Researchers from IBIMA Plataforma BIONAND and the UMA develop a useful algorithm for understanding the cellular processes involved in different diseases.

Home Page » News » Researchers from IBIMA Plataforma BIONAND and the UMA develop a useful algorithm for understanding the cellular processes involved in different diseases.

Thanks to this scientific work, genetic interactions can be identified with greater precision, resulting in innovative tools for more effective and personalised therapies.

A team of professionals from the Malaga Biomedical Research Institute and Nanomedicine Platform (IBIMA Plataforma BIONAND) and the University of Malaga (UMA) has developed an innovative methodology that promises to transform the way Gene Regulatory Networks (GRNs) are inferred. This advance, recently published in the journal Computers in Biology and Medicineintroduces a new tool called MO-GENECI, which optimises accuracy and reliability in the construction of these complex networks.

Gene Regulatory Networks are fundamental models in biology and medicine, as they describe how genes interact with each other and with other transcription factors, providing detailed insight into cellular processes and their relationship to various diseases. However, inferring these networks from gene expression data has historically been challenging due to the complexity of the data and limitations of existing techniques.

To address this challenge, the team led by Ismael Navas, a researcher from the ‘Knowledge and Data Analysis, Integration and Management (KHAOS)’ group at the UMA, has developed MO-GENECI, a multi-objective evolutionary algorithm that selects the best techniques for network inference, adapting to the particular characteristics of each dataset. This method not only improves accuracy in the identification of genetic interactions, but also mitigates uncertainty in the choice of the appropriate technique for each case.

Adrián Segura highlighted the importance of this advance, ‘since MO-GENECI represents a great step forward because it not only improves the results obtained by individual techniques, but also offers a flexible and adaptable solution that can be applied in different biological contexts’, which opens up, in the words of the pre-doctoral researcher himself, ‘a pathway open to new and more precise studies in the understanding of diseases and cellular processes’.

Likewise, researcher José M. García Nieto, co-author of the paper, emphasises the potential impact of this tool in biomedicine, ‘because MO-GENECI's multi-target approach allows us not only to select the best techniques, but also to optimise several crucial aspects of genetic network inference, as it could have significant implications for the development of more effective and personalised therapies’.

For his part, José F. Aldana, professor at the UMA's Institute of Software Technology and Engineering (ITIS), who coordinates this research group of IBIMA Plataforma BIONAND and the KHAOS group of the UMA, stresses that the development of MO-GENECI contributes to the growing importance of bioinformatics in biomedical research, where advanced computational tools like this one allow deciphering the complex mechanisms of gene regulation with unprecedented precision. This type of research not only contributes to scientific knowledge, but could also accelerate the development of new therapeutic strategies and improve the treatment of diseases.

The source code of MO-GENECI is publicly available, which facilitates its access to the global scientific community and promotes collaboration in future studies that seek to improve and apply this tool in other contexts. MO-GENECI is available in a software package implemented in one of the most popular programming languages and with a fairly intuitive and well-documented command hierarchy within the tool itself. The modularisation of the code allows for easy extension of objectives and incorporation of new inference techniques, even for people with basic programming skills.

Reference:

Segura-Ortiz A, García-Nieto J, Aldana-Montes JF, Navas-Delgado I. Multi-objective context-guided consensus of a massive array of techniques for the inference of Gene Regulatory Networks. Comput Biol Med. 2024 Jul 15;179:108850. doi: 10.1016/j.compbiomed.2024.108850. Epub ahead of print. PMID: 39013340.

Raúl J. Andrade Bellido, es Investigador Responsable del grupo consolidado ‘Hepatogastroenterología, Farmacología y Terapéutica Clínica Traslacional’ de IBIMA Plataforma BIONAND, Catedrático y Director del Departamento de Medicina en la Facultad de Medicina de la Universidad de Málaga, Jefe de Servicio Aparato Digestivo del Hospital Universitario Virgen de la Victoria en Málaga. Además, es el Responsable del Grupo Español de Hepatopatias asociadas a medicamentos (Spanish DILI Registry), el Coordinador de la Red Ibero-Americana de Hepatopatías asociadas a medicamentos (SLATINDILI) y también del Registro europeo de Hepatopatías asociadas a Medicamentos (Pro-Euro DILI Registry). Chair de la COST Action CA17112 – Prospective European Drug-Induced Liver Injury Network (PRO-EURO DILI NET) y del EASL DHILI Consortium. Horizonte2020. Framework Programme (European Union).

Dr. García Martín began her scientific career in the field of magnetic resonance imaging applied to biomedical research. In recent years, her research activity has been focused on nanotechnology applied to health. She completed her Ph.D. at the Sols-Morreale Biomedical Research Institute in Madrid (IIBM, CSIC), complementing her training with fellowships at several institutions in Europe and the United States of America. After completing her Ph.D., she joined the University of Arizona Cancer Center as a postdoctoral researcher, where she worked for three years until her return to the IIBM as a Ramón y Cajal researcher.

In 2011, she joined the Andalusian Center for Nanomedicine and Biotechnology (BIONAND)—now IBIMA Plataforma BIONAND—as leader of the Biomedical Magnetic Resonance Laboratory (BMRL) group, accredited by the Andalusian Agency of Knowledge as a consolidated group in the Andalusian Plan for Research, Development, and Innovation (PAIDI). From 2014 to 2019, she held the position of Deputy Chief Scientific Officer at BIONAND. She is currently the coordinator of the Nanodiagnostics Area at IBIMA Plataforma BIONAND and the scientific manager of the Nanoimaging Unit, a multimodal imaging platform accredited as a Singular Scientific and Technological Infrastructure (ICTS) by the Ministry of Science and Innovation as an independent hub of the ICTS NANBIOSIS.

Her current lines of research focus on the development of magnetic nanoparticles and other nanosystems for the diagnosis and treatment of tumors with special emphasis on malignant brain tumors and, on the other hand, the identification of metabolic biomarkers for the diagnosis and prognosis of various diseases, mainly cancer and neurodegenerative diseases, using NMR-based metabolomics.

Dr. Matas Rico earned a Ph.D. in biology from the University of Málaga in 2009 and trained for more than ten years at the prestigious Netherlands Cancer Institute research center in Amsterdam (The Netherlands). She was awarded the Ramón y Cajal program from the Ministry of Science, Innovation, and Universities in 2019 and became a permanent professor of the Department of Cell Biology, Genetics, and Physiology of the University of Málaga in 2024.

She is co-lead researcher of the Translational Research in Genitourinary Oncology group, with extensive experience in cell signaling pathways and their clinical impact. Her line of research focuses on the study of signaling pathways relevant to cancer progression, metastasis, and immunology. She has received funding from the Ministry of Science and Innovation and the Spanish Association Against Cancer Foundation. The results of her research have had great repercussion in the field of cancer cell biology and have been published in high impact factor journals such as ‘Cancer Cell,’ ‘Cell Reports,’ ‘Trends in Cancer,’ and ‘eLife,’ among others. In the research group, she participates in several clinical trials on urothelial bladder cancer. She is also a project assessor for the State Research Agency and the Spanish Association Against Cancer Foundation and participates in the review of articles and on different scientific evaluation committees.

As a lecturer at the University of Málaga, she teaches courses for the bachelor's degree in biology and biochemistry program; is a professor in the advanced biotechnology Ph.D. program; and supervises undergraduate, master's, and Ph.D. students.

Contact: elisa.matas@ibima.eu

Dr. Moreno Dueñas has been a full professor at the University of Málaga in the Department of Systems Engineering and Automation since 2023. He began his academic career with a bachelor's degree in telecommunication engineering from the University of Málaga in 2007 and a Ph.D. in mechatronics from the same institution in 2015.

He has worked in the Machine Perception and Intelligent Robotics Lab (MAPIR) group of the institute and the University of Málaga since 2006. He is currently co-lead investigator of the group, conducting projects focused on mobile robotics, computer vision, and artificial perception.

During his predoctoral career, he completed a research fellowship at the University of Bristol (2011) and collaborated with a research project at the University of Lincoln (2013), both in the United Kingdom. During these international experiences, he worked on the analysis and automatic description of images and the development of perception systems for agriculture, significantly influencing his doctoral work and subsequent research.

In regard to his scientific production, he has published 23 articles in ISI-JCR indexed journals and has made more than 20 contributions at conferences. Among his outstanding publications are articles on perception systems for mobile robots and widely cited multisensory datasets. He has also collaborated with other groups at the institute to develop systems for the automatic analysis and tracking of human movement, which resulted in the publication of a series of articles.

At the international level, he has participated in several European projects, especially those focused on support robotics for older adults and navigation systems for robots inside houses as well as on funded national projects on similar topics.

Dr. García Ranea is a professor at the Department of Molecular Biology and Biochemistry of the University of Málaga. From 1997 to 2001, he completed his Ph.D. degree in bioinformatics at the National Centre for Biotechnology (CNB-CSIC-Madrid). After a brief postdoctoral period at the National Centre for Biotechnology, he was subsequently hired in 2002 as a senior doctoral researcher at the University College London, where he worked until 2008, when he joined the University of Málaga as a Ramón y Cajal Researcher. He is a researcher at the Rare Diseases Networked Research Center (CIBERER-ISCIII), scientific coordinator of the Bioinformatics Common Research Support Service (ECAI) of the Biomedical Research Institute of Málaga (IBIMA), and leader of the National Institute of Bioinformatics (INB-ELIXIR) hub in Málaga. His research currently focuses on the areas of bioinformatics and systems biology applied to biomedicine and personalized precision medicine, with special attention to the study of rare diseases. He has authored more than 70 scientific publications in high impact journals; served as principal investigator on six national projects, three projects of excellence of the Regional Government of Andalusia, two European projects, and other projects; and holds contracts with universities, private foundations, and industry. In addition to serving as principal investigator on the aforementioned projects, he has also collaborated on more than 20 projects funded at regional, national, and European level during his professional career.

The research group he currently leads has experience in the prediction and modeling of complete interactomes and specific subnetworks based on biocomputational methods as well as on the use of these networks in the study of the molecular systems underlying the functioning of cellular systems and their implication in diseases. He also works on the modeling of drug-protein networks in order to generate hypotheses for compound repositioning as well as to predict the side effects and adverse effects of drugs. The group has an extensive track record working on the prediction of rare syndromes in patients and investigating the relationship between diseases and the mutations that produce them through the development and implementation of different workflows for the analysis and integration of multiomics data, with outstanding experience in the analysis of transcriptomic data.

Contact: ranea@uma.es

Dr. Mena Vázquez received her medical degree from the University of Málaga in 2010 and her Ph.D. from the University of Málaga in 2016. She has been a specialist physician in the Rheumatology Department at the Rheumatology Clinical Unit of the Regional University Hospital of Málaga since 2016 and has been Section Chief of the Rheumatology Clinical Unit at the Regional University Hospital of Málaga since 2021. In addition, she is co-lead researcher of the institute’s Inflammatory and Autoimmune Diseases research group, a member of the PAIDI CTS-1034 inflammatory rheumatic diseases study group since 2017, a collaborator in the Research Network on Rheumatic Diseases, collaborator in the Cooperative Research Networks Aimed at Health Outcomes, clinical coordinator of the Andalusian Research Network for Research on Rheumatic Diseases, and coordinator of the Research Unit of the Regional University Hospital of Málaga. She is a member and leader of the Spanish Society of Rheumatology research commission.

In addition, she has been a clinical tutor since 2014 and an honorary collaborator at the University of Málaga School of Medicine since 2020. She has research experience with previous contracts equivalent to the Juan Rodés contracts from 2018–2020, was the principal investigator for seven nationally competitive projects, and was a collaborator on more than ten projects. She participates as principal investigator in five clinical trials and collaborates on more than 40 clinical trials in phases II, III, and IV at the Immunologically-Mediated Diseases Research Unit.

In terms of scientific quality indicators, she has authored 66 publications since 2016, leading 45 of them. In addition, she has contributed to 21 other publications not as a leader. She has made more than 150 communications to conferences, edited of scientific article and a treatise on rheumatic diseases for the Spanish Society of Rheumatology, participated in six book chapters, and holds three patents. She has supervised seven medical degree final projects, two master’s degree final projects, and four doctoral theses. She also supervises researchers during their training

Contact: natalia.mena.sspa@juntadeandalucia.es

Dr. Moreno Peral holds a bachelor’s degree and Ph.D. in psychology from the University of Málaga. She is co-lead researcher of the Mental Health, Services, and Primary Care (SAMSERAP) group. Her lines of research focus on the prevention of depression and anxiety, the development of risk algorithms, and the use of information technology for personalized mental health interventions. She has published multiple articles in high impact journals, including studies on risk factors for anxiety disorders and the effectiveness of psychological and educational interventions.

In terms of research projects, has led projects such as “PrevANS,” focused on the prevention of anxiety and depression through personalized interventions based on risk algorithms and decision support system technologies.

On the international level, she participates in European networks such as the European Cooperation in Science & Technology (COST) for the study of perinatal depression and individualized psychotherapeutic treatments for young people. She has received several awards for her research work throughout her professional career. She is group leader for projects funded by the Ministry of Science, Innovation, and Universities.

Contact: patriciamorenoperal@uma.es

Dr. Bernal López earned her Ph.D. in biochemistry and molecular biology in 2002. She participated in the Miguel Servet Program of the Carlos III Institute of Health (2015–2023) and the Nicolás Monardes Program (2021) of the Andalusian Health Service. Since 2006, she has served as research coordinator of the Internal Medicine Clinical Unit of the Regional University Hospital of Málaga and professional tutor for the Advanced Vocational Training Course for Clinical Diagnosis Laboratory Technicians. In addition, she is an evaluator for national and international projects, including the Health Research Fund (FIS) and the National Agency for the Promotion of Science and Technology (FONCyT-ANPCyT).

She is co-lead investigator of the Research on Diabetes, Obesity, and Vascular Risk Factors group. Systemic Autoimmune Diseases and principal investigator for the Pathology of Atherosclerosis, Diabetes, and Obesity Group (CTS1023) of the Andalusian Research Plan. Furthermore, she has been a member of the Pathophysiology of Obesity and Nutrition Networked Research Center (CIBER) of the Carlos III Institute of Health since 2007.

Internationally, she has been a professional mentor for European medical students completing extracurricular internships at the University of Málaga. She has published more than 126 original articles in her line of research on diabetes, obesity, and cardiovascular risk factors. She has supervised seven doctoral theses in the last seven years. In regard to projects, she has led 16 national or regional projects and collaborated on 32 and has participated in six international projects. She has also coordinated 22 multicenter clinical trials on diabetes, obesity, and cardiovascular risk factors and holds two patents under evaluation.

Dr. Gómez Huelgas has been Chief of the Internal Medicine Clinical Unit of the Regional University Hospital of Málaga since 2005 and is a full professor at the Department of Medicine and Dermatology at the University of Málaga School of Medicine. In addition, he was President of the Spanish Society of Internal Medicine from 2017 to 2020 and is currently President of the European Federation of Internal Medicine. He is an associate researcher at the Pathophysiology of Obesity and Nutrition Networked Research Center (CIBER) and lead researcher of the Diabetes, Obesity, and Other Vascular Risk Factors. Systemic Autoimmune Diseases group.

On the international level, he is a national expert representative of the Joint Actions convened in the 2016 working plan of the European Directorate-General for Health and Consumers’ Third Health Programme.

He is the author of more than 160 original publications and participates in 13 national and two international projects. In addition, he participates in 18 multicenter clinical trials on diabetes, hyperlipidemia, and obesity and serves as coordinator for five of them. He has given more than 200 communications at regional and national conferences and more than one hundred communications at international conferences.

After completing her bachelor’s degree in biology in 2008, Dr. García Caballero completed a Ph.D. at the University of Málaga in which she focused on the search for new antiangiogenic and antitumor compounds. The results were included in a total of eight scientific articles and two book chapters. In addition, her collaboration with various pharmaceutical companies have led to four patents. She continued her training as a Marie Skłodowska-Curie researcher at the GIGA-Cancer GIGA-Cancer and the University of Liège (Belgium), where she developed a murine model for the study of lymphatic metastasis and characterized several inhibitors of the lymphangiogenic process. Subsequently, in 2017, she joined the Center for Cancer Biology and the Catholic University of Leuven (Belgium), where she completed her second postdoctoral fellowship focused on the study of endothelial metabolism.

In 2021, she joined the University of Málaga as a Beatriz Galindo Distinguished Researcher and Professor. She currently leads a research team at IBIMA Plataforma BIONAND, supervising several postdoctoral researchers, Ph.D. students, and master’s degree students. In addition, she teaches in the bachelor’s degree programs in biochemistry, biology, and chemistry and in the master’s degree in molecular and cellular biology program at the University of Málaga. She is co-author of more than 50 publications, most of which have been published in very high impact factor journals (Nature, Cell, Cell Metabolism, Cancer Cell, Nature Communications, Developmental Cell, Circulation Research, etc.). She is also an editor of two international journals, a scientific reviewer, participates in evaluation committees and panels, and has received 16 awards during her career.

Contact: melissa@uma.es

Dr. Serrano Criado has been working as a principal investigator at the institute through the Miguel Servet program and, since May 2023, as a researcher through the Nicolás Monardes program at the Mental Health Clinical Unit of the Regional University Hospital of Málaga. She has served as co-lead researcher of the Neuropsychopharmacology group and coordinator of Area 3: Neurosciences, Chronicity, Aging, and Health in Vulnerable Populations. Her lines of research focus on the characterization of lipid mediators in addictive disorders and comorbid mental illnesses through translational studies with the aim of identifying biomarkers and describing underlying molecular processes.

She has directed five national projects and one regional project and has participated in numerous national and international projects resulting in 137 scientific publications. She has also coauthored book chapters and presented numerous contributions at conferences. In addition, she has experience coordinating and tutoring students and technical staff and has collaborated on thesis committees, reviews for scientific journals, and the evaluation of national and international projects. She forms part of several stable research networks and structures, including the Research Network on Primary Care for Addictions (RIAPAd) and COST Action CA22111.

Contact: antonia.serrano@ibima.eu

Dr. Mayorga is a senior researcher through the Miguel Servet II, Nicolás Monardes, and Consolida programs. She works at the Allergology Clinical Unit of the Regional University Hospital of Málaga and the institute. She is coordinator of the research laboratory at the Civil Hospital of Málaga and co-lead researcher of the Allergic Diseases to Drugs and Allergens Research Group, recognized as a Center of Excellence by the World Allergy Organization (WAO). In addition, she is a founding member of Bioherent, a spin-off of the University of Málaga. In 2023, she was appointed a Fellow of the European Academy of Allergy and Clinical Immunology (EAACI).

Her research career focuses on the immunological mechanisms of adverse drug reactions and the improvement of in vitro tests as well as the identification of biomarkers in immunotherapy for food and respiratory allergies. She belongs to the Basic and Clinical Immunology Committee of the EAACI and the Spanish Society of Allergology and Clinical Immunology (SEAIC). She also participates in several European consortia, including EUROBAT and COST Action TD0802. She has been principal investigator for 18 projects and has collaborated in European projects such as AllerScreening and DIFAMEM. Her work has resulted in more than 250 publications in high impact journals and ten patents. In addition, she has directed 14 doctoral theses and supervises researchers in training. She is accredited as a full professor by ANECA.

Contact: lina.mayorga@ibima.eu

Dr. Yahyaoui Macías is a specialist in Clinical Biochemistry at the Regional University Hospital of Málaga and has been head of the Metabolopathies Laboratory and the Neonatal Screening Center of Eastern Andalusia since 2009. She has completed two training fellowships abroad at the Mayo Clinic and at the Connecticut Department of Public Health, specializing in advanced neonatal screening techniques. In 2021, she took on the role of healthcare coordinator of the Diagnostic and Treatment Unit for Congenital Metabolic Diseases at the Regional University Hospital of Málaga, which seeks to be designated a Reference Center, Department, or Unit (CSUR). In addition, she participates on the advisory group of the Andalusian Strategy for Personalized Precision Medicine and has coordinated line 2 of the new Andalusian Care Plan for Individuals with Rare Diseases (PAPER). She has been deputy coordinator of IBIMA-Rare since 2021. She has served as chief of the Clinical Analysis Department of the Regional University Hospital of Málaga since March 2024.

She has been a member of the Expert Panel on Newborn Screening of the Clinical Laboratory and Standards Institute (CLSI), contributing to the creation of clinical guidelines and international standards for neonatal screening. She has done research on the identification of new biomarkers in neonatal screening and the development of new technology for inherited metabolic diseases. In addition, she has received several awards and competitive research grants and has published more than 40 scientific articles, participated in more than 20 research projects, and supervised two doctoral theses at the University of Málaga.

Contact: raquel.yahyaoui.sspa@juntadeandalucia.es

Dr. Cuesta Vargas is a full professor at the University of Málaga, accredited as a dean by ANECA in 2022. He has 23 years of professional experience as a physical therapist. He has spent more than 15 years as a full-time teaching and research staff member (PDI) at the University of Jaén and the University of Málaga and 12 years at the Queensland University of Technology (Australia). He has published more than 250 contributions in JCR journals. He has codirected 29 doctoral theses and 75 master’s theses in the last ten years, leading the Clinimetry Research Group at the institute. In addition, he is part of the Research Network on Preventive Activities and Health Promotion (REDIAPP), funded by ISCIII from 2007 to 2020, and is principal investigator of the FUNNEL+ project, funded by ISCIII, and the iGAME project, funded by the European Union’s Horizon 2020 program.

He has been highly involved in education in the last ten years, teaching a total of 2,550 hours of undergraduate and 2,590 hours of postgraduate courses. He received the Educa-Abanca prize for the best teacher in Spain in the university category (all areas, 4th place) and is editor-in-chief of the journal BMC Sports Science, Medicine and Rehabilitation.

He currently focuses on the research, development, and transfer of clinical aspects related to human movement. His research ranges from the validation of indexes to the implementation of dashboards for clinical decisions to the transfer of therapeutic exercise programs that have a high impact on chronic conditions. This research incorporates the most advanced scientific methodology on the biomechanics, physiology, psychometrics, and epidemiology of physical therapy. He was included in the Stanford 2022 and 2023 lists of the top 2% of the world’s most influential scientists in the area of clinical medicine, based on citations for his scientific contributions over the past 25 years..

Contact: acuesta@uma.es

Dr. González is a Full Professor at the University of Málaga in the Department of Cell Biology, Genetics, and Physiology at the University of Málaga, a department she joined in 2016 through the prestigious Ramón y Cajal program of the State Research Agency. She is also the lead researcher of the Cellular Reprogramming and Cellular Models for Biomedical Applications group at IBIMA Plataforma BIONAND. She holds a bachelor’s degree in biology from the University of Seville and a Ph.D. in biomedicine from the University of Barcelona.

She has completed postdoctoral fellowships nationally, at the Institute for Biomedical Research of Barcelona, and internationally, at the Department of Neurosurgery of the University of California San Francisco, where she studied the role of the asymmetric division of cancer stem cells in oligodendriomas, as well as at Michigan State University, where she investigated cell reprogramming. A notable result of the latter was her article in Science on human oocyte factors and pluripotency.

She has been leading projects at the institute since 2016, including studies on multiple sclerosis, with recent publications. Her main line of research focuses on epigenetic phenomena during cellular reprogramming as well as their use to generate cellular models of disease, with funding from the Plan Retos of the Ministry of Economy, Commerce, and Companies; the Regional Ministry of Universities, Research, and Innovation; and the University of Málaga. Accredited by the I3 program, she has supervised ten master’s students and is supervising two Ph.D. students. She is a member of research ethics committees in Andalusia and collaborates with several national and international groups on cellular and biomedical research. She has published more than 22 international scientific publications of impact in JCR journals and has led six competitive research projects in the last five years.

Contact: egonmu@uma.es

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Researchers from IBIMA Plataforma BIONAND and the UMA develop a useful algorithm for understanding the cellular processes involved in different diseases.

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