Keynote Lectures

Vladimir Filkov, PhD
Professor at Computer Science Department, University of California, Davis, USA

Reconstructing Gene Networks of Forest Trees From Gene Expression Data

Abstract: Plants modify their growth and development in response to external stimuli. As trees grow, they integrate environmental and developmental signals using complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. Here I will present two of our recent systems biology studies in which we reconstruct gene networks active in wood tissue development and formation. To do that we used two different approaches. In the first, we integrated data from new and available transcriptome profiling, transcription factor binding, DNA accessibility and genome‐wide association mapping experiments, to identify relationships among genes expressed during wood formation. In the second, we more finely dissect the temporal changes in gene expression underlying wood formation in poplar tree stems. We used time‐series analysis of 7 time points over a 14‐day experiment to identify genes differentially expressed between tension wood (upper) and opposite wood (lower) sides of the leaning stems. We demonstrate that these approaches can be used for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.

Bio: Vladimir Filkov received his PhD in Computer Science from Stony Brook University in 2002. He is currently a Co-Director of the DECAL Lab and Full Professor of Computer Science at the University of California. His research interests lie in understanding the organization and effectiveness of large and complex systems, including biological organisms (mainly plants) and socio-technical systems of online teams (mainly computer programmers), using quantitative modeling methods on big data sets. Prof. Filkov's research has been funded by the USA NSF, USDA, USFS, AFOSR, and other agencies. Prof. Filkov's has been fortunate to have advised talented students and postdocs, who now work on the faculty at top universities in the world, and in leading research and industry organizations. His papers have received five best paper awards and other recognitions. Prof. Filkov is member of the ACM.

Susanne Hollmann, PhD
Scientific Manager at University of Potsdam, CEO of SB ScienceManagement, Germany

Standardisation in life-science research - crucially needed or unnecessary and annoying regulation?

Abstract: In the past, up to 98% of the research data generated have been lost by poor storage conditions, outdated or unusable formats, missing backup’s, incomplete or unpublished work and finally by inefficient documentation. This loss of data caused extremely high costs because the missing transparency and reproducibility of data required the repeated use of resources, time and manpower and was hindering a continuous advancement of knowledge and to innovation. The implementation of open access publication and FAIR data principles within the European Framework programs has been logical consequence and the first step to overcome this hurdles. It is now widely recognized that making research results more accessible to all societal actors contributes to better and more efficient science, and to innovation in the public and private sectors.

However, there are still some barriers to overcome: Looking to the FAIR data principles, you will realize that these principles mainly refer to the Meta data levels in research and the quality of the source data sets remains often unaddressed. Hence, even if the data sets are published following the FAIR data principles, the quality of the data might be insufficient and remains shrouded in mystery. Further calculations, analysis and proceedings based on such metadata needs to be questioned. The same applies for publications. The source data are not always being considered very critically.

But, in good laboratory practice well defined and precisely described techniques, methods and protocols are mandatory for optimal and reproducible conditions, for making possible any interlaboratory comparability of data and scientific results obtained and for further and future use of data sets.

The members of the COST Action CHARME therefore suggest implementing a SEAL OF QUALITY for the generation of data. But, is a seal of quality crucially needed or additional unnecessary and annoying regulation?

Bio: Dr. Susanne Hollmann is chemist and biochemist by training. She holds a Ph.D. in Biochemistry and used to work as a postdoc for both- industry and academia. Dr. Hollmann was one of the managers for the first German funding program FORSYS on systems biology and participated in the development of a business concept for a European infrastructure on systems biology. Dr. Hollmann is member of the ISO TC 276 on “Standardization in Biotechnology” and has long-term expertise in the development of standard operating procedures (SOP), which form the prerequisite for subsequent translation of research results into application. Dr. Hollmann is initiator and coordinator of the COST Action CHARME bringing together 30 countries to work on the harmonization of standards in the life sciences. She has long-term and outstanding expertise in the development and management of scientific projects, especially in EC programs and German funding initiatives. Dr. Hollmann does work as scientific manager for the Potsdam Research centre for Plant genomics and Systems Biology. In addition she works at her company SB-ScienceManagement UG, a spin-off of Potsdam University, founded in 2014.

Vesna Prchkovska, PhD
COO and Co-Founder of QMenta, Spain

The future of Brain Imaging

Abstract: Neuroimaging has advanced rapidly in the last two decades. The MRI scanners are getting more powerful offering rich data that can provide detailed insights on the brain structure and function. New computational tools are being developed at a fast pace, and machine learning and big data are the new trends in brain imaging. In this talk I will address some of the most notable advancements in the brain imaging in the recent years from reconstruction to visualisation and interaction techniques. Furthermore, I will talk about the future of brain imaging and patent care.

Bio: Vesna graduated with honors from the Faculty of Electrical Engineering at Ss. Cyril and Methodius University in Skopje, Macedonia, in 2006. After being awarded an NWO-Veni PhD Scholarship, she obtained her PhD at the Eindhoven University of Technology, Netherlands in 2010 and based her doctoral degree in novel diffusion-based MRI medical imaging models, specifically focusing on HARDI and DTI. Later, she was awarded the prestigious grant by European Commission - Marie Curie Intra-European fellowship and she became a postdoctoral research fellow at the Institut D’Investigacıons Biomediques August Pi i Sunyer at Hospital Clinic, in Barcelona from 2013 to 2015 where she researched neurological disorders, focused on brain connectomics, more specifically, modeling the disconnection syndrome in patients with Multiple Sclerosis. In 2013, she was a postdoctoral research fellow at the joint Department of Radiology of Mass General Hospital and Harvard Medical School where she explored network and graph- based theory applied to brain connectivity matrices from diffusion MRI and fMRI in healthy subjects and patients with Neurodegenerative diseases. After co-founding QMENTA, she is now the acting COO of the company, responsible for the day to day operations, R&D, communications with the scientific and medical communities, publications, and patenting algorithms.

Aleksandar Rodikj, PhD
Head of Robotics Laboratory Mihajlo Pupin Institute, Serbia

How far humans are from the time singular-point when robots will become superior?

Abstract: Human civilization is in its long history passed through many delicate phases of its development, fighting for their biological survival, surviving a brutal interethnic conflicts, natural disasters and large-scale epidemiological murders, experiencing their ups and downs through several techno-economic industrial revolutions globally stratifying divided into technologically developed and undeveloped communities (societies). Industrial revolutions in the 19th and 20th centuries contributed to the progress of humankind leaps and bounds, the rise of science and increasing the comfort and overall quality of life. Nowadays, on the scene is the so called 4th industrial revolution, whose main features are mass digitization, global communication and high automation and robotization of industry and society. On this wave of rapid development of mankind, Robotics as a highly interdisciplinary science, has built a sophisticated machines for the first time in the history of human civilization reached the level of skills, physical and intellectual, which can be comparable to the human skills. Are the robots created in the race for greater economic profit of rich industrialists or are they designed to help people in that times of major natural challenges (industrial pollution, climate change, risks from the Cosmos, etc.) to survive and prolong their biological type in the following centuries? This will be discussed within this presentation. There will also be exposed a substantial analysis meaning, can we expect (and when) the robots, as imitations of people (technology clones), once to become superior to their biological models – human beings?

Bio: Aleksandar Rodić (http://www.pupin.rs/RnDProfile/rodic.html) received BSc in Mechanical Engineering in 1985, MSc and PhD degrees in Electrical Engineering successively in 1992 and 1998 from the University of Belgrade, Serbia. Since 1987 he is with IMP Robotics Laboratory where he is currently at the position of Head of Department and Vicepresident of the Assembly of the Mihajlo Pupin Institute. Primary research interests of Prof. A. Rodić are in areas of robotics, bio-inspired and large scale dynamic systems, control and stability, cognitive autonomous systems, artificial intelligence, human-machine interface, etc. He is author of more than 140 scientific papers, several research monographs, editor of several books by Springer publishing house, member of three editorial boards of international scientific journals. He chaired international scientific meetings MeSRoB2013, RAAD 2016 and EIROBOTS2017. Dr. Rodić is member of the Scientific Board of the leading national conference on robotics and automation – ETRAN and International Scientific Committee of the RAAD (Robotics in Alpe-Adria-Danube Region). Thrice (2001/2002, 2005, 2015) he was Alexander von Humboldt research fellow (TU Braunschweig, TU Kaiserslautern). Visiting professor at the University of Reunion, France (2004-2014), Adjunct professor at the University of Szeged (Hungary) 2009, Visiting professor at the ANHUI University of Technology, China, from 2014. Currently, Prof. Rodić teaches robotics and autonomous systems at the Faculty of Electrical Engineering, University of Belgrade at the Doctoral studies program. Prof. Rodić was international memeber of several PhD committees for assesement doctoral theses of the candidates at the universities in France, Germany and Spain. He was member of National Scientific Council for Technology Development in Electronics, Telecommunication and Informatics with Serbian Ministry of Education, Science and Technology Development (2011-2016), from 2017 member of the Scientific Council for Technology Development in Mechanical Engineering and Industrial Software. Prof. Rodić has led many international and national research projects.