G. Jeliazkova,, Terry W. Schultz, Mark T. D. Cronin The Better Predictive Model: High q2 for the Training Set or Low Root Mean Square Error of Prediction for the Test Set?, QSAR and Combinatorial Science 2005, 24, 385-396 (2005)
• Nina Jeliazkova Slow Fingerprints?, CDK News (2005)

2004 and earlier

• Ovanes Mekenyan, Nina Nikolova, Patricia Schmieder, Gilman Veith COREPA-M: A Multi-Dimensional Formulation of COREPA QSAR & Combinatorial Science Volume 23, Issue 1, (2004) Pages 5-18
• Nikolova N., J. Jaworska. Approaches to Measure Chemical Similarity - a Review. QSAR Comb. Sci. 22, No. 9-10, 1006-1026 (2003)
• Ovanes Mekenyan, Nina Nikolova, Patricia Schmieder, Dynamic 3D QSAR techniques: applications in toxicology, Journal of Molecular Structure (Theochem) 622 (2003) 147–165
• Karabunarliev, S.H., Nikolova N., Nikolov N. and O.G. Mekenyan. Rule interpreter: A chemical language that implements decision rules based on molecular structure, Journal of Molecular Structure: THEOCHEM, Volume 622, Issues 1-2, 7 March 2003, Pages 53-62.
• Jaworska J., Dimitrov S., Nikolova N., Mekenyan O., Probabilistic assessment of biodegradability based on metabolic pathways: CATABOL system., SAR and QSAR in Environmental Research, 2002 vol. 13(2), pp. 307-323
• Mekenyan O.G. Dimitrov D. Nikolova N.,Karabunarliev S.H. Conformational Coverage by a Genetic Algorithm, J.Chem. Inf. Comput. Sci. 1999, 39/6, 997-1016.

Data mining, Pattern Recognition, Generalized Nets, Neural Networks

• Hristo S. Nikolov, Doyno I. Petkov, Nina Jeliazkova, Stela Ruseva and Kiril Boyanov Non-linear methods in remotely sensed multispectral data classification Advances in Space Research 2009
• N.Jeliazkova, S.Ruseva, K.Boyanov, H.Nikolov, D.Petkov, Application of Nonparametric Bayesian Classifier to Remote Sensing Data, Information Technologies and Control, No. 2, 2004, p 8-12
• Hadjitodorov S., Nikolova N.,Generalized net model of the self-organizing map of Kohonen classical training procedure", Advances in Modelling & Analysis, 2000, 1-B, Vol. 43
• Mateev, Pl., N. Nikolova and G. Angelova. Text Categorisation in an Internet Application for Document Management. Proc. Text Mining Workshop, IJCAI-99, Stockholm, August 1999.
• Nikolova N, Generalized Net representation of back-propagation Neural Network, AMSE Review, Vol. 1, No. 2, 1998

Internet, Networking

• N. Jeliazkova, L. Iliev, V. Jeliazkov, PerfsonarUI – a Standalone Graphical User Interface for Querying perfSONAR Services, IEEE 2006 John Vincent Atanasoff International Symposium on Modern Computing, Sofia, Oct 3-5 2006
• Egorov A., Nikolova N., Load balancing : A case study, in Proceedings of the 10th International Conference "Systems for Automation of Engineering and Research", (SAER '96), September 27-29, 1996, St. Konstantin resort, Varna, Bulgaria