Systems Biology of Aging external website

Bioinformatics & Structural Biochemistry Department

Systems Biology of Aging

The Systems Biology of Aging Group was founded by Dr. Robi Tacutu in 2016, and is part of the department of Bioinformatics and Structural Biochemistry at the Institute of Biochemistry of the Romanian Academy. The group is currently funded by a recently awarded EUR 1.9 million grant (Romanian/EU co-funded) for the project “Multi-omics Prediction System for Prioritization of Gerontological Interventions”.

The main areas of interest in the group include studying biology of ageing/biogerontology, systems biology and bioinformatics, overall the expertise required to acheive these spanning multiple research fields (from bioinformatics to synthetic biology).

With a highly multi-disciplinary team, the projects tackeled by the group include both computational aspects (data aggregation and processing, multi-dimensional data analysis, network-based methods, systems theory approaches, deep learning, etc.) as well as wet-lab experiments (in particular in-vivo testing of the computationally predicted interventions).

 

Robi Tacutu, Ph.D.
Robi Tacutu, Ph.D.

Group leader

A thorough, analytical and curiosity-driven scientist, with a multidisciplinary background in biology and computer science, Robi received his BSc in computer science from the University Politehnica Bucharest, and his MSc in biochemistry and molecular biology from the University of Bucharest. He has a long-term commitment and interest in the field of biogerontology (since 2005) and received his PhD in 2013 from the Ben-Gurion University of the Negev, in the lab of Prof. Vadim Fraifeld. His thesis was on an ageing-related topic: studying the relationships between aging and age-related diseases with the use of bioinformatics and network biology approaches, and More...

Alexandra Voinea, Mrs.
Alexandra Voinea, Mrs.

PhD student, Bioinformatics research assistant

Alexandra is a bioinformatics researcher at the Institute of Biochemistry, focussing on developing large screen analysis pipelines and automated tools for data and dataset annotation. She is also a PHD candidate at Univers More...

Anton Yurievich Kulaga, M.Phil.
Anton Yurievich Kulaga, M.Phil.

Bioinformatics research assistant

Anton has a formal background in international management and economics (Kyiv National Economic University, 2003 - 2008, M.A. with honors). Being passionate about programming since high school, he worked for many years as More...

Catalin-Florentin Ion
Catalin-Florentin Ion

Technician, Front-end developer

With a B.Sc. in Communication Sciences, Catalin joined the Computational Biology of Aging Group in order to aesthetically shape all of our web resources and interactions with the outside work. Aside from his formal educati More...

Constantina Filipciuc, Mrs.
Constantina Filipciuc, Mrs.

Project Manager

Without managerial help, our projects would surely fail, being swamped at the first sight of bureaucracy. Since Constantina (Tatiana for us) joined the Computational Biology of Aging Group, we have been able to properly fo More...

Costin Chiru, Ph.D.
Costin Chiru, Ph.D.

PhD. Eng. Costin-Gabriel Chiru (200+ citations, h-index 8) is an Associate Professor at the Faculty of Automatic Control and Computers from University Politehnica of Bucharest. In the past, he worked as a Teaching Assistan More...

Dan Mihaila, Mr.
Dan Mihaila, Mr.

Research assistant, Web developer

Dan Mihaila is a researcher in the Institute of Biochemistry of the Romanian Academy. Dan is currently working in Systems Biology of Aging in the Bioinformatics & Structural Biochemistry.

Dmitri Toren, Ph.D.
Dmitri Toren, Ph.D.

Assistant researcher

Dmitri is a bioinformatics researcher at the Institute of Biochemistry, focusing on curation for aging-related data, analysis of large screen datasets, dataset annotation and network-based analyses. He also holds a Ph.D. d More...

Eugen Ursu, Mr.
Eugen Ursu, Mr.

Junior Bioinformatician

Eugen Ursu is a researcher in the Institute of Biochemistry of the Romanian Academy. Eugen is currently working in Systems Biology of Aging in the Bioinformatics & Structural Biochemistry.

Gabriela Bunu, Mrs.
Gabriela Bunu, Mrs.

PhD student, Bioinformatics research assistant

Gabriela is a bioinformatics researcher at the Institute of Biochemistry, focussing on curation for aging-related data, analysis of large screen datasets and network-based analyses. She has a multidisciplinary background, More...

Ioan Valentin Matei, M.D., Ph.D.
Ioan Valentin Matei, M.D., Ph.D.

Scientific Researcher

Ioan has a background in regenerative medicine, cell therapies, stem cell biology, diabetes and aging. He has worked in endocrine pancreatic cell differentiation, starting with his Ph.D. at the Nippon Dental University Gra More...

Larisa Sârghie, PhD student
Larisa Sârghie, PhD student

Junior Bioinformatician

Larisa Sârghie is a researcher in the Institute of Biochemistry of the Romanian Academy. Larisa is currently working in Systems Biology of Aging in the Bioinformatics & Structural Biochemistry.

Laurentiu Spiridon, Dr.
Laurentiu Spiridon, Dr.

Laurentiu Spiridon is a researcher in the Institute of Biochemistry of the Romanian Academy. Laurentiu is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Simona Ghenea, Dr.
Simona Ghenea, Dr.

Researcher

Simona Ghenea is a researcher in the Institute of Biochemistry of the Romanian Academy. Simona is currently working in Molecular Cell Biology in the Molecular Cell Biology.

Teodora Bucaciuc
Teodora Bucaciuc

Teodora Bucaciuc is a researcher in the Institute of Biochemistry of the Romanian Academy. Teodora is currently working in Systems Biology of Aging in the Bioinformatics & Structural Biochemistry.

Vlad Constantinescu, Mr.
Vlad Constantinescu, Mr.

PhD student, Machine learning research assistant

Vlad is a senior software engineer (with more than 12 years experience), who has been involved in commercial projects for various partners in the EU, USA, Canada, and having a variety of roles in design, engineering and re More...

Year
  1. Har-Zahav A, Lixandru D, Cheishvili D, Matei IV, Florea IR, Aspritoiu VM, Blus-Kadosh I, Meivar-Levy I, Serban AM, Popescu I, Szyf M, Ferber S, Dima SOHar-Zahav A et al . "The role of DNA demethylation in liver to pancreas transdifferentiation", Stem cell research & therapy 13(1): 476, (2022)
    IF: 8.07
  2. Ghenea S, Chiritoiu M, Tacutu R, Miranda-Vizuete A, Petrescu SMGhenea S et al . "Targeting EDEM protects against ER stress and improves development and survival in C. elegans", PLoS genetics 18(2): e1010069, (2022)
    IF: 5.90
  3. Knyazer A, Bunu G, Toren D, Mracica TB, Segev Y, Wolfson M, Muradian KK, Tacutu R, Fraifeld VEKnyazer A et al . "Small molecules for cell reprogramming: a systems biology analysis", Aging 13(24): 25739-25762, (2021)
    IF: 5.68
  4. Matei IV, Samukange VNC, Bunu G, Toren D, Ghenea S, Tacutu RMatei IV et al . "Knock-down of odr-3 and ife-2 additively extends lifespan and healthspan in C. elegans", Aging 13(undefined), (2021)
    IF: 5.60
  5. Constantinescu V, Chiru C, Boloni T, Florea A, Tacutu RConstantinescu V et al . "Learning flat representations with artificial neural networks", Applied Intelligence: 2456–2470, (2021)
    IF: 5.09
  6. Kulaga AY, Ursu E, Toren D, Tyshchenko V, Guinea R, Pushkova M, Fraifeld VE, Tacutu RKulaga AY et al . "Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals", International journal of molecular sciences 22(3), (2021)
    IF: 4.56
  7. Toren D, Yanai H, Abu Taha R, Bunu G, Ursu E, Ziesche R, Tacutu R, Fraifeld VEToren D et al . "Systems biology analysis of lung fibrosis-related genes in the bleomycin mouse model", Scientific reports 11(1): 19269, (2021)
    IF: 4.38AI: 1.28
  8. Iacob R, Herlea V, Savu L, R Florea I, M Ilie V, Terinte-Balcan G, Gherghiceanu M, Uta M, Popa C, Iacob S, V Matei I, Jardan C, Lixandru D, Dima S, Meivar-Levy I, Ferber S, Popescu IIacob R et al . "Phenotypic assessment of liver-derived cell cultures during in vitro expansion", Regenerative medicine, (2021)
    IF: 2.59
  9. Matei IV, Meivar-Levy I, Lixandru D, Dima S, Florea IR, Ilie VM, Albulescu R, Popescu I, Ferber SMatei IV et al . "The effect of liver donors' age, gender and metabolic state on pancreatic lineage activation", Regenerative medicine, (2021)
    IF: 2.59
  10. Avelar RA, Ortega JG, Tacutu R, Tyler EJ, Bennett D, Binetti P, Budovsky A, Chatsirisupachai K, Johnson E, Murray A, Shields S, Tejada-Martinez D, Thornton D, Fraifeld VE, Bishop CL, de Magalhães JPAvelar RA et al . "A multidimensional systems biology analysis of cellular senescence in aging and disease", Genome biology 21(1): 91, (2020)
    IF: 10.81
  11. Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VEToren D et al . "Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination", Aging cell 19(7): e13158, (2020)
    IF: 7.24
  12. Bunu G, Toren D, Ion CF, Barardo D, Sârghie L, Grigore LG, de Magalhães JP, Fraifeld VE, Tacutu RBunu G et al . "SynergyAge, a curated database for synergistic and antagonistic interactions of longevity-associated genes", Scientific data 7(1): 366, (2020)
    IF: 5.54
  13. Bucaciuc Mracica T, Anghel A, Ion CF, Moraru CV, Tacutu R, Lazar GABucaciuc Mracica T et al . "MetaboAge DB: a repository of known ageing-related changes in the human metabolome", Biogerontology 21(6): 763-771, (2020)
    IF: 3.77
  14. Martin EC, Sukarta OCA, Spiridon L, Grigore LG, Constantinescu V, Tacutu R, Goverse A, Petrescu AJMartin EC et al . "LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers", Genes (Basel) 11(3): 286, (2020)
    IF: 3.33
  15. Tacutu R, Thornton D, Johnson E, Budovsky A, Barardo D, Craig T, Diana E, Lehmann G, Toren D, Wang J, Fraifeld VE, de Magalhães JPTacutu R et al . "Human Ageing Genomic Resources: new and updated databases", Nucleic acids research 46(D1): D1083-D1090, (2018)
    IF: 11.15
  16. Yanai H, Budovsky A, Barzilay T, Tacutu R, Fraifeld VEYanai H et al . "Wide-scale comparative analysis of longevity genes and interventions", Aging cell 16(6): 1267-1275, (2017)
    IF: 7.63
  17. Spiridon L, Minh DDL. "Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling", Journal of chemical theory and computation 13(10): 4649-4659, (2017)
    IF: 5.40
  18. Ruta LL, Lin YF, Kissen R, Nicolau I, Neagoe AD, Ghenea S, Bones AM, Farcasanu ICRuta LL et al . "Anchoring plant metallothioneins to the inner face of the plasma membrane of Saccharomyces cerevisiae cells leads to heavy metal accumulation", PloS one 12(5): e0178393, (2017)
    IF: 2.77
  19. Lixandru D, Alexandru P, Mihai A, Roşca A, Ionescu-Tîrgovişte C, Braşoveanu LI, Manuel-Y-Keenoy BLixandru D et al . "Decreased paraoxonase 2 enzymatic activity in monocyte/macrophages cells. A comparative in vivo and in vitro study for diabetes", Free radical research 51(6): 604-615, (2017)
  20. Sima F, Davidson P, Pauthe E, Sima LE, Gallet O, Mihailescu IN, Anselme KSima F et al . "Fibronectin layers by matrix-assisted pulsed laser evaporation from saline buffer-based cryogenic targets", Acta biomaterialia 7(10): 3780-8, (2011)
    IF: 4.87AI: 1.30
  21. de Magalhães JP, Lagger C, Tacutu Rde Magalhães JP et al . "Integrative Genomics of Aging", pp 151-171, Handbook of the Biology of Aging, Academic Press, Elsevier, (2021).
    ISBN: 978-0-12-815962-0
  22. Tacutu R, Toren D, Ursu E, Bunu G, Bucaciuc Mracica TTacutu R et al . "Healthy Biological Systems", pp 53-78, Explaining Health Across the Sciences, Springer, Cham, (2020).
    ISBN: 978-3-030-52662-7
Gerontomics: Multi-omics prediction system for prioritization of gerontological interventions 2016-2021
Acronym: Gerontomics
Project director: Robi Tacutu

Starting 02.09.2016, the Institute of Biochemistry of the Romanian Academy is implementing the project “Multi-omics prediction system for prioritization of gerontological interventions”, co-funded through European Fund for Regional Development, in accordance with the funding contract signed by the Ministry of National Education and Scientific Research. The total funding for the project is 8.524.757,50 lei, of which 8.502.557,50 lei represent non-reimbursable funding. The project’s duration is 48 months.

Microsoft Azure Research 2017-2018
Acronym: ML for Aging Research
Project director: Robi Tacutu

The Systems Biology of Aging team is grateful for the "Microsoft Azure for Research" sponsorship awarded to our group. We have received cloud computing resources worth the equivalent of 20,000$ credits, and this has greatly helped us to speed up some of our research projects.

Impact of Early life MetaBolic and psychosocial strEss on susceptibility to mental Disorders; from converging epigenetic signatures to novel targets for therapeutic intervention 2019-2022
Acronym: EMBED
Project director: Robi Tacutu

Starting 01.06.2019, the Institute of Biochemistry of the Romanian Academy is implementing the EMBED project, funded by UEFISCDI (contract 103, from 01.06.2019), through the ERA-NET COFUND-NEURON III grant call. The project aims to assess the shared molecular links between pre- and post-natal, metabolic and psychosocial stress, and the risks of depression later in life, and its duration will be 36 months.

Gene Transcriptional Signatures in Healthy Ageing and Related Pathologies 2020-2022
Acronym: GeT-SHARP
Budget: 431,900 RON
Project director: Robi Tacutu

The project aims to analyze and compare the age-related transcriptomics signatures in variuos tisues, both in healthy and pathological individuals, in order to identify shared or unique aging signature that drive aging or age-related diseases.

Automated Nematode Screening for Neurodegenerative Diseases 2020-2022
Acronym: ANS-ND
Budget: 600,000 RON
Project director: Robi Tacutu

The project aims to experimentally develop an integrated and automated solution for screening drugs and genetic interventions for neurodegenerative diseases, using the nematode C. elegans and ageing-related data.