simplebooklet thumbnail

of 0
2
ND
RSG
LUXEMBOURG
CONGRESS
“BIG-DATA ANALYSIS FOR
PRECISION MEDICINE”
FRIDAY, 6
TH
OCTOBER 2017
CONGRESS PROGRAM
Mobile devs for healthcare
Lamiece Hassan (Manchester U)
Amr Sobhy (PushBots, London)
Systems biology for precision medicine
Alessandra Carbone (UPMC, Paris)
Vehpi Yildirim (TU, Eindhoven)
Workshops
Finding and accessing human genome data
(Manuel Corpas, Repositive)
High performance computing
(Sarah Peter, LCSB)
Data visualization
(Fintan McGee, LIST)
Free registration
for bachelor,
master, and PhD
students
Save the date!
6th of October 20 17
Maison du savoir
Campus Belval
Luxembourg
Join our social event!
What
comes
next?
2nd RSG Luxembourg Congress
SC I-PUB
sc i en c e pu b quiz
LUXEMBOURG
Register here: rsg-luxembourg.iscbsc.org
Mobile devs for healthcare
Lamiece Hassan (Manchester U)
Amr Sobhy (PushBots, London)
Systems biology for precision medicine
Alessandra Carbone (UPMC, Paris)
Vehpi Yildirim (TU, Eindhoven)
Workshops
Finding and accessing human genome data
(Manuel Corpas, Repositive)
High performance computing
(Sarah Peter, LCSB)
Data visualization
(Fintan McGee, LIST)
Free registration
for bachelor,
master, and PhD
students
Save the date!
6th of October 20 17
Maison du savoir
Campus Belval
Luxembourg
Join our social event!
What
comes
next?
2nd RSG Luxembourg Congress
SC I-PUB
sc i en c e pu b quiz
LUXEMBOURG
Register here: rsg-luxembourg.iscbsc.org
2
WELCOME
The 2
nd
RSG Luxembourg Congress entitled “Big Data Analysis for
Precision Medicine” is a satellite event to the 4th International Systems
Biomedicine Symposium. Our congress focusses on recent developments
in the field of big data analysis with respect to their applications in
precision medicine. In particular, machine learning techniques for
diagnosis and disease stratification will be emphasized, bringing together
different approaches in bioinformatics and deep learning. Additionally,
innovative mobile solutions in healthcare will be addressed as their
generated data constitutes a big chunk of ‘Big Data’ in healthcare.
Following the success of the 1st RSG Luxembourg National Congress in
2016, where around 40 students and young researchers participated, the
RSG Luxembourg aims at establishing this yearly event as an
international reference for young researchers and students in the fields of
computational biology and bioinformatics.
3
PROGRAM OVERVIEW
9h00 9h20 Registration and reception
9h20 9h30 Opening
Session 1 Systems biology in precision medicine
9h30 10h15 Dr. Alessandra CARBONE
Learning about protein-protein interactions at a residue
resolution
10h15 11h00 Dr. Vehpi YILDRIM
Calcium Oscillation Frequency-Sensitive Gene Regulation
and Homeostatic Compensation in Pancreatic β-Cells
First Workshop Session (in parallel)
11h00 12h30 Workshop 1: Data visualization by Fintan McGee
Workshop 2: High performance computing by Sarah Diehl
12h30 13h00 RSG Award ceremony
Outreach Session
Company Presentations by Elixir Luxembourg and Digital
Inclusion Luxembourg
13h00 14h00 Lunch break
14h00 Group photo
Session 2 Mobile solutions for healthcare
14h00 14h45 Dr. Lamiece HASSAN
Citizen driven health: engaging citizens for trustworthy
health data science
14h45 15h30 Amy SOBHY
How technology is changing healthcare?
15h30 16h00 Coffee break
Second Workshop Session
16h00 17h15 Finding and accessing human genome data
by Manuel CORPAS
17h15 17h30 Concluding remarks
17h30 18h30 General assembly RSG Luxembourg
19h Social Event
Science pub quiz at Mix ‘n Cava Bar (MK Bar)
4
DETAILED PROGRAM
9H00 9H20 REGISTRATION AND RECEPTION
The congress registration will take place in the entrance area of Maison du
Savoir (MSA) at Campus Belval, Luxembourg.
Welcome refreshments are waiting on MSA 3
rd
Floor.
9H20 9H30 OPENING
Welcome session held by the RSG Luxembourg President Eugen Bauer.
9H30 11H00 SESSION 1: SYSTEMS BIOLOGY IN PRECISION MEDICINE
The first session of the congress is dedicated to the topic “Systems Biology in
precision medicine”.
Plenary 1: 9h30 10h15 (MSA Auditorium - 3.530)
“LEARNING ABOUT PROTEIN-PROTEIN INTERACTIONS AT
A RESIDUE RESOLUTION
Dr. Alessandra CARBONE
Pierre and Marie Cury University, Paris (France)
Alessandra Carbone is Distinguished Professor of Computer Science at
UPMC and she has led the Analytical Genomics team since 2003 and is
the director of the Department of Computational and Quantitative
Biology since 2009. Her group works on computational problems
concerning the functioning and evolution of biological systems.
Mathematical methods coming from statistics and combinatorics, as well
as algorithmic tools are employed to study fundamental principles of the
cellular functioning starting from genomic data. The projects are all
aimed at understanding the basic principles of evolution and co-evolution
of molecular structures in the cell. They concern sequence evolution of
entire genomes as well as protein evolution. Alessandra Carbone received
the Prix Joliot-Curie in 2010 from the Ministère de la Recherche et de
l’Enseignement Supérieur and from the EADS Foundation, and she was
distinguished in 2012 with the Grammaticakis-Neuman Prize of the
Académie
des Sciences for “Integrative Biology”. Since 2013 she is a senior
member of the Institut Universitaire de France.
5
Abstract: Biology entered a new era, with computational biology producing
biological data that are impossible nowadays to obtain with wet experiments.
Tackling biological questions with advanced engineering, new computer
algorithms and novel computational approaches is a challenge that will lead to
revolutionize biology and medicine through deeper, ubiquitous use of DNA
information.
A fundamental question is the extraction of evolutionary information from
DNA sequences. We consider protein sequences here and we shall describe how
a precise mapping between the one-dimensional representation of a protein (its
sequence) and its three-dimensional representation (its structure) revealed
important biological information on protein-protein binding sites and on
mechanical and allosteric properties of proteins. Fine combinatorial readings of
the conservation and co-evolution signals between residues in sequences can be
used to identify protein-protein interaction (PPI) networks and describe them at
the molecular level.
PPI are at the heart of the molecular processes governing life and constitute
an increasingly important target for drug design. Given their importance, it is vital
to determine which protein interactions have functional relevance and to
characterize the protein competition inherent to crowded environments. Suitable
mathematical approaches appear necessary to properly address these questions
and, in the talk, we shall highlight the new computational challenges.
Plenary 2: 10h15 11h00 (MSA Auditorium - 3.530)
CALCIUM OSCILLATION FREQUENCY-SENSITIVE GENE
REGULATION AND HOMEOSTATIC COMPENSATION IN
PANCREATIC Β-CELLS
Dr. Yehpi YILDRIM
Technische Universiteit Eindhoven
Dr. Vehpi Yildirim is a biomathematician, who uses computational
modeling to investigate the regulation of insulin, glucose and lipid
metabolisms. He uses mathematical modeling to explore the dynamics of
insulin secretion from pancreatic β-cells and development of metabolic
abnormalities. He is affiliated to the Eindhoven University Technology as
a partner in the Resolve project (http://www.resolve-diabetes.org/). He is
currently working on the long-term effects of the bariatric surgery on the
hepatic lipoprotein secretion and insulin sensitivity in obese patients.
Abstract: Insulin is secreted from Pancreatic β-cells in a pulsatile fashion in
response to elevated blood glucose. Pulsatile insulin secretion results from the
cytosolic Ca2+ oscillations driven by the bursting electrical activity of β-cells
6
and has physiological importance for normal blood glucose regulation. In the
initiation and modulation of the oscillations, ATP-sensitive K+ ion channels
(K(ATP) channels) play the key role by coupling cell metabolism to the
membrane potential. In humans, defects in K(ATP) channel expression leads to
spontaneous β-cell activity and excessive insulin secretion, resulting in
congenital hypoglycemia. However, in genetically engineered SUR1-/- mice β-
cells, which also do not express K(ATP) channels in their plasma membranes,
Ca2+ oscillations persist and these mice have almost normal blood glucose
levels. This is surprising because, in the wild type mouse β-cells, when K(ATP)
channels are blocked with pharmacological agents oscillations are terminated.
This shows that SUR1-/- mice can compensate fr the loss of K(ATP) current by
employing alternative mechanisms in their β-cells.
Recently, in a combined modeling and experimental study, we showed that an
inward-rectifying K+ channel (Kir2.1 channel) is upregulated in K(ATP)
channel deficient SUR1-/- β-cells. Furthermore, we showed that a sufficient
upregulation in this channel can rescue slow Ca2+ oscillations in SUR1-/--cells.
However, the questions of, “How upregulation is induced?”, “What is the
sufficient level of upregulation?” and “How is this level recognized by β-cells?”
remained unanswered. In this study, we aim to address these questions. With
mathematical modeling, we show that a Ca2+ oscillation frequency sensitive
gene regulation network can dynamically tune the Kir2.1 channel conductance
to the right level and establish homeostasis in the K(ATP) channel deficient β-
cells. We explore the frequency decoding properties of this gene transcription
network and investigate the compensation dynamics in detail. We also make
testable model predictions to guide future studies.
11H00 12H30 FIRST WORKSHOP SESSION (IN PARALLEL)
Workshop 1 (MSA Room 3.380)
DATA VISUALIZATION
Dr Fintan McGee
Dr Fintan McGee is a researcher of information visualisation, in the
eScience Unit of the Environmental Research and Innovation department
at the Luxembourg Institute of Science and Technology. He received his
doctorate in computer science from Trinity College, Dublin, in 2013 for
his thesis on the visualization of small world graphs. His current areas of
research include biological pathway visualisation, multilayer graph
visualisation, visualisation evaluation, as well as the use of machine
learning to improve graph layout. He is a work package leader and co-
author of the BLIZAAR project, which is jointly funded by L'Agence
7
Nationale de la Recherche (ANR), France, and Fonds National de la
Recherche (FNR), Luxembourg. This projects looks at developing
multilayer graph visual analytics techniques that can be applied in the
domain of digital humanities and biological network analysis.
Abstract: The goal of this workshop is to empower students to better
understand and visualise their data. We will examine the motivation behind data
visualization, why you should do it, and what benefits it offers. We will examine
the theoretical aspects and how they impact important design choices. Following
the why we will next look at the how, describing visualization approaches for
different types of data and different types of problems. We will examine several
freely available tools and technologies and demonstrate how they can be used to
visualize your data. We will also examine the concept of visual analytics, the
coupling of analytical techniques with powerful interactive visualizations.
Workshop 2 (MSA Room 3.390)
HIGH PERFORMANCE COMPUTING
Dr. Sarah Diehl
About Person
Abstract:
12H30 13H00 RSG AWARD CEREMONY & OUTREACH SESSION
(MSA AUDITORIUM - 3.530)
RSG Award
The 2017 International Society for Computational Biology Student
Council´s Regional Student Group Luxembourg award is attributed to Mr.
Venkata Pardhasaradhi SATAGOPAM for service to profession and
support to student groups in bioinformatics and computational biology.
Outreach session
ELIXIR LUXEMBOURG A DATA HUB FOR TRANSLATIONAL
MEDICINE
ELIXIR-LU, the Luxembourgish Node, focuses on long-term
sustainability of tools and data for Translational Medicine.
8
Translational Medicine data integrate clinical information with molecular
and cellular data for a better understanding of diseases. They bridge the
gap between the molecular level, findings from the laboratory, and the
clinical observations and applications.
ELIXIR-LU aims to facilitate long-term access to those research data and
to tools for scientists in both academia and industry. This will allow the
reuse of previously generated translational data to address new research
questions and dramatically save time and cost.
DIGITAL INCLUSION
Digital Inclusion a.s.b.l. is a non-profit organization in Luxembourg
seeking to help everybody access information technology and computing.
13H00 14H00 LUNCH BREAK & GROUP PHOTO
Please join us for the group photo 14h00 in the lunch area.
14H00 15H30 SESSION 2: MOBILE SOLUTIONS FOR
HEALTHCARE
Plenary 3: 14h00 14h45 (MSA Auditorium - 3.530)
HOW TECHNOLOGY IS CHANGING HEALTHCARE?
Amr SOBHI
Amr Sobhy is a multi-disciplinary Egyptian information activist and
entrepreneur. Amr formerly helped to shape youth policy at the World
Bank and advised on technology for Internews Europe. Sobhy has been
named by Forbes amongst the 30 Most Promising Young Entrepreneurs in
Africa 2017 for his work on PushBots a SaaS mobile startup serving
more than 70M people globally. In addition, He has been named amongst
the top 100 Influential Young Africans in August, 2017. Sobhy’s work in
the nexus between technology and advocacy includes him as the co-
creator of MorsiMeter; a digital online platform to document and monitor
the performance of Egyptian President, Mohamed Morsi and Mwazna; a
digital platform to open government budget to everyone for which he was
9
nominated for the Data Journalism Award 2016. Amr has a Masters
degree in Public Policy from Birkbeck, University of London.
Abstract: A 360 degree view on the different trends of exponential technologies
changing the health care process.
Plenary 4: 14h45 - 15h30 (MSA Auditorium - 3.530)
CITIZEN DRIVEN HEALTH: ENGAGING CITIZENS FOR
TRUSTWORTHY HEALTH DATA SCIENCE
Dr. Lamiece HASSAN
Dr Lamiece Hassan is a health services researcher and public
engagement expert at the Centre for Health Informatics at The University
of Manchester in England. There she leads digital health research with a
strong element of public involvement, engagement and/or participatory
methods across a range of health informatics projects including asthma,
dementia and childhood obesity. Her research interests include public
opinion on the reuse of health data, citizen science methodologies and
digital health co-design. Lamiece has a PhD in psychiatric epidemiology
and currently works for the Connected Health Cities programme, a major
government-funded initiative to trial learning health systems in the North
of England.
Abstract: Rapid advancements in data and data science mean that there are
more ways than ever to collect, combine, analyse and interpret data about our
health and care. Nonetheless, whilst ‘big data’ undeniably offers promise for
improving future population health, concerns about threats to privacy,
confidentiality and security remain. In this talk I will discuss the value of
engaging citizens in the design and delivery of health data science research to
understand public opinion and build public trust, providing examples from the
UK of how we have achieved this in the context of big data and m-health
research.
15H30 16H00 COFFEE BREAK
16H00 17H15 SECOND WORKSHOP SESSION
(MSA AUDITORIUM - 3.530)
10
FINDING AND ACCESSING HUMAN GENOME DATA
Dr. Manuel CORPAS
Dr. Corpas is an experienced community builder and scientific
communications strategist in Genomics and Computational Biology.
Currently based in Cambridge, UK, he is the Scientific Lead at
Repositive, a genome data sharing platform company. Before Repositive,
Corpas was a 2016 fellow of the Software Sustainability Institute and
Project Leader at The Genome Analysis Centre (now Earlham Institute,
Norwich, UK). There he was Technical Coordinator of the Bioinformatics
Research Infrastructure ELIXIR-UK, coordinator of the BioJS open
source community and Chair of the Technical Committee for the Global
Organisation for Bioinformatics Learning, Education and Training
(GOBLET). While doing he graduate studies he became Founder and
Inaugural Chair for the International Society for Computational Biology
(ISCB) Student Council (2004), the leading student body in
Computational Biology. Later in his career, he was elected ISCB Board of
Directors (2013-2016). He holds a Ph.D. in Computer Science from the
University of Manchester, UK, and did his postdoctoral work in clinical
genomics at the Wellcome Trust Sanger Institute, Cambridge, developing
the DECIPHER database, a widely-used clinical interpretation resource
for patients with rare genomic disorders. Dr. Corpas is a prolific author
and speaker, with circa 50 authored scientific publications and the
acclaimed ‘Perfect DNA’ book; a speculative futuristic novel exploring
the ethical and social implications of personal genetic testing in society.
His blog https://personalgenomics.zone/ is followed by ~3,000
subscribers and serves The Precision Medicine Podcast, a podcast about
current technological and ethical advancements and challenges in
Precision Medicine.
17H15 17H30 CONCLUDING REMARKS
17H30 18H30 GENERAL ASSEMBLY RSG LUXEMBOURG
11
SPONSORS
12
PICTURES FROM LAST YEARS CONGRESS
13