Leading Professional Society for Computational Biology and Bioinformatics
Connecting, Training, Empowering, Worldwide

UPCOMING DEADLINES & NOTICES

  • Virtual platform uploads open
    ISMB/ECCB 2025
    June 17, 2025
  • ISCB Offices Closed
    June 19, 2025
  • Deadline for Early Bird Registration
    INCOB 2025
    June 21, 2025
  • Final tutorial materials due for posting (You have until 23:59 Anywhere on Earth)
    ISMB/ECCB 2025
    June 25, 2025
  • Abstract acceptance notification
    INCOB 2025
    July 1, 2025
  • Deadline for submissions of final versions
    INCOB 2025
    July 1, 2025
  • Travel grant award notification
    INCOB 2025
    July 8, 2025
  • Last day to upload ANY/ALL files to the virtual platform (You have until 23:59 Anywhere on Earth) *no extensions*
    ISMB/ECCB 2025
    July 11, 2025
  • Deadline for early bird registration
    INCOB 2025
    July 21, 2025

Upcoming Conferences

A Global Community

  • ISCB Student Council

    dedicated to facilitating development for students and young researchers

  • Affiliated Groups

    The ISCB Affiliates program is designed to forge links between ISCB and regional non-profit membership groups, centers, institutes and networks that involve researchers from various institutions and/or organizations within a defined geographic region involved in the advancement of bioinformatics. Such groups have regular meetings either in person or online, and an organizing body in the form of a board of directors or steering committee. If you are interested in affiliating your regional membership group, center, institute or network with ISCB, please review these guidelines (.pdf) and send your exploratory questions to Diane E. Kovats, ISCB Chief Executive Officer (This email address is being protected from spambots. You need JavaScript enabled to view it.).  For information about the Affilliates Committee click here.

  • Communities of Special Interest

    Topically-focused collaborative communities

  • ISCB Member Directory

    Connect with ISCB worldwide

  • Green ISCB

    Environmental Sustainability Effort

  • Equity, Diversity, and Inclusion

    ISCB is committed to creating a safe, inclusive, and equal environment for everyone

Professional Development, Training, and Education

ISCBintel and Achievements

The ISCB-LATAM SoIBio CCBCOL 2024 conference  is pleased to announce a call for Volunteer Student Support Staff.

As a member of the Volunteer Student Support Staff, you will receive valuable first-hand experience at an academic association conference, a certificate of appreciation as well as a complimentary registration.

Here are the requirements of the Volunteer Support Staff:

  • Attend a volunteer meeting before the conference to ensure you are prepared for all volunteer responsibilities - likely Monday, November 11
  • Complete all assigned shifts
    • You will be notified of your shifts in advance of the conference and are required to sign and return in acknowledgement
Event Staff positions are:
    • Registration:
      • Handing out name badges, processing of invoices and assisting with on-site registration
    • Educational sessions:
      • Check in with the session leader at the beginning of the session and identify yourself as the volunteer to assist in that session
      • Checking badges for entrance to session rooms
      • Counting attendees in each educational session
      • Monitor session rooms, alerting conference manager of any AV or emergency needs during session
      • Moderate the online Q&A and chat room for our virtual audience and be the in-person voice for the virtual audience during any Q&A sessions
    • Other conference opportunities:
      • Numbering poster boards to include monitoring hanging up and taking down of poster boards by presenters
      • Assist attendees in locating various events throughout the conference
      • Answer questions about the scientific program and giving directions within the venue

Only a small number of students will be selected to participate on this team. Apply by 30 September 2024.

Apply to be Volunteer - Event Staff

 

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There will be a series of in-person and virtual tutorials prior to the start of the conference. Tutorial registration fees are shown at: https://www.iscb.org/latam2024/register#tutorials

In-person Tutorials (All times COT)

Virtual Tutorials: (All times COT) Presented through the conference virtual platform

 

Tutorial IP2: GA4GH: An introduction to federated genomics using the GA4GH Starter Kit and real-world data platforms

Room: TBD
Date: Tuesday, November 12, 09:00 - 13:00

Speakers:

  • Chen Chen, Global Alliance for Genomics and Health; Ontario Institute for Cancer Research
  • Alex Tsai, Global Alliance for Genomics and Health; Ontario Institute for Cancer Research
  • Dashrath Chauhan, Global Alliance for Genomics and Health; EMBL-EBI Cambridge, United Kingdom

Max Participants: 12

Description
The Global Alliance for Genomics and Health (GA4GH) is an international technical standards-setting organization, enabling genomic data sharing. Through its standards, GA4GH aims to promote a federated model of data sharing, in which researchers can seamlessly access data from multiple sources in an international network using common tools and protocols, and data providers can securely share data with trusted researchers while still maintaining ownership and control over their data. In this tutorial, we explore four GA4GH standardized API interfaces that enable federated data access and analysis. The first API standard, Data Repository Service (DRS), provides minimal metadata and access information about files that can be used as input to analytical workflows. The second standard, Workflow Execution Service (WES), enables researchers to remotely run workflows defined in Common Workflow Language (CWL), Workflow Description Language (WDL) or Nextflow on an input dataset of interest. The third standard, Data Connect, allows researchers to search and filter biomedical datasets based on criteria of interest. Lastly, GA4GH Passports grants researchers fine-grained permission sets for data and compute resources they are allowed to access and is used to control researcher access to resources behind the other three APIs.

In this tutorial, we deploy a server implementation network of the four API standards using a reference implementation suite known as the GA4GH Starter Kit. We run search, access, and analyze protocols on our local GA4GH network. Overall, we aim to give tutorial participants hands-on experience with the core GA4GH standards that enable federated analysis, from both the perspective of the researcher making use of these web services, and the data provider setting up secure, GA4GH-compliant services.

Learning Objectives

  • Gain an understanding of the key GA4GH standards in controlled data access,
  • data discovery, and workflow execution, and how they enable federated genomic
  • analysis
  • Set up a local network of GA4GH web services using out-of-the-box
  • implementations, the GA4GH Starter Kit.
  • Run the step-by-step tutorial to demonstrate federated analyses, data discovery
  • and controlled access to test datasets.

Intended Audience and Level
We expect attendees to be familiar with a programming language (code/script examples will mainly be done in Python), and have some understanding of web programming principles, such as REST APIs. Students should ideally have knowledge of containerization technologies such as Docker, as this will be used to set up the Starter Kit.

We do not require attendees to have any prior knowledge of GA4GH or GA4GH Standards.

Schedule
Coming soon

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Tutorial IP3: Multiomics integration: fundamentals and applications

Room: TBD
Date: Tuesday, November 12, 09:00 - 17:00

Speakers:

  • Natalia Pietrosemoli, Institut Pasteur, Université Paris Cité
  • Claudia Chica, Institut Pasteur, Université Paris Cité

Max Participants: 20

Description
This tutorial introduces students to methods for studying biological systems using various OMIC data types, employing a multi-omics approach. The goal is to identify potential interactions or correlations between entities across different OMIC layers. A given transcript, for instance (transcriptomic later), can be correlated with multiple proteins (proteomic layer). The methods explored in this tutorial are chosen based on the type of biological questions addressed and the available data types. These methods allow visualization, exploration, and summarization of relevant relationships among OMIC datasets.

The need for OMIC integration approaches is growing as more research projects simultaneously measure different types of high-dimensional data. Integrative analysis methods are crucial to handle this complexity, which in turns allows answering more complex questions and provides a more comprehensive understanding of biological systems.

In this training, we will first present the fundamental data pre-processing concepts and their impact on integration, including missing data and data distribution. Then, we will explore various multi-omic integration approaches, including:

  1. Data-driven, using existing functional annotations such as biological pathways.
  2. Dimensionality reduction, for example Multi-Omics Factor Analysis (MOFA) and Joint and Individual Variation Explained (JIVE).
  3. Network theory, for example Weighted Gene Co-expression Network Analysis WGCNA.

These approaches will result in different types of integrations, including horizontal, parallel, and hierarchical that are mainly dependent on the available OMICs. This course aims to equip participants with a robust understanding of current integration approaches, empowering them to address specific biological questions using available OMIC data. Upon completion, participants should identify questions suitable for multi-omics integration and choose appropriate methods tailored to their scenarios. More importantly, they should be able to tackle new questions as competent decision-makers.

We offer a multi-level tutorial suitable for trainees with both beginner and intermediate skills in OMIC data analysis. Each topic includes one or more exercises designed to deepen the understanding of critical concepts through hands-on experience on selected datasets. These hands-on exercises are designed to accommodate trainees with heterogeneous backgrounds (e.g., life sciences, computer sciences) and varying proficiency levels in OMIC data analysis. The material provided includes theoretical content and hands-on exercises with all necessary code, presented as R Markdowns. All materials are hosted in GitLab repositories, which will be publicly available. Materials are in English, but the course can be given in English or Spanish.

Participants will benefit from the teaching team's experience as computational biologists at the Bioinformatics and Biostatistics Hub of Institut Pasteur (IP) in Paris, collaborating with IP’s wet lab scientists. This collaboration encompasses data analysis, method development, and bioinformatics/biostatistics training for the campus. In addition to courses for PhD students at Institut Pasteur and for French universities, the teaching team has extensive experience in international training activities across Latin America (Ecuador, Colombia, Peru), Africa (Tunisia), Asia (Vietnam), and European consortiums.

Drawing from its experience as a lecturers and instructors, the teaching team believes that providing comprehensive training to students and researchers on the formal basis of bioinformatic and biostatistic methodologies is paramount for fostering successful collaboration between wet and dry lab environments. Indeed, regardless of the specific research subject in life sciences, there is a significant need for an advanced understanding on data analysis.

Learning Objectives

  • Become familiar with the principles, flavours and challenges of OMIC integration.
  • Understand fundamental data pre-processing concepts and their impact on integration,
  • including missing data (data imputation), and data distribution (normalization and
  • scaling).
  • Demystify the use of complex integrative methods through hands-on applying
  • statistical approaches such as dimensionality reduction, and network-based methods.
  • Develop an informed perspective on the key issues to make methodological choices
  • according to the data available and the biological question(s).
  • Apply and integrate good practices for data analysis in R/RStudio.

Intended Audience and Level
This tutorial is open to all scientists (students, postdocs, and researchers) involved in projects comprising various types of OMICs datasets. No prior knowledge of integration methods for OMICs data is required. However, previous experience with any OMICs data analysis (transcriptomics, proteomics, epigenomics) is highly encouraged. Familiarity with R/RStudio is necessary, including understanding the RStudio environment, R syntax, and package installation, though coding expertise is not mandatory.

Schedule
Coming soon

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Tutorial IP4: Bioinformatic tools for genome assembly and comparative genomics

Room: TBD
Date: Tuesday, November 12, 09:00 - 12:30

Speakers:

  • Jorge Duitama, PhD, Universidad de los Andes
  • Laura Gonzalez, PhD(c), Universidad de los Andes
  • Johanna Stepanian, MSc, Universidad de los Andes

Max Participants: 30

Description
The availability of new technologies to obtain accurate long DNA sequencing reads enabled the construction of high quality genome assemblies for complex organisms and streamlined the production of chromosome-level assemblies for most microorganisms. This course aims to provide basic knowledge on the current genome assembly process, including practical training on some of the tools available for assembling genomes from long reads (HiFiAsm, Flye and NGSEP). The course also includes practical training on common tools for evaluation of genome assemblies to obtain statistics such as N50, gene completeness and QV scores. Finally, we will cover some basic tools to align genomes and perform comparative genomics to provide further context on downstream analysis of genome assemblies.

Learning Objectives

  • Understand basic concepts of genomics and technologies for DNA sequencing and genome
  • assembly
  • Practice with bioinformatic tools for genome assembly, evaluation and comparative
  • genomics
  • Visualize and compare genomes

Intended Audience and Level
This tutorial is designed for individuals with basic knowledge in molecular biology and bioinformatics. Experience on command line usage is also required. Previous experience in genomics is desirable.

Schedule

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Tutorial VT1: Exploring the new Ensembl Genome Browser to retrieve genomic data

Date: Thursday, November 7, 10:00 - 14:00

Speakers:

  • Louisse Paola Mirabueno, Ensembl Outreach Officer, EMBL-EBI
  • Dr Jorge Batista da Rocha, Ensembl Outreach Project Leader, EMBL-EBI
  • Dr Juan Pablo Narváez Gómez, ARISE MSCA Research Fellow, EMBL-EBI

Max Participants: 40

Description
The Ensembl Genome Browser has been an indispensable tool in the field of genomics, aiding scientists around the world in their research for over 20 years. The Ensembl database provides visualisation and comprehensive analyses of integrated genomic data, including genes, variants, comparative genomics and gene regulation, for over 2,000 eukaryotic and over 30,000 prokaryotic genomes. With the rapid growth of genomic data in the past decades, a new Ensembl Genome Browser (https://beta.ensembl.org/) has been designed to provide a more robust and efficient platform. The new platform offers enhanced features, improved data visualisation, and a more intuitive user interface.

This online tutorial is an introduction to the new Ensembl genome browser, which presents genomic features for approximately 3,000 species with a new user interface, including visualisation of genes and variants on the Human Pangenome Reference Consortium (HPRC) assemblies. Participants will have the opportunity to learn about the range of data available through the new platform, gain hands-on experience in navigating the new Ensembl website to retrieve and interpret data and think about how this data might be informative for their research. The tutorial will also highlight the improvements in the new platform and how these enhancements can significantly aid in genomic research. Importantly, participants will also be able to engage with the Ensembl community, finding sources of help and documentation.

Learning Objectives
At the end of this course, participants will be able to:

  • Access the main data types through the new Ensembl web browser platform: genomes, genes and genetic variation.
  • View genomic regions and manipulate the view to add features.
  • Explore information about genes and their sequences.
  • Analyse genomic variants and associated phenotypes.

Intended Audience and Level
This is an introductory workshop that is aimed at wet-lab scientists and bioinformaticians from all levels who are new to using Ensembl, have not yet discovered the power and depth of the resource, or would like to explore the new browser platform

Schedule
Coming soon

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Tutorial VT3: Identification of Tissue Microenvironments using Spatial Transcriptomics

Date: Friday, November 8, 10:00 - 14:00

Speakers:

  • Karla Paniagua,  University of Texas at San Antonio
  • Mario Flores, University of Texas at San Antonio

Max Participants: 30

Description
In biomedical research, understanding the dynamics of microenvironments within tissues is crucial for unraveling disease mechanisms, identifying therapeutic targets, and developing personalized treatment strategies. Spatial transcriptomics technologies are recognized as powerful tools for visualizing and analyzing gene expression profiles within their spatial context in various tissues and disease conditions. However, deciphering the complex interactions between different cell types, their spatial organization, and gene expression patterns presents significant challenges. This tutorial aims to address these challenges by providing participants with a comprehensive understanding of spatial transcriptomics data analysis, through the use of deep learning algorithms. The tutorial will cover preprocessing techniques, integration of multimodal data, implementation of deep learning algorithms, and downstream analysis of identified microenvironments. By the end of the tutorial, participants will be equipped with the necessary skills to analyze spatial transcriptomics data, identify tissue microenvironments, and apply downstream analysis tools across different disease contexts. This will enable advancements in understanding the complex interplay within tissue microenvironments and its implications for disease progression, prognosis, and treatment strategies

Learning Objectives
Participants in this tutorial will gain a comprehensive understanding of key preprocessing methods for spatial transcriptomics data. They will learn innovative techniques to integrate multimodal data available with spatial transcriptomics and implement advanced deep-learning models, including a Transformer algorithm and a graph autoencoder. By interpreting the outputs of these models, participants will identify spatial microenvironments and apply downstream analysis tools to enhance their understanding of these microenvironments.

  • Utilize key preprocessing methods for spatial transcriptomics data.
  • Apply common deep-learning algorithms to process morphology images.
  • Explore new methods to integrate multimodal data provided by spatial transcriptomics.
  • Implement a deep-learning algorithm composed of a Transformer algorithm and a graph autoencoder to process the multimodal data representation.
  • Interpret the output of deep-learning models to identify spatial microenvironments.
  • Apply downstream analysis tools, such as differential gene expression (DGE), and enrichment analysis, to better understand the identified spatial microenvironments

Intended Audience and Level
This tutorial is aimed at researchers, data scientists, and bioinformaticians interested in spatial transcriptomics and its applications, in understanding microenvironments within tissues, and in learning the implementation of deep-learning algorithms to process spatial transcriptomics data. Basic Knowledge of Bioinformatics and Computational Biology concepts is expected.

Schedule
Coming soon

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Unfortunately, due to circumstances beyond our control, the walking tour has been CANCELLED.

Click schedule to download pdf

Click schedule to download pdf

Conference Chairs

Ana Tereza Vasconcelos
Conference Co-Chair
Steering Committee
National Laboratory for Scientific Computing
Brazil

Javier De Las Rivas
Conference Co-Chair
Steering Committee
Cancer Research Center (CiC-IBMCC, CSIC/USAL)
Spain

Yesid Cuesta-Astroz
Conference Co-chair
Program Committee Co-Chair
Universidad de Antioquia
Colombia

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Steering Committee

Ana Tereza Vasconcelos
Conference Co-Chair
Steering Committee
National Laboratory for Scientific Computing
Brazil

Alejandro Reyes Muñoz
Steering Committee
Tutorial & Workshop Committee Co-Chair
Universidad de los Andes
Colombia

Bel Hanson
Steering Committee
ISCB Director, Operations & Programs
United States

Diane Kovats
Steering Committee
ISCB Chief Executive Officer
United States

Javier De Las Rivas
Conference Co-Chair
Steering Committee
Cancer Research Center (CiC-IBMCC, CSIC/USAL)
Spain

Justine Morris
Steering Committee
ISCB Coordinator, Operations & Programs
United States

Norma Paniego
Steering Committee
Tutorial & Workshop Committee Co-Chair
Instituto Nacional de Tecnologia Agropecuaria
Argentina

Rebeca Campos
Steering Committee
Tutorial & Workshop Committee Co-Chair
University of Costa Rica
Costa Rica

Seth Munholland
Steering Committee
ISCB Lead Technologist
Canada

Vinicius Maracaja-Coutinho
Steering Committee
Universidad de Chile
Chile

Yalbi Itzel Balderas-Martinez
Steering Committee
Program Committee Co-Chair
Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas
Mexico

Yesid Cuesta-Astroz
Conference Co-chair
Program Committee Co-Chair
Universidad de Antioquia
Colombia

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Links within this page: Tutorials Organization | Compensation | Submitting a Tutorial Proposal | Review of Tutorial Proposals | Tutorial Materials | Recording of Tutorial Sessions | Copyright


Submit Tutorial Proposal

The purpose of the Tutorials program is to build knowledge and provide hands-on training in "cutting-edge" topics relevant to the bioinformatics field. Tutorials offer participants an opportunity to get an introduction to important established topics in bioinformatics, to learn about new areas of bioinformatics research, or to develop advanced skills in areas about which they are already knowledgeable.

Tutorials may include any form of presentation such as brief talks or panel discussions but should include hands-on exercises. Tutorials serve an educational function and are expected to provide a balanced perspective on a field of research. They should not focus on the presenters' own research or software, unless balanced with other tools in the same realm. However, tutorials on broadly used bioinformatics tools will be considered.

Potential topic areas may include but are not limited to the following:

  • Data analysis topics:
    • Single-cell
    • Multiomics integration
    • Spatial transcriptomics
    • Metagenomics
    • Proteomics
    • Alphafold and/or Structural biology
    • any other life sciences data
  • Data Science in Agriculture (breeding, diversity, soil, environment)
  • Data Science in One Health
  • Data visualization for bioinformatics
  • AI and Machine Learning for bioinformatics
  • Translational informatics: Opportunities for bioinformatics in the clinical realm
  • How to make your software sustainable and reusable for open access or commercial usage
  • Biological sciences for bioinformaticians (eg aimed at Comp-science graduates with less/no prior biology knowledge)
  • Data science in genomics
  • Workflow tools (eg Snakemake, NextFlow)
  • Bioinformatics on cloud platforms
  • Best practices (eg learning github, using pytorch, Python coding standard PEP8 etc)

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Tutorials organization

Tutorials can be planned to be either in-person or fully online, but should not be hybrid. (eg. tutorial presenters and participants should either be fully online or in-person).

Tutorials presented in-person will be held on November 12, 2024. Tutorials presented online will be held on a weekday (TBD) prior to the conference start. If submitting an online tutorial proposal you will be asked to confirm your preferred time zone for presentation.

Tutorials timing for full-day or half-day sessions:
In-person: November 14, 2024
Full Day Schedule: 9:00 am - 4:00 pm, (10:45-11:00 am Coffee; Lunch Break 1:00 pm - 2:00 pm)

Half Day Schedule: 9:00 am - 12:30 pm (Break at 10:45-11:00 am) or 1:00-4:00 pm (Break at 4:00 - 4:15 pm)

Virtual: TBD
Full Day Schedule: 9:00 am - 4:00 pm (Breaks 10:30-10:45am, 12-1pm, and 2:30-2:45pm)
Half Day Schedule: 9:00 am - 1:00 pm (Breaks at 10:30-10:45am and 11:45am-12:00pm)

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Compensation

The conference organizers are able to offer a complimentary conference registration for up to 2 tutorial presenters. Tutorial organizers may choose to share the value of the complimentary registration if the tutorial has additional presenters.

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Submitting a Tutorial Proposal

Tutorial proposals should contain the following information in a maximum of 4 pages:

  • Title of Tutorial
  • Abstract for Tutorial
  • Learning Objectives for Tutorial
  • Short promotional blurb for promotion if selected
  • Maximum number of attendees participating
  • Draft Schedule of the tutorial including coffee breaks (half-day or full-day schedule) - Include draft talk titles or draft content to be covered in each section
  • Identify and highlight blocks of hands-on content in your submission
  • Draft List of Tutorial Speakers with titles and affiliations
  • Intended audience and level - Describe the audience for which the Tutorial is aimed, and at which level it would be taught (e.g. beginner, past experience, advanced knowledge).

The final proposal must be uploaded as a PDF file only.

Deadline for Tutorial Proposals: June 3, 2024

During the submission process be sure to provide a brief description of the tutorial that will be used on the website to promote it to delegates, and to confirm that if selected, you will submit draft and final tutorial materials for committee review by the listed deadlines.

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Review of Tutorial Proposals

All tutorial submissions will be evaluated by a committee, which will consider the following criteria:

  • Relevance, interest, and value of the topic to ISMB attendees and COSI communities
  • The tutorial should achieve a good balance between the theoretical component and hands-on exercises
  • Completeness, clarity, and quality of the proposal and materials including schedule of tutorial
  • Educational value and effectiveness of the proposed presentation approach
  • Educational value and effectiveness of the proposed presentation approach and FAIRness of the data, tools and content

Successful tutorial proposals will be notified by July 1, 2024 (no later than 17:00 Eastern Time (ET).

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Tutorial Materials

The tutorial speakers agree to provide participants with teaching materials that include:

  • Copies of the final slides in Powerpoint or PDF format for posting online.
  • Copies of relevant articles/book chapters published by the presenters provided as Supplementary
  • Information. Presenters will have to obtain copyright permission from their publishers, as required.
  • Links to repositories containing training materials.
  • Make your training materials FAIR (Findable, Accessible, Interoperable, and Reusable), as much as possible.

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Recording of Tutorial Sessions

Tutorials programs will be recorded to serve as online learning tools following the conference. All presenters must agree to allow ISCB to post the recordings of the Tutorials program as a requirement of acceptance.

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Copyright

The authors will grant copyright to tutorial materials to the ISCB for a period to extend from acceptance through December 31, 2024, and they agree that their materials may be made available for use in perpetuity through ISCB.

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Pierre Baldi
University of California, Irvine
United States

Pierre Baldi earned MS degrees in Mathematics and Psychology from the University of Paris, and a PhD in Mathematics from the California Institute of Technology. He is currently Distinguished Professor in the Department of Computer Science, Director of the AI in Science Institute, and Associate Director of the Center for Machine Learning and Intelligent Systems  at the University of California Irvine. The long term focus of his research is on understanding intelligence in brains and machines. He has made several contributions to the theory of AI and deep learning, and developed and applied AI and deep learning methods for the natural sciences, to address problems in  physics (e.g., exotic particle detection), chemistry (e.g., reaction prediction), and bio-medicine (e.g., circadian rhythm analyses, biomedical imaging analyses). He recently published his fifth book: Deep Learning in Science, Cambridge University Press (2021). His honors include the 1993 Lew Allen Award at JPL, the 2010 E. R. Caianiello Prize for research in machine learning, the 2023 Dennis Gabor Prize of the International Neural Network Society, and election to Fellow of the AAAS, AAAI, IEEE, ACM, and ISCB.
He has co-founded several startup companies.

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Maryam Chaib De Mares
National University of Colombia
Colombia

Maryam Chaib De Mares is an assistant professor at the National University of Colombia. She studies the evolutionary and molecular basis of symbiotic relationships between animal hosts and microorganisms. She is also interested in understanding how ecological conditions modify the dynamics of these interspecific interactions. Maryam holds a Master's degree in Ecology and Evolutionary Biology from the University of Montpellier 2 in France and the University of Groningen in the Netherlands. At the latter university, she advanced her doctoral training in Microbial Ecology and Bioinformatics.

As a postdoctoral researcher in the Computational Biology and Microbial Ecology research group at the Universidad de los Andes, she taught undergraduate and masters classes in Genomics, Microbial Ecology and Bioinformatics and started working on the integration of sequence analysis with mathematical modeling in artificial microbial consortia from the human gut. Currently, Maryam leads the Theoretical and Evolutionary Molecular Biology Research Group at Universidad Nacional de Colombia. She is combining interdisciplinary approaches that integrate computation and wet-lab experiments to design and understand how gene circuits from communities of microorganisms have the ability to modulate animal host physiology.

Maryam also is a consultant in statistics and data analysis for the private sector. In addition, since her doctoral studies she has been trained in research data management, leading the adoption of reproducibility practices in computational biology. Beyond biology research, she has participated in open data initiatives to bring these skills to all interested citizens.

Molecular and Evolutionary Insights into Host-Microbe Symbiosis: A Computational Perspective
Understanding the intricate interactions that take place between hosts and microbes is essential for uncovering how microbial communities influence host physiology, adaptation, and health. This keynote will present computational strategies to decode these complex interactions by integrating functional genomics data analyses with ecological modeling. Focusing on secreted bacterial proteins, small RNAs, and their genetic targets in emerging model organisms, notably invertebrates, I explore the molecular mechanisms underlying symbiosis. The methodologies combine comparative and functional genomics with dynamic modeling to predict microbial processes such as competition, cooperation, and functional complementarity, and their effects on host traits like stress response and immunity. Co-divergence analyses will also be highlighted, tracing the evolutionary history of hosts and their symbionts to reveal the co-evolutionary dynamics that shape these associations. Through case studies, this presentation will showcase how computational tools can bridge molecular mechanisms and broader ecological processes, offering new insights into microbial contributions to host biology across scales. This integrated approach underscores the value of computational methods in advancing our understanding of symbiosis, with broader implications that demonstrate how these tools can identify key microbial players and pathways, supporting the development of new approaches to modulate host-microbiome interactions, potentially enhancing animal health and nutrition.

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Valeria Faggioli
Instituto Nacional de Tecnología Agropecuaria
Argentina

Valeria Faggioli is a Researcher at the Instituto Nacional de Tecnología Agropecuaria (INTA), Argentina, in the Department of Soil Science and Crop Production (Marcos Juarez, Cordoba Province). She obtained her BSc in Agronomy, MSc in Soil Fertility, and PhD in Natural Science. During her post-doctoral studies, she performed training in bioinformatics at the European Bioinformatics Institute in Hinxton, UK (EMBL). The goal of her current investigations is to elucidate the impact of agricultural practices in microbial biodiversity studying long-term experiments.

Preservation of local biodiversity is a key factor in sustainable production. Agricultural soils can harbour diverse communities of microorganisms providing key ecosystem services such as nutrient cycling, chemistry and structure of soil, and plant productivity. To carry out sustainable agriculture, the understanding of the composition of microbial communities as well as changes induced by human practices demands the generation of experimental evidence.

As a member of CABANAnet project, the aim of her project is to investigate the impact of long-term anthropogenic practices on soil bacterial and fungal communities using high throughput sequencing techniques in emblematic agroecosystems of Argentina, Colombia, Costa Rica and Peru. This study pursues a complete taxonomic classification of the existing taxa and will represent an unprecedented dataset from Latin America.

Unveiling Soil Microbiome: From NGS Data to Sustainable Agriculture
The twenty-first century is the era of omics technologies, which are primarily focused on the generation and analysis of molecular data within organisms. In the last two decades, researchers in laboratories have generated enormous amounts of data due to the rapid development of high-throughput next-generation sequencing (NGS) technologies. The data generated by these technologies can be directly applied to agricultural developments. The agricultural system, which is directly connected to the soil, can promote plant growth either in a free-living state or associated with the rhizosphere region. Pathogenic organisms can affect plant health and remain in the soil for decades, rendering it unproductive. Additionally, a great variety of species remain in grains after harvest, altering further processes such as fermentation, storage, and commercialization. Identification through DNA barcoding in soil microorganisms is also a new avenue, assisted by various bioinformatics tools. Microbial systems biology provides another means to explore data from different metabolic pathways and taxonomic genes for valid conclusions about microbial activity. Overall, in silico tools, including databases and software, can help reduce the "microbial knowledge gap" and support the broad-spectrum study of soil microorganisms and their application toward sustainable agriculture.

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Rob Finn, Ph.D.
Team Leader and Senior Scientist
EMBL-EBI
United Kingdom

Dr Rob Finn leads EMBL-EBI’s Microbiome Informatics team, which is responsible for the MGnify resource, which provides access to the metagenomics, metatranscriptomics and assembly analysis services.  The functional and taxonomic profiles of these datasets, once made public, can be access by all via the MGnify website. The team is also responsible for the HMMER website, which enables fast proteins sequence similarity searches against a range of sequence and profile HMM databases. Rob also has a small research group that probes the functions of microbial 'dark matter'.

Rob joined EMBL-EBI from the Janelia Research Campus in the US, where he led a group that designed fast, web-based, interactive protein-sequence searches and annotations. Between 2001 and 2010, he was the project leader for Pfam at the Wellcome Sanger Institute in the UK. Rob’s academic background is in microbiology and he holds a PhD in biochemistry from Imperial College, London.

Studying of diverse microbiomes through MGnify
Metagenomics, the analysis of the sum of genetic material from a sample, has started to shed light on the huge diversity of micro-organisms that occupy different such as the human body, soil and ocean environment. For example, humans host trillions of microbes, which have adapted to a range of body sites, such as the gut, oral cavity and skin. It is only since the application of metagenomic approaches have we started to understand the huge diversity of micro-organisms that occupy these different environments provided by the human host. MGnify hosts the catalogs of genomes, which is driving new avenues of research, especially with the aim to develop new model organisms and experimental systems.  We have also conducted parallel research to recover genomes from the human skin microbiome, which not only harbours a very distinct microbial composition compared to the gut, but also carries additional challenges such as low DNA yield. Nevertheless, this analysis has provided multi-kingdom catalogues from the skin. Finally, the same approaches have started to reveal the diversity harboured in the marine environment. While this dataset is by no means complete, we are starting to understand how this data can be utilised to identify potential new products or enzymes tractable for bioremediation.

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Alejandra Medina Rivera
Laboratorio Internacional de Investigación sobre el Genoma Humano
Universidad Nacional Autónoma de México, Campus Juriquilla
Mexico

Alejandra obtained her Ph.D. in 2012 from the Biomedical Sciences Program at the National University of Mexico (UNAM), with a project developed under a cotutorship between Dr. Collado, at UNAM, and Dr. van Helden at the Université libre de Bruxelles. Since her Ph.D., she has been focused on developing bioinformatic tools, and strategies to study gene regulatory mechanisms, most of the developed tools are now part of the Regulatory Sequence and Analysis Tools suite (RSAT, http://rsat.eu/), where she still collaborates as a developer. Currently, using computational approaches, her research will incorporate functional genomics data into Genome Wide Association Studies (GWAS), aiming to identify variants that lead to misregulation of gene expression.

Unlocking the power of community data: LupusRGMX and immune cell research In LATAM
Patient registries are structured systems designed to collect, store, and analyze information about individuals living with specific health conditions. When combined with genomic data, they create new opportunities for genomic medicine and research. The MexOMICS Consortium was established to develop infrastructure that integrates electronic databases, enabling the collection, comparison, cross-referencing, and sharing of valuable information on various health conditions in the Mexican population, including the Mexican Lupus Registry (LupusGMX).

LupusRGMX is a digital data platform created to enhance understanding of the characteristics of Mexican people with Systemic Lupus Erythematosus (SLE) and to support longitudinal studies. Led by a multidisciplinary research team and engaging patient communities, the platform offers tailored surveys focusing on different aspects of patients' lives. This resource has empowered demographic, socioeconomic, and genomic research.

Building on the insights gained from MexOMICS and LupusRGMX, we have launched the JAGUAR project to map the immune cell diversity across Latin America.

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Helder Nakaya, Ph.D.
Associate Professor
School of Pharmaceutical Sciences
University of São Paulo
Brazil

Passionate about science, soccer, teaching, travel, and of course, gorgonzola, Helder Nakaya is a senior researcher at Hospital Israelita Albert Einstein in São Paulo and an associate professor at the University of São Paulo, Brazil. He holds a PhD in Molecular Biology and has extensive training in Bioinformatics. An expert in Systems Immunology, he works at the intersection of system-wide measurements, networks, and predictive modeling, particularly as they relate to vaccines and infectious diseases. His lab concentrates on investigating the foundations of infectious diseases through computational systems biology. Additionally, Dr. Nakaya serves as an adjunct professor at Emory University School of Medicine, in the Department of Pathology.

AI-Driven Precision Medicine: Unveiling Human Diseases through Single-Cell Systems Biology and Spatial Transcriptomics
In this seminar, I will explore the transformative role of Artificial Intelligence (AI) in medicine, focusing on its integration with systems biology at the single-cell level. We will show how spatial transcriptomics is revolutionizing our understanding of tissue architecture and disease progression. By leveraging these cutting-edge technologies, we aim to uncover new insights into human diseases and advance precision medicine approaches.

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Gosia Trynka
Head of Immune Genomics Group, Wellcome Sanger Institute
Science Director, Open Targets
Wellcome Genome Campus
UK

Dr. Trynka strongly believes that interdisciplinary approaches are essential to achieve meaningful insights into biological processes. The combination of molecular techniques, genomic assays, and computational methods that we develop and apply to study the immune system is a reflection of their own career path through several disciplines within biology and genetics.

With a background in molecular biology, they became interested in medical and population genetic approaches to study genetic determinants for immune related diseases. They joined Prof. Cisca Wijmenga’s group where they were a co-lead analyst for the genome-wide association study (GWAS) and an Immunochip study for coeliac disease (an immune disease of the small intestine resulting from intolerance to gluten). These studies resulted in identification of tens of disease risk loci and pointed to strong shared genetic background between celiac disease and a range of other common immune conditions, including type-1 diabetes, rheumatoid arthritis, and inflammatory bowel disease.

Despite their great success in mapping disease risk variants, they were disappointed by the limited insights that they gained in understanding biology of complex immune diseases. They therefore carried out their postdoctoral research at Brigham and Women’s Hospital, Harvard Medical School, and Broad Institute where they joined Dr. Soumya Raychaudhuri’s and Dr. Robert Plenge’s groups. They invested their time in developing statistical methods that allow translation of GWAS associations into biological functions. By integrating disease-associated variants with functional genomics data, these approaches pointed to specific cell types being relevant in the pathogenesis of numerous complex traits, including immune diseases. Their group at the Sanger Institute continuous with experimental and computational efforts to further map and translate immune disease genetic variants to function.

Using genetics to nominate, accelerate and deprioritise drug targets – a perspective from Open Targets Consortium

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Please note:
Due to a significantly higher number of submissions than we typically receive, it is taking a bit more time than expected to review and decide upon submissions. Thank you in advance for your patience and understanding.

Proceedings Paper Submissions

Bioinformatics Advances Journal has committed to considering publication of a special issue for peer-reviewed articles from the conference.

Bioinformatics Advances will have the opportunity to review the papers and provide comments. We will give authors one month to reply to comments in order to have the list of accepted proceedings papers at the end of September. Outstanding proceedings papers will be selected for featured talks (15 total minutes in length with 2 minutes reserved for Q&A).

Authors are responsible for the processing charges associated with the publication of the proceedings paper.  The processing charges are:

CC BY license (non-member): $2,620
CC BY license (ISCB member): $2,077
Free developing country charge*: $0

*Visit the journal's APC waiver policy page for more information on eligibility for geographic-based waivers.  

Submit a Proceedings Paper

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Abstract Talk and Poster Submissions

This is an invitation to scientists and professionals working in the fields of bioinformatics and computational biology to submit high quality original research papers for presentation at ISCB-LATAM SOiBiO CCBCOL 2024.

Abstract talks and posters will be organized according to scientific topics, which are covered by the conference (see below). Please note, abstracts are not limited to the listed conference topics and if the topic of your submission falls outside the listed ones you can choose the "General Computational Biology" area. Your abstract should convey a scientific result and should not be an advertisement for any commercial software package. Commercial software packages wishing to present at the conference should contact This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Agrobiological Omics
  • Biomedical Omics
  • Bioinformatics of Microbes and Microbiomes
  • Bioinformatics Education
  • Comparative and Population Genomics
  • Evolutionary & Comparative Genomics
  • Macromolecular Sequence, Structure, Function, and Interactions
  • Single-cell Omics
  • Systems and Network Biology
  • General Bioinformatics & Computational Biology
  • Machine Learning and Deep Learning applied to biodata

Abstracts for Oral Presentation and/or poster submissions to ISCB-LATAM SOiBiO CCBCOL 2024 should be approximately 400 words and have no figures. Adding references to already published papers is recommended where appropriate. Submission deadline in Easychair is https://easychair.org/conferences/?conf=iscblatamsoibioccbco24

For a variety of reasons, ISCB-LATAM SOiBiO CCBCOL 2024 strongly prefers that scientific research accepted for oral presentation be presented in-person at the conference venue. We understand that some presenters will have valid reasons to avoid in-person attendance. ISCB will grant remote presentation options for reasons associated with maternity/paternity leave, care for a family member, personal/medical disability, sickness, financial hardship, or potential visa problems. If your research is accepted for oral presentation and you are unable to present in person, ISCB-LATAM SOiBiO CCBCOL 2024 requires notification at the time of acceptance and no later than September 30, 2024. You will be asked during your confirmation of participation to confirm your in-person participation. If unable to participate you will need to request a waiver by writing This email address is being protected from spambots. You need JavaScript enabled to view it.

Any abstracts submitted after the deadline will be included only at the discretion of the conference chairs, and will be eligible for poster presentations only. Please also note that we can only allow one abstract per presenting author.

All talks will be recorded and available to participants as well as included in a live broadcast schedule as part of the virtual platform. All schedules will be posted on the ISCB-LATAM SOiBiO CCBCOL 2024 website.

In-Person Poster Hall: When preparing accepted posters please note that your printed poster should not exceed the following dimensions: 1.1 meters x 1.5 meters. There will be 1or 2 poster per side on the each poster board. Additionally, we ask that you also follow the Virtual Poster Theater information below in addition to your in-person presentation. This ensures all posters are viewable to both in-person and virtual attendees thus providing more exposure to your work.

Virtual Poster Theater: When preparing accepted posters please note that your poster will need to be uploaded via the virtual platform portal in two formats - a PDF of the poster and a 5-7 minute flash talk video not to exceed 100MB. Poster portal information will be sent to all approved posters closer to the conference and after the notification deadline. All presentations MUST be uploaded on specific dates the week of October 30 - November 5*. More specific dates will be given closer to the conference.
*Late Breaking posters will have a very short turn-around.

Authors selected for presentation (talk or poster) will be required to register for the conference.

Poster Submission Deadline is September 30, 2024

Please note: the official language of the conference is English.

Submit an Abstract

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