For all publications please see: https://orcid.org/0000-0002-2779-7174
Publications
2026
Scholarly publications
Chen, M., Lakbir, S., Jeon, M., Mazur, V., Abeln, S., & Mouhib, H. (2026). Beyond olfaction: New insights into human odorant binding proteins. Protein Science, 35(2), e70451. [DOI]
Bentivenga, G. M., Mammana, A., Gogishvili, D., Baiardi, S., Vittoriosi, E., Mastrangelo, A., Ranieri, A., Houtkamp, I. M., Brockmann, K., Abeln, S., Capellari, S., & Parchi, P. (2026). Distinct cerebrospinal fluid proteomic signatures define clinicopathological subtypes of sporadic Creutzfeldt-Jakob disease and predict patient survival. Acta neuropathologica communications, 14(1), Article 14. [DOI] [Portal]
2025
Scholarly publications
Losa, J., Simon, F., Linnik, D., Kaya, S. G., Stuart, M. C. A., Stetsenko, A., Boer, R. D., Ho, F. Y., Incarnato, D., Stevens, J., Eck, J. V., Fraaije, M. W., Weiss, L. E., Teeffelen, S. V., Abeln, S., Guskov, A., Marrink, S.-J., Poolman, B., & Heinemann, M. (2025). Condition-dependent, amorphous protein agglomerates control cytoplasmic rheology. bioRxiv, 2025.06.17.660151.
Eijpe, A., Lakbir, S., Erdal Cesur, M., Oliveira, S. P., Abeln, S., & Silva, W. (2025). Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction. In J. C. Gee, J. Hong, C. H. Sudre, P. Golland, J. Park, D. C. Alexander, J. E. Iglesias, A. Venkataraman, & J. H. Kim (Eds.), Medical Image Computing and Computer Assisted Intervention, MICCAI 2025 - 28th International Conference, 2025, Proceedings (pp. 117-127). (Lecture Notes in Computer Science; Vol. 15973 LNCS). Springer. [DOI]
Halma, M. T. J., Kumar, S., van Eck, J., Abeln, S., Gates, A., & Wuite, G. J. L. (2025). FAIR data for optical tweezers experiments. Biophysical Journal, 124(8), 1255-1272. [DOI]
Lakbir, S., de Wit, R., de Bruijn, I., Kundra, R., Madupuri, R., Gao, J., Schultz, N., Meijer, G. A., Heringa, J., Fijneman, R. J. A., & Abeln, S. (2025). Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers. npj Precision Oncology, 9( 1), Article 140. [DOI] [Portal]
Coppens, S., Gogishvili, D., Faustinelli, V., Scollo, E., Hopley, C., Abeln, S., Dalby, P., Goenaga-Infante, H., Luckau, L., Vialaret, J., Lehmann, S., Hirtz, C., & Illes-Toth, E. (2025). Neurofilament Light Chain under the Lens of Structural Mass Spectrometry. ACS Chemical Neuroscience, 16(2), 141-151. [DOI] [Portal]
2024
Scholarly publications
Lakbir, S., de Wit, R., de Bruijn, I., Kundra, R., Madupuri, R., Gao, J., Schultz, N., Meijer, G. A., Heringa, J., Fijneman, R. J. A., & Abeln, S. (2024). Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers. bioRxiv. [DOI] [Portal]
Lorentz workshop on epistasis, Balvert, M., Cooper-Knock, J., Stamp, J., Byrne, R. P., Mourragui, S., van Gils, J., Benonisdottir, S., Schlüter, J., Kenna, K., Abeln, S., Iacoangeli, A., Daub, J. T., Browning, B. L., Taş, G., Hu, J., Wang, Y., Alhathli, E., Harvey, C., ... Twine, N. A. (2024). Considerations in the search for epistasis. Genome Biology, 25(1), Article 296. [DOI] [Portal]
Rubio-Alarcón, C., Stelloo, E., Vessies, D. C. L., van 't Erve, I., Mekkes, N. J., Swennenhuis, J., Lakbir, S., van Bree, E. J., Tijssen, M., Diemen, P. D., Lanfermeijer, M., Linders, T., van den Broek, D., Punt, C. J. A., Heringa, J., Meijer, G. A., Abeln, S., Feitsma, H., & Fijneman, R. J. A. (2024). High prevalence of chromosomal rearrangements and LINE retrotranspositions detected in formalin-fixed paraffin-embedded colorectal cancer tissue. Journal of Molecular Diagnostics, 26(12), 1065-1080. [DOI] [Portal]
Lakbir, S., Buranelli, C., Meijer, G. A., Heringa, J., Fijneman, R. J. A., & Abeln, S. (2024). CIBRA identifies genomic alterations with a system-wide impact on tumor biology. arXiv. [DOI] [Repository]
Dusoswa, S. A., Verhoeff, J., van Asten, S., Lübbers, J., van den Braber, M., Peters, S., Abeln, S., Crommentuijn, M. H. W., Wesseling, P., Vandertop, W. P., Twisk, J. W. R., Würdinger, T., Noske, D., van Kooyk, Y., & Garcia-Vallejo, J. J. (2024). The immunological landscape of peripheral blood in glioblastoma patients and immunological consequences of age and dexamethasone treatment. Frontiers in Immunology, 15, Article 1343484. [DOI] [Repository]
Gogishvili, D., Illes-Toth, E., J, MH., Hopley, C., E, CT., & Abeln, S. (2024). Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP). Proteins: Structure, Function and Bioinformatics, 92(5), 649-664. [DOI] [Repository]
2023
Scholarly publications
Gavaldá-Garciá, J., Stringer, B., Ivanova, O., Abeln, S., Feenstra, K. A., & Mouhib, H. (2023). Data Resources for Structural Bioinformatics. In Introduction to Structural Bioinformatics [DOI]
Waury, K., Gogishvili, D., Nieuwland, R., Chatterjee, M., Teunissen, C. E., & Abeln, S. (2023). Proteome encoded determinants of protein sorting into extracellular vesicles. (pp. 1-22). bioRxiv. [DOI]
Rubio-Alarcon, C., Stelloo, E., Vessies, D. C., van ‘t Erve, I., Mekkes, N., Swennenhuis, J., Lakbir, S., van Bree, E., Tijssen, M., Delis-van Diemen, P., Lanfermeijer, M., Linders, T. C., van den Broek, D., Punt, C. J., Heringa, J., Meijer, G. A., Abeln, S., Feitsma, H., & Fijneman, R. J. (2023). Abstract 222: High frequency of structural variants in FFPE colorectal cancer tissue detected by targeting selected common fragile site genes and LINE transposable elements. 222-222. [DOI]
Gils, J. H. M. V., Mouhib, H., Dijk, E. V., Dijkstra, M., Houtkamp, I., Goetzee, A., Abeln, S., & Feenstra, K. A. (2023). Thermodynamics of Protein Folding. In Introduction to Structural Bioinformatics [DOI]
Ivanova, O., Gavaldá-Garciá, J., Gogishvili, D., Houtkamp, I., Bouwmeester, R., Feenstra, K. A., & Abeln, S. (2023). Structure Alignment. In Introduction to Structural Bioinformatics [DOI]
Gils, J. H. M. V., Dijkstra, M., Mouhib, H., Rauh, A. S., Vreede, J., Feenstra, K. A., & Abeln, S. (2023). Monte Carlo for Protein Structures. In Introduction to Structural Bioinformatics [DOI]
Mouhib, H., Gils, J. H. M. V., Gavaldá-Garciá, J., Hou, Q., May, A., Rauh, A. S., Vreede, J., Abeln, S., & Feenstra, K. A. (2023). Molecular Dynamics. In Introduction to Structural Bioinformatics [DOI]
Jacobsen, A., Dijk, E. V., Mouhib, H., Stringer, B., Ivanova, O., Gavaldá-Garciá, J., Hoekstra, L., Feenstra, K. A., & Abeln, S. (2023). Introduction to Protein Structure. In Introduction to Structural Bioinformatics [DOI]
Gils, J. H. M. V., Dijk, E. V., May, A., Mouhib, H., Bijlard, J., Jacobsen, A., Houtkamp, I., Feenstra, K. A., & Abeln, S. (2023). Introduction to Protein Folding. In Introduction to Structural Bioinformatics [DOI]
Stringer, B., Jacobsen, A., Hou, Q., Ferrante, H. D., Ivanova, O., Waury, K., Gavaldá-Garciá, J., Abeln, S., & Feenstra, K. A. (2023). Function Prediction. In Introduction to Structural Bioinformatics [DOI]
Teunissen, C. E., Kimble, L., Bayoumy, S., Bolsewig, K., Burtscher, F., Coppens, S., Das, S., Gogishvili, D., Gomes, B. F., de San José, N. G., Mavrina, E., Meda, F. J., Mohaupt, P., Mravinacová, S., Waury, K., Wojdała, A. L., Abeln, S., Chiasserini, D., Hirtz, C., ... Zetterberg, H. (2023). Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias. Molecular and Cellular Proteomics, 22(10), Article 100629. [DOI] [Repository]
Bridel, C., Gils, J. H. M. V., Miedema, S. S. M., Hoozemans, J. J. M., Pijnenburg, Y. A. L., Smit, A. B., Rozemuller, A. J. M., Abeln, S., & Teunissen, C. E. (2023). Clusters of co-abundant proteins in the brain cortex associated with fronto-temporal lobar degeneration. Alzheimer's Research and Therapy, 15(1), Article 59. [DOI] [Repository]
Gogishvili, D., Vromen, E. M., Hertog, S. K., Lemstra, A. W., Pijnenburg, Y. A. L., Visser, P. J., Tijms, B. M., Campo, M. D., Abeln, S., Teunissen, C. E., & Vermunt, L. (2023). Discovery of novel CSF biomarkers to predict progression in dementia using machine learning. Scientific Reports, 13(1), Article 6531. [DOI] [Repository]
Waury, K., de WIt, R., Verberk, IMW., Teunissen, CE., & Abeln, S. (2023). Deciphering Protein Secretion from the Brain to Cerebrospinal Fluid for Biomarker Discovery. Journal of Proteome Research, 22(9), 3068-3080. [DOI] [Repository]
2022
Scholarly publications
Stringer, B., de Ferrante, H., Abeln, S., Heringa, J., Feenstra, K. A., & Haydarlou, R. (2022). PIPENN: protein interface prediction from sequence with an ensemble of neural nets. Bioinformatics (Oxford, England), 38(8), 2111-2118. [DOI]
Verhoeff, J., Abeln, S., & Garcia-Vallejo, J. J. (2022). INFLECT: an R-package for cytometry cluster evaluation using marker modality. BMC Bioinformatics, 23(1), Article 487. [DOI]
Lakbir, S., Lahoz, S., Cuatrecasas, M., Camps, J., Glas, R. A., Heringa, J., Meijer, G. A., Abeln, S., & Fijneman, R. J. A. (2022). Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer. European Journal of Cancer, 177, 94-102. [DOI]
Halma, M. T. J., Wever, M. J. A., Abeln, S., Roche, D., & Wuite, G. J. L. (2022). Therapeutic potential of compounds targeting SARS-CoV-2 helicase. Frontiers in Chemistry, 10, 1-12. [DOI]
Waury, K., Willemse, E. A. J., Vanmechelen, E., Zetterberg, H., Teunissen, C. E., & Abeln, S. (2022). Bioinformatics tools and data resources for assay development of fluid protein biomarkers. Biomarker Research, 10(1), Article 83. [DOI]
Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., & Goble, C. (2022). Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Communications of the ACM, 65(6), 54-63. [DOI] [Repository]
Gils, J. H. M. V., Gogishvili, D., Eck, J. V., Bouwmeester, R., Dijk, E. V., & Abeln, S. (2022). How sticky are our proteins? Quantifying hydrophobicity of the human proteome. Bioinformatics Advances, 2(1). [DOI] [Repository]
Capel, H., Feenstra, A., & Abeln, S. (2022). Multi-task learning to leverage partially annotated data for PPI interface prediction. Scientific Reports, 12. [DOI] [Repository]
2021
Scholarly publications
Mouhib, H., Stringer, B., Ingen, H. V., Gavaldá-García, J., Waury, K., Abeln, S., & Feenstra, K. A. (2021). Structure determination. In Introduction to Protein Structural Bioinformatics
Hou, Q., Stringer, B., Waury, K., Capel, H., Haydarlou, R., Xue, F., Abeln, S., Heringa, J., & Feenstra, K. A. (2021). SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. Bioinformatics (Oxford, England), 37(20), 3421-3427. [DOI]
2020
Scholarly publications
Gils, J. H. M. V., Dijk, E. V., Peduzzo, A., Hofmann, A., Vettore, N., Schützmann, M. P., Groth, G., Mouhib, H., Otzen, D. E., Buell, A. K., & Abeln, S. (2020). The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Computational Biology, 16(5). [DOI] [Repository]
2019
Scholarly publications
Abeln, S., Feenstra, K. A., & Heringa, J. (2019). Protein three-dimensional structure prediction. In S. Ranganathan (Ed.), Encyclopedia of Bioinformatics and Computational Biology (Vol. 2, pp. 497-511). Elsevier. [DOI]
Mouhib, H., Higuchi, A., Abeln, S., Yura, K., & Feenstra, K. A. (2019). Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using consdyn enhanced sampling [version 1; peer review: 1 approved with reservations, 1 not approved]. F1000Research, 8, 1-14. [DOI]
Fijneman, R. J. A., Mekkes, N., Broek, E. V. D., Stringer, B., Glas, R. A., Komor, M. A., Rausch, C., Lieshout, S. V., Cuppen, E., Smith, M. L., Sebra, R. P., Rowell, W. J., Ashby, M., Carvalho, B., Heringa, J., Meijer, G. A., & Abeln, S. (2019). Abstract 1738: Characterization of structural variants within MACROD2 in the pathogenesis of colorectal cancer. [DOI]
Willems, S. M., Abeln, S., Feenstra, K. A., de Bree, R., van der Poel, E. F., Baatenburg de Jong, R. J., Heringa, J., & van den Brekel, M. W. M. (2019). The potential use of big data in oncology. Oral Oncology, 98, 8-12. [DOI]
Hou, Q., De Geest, P. F. G., Griffioen, C. J., Abeln, S., Heringa, J., & Feenstra, K. A. (2019). SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. Bioinformatics, 35(22), 4794-4796. [DOI]
Dijkstra, M. J. J., van der Ploeg, A. J., Feenstra, K. A., Fokkink, W. J., Abeln, S., & Heringa, J. (2019). Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinformatics (Oxford, England), 35(24), 5315-5317. [DOI]
2018
Scholarly publications
Jacobsen, A., Bosch, L. J. W., Martens-De Kemp, S. R., Carvalho, B., Sillars-Hardebol, A. H., Dobson, R. J., De Rinaldis, E., Meijer, G. A., Abeln, S., Heringa, J., Fijneman, R. J. A., & Feenstra, K. A. (2018). Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer. Scientific Reports, 8(1), Article 7522. [DOI]
Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J., & Heringa, J. (2018). Training for translation between disciplines: A philosophy for life and data sciences curricula. Bioinformatics, 34(13), i4-i12. [DOI]
Dijkstra, M., Bawono, P., Abeln, S., Feenstra, K. A., Fokkink, W., & Heringa, J. (2018). Motif-Aware PRALINE: Improving the alignment of motif regions: Improving the alignment of motif regions. PLoS Computational Biology, 14(11), 1-19. [DOI]
Dijkstra, M. J. J., Fokkink, W. J., Heringa, J., van Dijk, E., & Abeln, S. (2018). The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein. Molecular Physics, 116(21-22), 3173-3180. [DOI]
2017
Scholarly publications
Broek, E. V. D., Dijkstra, M. J. J., Voorham, Q. J. M., Carvalho, B., Wiel, M. A. V. D., Abeln, S., Meijer, G. A., & Fijneman, R. J. A. (2017). Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression. Cancer Research, 77(3_Supplement), Article A07. [DOI]
Fijneman, R. J. A., van den Broek, E., van Lieshout, S., Rausch, C., Ylstra, B., van de Wiel, M. A., Meijer, G. A., & Abeln, S. (2017). GeneBreak: Detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. F1000Research, 5, Article 2340. [DOI]
Zhang, C., Bijlard, J., Staiger, C., Scollen, S., van Enckevort, D., Hoogstrate, Y., Senf, A., Hiltemann, S., Repo, S., Pipping, W., Bierkens, M., Payralbe, S., Stringer, B., Heringa, J., Stubbs, A., Bonino Da Silva Santos, L. O., Belien, J., Weistra, W., Azevedo, R., ... Abeln, S. (2017). Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research, 6, Article 1488. [DOI]
2016
Scholarly publications
May, A., Brandt, B. W., El-Kebir, M., Klau, G. W., Zaura, E., Crielaard, W., Heringa, J., & Abeln, S. (2016). MetaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics, 32(11), 1678-1685. [DOI]
Spalding, D., Hoogstrate, Y., Zhang, C., Senf, A., Bijlard, J., Hiltemann, S., van Enckevort, D., Repo, S., Heringa, J., Jenster, G., Fijneman, R. J. A., Boiten, J. W., Meijer, G. A., Stubbs, A., Rambla, J., & Abeln, S. (2016). Integration of EGA secure data access into Galaxy. F1000Research, 5, Article 2841. [DOI]
Haydarlou, R., Jacobsen, A., Bonzanni, N., Feenstra, K. A., Abeln, S., & Heringa, J. (2016). BioASF: A framework for automatically generating executable pathway models specified in BioPAX. Bioinformatics, 32(12), i60-i69. [DOI]
Stringer, B., Meroño-Peñuela, A., Abeln, S., Van Harmelen, F., & Heringa, J. (2016). SCRY: Extending SPARQL with custom data processing methods for the life sciences. CEUR Workshop Proceedings, 1795.
Baclayon, M., Van Ulsen, P., Mouhib, H., Shabestari, M. H., Verzijden, T., Abeln, S., Roos, W. H., & Wuite, G. J. L. (2016). Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates. ACS Nano, 10(6), 5710-5719. [DOI]
Rajendran, R., May, A., Sherry, L., Kean, R., Williams, C., Jones, B. L., Burgess, K. V., Heringa, J., Abeln, S., Brandt, B. W., Munro, C. A., & Ramage, G. (2016). Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping. Scientific Reports, 6, Article 35436. [DOI]
Van Dijk, E., Varilly, P., Knowles, T. P. J., Frenkel, D., & Abeln, S. (2016). Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation. Physical Review Letters, 116(7), Article 078101. [DOI]
Bawono, P., Dijkstra, M., Pirovano, W., Feenstra, A., Abeln, S., & Heringa, J. (2016). Multiple sequence alignment. In Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution (2 ed., Vol. 1, pp. 167-189). (Methods in Molecular Biology; Vol. 1525). Humana Press. [DOI]
Heringa, J., Reinders, M., Abeln, S., & De Ridder, J. (2016). ECCB 2016: The 15th European Conference on Computational Biology. Bioinformatics, 32(17), i389-i392. [DOI]
2015
Scholarly publications
May, A., Abeln, S., Buijs, M. J., Heringa, J., Crielaard, W., & Brandt, B. W. (2015). NGS-eval: NGS error analysis and novel sequence VAriant detection tooL. Nucleic Acids Research, 43(W1), W301-W305. [DOI]
Van Den Broek, E., Dijkstra, M. J. J., Krijgsman, O., Sie, D., Haan, J. C., Traets, J. J. H., Van De Wiel, M. A., Nagtegaal, I. D., Punt, C. J. A., Carvalho, B., Ylstra, B., Abeln, S., Meijer, G. A., & Fijneman, R. J. A. (2015). High prevalence and clinical relevance of genes affected by chromosomal breaks in colorectal cancer. PLoS One, 10(9), Article e0138141. [DOI]
van Dijk, E., Hoogeveen, A., & Abeln, S. (2015). The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures. PLoS Computational Biology, 11(5), Article e1004277. [DOI]
Bawono, P., Van Der Velde, A., Abeln, S., & Heringa, J. (2015). Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. PLoS One, 10(5), 1-19. Article e0127431. [DOI]
Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S., & Heringa, J. (2015). To SCRY Linked data: Extending SPARQL the easy way. CEUR Workshop Proceedings, 1501, 8-14.
Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S., & Heringa, J. (2015). SCRY: Enabling quantitative reasoning in SPARQL queries. CEUR Workshop Proceedings, 1546, 214-215.
Stringer, B., Dijkstra, M., Feenstra, A., Abeln, S., & Heringa, J. (2015). Explaining disease using big data: How valid is your pathway? In W. W. Smari, & V. Zeljkovic (Eds.), Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015 (pp. 662-664). Article 7237114 (Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015). IEEE. [DOI]
Kukic, P., Kannan, A., Dijkstra, M. J. J., Abeln, S., Camilloni, C., & Vendruscolo, M. (2015). Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. PLoS Computational Biology, 11(10), Article e1004435. [DOI]
Ni, R., Kleijn, J. M., Abeln, S., Cohen Stuart, M. A., & Bolhuis, P. G. (2015). Competition between surface adsorption and folding of fibril-forming polypeptides. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 91(2), Article 022711. [DOI]
2014
Scholarly publications
Abeln, S., Vendruscolo, M., Dobson, C. M., & Frenkel, D. (2014). A simple lattice model that captures protein folding, aggregation and amyloid formation. PLoS One, 9(1), Article e85185. [DOI]
May, A., Pool, R., Van Dijk, E., Bijlard, J., Abeln, S., Heringa, J., & Feenstra, K. A. (2014). Coarse-grained versus atomistic simulations: Realistic interaction free energies for real proteins. Bioinformatics, 30(3), 326-334. [DOI]
May, A., Abeln, S., Crielaard, W., Heringa, J., & Brandt, B. W. (2014). Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics, 30(11), 1530-1538. [DOI]
2013
Scholarly publications
Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C. J., Teusink, B., & Heringa, J. (2013). Bioinformatics and systems biology: Bridging the gap between heterogeneous student backgrounds. Briefings in Bioinformatics, 14(5), 589-598. [DOI]
Ni, R., Abeln, S., Schor, M., Cohen Stuart, M. A., & Bolhuis, P. G. (2013). Interplay between folding and assembly of fibril-forming polypeptides. Physical Review Letters, 111(5), Article 058101. [DOI]
Edwards, H., Abeln, S., & Deane, C. M. (2013). Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies. PLoS Computational Biology, 9(11), Article e1003325. [DOI]
2012
Scholarly publications
Bonder, M. J., Abeln, S., Zaura, E., & Brandt, B. W. (2012). Comparing clustering and pre-processing in taxonomy analysis. Bioinformatics, 28(22), 2891-2897. [DOI]
2011
Scholarly publications
Abeln, S., & Frenkel, D. (2011). Erratum: Correction (Biophysical Journal (2011) 100 (693-700)). Biophysical Journal, 101(4), 1014. [DOI]
Abeln, S., & Frenkel, D. (2011). Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins. Biophysical Journal, 100(3), 693-700. [DOI]
2010
Scholarly publications
Pirovano, W., Abeln, S., Feenstra, K. A., & Heringa, J. (2010). Multiple alignment of transmembrane protein sequences. In Structural Bioinformatics of Membrane Proteins (pp. 103-122). Springer. [DOI]
2008
Scholarly publications
Abeln, S., & Frenkel, D. (2008). Disordered flanks prevent peptide aggregation. PLoS Computational Biology, 4(12), Article e1000241. [DOI]
2007
Scholarly publications
Abeln, S., Teubner, C., & Deane, C. M. (2007). Using phylogeny to improve genome-wide distant homology recognition. PLoS Computational Biology, 3(1), 73-83. [DOI]
2005
Scholarly publications
Abeln, S., & Deane, C. M. (2005). Fold usage on genomes and protein fold evolution. Proteins: Structure, Function and Genetics, 60(4), 690-700. [DOI]
Winstanley, H. F., Abeln, S., & Deane, C. M. (2005). How old is your fold? Bioinformatics, 21(SUPPL. 1), i449-i458. [DOI]