MODIMO
(2nd edition)

Workshop on Multi-Omics Data Integration for Modelling Biological Systems

in conjunction with ACM CIKM 2023

Multi-omics analysis aims at extracting previously uncovered biological knowledge by integrating information across multiple single-omic sources. Past approaches have focused on the simultaneous analysis of a small number of omic data sets. Current challenges face the problem of integrating multiple omic sources into a unified complex model, or of combining already available tools for two-by-two omics analyses and merging their outcomes. By doing so and leveraging integrated system-level knowledge, multi-omic approaches ought to enable the development of better qualitative and quantitative models for descriptive and predictive analyses. To move this area forward, new statistical and algorithmic frameworks are needed, for example for generalizing classical graph theory results to heterogeneous networks, and applying them to diverse problems such as drug repurposing or understanding the immune response to infections. Thus, in short, this workshop aims at investigating novel methodologies for providing crucial insights into multi-omics data management, integration, and analysis in order to enable biological discoveries.

The workshop will be sponsored by InfoLife CINI National Laboratory (https://www.consorzio-cini.it/index.php/en/).

Workshop Theme and Topics

The relevant topics include the following (but not limited to):

mutli-omics data analysis
multi-omics data integration
system biology
computational biology
biological network construction and analysis
biological knowledge graphs
heterogeneous networks
modelling of biochemical pathways and biological networks
big bio- or clinical-data analytics
Integration of structured and unstructured resources for biomedical applications
mining multi-relational data
information retrieval from large biomedical data collections

Important Dates

Full paper deadline 18 August 2023 6 September 2023

Short paper deadline 18 August 2023 6 September 2023

Paper Notification 15 September 2023

Workshop date 22 October 2023

Organizing Committee

Program Chairs and Co-Chairs

Marco Beccuti, University of Turin, Italy

Vincenzo Bonnici, University of Parma, Italy

Rosalba Giugno, University of Verona, Italy

Pernice Simone, University of Turin, Italy,

Simone Avesani, University of Verona, Italy

Program Committee

Ivan G. Costa, RWTH Aachen University

Alberto Policriti, University of Udine

Andre Altmann, University College London

Davide Chicco, University of Udine

Workshop Contact Person

Vincenzo Bonnici

Department of Mathematical, Physical and Computer Sciences

Parco area delle Scienze, 53/A, 43124 Parma, Italy

+39 0521 906909

vincenzo.bonnici[at]unipr.it

https://personale.unipr.it/en/ugovdocenti/person/230820

Progam

22th October, 2023

2:00 pm - 2:25 pm | Welcome and Open session

2:25 pm - 2:30 pm | Openings

2:30 pm - 3:30 pm | Invited speaker - Elham Azizi (Columbia University)

Probabilistic modeling of dynamics in the tumor microenvironment

3:30 pm - 5:00 pm | Paper session

RASpy: Metabolic Reaction Activity Analysis with Scanpy
Towards a Computational Approach to Quantification of Allele Specific Expression at Population Level
EasyCircR: Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

5:00 pm - 5:05 pm | Closing remarks

All times are UK (UTC+1) timezone.

Venue

The University of Birmingham, Alan Walters Building, Seminar Room 2 (111)

Invited speakers

Elham Azizi, Columbia University, USA.

Azizi holds a BSc in Electrical Engineering from Sharif University of Technology (2008), an MSc in Electrical Engineering (2010), and a PhD in Bioinformatics (2014) from Boston University. She was a postdoctoral fellow at Columbia University and Memorial Sloan Kettering Cancer Center (2014-2019). She joined the faculty of Columbia Biomedical Engineering and Irving Institute of Cancer Dynamics in 2020. She is also affiliated with the Department of Computer Science, Data Science Institute, and the Herbert Irving Comprehensive Cancer Center.

Characterizing various interacting cell types in the tumour microenvironment, and unraveling their underlying mechanisms can guide the development of improved and personalized cancer treatments. Azizi’s approach involves leveraging genomic profiling at single-cell resolution and developing machine learning and statistical method to analyze and integrate high-dimensional genomic data.

Submission guidelines

Authors are invited to submit original work in the form of short and full papers, describing research results that are unpublished and not under consideration for publication elsewhere.

Members of the Program Committee will review the submissions and select papers for poster or talk presentation at the conference based on their novelty, technical quality, potential impact, clarity, and reproducibility.

Accepted papers will be invited for presentation during the workshop. Presentation time and format (talk or poster) will be allocated based on the presented contribution.

Manuscripts should be submitted to the MODIMO 2023 Easychair site (https://easychair.org/conferences/?conf=modimo2023) in PDF format formatted in CEUR style guidelines (http://ceur-ws.org/Vol-XXX/CEURART.zip also available as an Overleaf template ). The page limit is 9 pages for full papers and 4 pages for short papers, plus references. At least one of the authors of each accepted paper must be available to present in person. In case of traveling restrictions (COVID related or otherwise), an exception may be made to allow registered authors to present the work remotely.

Workshop papers will not be included in the ACM proceedings. Selected full papers will be invited for a special issue of selected journals in the fields of Computer Science and Bioinformatics.