Irena Roterman | Computational Neuroscience | Best Researcher Award

Prof. Dr. Irena Roterman | Computational Neuroscience | Best Researcher Award

Prof. Dr. Irena Roterman, Jagiellonian University Medical College, Poland.

Prof. Irena Roterman-Konieczna is a distinguished scientist whose academic roots in theoretical chemistry and biochemistry evolved into groundbreaking contributions in bioinformatics. With a Ph.D. and habilitation in biochemistry, and a postdoctoral fellowship at Cornell University, she developed a unique perspective on protein structure and folding. Her most notable innovation is the Fuzzy Oil Drop (FOD) model, which simulates protein folding by incorporating environmental effects using a 3D Gaussian function to map hydrophobicity distribution. This model has wide applicability—from understanding membrane proteins and amyloids to analyzing domain-swapping and receptor anchoring.

Profile

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🎓 Early Academic Pursuits

Irena Roterman-Konieczna began her academic journey in theoretical chemistry at the prestigious Jagiellonian University, graduating from the Faculty of Chemistry in 1974. Her early interest in molecular structure and the physicochemical underpinnings of biological systems laid a strong foundation for her interdisciplinary career. She deepened her scientific expertise by earning a Ph.D. in biochemistry in 1984 from Nicolaus Copernicus Medical Academy in Krakow, focusing on the structure of the recombinant IgG hinge region. Her postdoctoral studies at Cornell University from 1987 to 1989, under the mentorship of Harold A. Scheraga, further shaped her academic development. There, she explored force fields used in prominent computational programs like AMBER, CHARMM, and ECEPP, bridging theoretical modeling with biomolecular reality.

🧬 Professional Endeavors in Bioinformatics

Throughout her career, Prof. Roterman-Konieczna has been at the forefront of bioinformatics, dedicating herself to unraveling the mysteries of protein structure and amyloid formation. Following her habilitation in biochemistry at the Jagiellonian University Faculty of Biotechnology in 1994 and the conferment of her professorial degree in medical sciences in 2004, she continued to pioneer innovative methods in structural bioinformatics. Her hallmark contribution, the Fuzzy Oil Drop (FOD) model, revolutionized the understanding of protein folding. The model uniquely incorporates environmental influence into folding simulations by using a 3D Gaussian function to describe hydrophobicity distribution—proposing that hydrophobic residues form a central core while hydrophilic residues remain exposed. This paradigm introduced a more realistic, dynamic framework for simulating in silico protein folding.

🧪 Contributions and Research Focus

Prof. Roterman-Konieczna’s research has explored how proteins behave not only in aqueous environments but also within membranes and under the influence of external force fields. By modifying the Gaussian-based FOD model, she extended its applicability to membrane proteins, enabling quantification of their anchoring mechanisms and mobility. Her investigations into chaperonins and domain-swapping phenomena further illustrate the power of her model to decode complex folding and protein-protein interactions. She introduced a dual-variable simulation function—accounting for both internal forces (non-bonded interactions within the protein chain) and external forces (environmental effects)—to guide structural transformation toward energy minima. These ideas are foundational in modern computational biology, where realistic folding predictions are critical for understanding disease mechanisms and therapeutic targeting.

📘 Scholarly Publishing and Intellectual Outreach

A prolific author, Prof. Roterman-Konieczna has made significant contributions to scientific literature. She has authored several influential books, many published in Open Access to promote knowledge sharing. These works include “Protein Folding In Silico” (Elsevier), “Systems Biology – Functional Strategies of Living Organism” (Springer), and “From Globular Proteins to Amyloids” (Elsevier, 2020). Her books elegantly communicate complex bioinformatic strategies, such as ligand binding site identification, protein-protein interactions, and computer-aided diagnostics. Moreover, her editorial leadership from 2005 to 2020 as Chief Editor of the journal Bio-Algorithms and Med-Systems cemented her influence in shaping interdisciplinary dialogues at the intersection of medicine, biology, and computation.

🏆 Accolades and Recognition

Prof. Roterman-Konieczna’s work has earned international acclaim. Notably, she is listed among the Top 2% scientists worldwide by Stanford University and Elsevier—a testament to her influential research and academic reputation. With 149 publications indexed in PubMed, her impact on the bioinformatics community is both broad and profound. Over the course of her career, she has also served as a mentor to 14 doctoral students, many of whom continue to contribute to research and innovation across various fields of biomedicine.

🌐 Impact and Influence

Her research has advanced global understanding of how proteins fold, interact, and misfold—a process central to neurodegenerative diseases such as Alzheimer’s. The FOD model continues to provide a computational lens for studying amyloid formation and supramolecular assemblies. Her model is also pivotal in studying receptor anchoring in membranes and exploring domain-swapping mechanisms critical to protein complex formation. By integrating thermodynamic theory, statistical modeling, and structural biology, her work bridges theoretical research with biomedical applications, pushing the boundaries of in silico experimentation.

🧭 Legacy and Future Contributions

Prof. Irena Roterman-Konieczna’s legacy is rooted in her visionary approach to molecular biology, championing models that blend computational precision with biological realism. Her commitment to open access publishing and academic mentoring reflects a deep dedication to inclusive, sustainable scientific progress. As systems biology and personalized medicine continue to evolve, her models and insights will remain cornerstones for future explorations in disease modeling, drug design, and molecular diagnostics. Her career exemplifies how interdisciplinary thinking and computational ingenuity can transform the life sciences, leaving a legacy that will guide future generations of scientists.

Publication

  • Title: Aquaporins as Membrane Proteins: The Current Status
    Authors: I.K. Roterman (Irena K.), K. Stapor (Katarzyna), D. Dułak (Dawid), G. Szoniec (Grzegorz), L. Konieczny (Leszek)
    Year: 2025

 

  • Title: DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction
    Authors: K. Kotowski (Krzysztof), I.K. Roterman (Irena K.), K. Stapor (Katarzyna)
    Year: 2025

 

  • Title: Protein folding: Funnel model revised
    Authors: I.K. Roterman (Irena K.), M. Slupina (Mateusz), L. Konieczny (Leszek)
    Year: 2024

 

  • Title: Domain swapping: a mathematical model for quantitative assessment of structural effects
    Authors: I.K. Roterman (Irena K.), K. Stapor (Katarzyna), D. Dułak (Dawid), L. Konieczny (Leszek)
    Year: 2024

 

  • Title: Chameleon Sequences─Structural Effects in Proteins Characterized by Hydrophobicity Disorder
    Authors: I.K. Roterman (Irena K.), M. Slupina (Mateusz), K. Stapor (Katarzyna), K. Gądek (Krzysztof), P. Nowakowski (Piotr)
    Year: 2024

 

  • Title: Transmembrane proteins—Different anchoring systems
    Authors: I.K. Roterman (Irena K.), K. Stapor (Katarzyna), L. Konieczny (Leszek)
    Year: 2024

 

  • Title: External Force Field for Protein Folding in Chaperonins─Potential Application in In Silico Protein Folding
    Authors: I.K. Roterman (Irena K.), K. Stapor (Katarzyna), D. Dułak (Dawid), L. Konieczny (Leszek)
    Year: 2024

 

  • Title: Structural features of Prussian Blue-related iron complex FeT of activity to peroxidate unsaturated fatty acids
    Authors: M. Lasota (Małgorzata), G. Zemanek (Grzegorz), O. Barczyk-Woźnicka (Olga), L. Konieczny (Leszek), I.K. Roterman (Irena K.)
    Year: 2024

 

  • Title: Editorial: Structure and function of trans-membrane proteins
    Authors: I.K. Roterman (Irena K.), M.M. Brylinski (Michal Michal), F. Polticelli (Fabio), A.G. de Brevern (Alexandre G.)
    Year: 2024

 

  • Title: Model of the external force field for the protein folding process—the role of prefoldin
    Authors: I.K. Roterman (Irena K.), K. Stapor (Katarzyna), L. Konieczny (Leszek)
    Year: 2024

 

🧠 Conclusion

Prof. Roterman-Konieczna’s career stands as a testament to how deep scientific insight and computational innovation can revolutionize biological understanding. Her FOD model not only enriches the study of protein dynamics but also provides a versatile framework for medical and pharmaceutical applications. With a legacy built on rigorous research, educational outreach, and academic leadership, her influence will continue to guide future advances in molecular biology, bioinformatics, and biomedical science.

 

Francisco Mena | Computational Neuroscience | Best Researcher Award

Mr. Francisco Mena | Computational Neuroscience | Best Researcher Award

Mr. Francisco Mena, University of Kaiserslautern-Landau, Germany.

Francisco Mena is a dynamic researcher in the field of machine learning, currently pursuing a PhD at the University of Kaiserslautern-Landau (RPTU), Germany. His academic roots trace back to Federico Santa María Technical University (UTFSM) in Chile, where he developed a strong foundation in computer engineering and data science. With a specialization in unsupervised learning, deep learning, and multi-view data fusion, his work focuses on building robust and scalable models that minimize human intervention and adapt to incomplete or noisy datasets—particularly in the context of Earth observation and crowdsourced data. He has worked across international research institutes like DFKI in Germany and Inria in France, contributing to global advancements in AI and data science. His teaching and mentoring roles, combined with his innovative research, mark him as a rising contributor to the future of intelligent systems.

Profile

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🎓 Early Academic Pursuits

Francisco Mena’s academic journey began with a strong foundation in computer engineering at Federico Santa María Technical University (UTFSM) in Chile. Demonstrating exceptional academic performance, he ranked in the top 10% of his class, securing the 4th position among 66 students. He pursued an integrated path that led him to obtain a Bachelor of Science, a Licenciado, and later the Ingeniería Civil en Informática degree. Driven by curiosity and a passion for machine learning, he transitioned seamlessly into postgraduate studies, earning a Magíster en Ciencias de la Ingeniería Informática at UTFSM. His master’s thesis, focused on mixture models in crowdsourcing scenarios, set the stage for his growing interest in unsupervised learning and probabilistic models.

💼 Professional Endeavors

Alongside his studies, Francisco actively engaged in diverse professional roles that enriched his technical and academic expertise. He served as a research assistant at the Chilean Virtual Observatory (CHIVO), contributing to astroinformatics projects by processing and organizing astronomical datasets from ALMA and ESO observatories. His early professional stint as a front-end and back-end developer provided him with hands-on industry experience. In academia, he held several teaching roles, progressing from laboratory assistant to lecturer in key courses such as computational statistics, artificial neural networks, and machine learning. Currently, as a Student Research Assistant at the German Research Centre for Artificial Intelligence (DFKI), he contributes to Earth observation projects, enhancing models for crop yield prediction using multi-view data.

🔬 Contributions and Research Focus

Francisco’s research is anchored in machine learning with a special emphasis on unsupervised learning, deep neural architectures, multi-view learning, and data fusion. His doctoral work at University of Kaiserslautern-Landau (RPTU) focuses on handling missing views in Earth observation data, an increasingly important issue in remote sensing. He explores innovative methods that challenge traditional domain-specific models by advocating for approaches that minimize human intervention and labeling. His core research areas include autoencoders, deep clustering, dimensionality reduction, and latent variable modeling, with applications extending to vegetation monitoring, neural information retrieval, and crowdsourcing.

🌍 Global Collaborations

Francisco’s commitment to impactful research is evident in his international collaborations. In addition to his work in Germany, he undertook a research visit to Inria in Montpellier, France, where he explored cutting-edge topics such as multi-modal co-learning, multi-task learning, and mutual distillation. These collaborations allow him to expand the practical relevance of his research across geographical and disciplinary boundaries, contributing to global discussions in artificial intelligence and data science.

🧠 Impact and Influence

Through his extensive academic involvement, Francisco has shaped the understanding of machine learning models that are both scalable and adaptable to real-world challenges. His contributions in crowdsourcing, particularly the use of latent group variable models for large-scale annotations, reflect his commitment to developing resource-efficient models. His influence extends into education, where he has mentored students and shaped curriculum delivery in machine learning-related subjects. By leveraging tools like PyTorch, QGIS, and Slurm, he ensures his work remains at the cutting edge of technological advancement.

🏆 Recognition and Growth

Francisco’s academic excellence is evident from his consistent achievements and recognition. His GPA of 94% during his master’s program stands as a testament to his dedication and intellect. Being ranked #4 in his undergraduate program highlights his sustained academic brilliance. His teaching roles at UTFSM and lecturing at RPTU further underscore the trust institutions place in his knowledge and teaching abilities.

🚀 Legacy and Future Contributions

With a clear research vision and a strong international presence, Francisco Mena is poised to leave a lasting impact in the field of artificial intelligence, particularly in unsupervised learning and Earth observation. His focus on reducing dependency on human intervention, increasing model generalizability, and handling incomplete or noisy data reflects a future-forward approach. As his doctoral journey progresses, he is expected to continue influencing how machine learning models are conceptualized, designed, and deployed in real-world applications—especially those that require scalable, domain-agnostic solutions.

Publication

 

  • Harnessing the power of CNNs for unevenly-sampled light-curves using Markov Transition Field – M Bugueño, G Molina, F Mena, P Olivares, M Araya – 2021

 

  • Common practices and taxonomy in deep multiview fusion for remote sensing applications – F Mena, D Arenas, M Nuske, A Dengel – 2024

 

  • A binary variational autoencoder for hashing – F Mena, R Ñanculef – 2019

 

  • Refining exoplanet detection using supervised learning and feature engineering – M Bugueño, F Mena, M Araya – 2018

 

  • Predicting crop yield with machine learning: An extensive analysis of input modalities and models on a field and sub-field level – D Pathak, M Miranda, F Mena, C Sanchez, P Helber, B Bischke, … – 2023

 

  • Adaptive fusion of multi-modal remote sensing data for optimal sub-field crop yield prediction – F Mena, D Pathak, H Najjar, C Sanchez, P Helber, B Bischke, P Habelitz, … – 2025

 

  • A comparative assessment of multi-view fusion learning for crop classification – F Mena, D Arenas, M Nuske, A Dengel – 2023

 

  • Self-supervised Bernoulli autoencoders for semi-supervised hashing – R Ñanculef, F Mena, A Macaluso, S Lodi, C Sartori – 2021

 

  • Impact assessment of missing data in model predictions for Earth observation applications – F Mena, D Arenas, M Charfuelan, M Nuske, A Dengel – 2024

 

  • Increasing the robustness of model predictions to missing sensors in Earth observation – F Mena, D Arenas, A Dengel – 2024

 

🧩 Conclusion

Driven by curiosity and innovation, Francisco Mena is reshaping the landscape of machine learning through his pursuit of generalizable, efficient, and human-independent models. His research not only addresses technical limitations but also responds to the growing need for AI systems that are adaptable across domains and disciplines. With a solid academic background, global collaborations, and a clear research vision, he is set to make lasting contributions to unsupervised learning and its applications in critical areas like Earth observation and neural information retrieval. As he continues to build on his expertise, his work promises to influence both the academic world and the practical deployment of intelligent systems in complex, real-world scenarios.