Non-globular proteins in the era of Machine Learning

COST Action CA21160

MEET THE TEAM

CORE GROUP

Dr. Alexander MONZON

Action Chair

Department of Information Engineering University of Padova, Italy

Dr. Alexander MONZON

Action Chair

Alexander Monzon is an associate professor (RTDA researcher) in the Department of Information Engineering at the University of Padova, Italy. He obtained his Bioinformatics degree (BSc/MSc) in 2012 from the National University of Entre Ríos (Oro Verde, Entre Ríos, Argentina) and his PhD in Basic and Applied Sciences in 2018 from the National University of Quilmes (Buenos Aires, Argentina). After completing his doctoral studies, Alexander received the MSCA “Seal of Excellence” fellowship at the University of Padova and joined the research group of Prof. Silvio Tosatto at the Department of Biomedical Sciences. He spent four years as a postgraduate researcher before being appointed to a Junior Faculty position in 2022 within the Department of Information Engineering at the University of Padova. During his doctoral training, Alexander specialized in the field of Structural Bioinformatics under the guidance of Dr. Gustavo Parisi. He focused on developing the CoDNaS database, which explores conformational diversity in the native state of proteins. His work in this area resulted in several publications in high-impact journals. Alexander continued his postdoctoral training in Prof. Silvio Tosatto’s group, where he currently conducts research on non-globular proteins, specifically disordered and repetitive proteins. Alexander has made significant contributions to the field of Bioinformatics and has co-authored several important databases, including DisProt, RepeatsDB, MobiDB, PED, and FuzDB. These databases represent the current state-of-the-art knowledge in the structural biology of non-globular proteins. He actively participates in various networks, scientific societies, and international consortia, such as the ISCB student council, A2B2C, COST-action “NGP-net,” MSCA RISE “IDPfun” and “REFRACT”, and the H2020 Twinning project “PhasAGE” Additionally, he was the main proposer of the COST action “ML4NGP.”

Phone:+390498276269
Email:alexander.monzon@unipd.it

Dr. Zuzana BEDNÁRIKOVÁ

Action Vice-Chair

Institute of Experimental Physics, Slovak Academy of Sciences, Slovakia

Dr. Zuzana BEDNÁRIKOVÁ

Action Vice-Chair

Zuzana Bednarikova is a postdoctoral researcher at the Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences in Košice. She obtained her PhD in Biochemistry from Safarik University in Košice in 2016. Afterwards, she received a long-term postdoctoral fellowship awarded by the Slovak Academy of Sciences (2017-2021). As a member of the Dr. Zuzana Gazova research group, she is working on the mechanism of intrinsically disordered protein amyloid formation, focusing on Amyloid β peptides and identification of potential inhibitors with implications for Alzheimer's disease novel treatment strategies.

Phone:+421557204137
Email:bednarikova@saske.sk

Dr. Pavel KADEŘÁVEK

Working Group Leader (WP1)

Central European Institute of Technology, Masaryk University, Czech Republic

Dr. Pavel KADEŘÁVEK

Working Group Leader (WP1)

Pavel Kadeřávek is a researcher at the Central European Institute of Technology (CEITEC) at Masaryk University in Brno. He obtained her PhD in Biomolecular chemistry at Masaryk University in Brno in 2013 under the supervision of doc. Radovan FIala, then he worked as a postdoc at EPFL in Lausanne (École Polytechnique Fédérale de Lausanne) under the supervision of Prof. Geoffrey Bodenhausen, at Masaryk University in Brno under the supervision of Prof. Lukáš Žídek, and at École Normale Supérieure (ENS) in Paris under the supervision of Prof. Fabien Ferrage. His main research interest is focused on investigation of biomolecules using nuclear magnetic resonance (NMR), development NMR methodology and design of new NMR experiments. Particularly he is interested in studies of dynamics of proteins at various timescales including intrinsically disordered proteins and regions present for example within bacterial RNA polymerase or represented by neuronal microtubule associated proteins.

Phone:+420549496425
Email:pavel.kaderavek@ceitec.muni.cz

Dr. Dana REICHMANN

Working Group Co-Leader (WP1)

The Hebrew University of Jerusalem, Israel

Dr. Dana REICHMANN

Working Group Co-Leader (WP1)

Dana Reichmann is an Associate Professor at the Hebrew Univeristy of Jerusalem and the Vice President of the Israel Society of Biochemistry and Molecular Biology. The Reichmann’s lab is interested in molecular structures and dynamic protein assemblies, formed during physiological stress conditions and aging. One of the major focuses of her lab is understanding how cells maintain their “healthy” and complex protein structures during increased oxidation, which is one of the main hallmarks of aging and age-related diseases (e.g., Alzheimer, Parkinson and others). The Reichmann lab aims to unravel the mystery of the cellular “redox code” in the context of protein quality control. To archive this goal, the lab is utilizing and developing an extensive toolbox of technologies including in-vivo fluorescence-based sensors and cutting-edge mass spectrometry technology to map conformational changes in proteins upon interactions, modifications and stress conditions.

Phone:(+972) 2-658-6952
Email:danare@mail.huji.ac.il

Dr. Zsuzsanna DOSZTÁNYI

Working Group Leader (WP2)

Institute of Biology, Hungary

Dr. Zsuzsanna DOSZTÁNYI

Working Group Leader (WP2)

Phone:+303079335
Email:zsuzsanna.dosztanyi@ttk.elte.hu

Dr. Javier GARCIA-PARDO

Working Group Co-Leader (WP2)

Universitat Autònoma de Barcelona, Spain

Dr. Javier GARCIA-PARDO

Working Group Co-Leader (WP2)

Javier Garcia-Pardo is currently a Juan de la Cierva Scientist at the Institut de Biotecnologia i de Biomedicina (Universitat Autònoma de Barcelona, IBB-UAB, Spain). During his PhD, he studied structure and function of relevant human proteases and their inhibitors under the supervision of Prof. FX Avilés at IBB-UAB. After the PhD, he visited the lab of Sir. T. Blundell (University of Cambridge, UK), where he obtained large skills in structural biology. One of the major achievements of his career during this period was the discovery of a pivotal mechanism regulating the substrate specificity of carboxypeptidase O, a novel digestive enzyme with a unique affinity for acidic residues. This groundbreaking discovery was the result of collaborative efforts with Prof. R. Huber at the Max Planck Institute, Germany, and Prof. David Reverter at IBB-UAB. In 2018, he moved to Frankfurt am Main to join the group of Prof. Ivan Dikic at the Buchman Institute for Molecular Life Sciences (BMLS, Germany) as a senior scientist. During his time in Frankfurt, Javier concentrated his research on identifying novel compounds that target the NF-kB pathway and on providing structural insights into reticulons, a group of conserved ER-resident proteins involved in membrane curving. More recently, Javier has returned to IBB-UAB, where he currently leads various research projects focused on the structural characterization of amyloid fibrils using cryo-EM, as well as their applications in Nanotechnology. Additionally, he is actively engaged in the development of innovative computational tools to study protein disorder and aggregation.

Email:javiergarciapardo@msn.com

Dr. Jovana KOVAČEVIĆ

Working Group Leader (WP3)

Faculty of Mathematics, Belgrade University, Serbia

Dr. Jovana KOVAČEVIĆ

Working Group Leader (WP3)

Jovana is an assistant professor at the Department for Computer Science and Informatics, Faculty of Mathematics, Belgrade University, Serbia, where she received her Ph.D. in bioinformatics. The key area of her scientific interest is the application of machine learning techniques on biological data with emphasis on protein function and disordered proteins. Her lecturing activities include bioinformatics courses at the master and Ph.D. study programmes.

Phone:381648650190
Email:jovana@matf.bg.ac.rs

Dr. Milana GRBIC

Working Group Co-Leader (WP3)

Faculty of Natural Science and Mathematics, University of Banja Luka, Bosnia & Herzegovina

Dr. Milana GRBIC

Working Group Co-Leader (WP3)

Milana is an assistant professor at the Department for Mathematics and Computer Science, Faculty of Natural Science and Mathematics, University of Banja Luka. She received her Ph.D. in bioinformatics at the Faculty of Mathematics, University of Belgrade, Serbia. The key area of her scientific interest is the application of machine learning and combinatorial optimization techniques for the analysis of biological networks. Her lecturing activities include bioinformatics and data mining courses at the bachelor's and master's study programs.

Phone:0038765828713
Email:milana.grbic@pmf.unibl.org

Dr. Gonzalo PARRA

Working Group Leader (WP4)

Barcelona Supercomputing Center, Spain.

Dr. Gonzalo PARRA

Working Group Leader (WP4)

R. Gonzalo Parra is an Argentinian postdoctoral researcher within the Computational Biology group led by Prof. Alfonso Valencia. His research mainly focuses on Structural Bioinformatics and Single Cell Multiomics data. He obtained his PhD from Buenos Aires University in 2016 under Prof. Diego Ferreiro’s supervision. He obtained a EMBO long-term postdoctoral fellowship and joined the group of Dr. Johannes Soeding at the Max Planck Institute for Biophysical Chemistry in Goettingen Germany (2016-2018). Afterwards, he joined the group of Prof. Oliver Stegle at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany (2018-2021). In addition, Gonzalo participates in different international organizations that promote bioinformatics. He is the current ISCB Student Council Board of Directors Representative and participates in the advisory boards of the Bioinfo4Women initiative and the 3DBioinfo Elixir Community.

Phone:+34934137716
Email:parra.gonzalo@gmail.com

Dr. Ana MELO

Working Group Co-Leader (WP4)

Instituto Superior Técnico, University of Lisbon, Portugal

Dr. Ana MELO

Working Group Co-Leader (WP4)

Ana M Melo is a Young PI at Institute for Bioengineering and Bioscience (iBB) of Instituto Superior Técnico (IST), University of Lisbon (ULisbon). She is currently an Independent Junior Researcher under CEEC-Individual call – 1st Edition funded by FCT (PT Science Foundation). In addition, she is an Invited Assistant Professor at the Department of Bioengineering at IST. Ana M Melo holds a BSc and MSc in Biochemistry (2007 and 2009) from Faculty of Sciences, ULisbon. She obtained her PhD in Chemistry (Jan 2014) at IST- ULisbon under supervision of Prof. Manuel Prieto / Ana Coutinho. She was then a Postdoc at the Laboratory of Prof. Elizabeth Rhoades (USA) - initially at Yale University and later at University of Pennsylvania (Feb 2014–Sept 2017). To pursue her scientific independence, Ana M Melo returned to Portugal in Oct 2017. She secured highly competitive fundings as PI of 3 grants (total 318.2K Eur) that allowed her to build the first smFRET microscope in Portugal and implement a new research line at iBB-IST. Her research is focused on the development of innovative single-molecule based approaches to study aggregation-prone IDPs involved in neurodegeneration, including tau protein (Alzheimer´s disease) and huntingtin exon 1 (Huntington´s disease).

Email:anammelo@tecnico.ulisboa.pt

Dr. Rita VILAÇA

Working Group Leader (WP5) Science Communication Coordinator

Instituto de Investigação e Inovação em Saúde (i3S), Portugal

Dr. Rita VILAÇA

Working Group Leader (WP5) Science Communication Coordinator

Rita Vilaça has a PhD in Biomedical Sciences from University of Porto and performed post-doc studies at Center for Neuroscience and Cell Biology at University of Coimbra. She has a solid research background on cell signaling modulation in aging and age-related disorders, particularly lysosomal storage diseases and polyglutamine disorders. Rita has more than 15 years working in science education and communication and is certified with Trainer Accreditation in Biology and Health Sciences.

Phone:+351 226 074 900
Email:ritavilacawork@gmail.com

Prof. Silvio TOSATTO

Grant Holder Scientific Representative

Department of Biomedical Sciences, University of Padova, Italy

Prof. Silvio TOSATTO

Grant Holder Scientific Representative

Silvio Tosatto’s research covers several aspects of what is generally termed bioinformatics and computational biology. The lab’s main aim is to integrate the development of novel methods and their application to biologically relevant issues.

Dr. Darius ŠULSKIS

Grant Awarding Coordinator

Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania

Dr. Darius ŠULSKIS

Grant Awarding Coordinator

Darius Šulskis is a postdoctoral researcher at the Institute of Biotechnology, Life Science Center, Vilnius University. He obtained a PhD at the University of Gothenburg in 2022, specializing in various biochemistry, and biophysics techniques. His project involved deciphering bacterial protease DegP activation mechanism using high-resolution NMR spectroscopy. Currently, he is investigating how various proteins form amyloid fibrils, interact with each other and learning to solve their structures with Cryo-EM.

Phone:+37069221885
Email:sulskis.d@gmail.com