Gomaz, B., Pandini, A., Maršavelski, A. and Štefanić, Z. (2024) 'MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams'. Journal of Chemical Information and Modeling, 64 (15). pp. 5742 - 5748. ISSN: 1549-9596

Verbeek, H., Ayad, LAK., Loukides, G. and Pissis, SP. (2024) 'Minimizing the Minimizers via Alphabet Reordering'. Leibniz International Proceedings in Informatics, LIPIcs. ISSN: 1868-8969

Kliza, KW., Song, W., Pinzuti, I., Schaubeck, S., Kunzelmann, S., Kuntin, D., Fornili, A., Pandini, A., Hofmann, K., Garnett, JA., Stieglitz, B. and Husnjak, K. et al. (2024) 'N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling'. Cell Death Discovery, 10 (1). pp. 1 - 15. ISSN: 2058-7716 Open Access Link

Bibik, P., Alibai, S., Pandini, A. and Dantu, SC. (2024) 'PyCoM: a python library for large-scale analysis of residue-residue coevolution data'. Bioinformatics, 40 (4). pp. btae166. ISSN: 1367-4803 Open Access Link

Ayad, LAK., Loukides, G., Pissis, SP. and Verbeek, H. (2024) 'Sparse Suffix and LCP Array: Simple, Direct, Small, and Fast'.16th Latin American Symposium. Puerto Varas, Chile. 6 - 22 March. Springer Nature Switzerland. pp. 162 - 177. ISSN: 0302-9743 Open Access Link

Ayad, LAK., Chikhi, R. and Pissis, SP. (2023) 'Seedability: optimizing alignment parameters for sensitive sequence comparison'. Bioinformatics Advances, 3 (1). pp. vbad108. ISSN: 2635-0041 Open Access Link

Ayad, L., Pissis, S. and Loukides, G. (2023) 'Text Indexing for Long Patterns: Anchors are All you Need'. Proceedings of the VLDB Endowment, 16 (9). pp. 2117 - 2131. ISSN: 2150-8097 Open Access Link

Oues, N., Dantu, SC., Patel, RJ. and Pandini, A. (2023) 'MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations'. Bioinformatics, 39 (7). pp. btad427. ISSN: 1367-4803 Open Access Link

Morra, G., Meli, M., Moroni, E. and Pandini, A. (2023) 'Editorial: Computational drug discovery for targeting of protein-protein interfaces—Volume II'. Frontiers in Chemistry, 11. pp. 1 - 2. ISSN: 2296-2646 Open Access Link

Pandini, A., Schulman, H. and Khan, S. (Accepted) 'Subunit Capture Mechanics in Calcium Calmodulin Dependent Kinase II'. SSRN Electronic Journal.

Li, T., Motta, S., Stevens, AO., Song, S., Hendrix, E., Pandini, A. and He, Y. et al. (2022) 'Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex'. JACS Au, 2 (8). pp. 1935 - 1945. ISSN: 2691-3704 Open Access Link

Motta, S., Callea, L., Bonati, L. and Pandini, A. (2022) 'PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations'. Journal of Chemical Theory and Computation, 18 (3). pp. 1957 - 1968. ISSN: 1549-9618 Open Access Link

Cho, E., Rosa, M., Anjum, R., Mehmood, S., Soban, M., Mujtaba, M., Bux, K., Moin, ST., Tanweer, M., Dantu, S., Pandini, A., Yin, J., Ma, H., Ramanathan, A., Islam, B., Mey, ASJS., Bhowmik, D. and Haider, S. et al. (2021) 'Dynamic Profiling of β-Coronavirus 3CL M^proProtease Ligand-Binding Sites'. Journal of Chemical Information and Modeling, 61 (6). pp. 3058 - 3073. ISSN: 1549-9596 Open Access Link

Marchetti, F., Moroni, E., Pandini, A. and Colombo, G. (2021) 'Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics'. The Journal of Physical Chemistry Letters, 12 (15). pp. 3724 - 3732. ISSN: 1948-7185 Open Access Link

Cho, E., Rosa, M., Anjum, R., Mehmood, S., Soban, M., Mujtaba, M., Bux, K., Dantu, S., Pandini, A., Yin, J., Ma, H., Ramanathan, A., Islam, B., Mey, ASJS., Bhowmik, D. and Haider, S. et al. (2021) 'Structural dynamics of the β-coronavirus M^pro protease ligand binding sites'. bioRxiv. pp. 1 - 42.Open Access Link

Motta, S., Pandini, A., Fornili, A. and Bonati, L. (2021) 'Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks'. Journal of chemical theory and computation, 17 (4). pp. 2080 - 2089. ISSN: 1549-9618 Open Access Link

Meli, M., Pandini, A. and Morra, G. (2021) 'Editorial: Computational Drug Discovery for Targeting of Protein-Protein Interfaces'. Frontiers in Chemistry, 9. pp. 1 - 2. ISSN: 2296-2646 Open Access Link

Ayad, LAK., Badkobeh, G., Fici, G., Héliou, A. and Pissis, SP. (2020) 'Constructing Antidictionaries of Long Texts in Output-Sensitive Space'. Theory of Computing Systems, 65 (5). pp. 777 - 797. ISSN: 1432-4350 Open Access Link

Ayad, LAK., Charalampopoulos, P. and Pissis, SP. (2020) 'SMART: SuperMaximal approximate repeats tool'.BCB '20: 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Virtual. 21 - 24 September. ACM. pp. 1 - 1.

Ayad, LAK., Dourou, A-M., Arhondakis, S. and Pissis, SP. (2020) 'IsoXpressor: A tool to assess transcriptional activity within isochores'. Genome Biology and Evolution, 12 (9). pp. 1573 - 1578. ISSN: 1759-6653 Open Access Link

Wheatley, P., Gupta, S., Pandini, A., Chen, Y., Petzold, CJ., Ralston, CY., Blair, DF. and Khan, S. et al. (2020) 'Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM'. Biophysical Journal, 119 (6). pp. 1108 - 1122. ISSN: 0006-3495 Open Access Link

Akere, A., Chen, SH., Liu, X., Chen, Y., Dantu, SC., Pandini, A., Bhowmik, D. and Haider, S. et al. (2020) 'Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana Glycosyltransferases'. Biochemical Journal, 477 (15). pp. 2791 - 2805. ISSN: 0264-6021 Open Access Link

Portlock, TJ., Tyson, JY., Dantu, SC., Rehman, S., White, RC., McIntire, IE., Sewell, L., Richardson, K., Shaw, R., Pandini, A., Cianciotto, NP. and Garnett, JA. et al. (2020) 'Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System'. Frontiers in Molecular Biosciences, 7 (112). pp. 1 - 17. ISSN: 2296-889X Open Access Link

Ayad, LAK., Charalampopoulos, P. and Pissis, SP. (2020) 'SMART: SuperMaximal approximate repeats tool'. Bioinformatics, 36 (8). pp. 2589 - 2591. ISSN: 1367-4803

Ayad, LAK., Bernardini, G., Grossi, R., Iliopoulos, CS., Pisanti, N., Pissis, SP. and Rosone, G. et al. (2020) 'Longest property-preserved common factor: A new string-processing framework'. Theoretical Computer Science, 812. pp. 244 - 251. ISSN: 0304-3975

Motta, S., Pandini, A., Fornili, A. and Bonati, L. (2020) 'Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations'.64th Annual Meeting of the Biophysical-Society. San Diego, CA. 7 - 19 February. CELL PRESS. pp. 297A - 297A. ISSN: 0006-3495

Alzamel, M., Ayad, LAK., Bernardini, G., Grossi, R., Iliopoulos, CS., Pisanti, N., Pissis, SP. and Rosone, G. et al. (2020) 'Comparing Degenerate Strings'. Fundamenta Informaticae, 175 (1-4). pp. 41 - 58. ISSN: 0169-2968

Wheatley, P., Gupta, S., Pandini, A., Chen, Y., Petzold, CJ., Ralston, CY., Blair, DF. and Khan, S. et al. (2019) 'Allosteric priming ofE. coliCheY by the flagellar motor protein FliM'. .

Pandini, A., Schulman, H. and Khan, S. (2019) 'Conformational coupling by trans-phosphorylation in calcium-calmodulin-dependent kinase II'. PLoS Computational Biology, 15 (5). pp. e1006796 - e1006796. ISSN: 1553-734X Open Access Link

Ayad, LAK., Badkobeh, G., Fici, G., Heliou, A. and Pissis, SP. (2019) 'Constructing Antidictionaries in Output-Sensitive Space'.2019 Data Compression Conference (DCC). Snowbird, UT. 10 - 29 March. IEEE. pp. 538 - 547. ISSN: 1068-0314

Pandini, A., Schulman, H. and Khan, S. (2019) 'Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II'. .

Teletin, M., Czibula, G., Bocicor, M-I., Albert, S. and Pandini, A. (2018) 'Deep Autoencoders for Additional Insight into Protein Dynamics'.International Conference on Artificial Neural Networks ICANN 2018. Rhodes, Greece. 26 - 7 October. Springer International Publishing. pp. 79 - 89. ISSN: 0302-9743 Open Access Link

Ayad, LAK., Chemillier, M. and Pissis, SP. (2018) 'Creating improvisations on chord progressions using suffix trees'. Journal of Mathematics and Music, 12 (3). pp. 233 - 247. ISSN: 1745-9737

Ayad, LAK., Pissis, SP. and Polychronopoulos, D. (2018) 'CNEFinder: Finding conserved non-coding elements in genomes'.The 17th European Conference on Computational Biology (ECCB 2018). Athens, Greece. 1 - 12 September. Oxford University Press (OUP). pp. i743 - i747. ISSN: 1367-4803 Open Access Link

Ayad, L., Barton, C. and Iliopoulos, C. (2018) 'The 27th London Stringology Days & London Algorithmic Workshop (LSD & LAW) 2019'.LSD & LAW 2019. King's College London.

Alzamel, M., Ayad, LAK., Bernardini, G., Grossi, R., Iliopoulos, CS., Pisanti, N., Pissis, SP. and Rosone, G. et al. (2018) 'Degenerate string comparison and applications'. Leibniz International Proceedings in Informatics, LIPIcs. ISSN: 1868-8969

Motta, S., Minici, C., Corrada, D., Bonati, L. and Pandini, A. (2018) 'Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics'. PLoS Computational Biology, 14 (2). pp. e1006021 - e1006021. ISSN: 1553-734X Open Access Link

Tiberti, M., Pandini, A., Fraternali, F. and Fornili, A. (2018) 'In Silico Identification of Rescue Sites by Double Force Scanning'.62nd Annual Meeting of the Biophysical-Society. San Francisco, CA. 2 - 21 February. CELL PRESS. pp. 43A - 43A. ISSN: 0006-3495

Ayad, LAK., Barton, C., Charalampopoulos, P., Iliopoulos, CS. and Pissis, SP. (2018) 'Longest common prefixes with k-errors and applications'.25th International Symposium on String Processing and Information Retrieval (SPIRE). Lima, PERU. 1 - 11 October. Springer International Publishing. pp. 27 - 41. ISSN: 0302-9743

Ayad, LAK., Bernardini, G., Grossi, R., Iliopoulos, CS., Pisanti, N., Pissis, SP. and Rosone, G. et al. (2018) 'Longest property-preserved common factor'.25th International Symposium on String Processing and Information Retrieval (SPIRE). Lima, PERU. 1 - 11 October. Springer International Publishing. pp. 42 - 49. ISSN: 0302-9743

Alamro, H., Ayad, LAK., Charalampopoulos, P., Iliopoulos, CS. and Pissis, SP. (2018) 'Longest common prefixes with k-mismatches and applications'.44th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM). Danube Univ Krems, Krems, AUSTRALIA. 1 - 2 February. Springer International Publishing. pp. 636 - 649. ISSN: 0302-9743

Tiberti, M., Pandini, A., Fraternali, F. and Fornili, A. (2017) 'In silico identification of rescue sites by double force scanning'. Bioinformatics, 34 (2). pp. 207 - 214. ISSN: 1367-4803 Open Access Link

Ayad, LAK., Barton, C. and Pissis, SP. (2017) 'A faster and more accurate heuristic for cyclic edit distance computation'. Pattern Recognition Letters, 88. pp. 81 - 87. ISSN: 0167-8655

Ayad, LAK. and Pissis, SP. (2017) 'MARS: Improving multiple circular sequence alignment using refined sequences'. BMC Genomics, 18 (1). pp. 86. ISSN: 1471-2164

Pernigo, S., Fukuzawa, A., Beedle, AEM., Holt, M., Round, A., Pandini, A., Garcia-Manyes, S., Gautel, M. and Steiner, RA. et al. (2016) 'Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection'. Structure, 25 (1). pp. 107 - 120. ISSN: 0969-2126 Open Access Link

Ayad, LAK., Pissis, SPP. and Retha, A. (2016) 'libFLASM: A software library for fixed-length approximate string matching'. BMC Bioinformatics, 17 (1). pp. 454. ISSN: 1471-2105

Pandini, A., Morcos, F. and Khan, S. (2016) 'The Gearbox of the Bacterial Flagellar Motor Switch'. Structure, 24 (7). pp. 1209 - 1220. ISSN: 0969-2126 Open Access Link

Pandini, A. and Fornili, A. (2016) 'Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in Proteins'.60th Annual Meeting of the Biophysical-Society. Los Angeles, CA. 16 - 2 March. Elsevier BV. pp. 187a - 188a. ISSN: 0006-3495 Open Access Link

Pandini, A. and Fornili, A. (2016) 'Using Local States to Drive the Sampling of Global Conformations in Proteins'. Journal of Chemical Theory and Computation, 12 (3). pp. 1368 - 1379. ISSN: 1549-9618 Open Access Link

Pandini, A., Kleinjung, J., Rasool, S. and Khan, S. (2015) 'Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor'. PLoS One, 10 (11). pp. 1 - 1. ISSN: 1932-6203 Open Access Link