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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="">
<meta name="author" content="">
<title>DALS 2022</title>
<!-- Bootstrap core CSS -->
<link href="vendor/bootstrap/css/bootstrap.min.css" rel="stylesheet">
<!-- Custom styles for this template -->
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<body id="page-top">
<!-- Navigation -->
<nav class="navbar navbar-expand-lg navbar-dark bg-dark fixed-top" id="mainNav">
<div class="container">
<a class="navbar-brand js-scroll-trigger" href="#page-top">DALS 2022</a>
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<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="navbar-nav ml-auto">
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#about">About</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#topics">Topics of Interest</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#submission">Submission</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#special_issue">Special Issue</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#dates">Important Dates</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#Chairs">Chairs</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#committee">Committee</a>
</li>
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<a class="nav-link js-scroll-trigger" href="#program">Program</a>
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<!-- <li class="nav-item">-->
<!-- <a class="nav-link js-scroll-trigger" href="#collaborations">Collaborations</a>-->
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<header class="text-black-50" style="background-image: url('imgs/scenario_bg.jpg'); min-height: 27rem;">
<div class="container text-center">
<h1>The 1<sup>st</sup> International Workshop <br> on Data Analysis in Life Science</h1>
<!-- <img src="imgs/logo2022.png" alt="Logo CMLS" class="logo-cmls" width="320">-->
<br><br>
<h3>19-23 September, 2022 in Grenoble, France</h3>
<h4 style="color:red;opacity: 0.7;">Online workshop</h4>
<!--<h3 style="color:red">Held virtually</h3>-->
<br>
<h4>In conjunction with the
European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases
(ECML PKDD 2022)</h4>
</div>
</header>
<section id="about">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>About</h2>
<p class="text-justify lead">
Data Scientists play a fundamental role in analyzing biological, genomics, and health care data, in
particular, to pave the ground to personalized medicine. Indeed, such data need to be properly
managed, integrated, and analyzed employing statistical inference tools as well as machine learning,
data mining, and deep learning methods. Indeed, an increasing number of data scientists are actively
working with bio-data, with many different goals, including patient stratification, personalized
medicine, drug, and therapy design. Furthermore, analyzing and mining the public large biological
and clinical databases (e.g.,
<a href="https://www.encodeproject.org/">ENCODE</a>,
<a href="https://sites.broadinstitute.org/ccle/">CCLE</a>,
<a href="https://portal.gdc.cancer.gov/">GDC</a>,
and
<a href="https://mimic.mit.edu/">MIMIC</a>)
have already proven to be paramount for
knowledge discovery. Thus, the Data Science community may benefit from learning and sharing the
various approaches that have been developed to deal with biological and clinical data.
</p>
<p class="text-justify lead">
The workshop will gather researchers with expertise in data management and analysis, machine
learning, and knowledge discovery applied to bioinformatics, healthcare, and life science problems.
This workshop aims to share current cutting-edge data science methodologies and their applications.
It will be an opportunity for researchers to meet and share their ideas on improving data-driven
personalized medicine, genetic data management, and health care system advancement. </p>
</p>
</div>
</div>
</div>
</section>
<section id="topics">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Topics of interest</h2>
<p class="text-justify lead">The topics of interest include, but are not limited to:</p>
<ul class="lead">
<li>Visualization and exploratory analysis methods for genomic and health care data</li>
<li>Data analysis of genomics and molecular biology data</li>
<li>Knowledge discovery from biological and clinical databases</li>
<li>Analysis of electronic health records (EHR)</li>
<li>Data analysis of heterogeneous health information systems and databases</li>
<li>Natural language processing methods applied to genomics and healthcare data</li>
<li>Tracking and visualization of the viral sequences</li>
<li>Machine learning methods applied to viral sequences</li>
<li>Deep learning methods for bioinformatics and biomedical images</li>
<li>Data pre-processing approaches for single-cell data</li>
<li>Single-cell data analysis</li>
<li>Data integration practices for precision medicine</li>
<li>Network-based approaches for genomic data analysis</li>
</ul>
<p class="text-justify lead">
We invite contributions from both industry and academia to share their research and experience in
using data science, machine learning and database knowledge practices with biological and clinical
data.
</p>
</div>
</div>
</div>
</section>
<section id="program">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Program</h2>
<p class="text-justify">DALS 2022 will take place Monday, September the 19th starting at 9:00AM (CET). The program of the workshop follows:</p>
<div class="col-lg-8 mx-auto">
<p class="lead">
<b>9:00-9:15</b>, Welcome and Introduction
</p>
<p class="lead">
<b>9:15-10:15</b>, Keynote by Anna Bernasconi: Data analysis for unveiling the SARS-CoV-2 evolution<br>
<b>Abstract: </b> The COVID-19 epidemic has brought enormous attention to the genetics of viral infection and the corresponding disease. In this seminar, I will provide a viral genomic primer. Then, I will discuss the potential of big data in this domain, especially when millions of SARS-CoV-2 sequences are available on open databases.
I will present a collection of current analysis problems, focusing on viral evolution, monitoring of variants, and the categorization of their effects. Finally, I will hint at open problems that should attract the interest of data scientists.<br>
<b>Biography: </b> Anna Bernasconi is a postdoctoral researcher with the Dipartimento di Elettronica, Informazione e Bioingegneria at Politecnico di Milano and a visiting researcher at Universitat Politècnica de València. Her research areas are Bioinformatics, Databases, and Data Science, where she applies conceptual modeling, data integration, and semantic web technologies to biological and genomic data. Starting from a Ph.D. thesis on the modeling and integration of data and metadata of human genomic datasets, she has then extended her expertise to the fastly growing field of viral genomics, particularly relevant since the COVID-19 pandemic outbreak. She is active in the conceptual modeling and database communities, with several paper presentations and the organization of tutorials and workshops.
</p>
<p class="lead">
<b>10:15-10:45</b>, Paper presentation: I-CONVEX: Fast and Accurate de Novo Transcriptome Recovery from Long Reads.
</p>
<p class="lead">
<b>10:45-11:15</b>, Paper presentation: Italian debate on measles vaccination: how Twitter data highlight communities and polarity.
</p>
</div>
</div>
</div>
</div>
</section>
<!--<section id="accepted">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Accepted papers</h2>
<p class="text-justify lead">
This is the list of accepted papers for CMLS 2020:</p>
<ul class="lead">
<li>Mireia Costa, Ana León, and Óscar Pastor. <i>The Importance of the Temporal Dimension in
Identifying Relevant Genomic Variants: a Case Study</i></li>
<li>Alberto García and Juan C. Casamayor. <i>Towards the Generation of a Species-Independent
Conceptual Schema of the Genome</i></li>
<li>Mohammed R. Elkobaisi, Heinrich C. Mayr, and Vladimir A. Shekhovtsov. <i>Conceptual Human
Emotion Modeling (HEM)</i></li>
<li>Pietro Crovari, Sara Pidò, and Franca Garzotto. <i>Towards an Ontology for Bioinformatics
Research Process</i></li>
<li>Giuseppe Agapito and Mario Cannataro. <i>Using BioPAX-Parser (BiP) to annotate lists of
biological entities with pathway data</i></li>
<li>Cristian Tristão and Antonio Basilio de Miranda, Edward Hermann Haeusler, Sergio Lifschitz. <i>Relational
Text-type for Biological Sequences</i></li>
</ul>
</div>
</div>
</div>
</section>-->
<section id="submission">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Paper submission guidelines</h2>
<p class="text-justify lead">
Papers must be written in English and formatted according to the
<a href="http://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines">Springer
LNCS guidelines</a>.
<br>
Authors can submit their manuscript using the <a href="https://easychair.org/conferences/?conf=dals2022">EasyChair platforms.</a>.<br/>
Submissions may not exceed 12 pages in PDF format for full papers, respectively 6 pages for
short or demo papers, including figures and references.
Submitted papers must be original work that has not appeared in and is not under consideration for
another conference or journal. Work in progress is welcome, but preliminary results should be made
available as a proof of concept. Submissions only consisting of a proposal will be rejected.
<br>
At least one author should commit to present their work at the workshop.
</p>
</div>
</div>
</div>
</section>
<!--<section id="cameraready">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<strike><h2>Camera-ready guidelines</h2></strike>
<strike><p class="text-justify lead">
For the preparation of their manuscript camera-ready version, authors should consult <a
href="ftp://ftp.springernature.com/cs-proceeding/svproc/guidelines/Springer_Guidelines_for_Authors_of_Proceedings.pdf">Springer’s
authors’ guidelines</a>
and use their <a
href="https://www.springer.com/de/it-informatik/lncs/conference-proceedings-guidelines">proceedings
templates</a>, either for LaTeX or for Word,
for the preparation of their papers. The page limit for workshop papers is 10 pages, as for the
previously submitted version.
Springer encourages authors to include their ORCIDs in their papers.
<br><br>
In addition, the corresponding author of each paper, acting on behalf of all of the authors of that
paper,
must complete and sign a <a
href="https://drive.google.com/file/d/1FL5_jFrqayqbPRZ2nTuNKaY55_8L8xD8/view?usp=sharing">Consent-to-Publish
form</a>.
The corresponding author signing the copyright form
should match the corresponding author marked on the paper.
Once the files have been sent to Springer, changes relating to the authorship of the papers cannot
be made.
</p></strike>
</div>
</div>
</div>
</section>
-->
<section id="special_issue">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Post-conference publication</h2>
<p class="text-justify lead">
<!--The papers accepted to the workshop's last edition CMLS 2022,
published within the Springer volume <a
href="https://link.springer.com/book/10.1007/978-3-030-65847-2">Advances in Conceptual
Modeling</a>,
have been invited to submit a revised and extended version
for a post-conference supplement in the journal
<a
href="https://bmcbioinformatics.biomedcentral.com/" target="_blank"><b>BMC
Bioinformatics</b></a>
journal (2-year IF 2.511, SJR 1.374).
We are working towards an agreement with the same journal also for this year.-->
Accepted papers will be published by Springer as joint proceedings of several ECML PKDD workshops.
We are working towards a preliminary agreement with <a
href="https://bmcbioinformatics.biomedcentral.com/" target="_blank"><b>BMC
Bioinformatics</b></a> journal (2-year Impact Factor: 3.169)
for a <b>post-conference supplement</b> related to Data modeling, Processing and Analysis for Life Sciences.
If the agreement is reached, all the papers accepted to our workshop will be invited
to submit a revised and extended version to the journal supplement.
</p>
<!--<p class="text-justify lead">For the <b>best paper</b> of the workshop (as assessed by the evaluations
of the members of the Program Committee) the <b>Article Processing Charges of the BMC Bioinformatics
supplement will be fully covered</b> by the organizers (GeCo at Politecnico di Milano & PROS at
Universitat Politècnica de València).-->
</p>
</div>
</div>
</div>
</section>
<section id="dates">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Important dates</h2>
<p class="lead">
The following deadlines are in AoE time zone (UTC – 12).
<ul class="lead">
<li>Paper submission: 31 August 2022
<span style="color:red;opacity: 0.7;text-decoration: line-through;">20 June 2022</span>
</li>
<li>Notification: 10 September 2022
<span style="color:red;opacity: 0.7;text-decoration: line-through;">13 July 2022</span>
</li>
<li>ECML PKDD Conference dates: September 17-20, 2022</li>
</ul>
</p>
</div>
</div>
</div>
</section>
<!--<section id="registration">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Registration</h2>
<p class="lead">
The registration for the workshop is open via the <a
href="https://er2020.big.tuwien.ac.at/registration/">ER website</a>.
At least one of the authors for each accepted paper must have an "Author Registration" (registration
fee of € 150,-.)
and attend the online conference for paper presentation.
</p>
</div>
</div>
</div>
</section>-->
<section id="Chairs">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Chairs</h2>
<p class="lead">
<b>Arif Canakoglu</b>,
Dipartimento di Anestesia, Rianimazione ed Emergenza-Urgenza,
<br>Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
<br>
<a href="mailto:[email protected]">[email protected]</a>
</p>
<p class="text-justify">
Arif Canakoglu currently works as a data scientist at Policlinico di Milano; and he works mainly on
the electronic health record of the intensive care unit's patients in the Lombardy region. He is
leading the research with the support of the medical group, analyzing the life quality of the
patients after the hospital discharge. Previously, he was involved in the "Data-driven Genomic
Computing" ERC Awarded project (2016-2021), where he contributed to developing integration of
heterogeneous genomic data and for developing computational methods for genomic applications. In
2016, he received his PhD on biomolecular knowledge data integration by using the modular schema
data warehouse. His research interests include data integration and data driven genomic computing,
big data analysis and processing on cloud computing, artificial intelligence applications. His main
areas of expertise are heterogeneous data integration and data driven models and machine learning
approaches in genomic, and big data processes, especially on cloud computing.
<p><br><br>
<p class="lead">
<b>Gaia Ceddia</b>, Life Sciences, Integrative Computational Network Biology
<br> Barcelona Supercomputing Center (BSC), Barcelona, Spain
<br>
<a href="mailto:[email protected]">[email protected]</a>
</p>
<p class="text-justify">
Gaia Ceddia is a Recognised Researcher at Barcelona Supercomputing Center. She is currently working
for the Integrative Computational Network Biology group directed by Prof. Nataša Pržulj. She
received his PhD cum laude in 2021, with a thesis titled “Computational Methods for Data-driven
Predictions and Understanding of Biological Interactions” at Politecnico di Milano. Her research
interests include the design of novel network science and machine learning algorithms to extract new
biomedical information and uncover molecular mechanisms of disease from biological data.
</p><br><br>
<p class="lead">
<b>Sara Pido</b>,
Laboratory for Information and Decision Systems (LIDS)
<br> Massachussets Institute of Technology, US
Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
<br> Politecnico di Milano, Italy
<br>
<a href="mailto:[email protected]">[email protected]</a>
</p>
<p class="text-justify">
Sara Pido is a Ph.D. candidate at Politecnico di Milano in Data Analytics and Decision Sciences
supervised by the professor Stefano Ceri. She is currently a visiting student at Laboratory of
Information and Decision Systems, Massachusetts Institute of Technology, under the supervision of
Kalyan Veeramachaneni. She obtained her master degree at Politecnico di Milano under the supervision
of the professor Marco Masseroli with a thesis on the analysis of gene expression data through the
use of complex networks. She is currently working on drug repurposing techniques and on automatic
data science methods.
</p><br><br>
<p class="lead">
<b>Pietro Pinoli</b>,
Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
<br> Politecnico di Milano, Italy
<br>
<a href="mailto:[email protected]">[email protected]</a>
</p>
<p class="text-justify">
Pietro Pinoli works as Researcher Fellow and lecturer at the Department of Electronics, Information
and Bioengineering at the Politecnico di Milano (Italy). He received his PhD cum laude in 2017, with
a thesis titled “Modeling and Querying Genomic Data” where he proposed and benchmarked data
structures and algorithms to manage, search and elaborate huge collections of genomic datasets, by
means of cloud and distributed technologies. He has been visiting PhD candidate at Harvard
University (Cambridge, MA, US). His research interests include bioinformatics and computational
biology, data bases and data management, big data technology and algorithms, machine learning and
natural language processing, and drug repurposing. He participated in the Italian PRIN GenData, ERC
GeCo and EIT VirusLab projects. In recent years he delivered talks at IBM Research in Almaden, Broad
Institute of Boston, University of Trento, University of Lausanne, IBM Research Zurich. He
co-organized tutorials sections at ER and EDBT, workshop at ICWE and he served as guest editor for
MDPI Biotech and BMC Supplements.
</p><br><br>
</div>
</div>
</div>
</section>
<section id="committee">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Program Committee</h2>
<p class="lead">
TBD
<!--<ul class="lead">
<li>Giuseppe Agapito, Magna Graecia University</li>
<li>Raffaele Calogero, University of Turin</li>
<li>Mario Cannataro, Magna Graecia University</li>
<li>Matteo Chiara, University of Milan</li>
<li>Johann Eder, University of Klagenfurt</li>
<li>Jose Luis Garrido, University of Granada</li>
<li>Giancarlo Guizzardi, Free University of Bozen-Bolzano</li>
<li>Carlos Íñiguez-Jarrín, National Polytechnic School</li>
<li>Sergio Lifschitz, Pontifical Catholic University of Rio de Janeiro
</li>
<li>Paolo Missier, Newcastle University</li>
<li>Ignacio Panach, University of Valencia</li>
<li>Barbara Pernici, Polytechnic University of Milan</li>
<li>Rosario Michael Piro, Polytechnic University of Milan</li>
<li>Sudha Ram, University of Arizona</li>
<li>Maria Rodriguez Martinez, IBM Zurich Research Laboratory</li>
<li>Pietro Pinoli, Politecnico di Milano</li>
</ul>-->
</p>
</div>
</div>
</div>
</section>
<!--<section id="invited">
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 mx-auto">
<h2>Invited Talk</h2>
<p class="text-justify">
We are glad to announce the CMLS 2020 Keynote Talk by <a
href="https://www.ncl.ac.uk/computing/people/profile/paolomissier.html#background">
Paolo Missier</a>: "<b>Optimising the re-execution of analytics pipelines in response to
changes in the data: current results, open problems, and opportunities</b>".
<br><br>
<a
href="https://www.ncl.ac.uk/computing/people/profile/paolomissier.html#background">
Paolo Missier</a> is Professor of Big Data Analytics
with the School of Computing at Newcastle University,
with 20 years experience in CS research, development, and research management.
<br>
The broad goal of his research is to understand the role of metadata, most notably data provenance,
in making sense of the underlying (big) data as well as improving and optimising the processes that
produce and extract added value from the data (i.e. through "big data" analytics)—he calls
this
metadata analytics.
<br>
He has been leading (as Principal Investigator) the ReComp project (2016-2019, EPSRC) focused on
preserving value from large-scale data analytics over time through selective re-computation
(<a href="http://recomp.org.uk/">http://recomp.org.uk/</a>)
where the challenge of collecting provenance metadata and extracting value from it through
analytics techniques is central to the research.
<br>
His talk will be focused on — but not limited to — the results of ReComp project and
explain
its application to Genomics and to the Simple Variant Interpretation (SVI) workflow.
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<h2>Program</h2>
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TBD
<!--<h4>CMLS session is on Tuesday October 19th, 17:30-19:00 (CEST)</h4>
17:30-17:35
<br>Welcome and introduction to the workshop
<br>
<br>17:35-17:50
<br>Roman Lukyanenko, Veda Storey and Oscar Pastor Lopez:
<br>The Notion of “System” as a Core Conceptual Modeling Construct for Life Sciences.
<a target="_blank" class="pdf" href="presentations/1-TristaoEtAl.pdf">Slides</a>
<a target="_blank" class="video" href="https://youtu.be/Y74YXHj8-mE">Video</a>
<br>
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<br>17.50-18.05
<br>Alberto García S., Mireia Costa Sánchez and Oscar Pastor Lopez:
<br>Characterization and Treatment of the Temporal Dimension of Genomic Variations: a Conceptual
Model-based approach.
<br>
<br>18.05-18.20
<br>Federico Comolli:
<br>Extension of the Genomic Conceptual Model to integrate Genome-Wide Association Studies.
<br>
<br>18.20-18.35
<br>Sara Balderas-Díaz, María José Rodríguez Fórtiz, Gabriel Guerrero-Contreras, Mercedes
Bellido-González and Jose Luis Garrido:
<br>Design of an Adaptable mHealth System Supporting a Psycho-Educational Program for Pregnant Women
with SGA Foetuses.
<br>
<br>18.35-19.00
<br>Oscar Pastor (<b>Keynote talk</b>):
<br>New directions for clinical and genomic problems in different diseases: A Conceptual Modeling-based
Approach
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<h2>Accepted papers</h2>
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This is the list of accepted papers for CMLS 2021:</p>
<ul class="lead">
<li>Roman Lukyanenko, Veda Storey and Oscar Pastor Lopez. <i>The Notion of “System” as a Core Conceptual Modeling Construct for Life Sciences</i></li>
<li>Alberto García S., Mireia Costa Sánchez and Oscar Pastor Lopez. <i>Characterization and Treatment of the Temporal Dimension of Genomic Variations: a Conceptual Model-based approach</i></li>
<li>Federico Comolli. <i>Extension of the Genomic Conceptual Model to integrate Genome-Wide Association Studies</i></li>
<li>Sara Balderas-Díaz, Rodríguez Fórtiz María José, Gabriel Guerrero-Contreras, Mercedes Bellido-González and Jose Luis Garrido. <i>Design of an Adaptable mHealth System Supporting a Psycho-Educational Program for Pregnant Women with SGA Foetuses</i></li>
</ul>
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