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I obtained a Bachelor Degree in Physics in March 1993 and a PhD in Physics in 1997 at the University of Turin (Italy); then I was hired as a postdoc by the Italian National Institute of Matter Physics (2 years), by the Politecnico of Turin (4 years), and by the the International Center of Theoretical Physics of Trieste (5 months, visiting scientist). I moved to the University of Zaragoza in 2003, as a "Ramón y Cajal" research fellow for the area of "Molecular, Cellular and Genetic Biology". I'm a member of the Institute of Biocomputation and Physics of Complex Systems (BIFI), and of the Department of Theoretical Physics; from 2008 to 2019 I have been a Lecturer ("Profesor Contratado Doctor") and since 2019 I am a Senior Lecturer ("Profesor Titular") at the University of Zaragoza.
My research lines deals with statistical physics applied to biological problems: protein folding, design and sequencing, antibody design and antibody humanization for biomedical purposes; polymer translocation; systems biology. Past research interests include the modelling of hydrophobic/hydrophilic species and polymers in water.
Research approach and theoretical tools: discrete Hamiltonian models, graphical models and generalized mean field techniques, Bayesian inference, Monte Carlo methods, analytical calculus techniques, Markov network, master equation.
I'm interested both in the search for universal properties of the models under study, and in their application to the prediction and quantitative analysis of experimental results, in close collaboration with biochemists and biophysicists.
Since 2010, I've lead 1 coordinated project within the National Plan for Scientific Innovation, I've participated in 15 national, regional and university projects, I' ve authored 10 publications in international journals (3 in D1, 4 in Q1; H-index 7) and I've presented contributions within 12 national and international conferences.
Globally, I have lead 3 coordinated projects within the National Plan for Scientific Innovation, and I have participated in 20 national, regional and university projects. I've authored 26 publications in international journals (16 in quartile Q1, 6 in decile D1). H-index: 11); I have presented contributions at 44 national and international conferences.
I have four 6-years research merits acknowledged by the National Committee of Evaluation of Research Activity (CNEAI: 1996-2001, 2002-2007, 2008-2013, 2014-2019).
I'm member of the faculty of the Degree Program in Physics, of the Master in Quantitative Biotechnology and of the PhD Program of the University of Zaragoza. I've directed one PhD thesis, 4 MPhil dissertations, 8 Undergraduate Dissertations (+4 in progress) and 5 Master Thesis (+2 in progress). I've been an Examiner for 9 PhD theses, I'm referee for 5 international journals (PRE, PRL, Physica A, Physical Biology, Entropy). Since February 2019 I am the Academic Secretary of the BIFI Institute and the Coordinator of the Master Program in "Quantitative Biotechnology"; I have led in 2019-20 the proposal for a new Master Program, that has been approved and will start on 2021-22.
Four 6-years research merits acknowledged by the National Committee of Evaluation of Research Activity (CNEAI: 1996-2001, 2002-2007, 2008-2013, 2014-2019);
Supervisor of 1 PhD Thesis (2011)
Publications since 2010: 10 (3 in D1, 4 in Q1, 3 in Q2)
Citations since 2010: 130
Average citations/year (since 2010): 13
H-index, since 2010: 7
Journal articles
- Luna-Cerralbo, David; Blasco-Machín, Irene; Adame-Pérez, Susana; Lampaya, Verónica; Larraga, Ana; Alejo, Teresa; Martínez-Oliván, Juan; Broset, Esther; Bruscolini, Pierpaolo. A statistical-physics approach for codon usage optimisation. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 2024. DOI: 10.1016/j.csbj.2024.07.020
- Di Mambro, T.; Vanzolini, T.; Bruscolini, P.; Perez-Gaviro, S.; Marra, E.; Roscilli, G.; Bianchi, M.; Fraternale, A.; Schiavano, G.F.; Canonico, B.; Magnani, M. A new humanized antibody is effective against pathogenic fungi in vitro. SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP). 2021. DOI: 10.1038/s41598-021-98659-5
- Alonso, J.L.; Bruscolini, P; Castro, A; Clemente-Gallardo, J.; Cuchí, J. C.; Jover-Galtier, J.A. Ehrenfest Statistical Dynamics in Chemistry: Study of Decoherence Effects. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2018. DOI: 10.1021/acs.jctc.8b00511
- Clavero-Alvarez, A.; Di Mambro, T.; Perez-Gaviro, S.; Magnani, M.; Bruscolini, P. Humanization of Antibodies using a Statistical Inference Approach. SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP). 2018. DOI: 10.1038/s41598-018-32986-y
- Hutton, R. D.; Wilkinson, J.; Faccin, M.; Sivertsson, E. M.; Pelizzola, A.; Lowe, A. R.; Bruscolini, P.; Itzhaki, L. S. Mapping the Topography of a Protein Energy Landscape. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2015. DOI: 10.1021/jacs.5b07370
- Martínez-Oliván, J; Arias-Moreno, X; Hurtado-Guerrero, R; Carrodeguas, Ja; Miguel-Romero, L; Marina, A; Bruscolini, P; Sancho, J. The closed conformation of the LDL receptor is destabilized by the low Ca(++) concentration but favored by the high Mg(++) concentration in the endosome. FEBS LETTERS. 2015. DOI: 10.1016/j.febslet.2015.10.014
- Lira-Navarrete, E.; Rivas, M.de Las; Compañón, I.; Pallarés, M.C.; Kong, Y.; Iglesias-Fernández, J.; Bernardes, G.J.L.; Peregrina, J.M.; Rovira, C.; Bernadó, P.; Bruscolini, P.; Clausen, H.; Lostao, A.; Corzana, F.; Hurtado-Guerrero, R. Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation. NATURE COMMUNICATIONS. 2015. DOI: 10.1038/ncomms7937
- Faccin, M.;Bruscolini, P. MS/MS spectra interpretation as a statistical-mechanics problem. ANALYTICAL CHEMISTRY. 2013. DOI: 10.1021/ac4005666
- Bastolla,U.;Bruscolini,P.;Velasco,J. L. Sequence determinants of protein folding rates: Positive correlation between contact energy and contact range indicates selection for fast folding. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2012. DOI: 10.1002/prot.24118
- Bruscolini, P.;Naganathan, A. N. Quantitative prediction of protein folding behaviors from a simple statistical model. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2011. DOI: 10.1021/ja110884m
- Faccin, M.;Bruscolini, P. ;Pelizzola, A. Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin. JOURNAL OF CHEMICAL PHYSICS. 2011. DOI: 10.1063/1.3535562
- Larriva, M.;Prieto, L.;Bruscolini, P. ;Rey, A. A simple simulation model can reproduce the thermodynamic folding intermediate of apoflavodoxin. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2010
- Sciretti, D.;Bruscolini,P.;Pelizzola,A.;Pretti,M.;Jaramillo,A. Computational Protein Design with Side-Chain Conformational Entropy. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2009
- Bruscolini, P.;Pelizzola,A.;Zamparo,M. Rate Determining Factors in Protein Model Structures. PHYSICAL REVIEW LETTERS. 2007
- Bruscolini, P.;Pelizzola,A.;Zamparo,M. Downhill Versus Two-State Protein Folding in a Statistical Mechanical Model. JOURNAL OF CHEMICAL PHYSICS. 2007
- Cotallo-Aban, M.; Prada‐Gracia, D.;Mazo, J. J.; Bruscolini P.; Falo, F.;Sancho, J. Analysis of Apoflavodoxin Folding Behavior with Elastic Network Models. AIP CONFERENCE PROCEEDINGS. 2006. DOI: 10.1063/1.2345631
- Bruscolini, P.;Cecconi, F. Analysis of Pin1ww Domain Through a Simple Statistical Mechanics Model. BIOPHYSICAL CHEMISTRY. 2005
- Bruscolini, P.; Pelizzola, A.; Casetti, L. Phase Diagram of a Simple Model of Water: a CVM and Monte Carlo Analysis. AIP CONFERENCE PROCEEDINGS. 2003
- Bruscolini, P.; Pelizzola, A. The Muñoz Eaton Model for Protein Folding and its Exact Solution. AIP CONFERENCE PROCEEDINGS. 2003
- Bruscolini, P.; Cecconi, F. Mean Field Approach for a Statistical Mechanical Model of Proteins. JOURNAL OF CHEMICAL PHYSICS. 2003. DOI: 10.1063/1.1580108
- Bruscolini, P.; Buzano, C.; Pelizzola, A.; Pretti, M. Lattice model for polymer hydration: collapse of poly(N-isopropylacrylamide). MACROMOLECULAR SYMPOSIA. 2002. DOI: 10.1002/1521-3900(200205)181:1<261::AID-MASY261>3.0.CO;2-Z
- Bruscolini, P.; Pelizzola, A.; Casetti, L. Comment on Novel phase behavior in a two dimensional network forming lattice fluid. PHYSICAL REVIEW LETTERS. 2002
- Bruscolini, P.; Pelizzola, A. Exact Solution of the Muñoz-Eaton Model for Protein Folding. PHYSICAL REVIEW LETTERS. 2002
- Bruscolini, P.; Casetti, L. Modeling Hydration Water and Its Role in Polymer Folding. JOURNAL OF BIOLOGICAL PHYSICS. 2001
- Bruscolini, P.; Buzano, C.; Pelizzola, A.; Pretti, M. Bethe Approximation for a Model of Polymer Solvation. PHYSICAL REVIEW E - STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS. 2001
- Bruscolini, P.; Casetti, L. Model for the Hydration of Nonpolar Compounds and Polymers. PHYSICAL REVIEW E - STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS. 2001
- Bruscolini, P.; Casetti, L. Lattice model for cold and warm swelling of polymers in water. PHYSICAL REVIEW E - STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS. 2000. DOI: 10.1103/PhysRevE.61.R2208
Conference presentations
- Sciretti, D.;Bruscolini,P.;Pelizzola,A.;Pretti,M.;Jaramillo,A. Protein Design at Room Temperature: The Role of Side-Chain Conformational Entropy. AIP CONFERENCE PROCEEDINGS. 2008
Scientific chapters
- PHASE DIAGRAM OF A SIMPLE MODEL OF WATER: A CVM AND MONTE CARLO ANALYSIS. Bruscolini, P.; Pelizzola, A.; Casetti, L. MODELING OF COMPLEX SYSTEMS: SEVENTH GRANADA LECTURES. 2003
Projects
- TERAPIAS DE RNA, INMUNOTERAPIA Y DIAGNÓSTICO AVANZADO FRENTE A LAS RESISTENCIAS ANTIMICROBIANAS. 01/01/25 - 31/12/28
- CONVIVEN-CI-IA. APRENDIZAJE DE COMPETENCIAS SOCIOEMOCIONALES PARA LA CIBERCONVIVENCIA A TRAVÉS DE LA INTEGRACIÓN DE HERRAMIENTAS DE INTELIGENCIA ARTIFICIAL (IA) + INTELIGENCIA COLECTIVA (IC) EN CENTROS EDUCATIVOS. 01/09/24 - 31/12/26
- PID2023-147734NB-I00: Complejidad a través de escalas espacio-temporales: de átomos a sociedades humanas. 01/09/24 - 31/12/28
- E30_23R: Supercomputación y Física de Sistemas Complejos y Biológicos (COMPHYS). 01/01/23 - 31/12/25
- EUROCC2 / National competence centres in the framework of EuroHPC Phase 2 (DIGITAL-EUROHPC-JU-2022-NCC-01). 01/01/23 - 31/12/25
- TED2021-130302B-C21: Transformación digital y pensamiento crítico en estudiantes mediante la interacción on-line en la plataforma THINKUB de inteligencia colectiva. 01/12/22 - 31/05/25
- TED2021-131518B-C31: Modelos predictivos para la estimación del riesgo de pérdida mineral ósea. 01/12/22 - 30/11/24
- PID2020-113582GB-I00: Abordando la emergencia a través de Múltiples Escalas. 01/09/21 - 28/02/25
- EUROCC / National Competence Centres in the framework of EuroHPC. 01/09/20 - 31/12/22
- E30_20R: Supercomputación Y Física De Sistemas Complejos Y Biológicos (COMPHYS). 01/01/20 - 31/12/22
- FCT-17-12577: MICROMASCOTAS II. 01/04/18 - 31/03/19
- FIS2017-87519-P. ABORDANDO LA COMPLEJIDAD DE SISTEMAS SOCIOTÉCNICOS, BIOLÓGICOS Y NATURALES. 01/01/18 - 30/09/21
- GRUPO DE REFERENCIA SUPERCOMPUTACIÓN Y FÍSICA DE SISTEMAS COMPLEJOS Y BIOLÓGICOS (COMPHYS). 01/01/17 - 31/12/19
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACION Y FISICA DE SISTEMAS COMPLEJOS. 01/01/16 - 31/12/16
- FIS2014-55867-P: SocioBioTec: FÍSICA ESTADÍSTICA Y NO LINEAL APLICADA A SISTEMAS SOCIALES, BIOLÓGICOS Y TECNOLÓGICOS. 01/01/15 - 31/07/18
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACIÓN Y FÍSICA DE SISTEMAS COMPLEJOS. 01/01/15 - 31/12/15
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACION Y FISICA DE SISTEMAS COMPLEJOS. 01/01/14 - 31/12/14
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACIÓN Y FÍSICA DE SISTEMAS COMPLEJOS. 01/01/13 - 31/12/13
- UZ2012-CIE-06: SIMPLIFICAR LA COMPLEJIDAD: DESDE LAS MOLÉCULAS A LOS SISTEMAS DE MUCHOS AGENTES. 01/01/13 - 31/12/13
- V.I. EXCELENCIA 2011.ESTANCIA ALESSANDRO PELIZZOLA DEL POLITECNICO DE TORINO (ITALIA). 01/01/12 - 31/12/12
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACIÓN Y FÍSICA DE SISTEMAS COMPLEJOS. 01/01/11 - 31/12/12
- SUB. NO SUJETA A CONV. 2011. V CONGRESO NACIONAL DEL INSTITUTO DE BIOCOMPUTACION Y FISICA DE SISTEMAS COMPLEJOS. 01/01/11 - 14/11/11
- VI CONGRESOS 2010"V CONGRESO NACIONAL BIFI 2011". 01/01/11 - 31/12/11
- COMPLEX ENERGY LANDSCAPES:COMPUTATIONAL AND STATISTICAL METHODS OF SOFT MATTER. 01/05/10 - 01/09/10
- FIS2009-13364-C02-01. ACERCAMIENTO COMPUTACIONAL A LA COMPLEJIDAD EN REDES,PROTEINAS, Y SISTEMAS DE MUCHOS AGENTES. 01/01/10 - 30/09/13
- PI065/08. ACCIONES DE SOPORTE PARA EL PROYECTO DE GRID REGIONAL ARAGRID. 01/10/08 - 30/09/10
- GRUPO EXCELENTE E24/3 BIOCOMPUTACIÓN Y FISICA DE SISTEMAS COMPLEJOS. 01/01/08 - 31/12/10
- FIS2006-12781-C02-01 COMPLEJIDAD EN PROTEÍNAS, REDES Y SISTEMAS DE MUCHOS AGENTES. 01/10/06 - 31/12/09
- PM057/2006 ACELERACIÓN DEL CRIBADO VIRTUAL PARA EL DESARROLLO DE FÁRMACOS EN UN SUPERORDENADOR DE FPGAs. 01/10/06 - 30/09/08
- GRUPO EXCELENTE E24/3 BIOCOMPUTACION Y FISICA DE SISTEMAS COMPLEJOS. 01/01/06 - 31/12/07
- INF2005-CIEN-016. TARJETA DE DESARROLLO DE FPGA-XILINX. 13/07/05 - 31/12/05
- GRUPO CONSOLIDADO E24/3 BIOCOMPUTACION Y FISICA DE SISTEMAS COMPLEJOS. 01/01/05 - 31/12/05
- VI EXCELENCIA 2004 CASETTI, LAPO. 01/01/05 - 31/12/05
- VI INFRAESTRUCTURA 2004. INF2004-CIE-04. 01/01/05 - 31/12/05
- FIS2004-05073-C04-01. CARACTERIZACION Y ANALISIS DE FENOMENOS COOPERATIVOS EN SISTEMAS COMPLEJOS IDEALES Y REALES. 13/12/04 - 12/12/06
- RAMON Y CAJAL 2003. 17/11/03 - 16/11/04
PhD supervision
- Analysis and Development of Algorithms for the Characterization of Biopolymers and Application to Protein Sequencing and Protein Folding. Universidad de Zaragoza. Sobresaliente cum laude. 28/10/11
Supervision of undergraduate dissertations
- Aplicaciones de técnicas de campo medio generalizado a problemas de biofísica. Universidad de Zaragoza. Matrícula de honor. 04/12/24
- Extensión del modelo WSME del plegamiento de proteínas al caso de tres estados. Universidad de Zaragoza. Sobresaliente. 18/09/24
- Inclusión de Interacciones electrostáticas en el modelo WSME del desplegamiento de proteínas y aplicación a proteínas relevantes. Universidad de Zaragoza. Matrícula de honor. 14/09/23
- Desarrollo de un método para la inferencia de trayectorias de diferenciación celular en tejidos complejos. Universidad de Zaragoza. Notable. 16/12/22
- Desarrollo de una aproximación variacional para la cinética de procesos markovianos en grafos. Aplicación a redes de regulación genética. Universidad de Zaragoza. Sobresaliente. 26/09/22
- Estudio de la cromatina con modelos sencillos de física estadística. Universidad de Zaragoza. Notable. 15/12/21
- Validación de un modelo estadístico para la clasificación y humanización de anticuerpos con databases de secuencias naturales y artificiales. Universidad de Zaragoza. Sobresaliente. 22/09/21
- Estudios de redes de regulación genéticas con modelos discretos. Universidad de Zaragoza. Sobresaliente. 22/09/21
- Análisis de transcriptomas a resolución de célula única aplicados a la inferencia de trayectorias de diferenciación celular en tejidos complejos. Universidad de Zaragoza. Notable. 09/07/21
- Biología de Sistemas: Circuitos genéticos oscilatorios y sincronización. Universidad de Zaragoza. Sobresaliente. 11/09/20
- Estudio de la translocación de biopolímeros con modelos sencillos y simulaciones. Universidad de Zaragoza. Notable. 21/07/20
- Métodos computacionales para la caracterización de relaciones causales entre genotipo y fenotipos: heredabilidad de la expresión y coexpresión genética. Universidad de Zaragoza. Sobresaliente. 21/07/20
- Validación y refinamiento de un modelo estadístico para la clasificación y humanización de anticuerpos. Universidad de Zaragoza. Sobresaliente. 20/07/20
- Estructura celular y patrones en biología: un enfoque de biología de sistemas. Universidad de Zaragoza. Sobresaliente. 11/07/19
- Sistemas dinámicos y expresión de genes: cómo se forman los patrones celulares. Universidad de Zaragoza. Matrícula de honor. 12/07/16
- Estudio del comportamiento de las proteínas modulares en función del número de módulos repetidos. Universidad de Zaragoza. Sobresaliente. 08/07/16
Supervision of master's theses
- Desarrollo de un modelo Loopy-WSME y aplicación a proteínas sencillas. Universidad de Zaragoza. Matrícula de honor. 12/02/25
- Study of the translocation and degradation of repeat proteins by the protein complex ClpXP. Universidad de Zaragoza. Matrícula de honor. 07/07/21
- Application of a statistical inference model to the prediction of antibody affinity from sequence analysis. Universidad de Zaragoza. Sobresaliente. 07/07/21
- Characterization of molecular heterogeneity in celiac disease patients. Universidad de Zaragoza. Sobresaliente. 24/09/20
- Ajuste de un modelo estadístico para la humanización de anticuerpos. Universidad de Zaragoza. Matrícula de honor. 26/09/19
- Study of the structure-propensities of the alpha-synuclein sequence. Universidad de Zaragoza. Sobresaliente. 10/07/19
- Study of the behavior of repeat proteins with simple native-centric models. Universidad de Zaragoza. Aprobado. 28/09/18
- Modelización matemática de problemas biológicos. Universidad de Zaragoza. Sobresaliente. 15/12/17
UNIZAR teaching of the last six courses
- Undergraduate dissertation. Joint Program in Physics and Mathematics. During academic year 2024-25
- Master project. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. During academic year 2024-25
- Master's dissertation. Master's in Modeling, Mathematical Research, Statistics and Computing. From the 2023-24 course to the 2024-25 course
- Systems & synthetic biology. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. From the 2021-22 course to the 2024-25 course
- Modelling of biological systems. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. From the 2021-22 course to the 2024-25 course
- Molecular biotechnology: instrumental techniques. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. From the 2021-22 course to the 2024-25 course
- Algebra II. Degree in Physics. From the 2019-20 course to the 2024-25 course
- Algebra II. Joint Program in Physics and Mathematics. From the 2019-20 course to the 2024-25 course
- Introduction to computational methods in biology. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. During academic year 2023-24
- Practical training in external companies/centres. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. During academic year 2023-24
- Simulations of biomolecules. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. During academic year 2023-24
- Undergraduate dissertation. Joint Program in Physics and Mathematics. During academic year 2023-24
- Big data in biology. Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology. From the 2022-23 course to the 2023-24 course
- Systems & synthetic biology. Master's in Quantitative Biotechnology. From the 2019-20 course to the 2020-21 course
- Biological modelling. Master's in Quantitative Biotechnology. From the 2019-20 course to the 2020-21 course
- Molecular biotechnology: instrumental techniques. Master's in Quantitative Biotechnology. From the 2019-20 course to the 2020-21 course
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