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  • News & Commentary - News

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    Submitter

    October 10-12, 2024
    Houston, TX, USA
    https://icibm2024.iaibm.org

    We are pleased to announce the 12th International Conference on Intelligent Biology and Medicine (ICIBM 2024), which will take place in Houston, TX, USA. ICIBM is a high-caliber conference that brings together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, and experimentalists interested in the application of computational methods in biomedical studies. The purpose of the ICIBM is to provide a congenial atmosphere highly conducive to extensive discussion and networking. You are invited to submit papers and abstracts with unpublished, original work describing recent advances in all aspects of Bioinformatics, Intelligent Computing, Systems Biology, and Medical Informatics, including but not restricted to the following topics:

    Bioinformatics:
    • Genomics and genetics/epigenetics, including integrative & functional genomics, genome evolution, GWAS.
    • Next-generation sequencing data analysis, 3D genome.
    • Big data science including storage, analysis, modeling, visualization, and cloud.
    • Precision medicine, translational bioinformatics, and medical informatics.
    • Drug discovery, design, and re-purposing.
    • Proteomics, and protein structure prediction, function, and interactions.
    • Single-cell sequencing data analysis.
    • Microbiome and Metagenomics.
    Intelligent Computing and Data Science:
    • Artificial intelligence, machine learning, deep learning, data mining, knowledge discovery.
    • Large language model, foundation model, and computer vision in biomedical.
    • Natural language processing, literature mining, semantic ontology, and health informatics.
    • Neural computing, kernel methods, feature selection/extraction.
    • Evolutionary computing, swarm intelligence / optimization, ensemble methods.
    • Artificial life and artificial immune system.
    • Biomedical image analysis and processing.
    Systems Biology:
    • Modeling and simulation of biological processes, pathways, networks, and interactomes.
    • Modeling of cellular and multi-cellular interaction systems.
    • Multi-dimensional omics data integration.
    • Synthetic biological systems.
    • Metabolomics, microbiome, and lipidomics.
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.).
    Medical Informatics:
    • Cohort discovery, EHR-based phenotyping, predictive modeling.
    • Data quality assessment or validation.
    • Clinical decision support solutions.
    • Informatics to address disparities in health and health care.
    • Interoperability (e.g., ontology, terminology, standards, and others).
    • Machine learning for clinical applications, genome, and phenome analysis/associations.
    • Mobile health and wearable devices.
    • Human-computer interaction and human factors
    Paper Submission and Publication:

    Prospective authors are invited to submit unpublished work to ICIBM 2024. All papers and abstracts will be initially submitted through the EasyChair Conference System. Selected papers of the registered authors will be recommended to be published in special issues in the following journals, subject to additional editorial approval and expected additional review by each journal: Patterns (impact factor: 6.5), Computational and Structural Biotechnology Journal (CSBJ, impact factor: 6.0), International Journal of Molecular Sciences (IJMS, impact factor: 5.6), Quantitative Biology (impact factor 3.1), Information (impact factor 3.1), Cancers (impact factor 5.2).

    Abstract Submission:

    Conference participants are invited to submit abstracts to ICIBM 2024. Abstract submitted to the conference should be formatted using the Abstract Template. The abstract body should be no more than 400 words. We welcome submissions of highlight papers that have been recently published or accepted for publication. In this case, the abstract should include a complete reference to the published paper. A group of experts will evaluate the submissions and select the abstracts to be presented orally or as a poster. Please submit your abstract to icibm2024.abstract[at]gmail.com.

    Travel Awards:

    The Travel Award, which pending on a grant application, is to encourage young scientists in training, including graduate, undergraduate and high school students, as well as postdoctoral fellows. Specific consideration will be given to qualified applicants from underrepresented populations, minority institutes, female trainees, or those who needs special financial support to attend ICIBM 2024.

    IMPORTANT DATES

    Deadline for original paper submission: July 5 (Fri), 2024
    Notification to authors of papers: August 23 (Fri), 2024
    Deadline for abstract submission: August 30 (Fri), 2024
    Conference early registration opens: June 20 (Thurs), 2024
    Conference early registration deadline: September 10 (Tues), 2024
    Deadline for travel award application: September 11 (Wed), 2024
    Conference regular registration: September 11 – October 10, 2024
    Research: A genomic language model (gLM) artificial intelligence
    Submitted by J.W. Bizzaro; posted on Thursday, April 04, 2024

    Submitter

    In a new Nature Communications article, researchers describe a genomic language model (gLM) capable of predicting protein co-regulation and function. The gLM, which was trained on millions of metagenomic scaffolds, has learned to interpret the language of genes, revealing the intricate dance of protein regulation and enzymatic functions. This approach is a leap forward in our understanding of the genomic blueprint and its regulatory networks.

    CITATION

    Hwang, Y., Cornman, A.L., Kellogg, E.H. et al. Genomic language model predicts protein co-regulation and function. Nat Commun 15, 2880 (2024). https://doi.org/10.1038/s41467-024-46947-9
    Proteopedia.Org Seeks Help
    Submitted by Eric Martz; posted on Wednesday, April 03, 2024

    Submitter

    https://Proteopedia.Org needs a major upgrade. Proteopedia.org (free, open source) was created in 2007 as a wiki encyclopedia of protein molecular structure incorporating JSmol (http://Jmol.Org). It is by far the easiest place to create customized interactive molecular scenes, which are then immediately online for anyone to see. "Green links" illustrate statements in text with interactive molecular scenes in JSmol. Proteopedia's pages have been visited >230 million times. Users have authored thousands of articles, >100 of which have been visited >50,000 times each. Professors and students are major users, as well as researchers. Over 5,000 people have set up free accounts. A brief introductory overview of Proteopedia is here:

    https://proteopedia.org/w/Proteopedia:Overview

    Rejuvenation will involve upgrading the obsolete versions of linux, MySQL, and Wikimedia that it now runs with on Amazon Web Services, and making all its customized features work with the new infrastructure. Those features include support to run JSmol within Wikimedia, the Scene Authoring Tools (https://www.youtube.com/watch?v=90jonYOzzCY), green links, etc. Then the content in the present implementation could be imported into the new system using an automated script that would also need to be developed. Jaime Prilusky, who created most of the present system and has maintained it until now, would very much like help from someone familiar with the components of the infrastructure, especially current MySQL. Limited funding may be available.

    Thanks from the Proteopedia Team, https://proteopedia.org/w/Proteopedia:Team

    Submitter

    The ARC Opportunity is seeking innovative approaches to tackle the challenge of the "Unknome" – a collection of genes that have been overlooked in research for over 20 years. These genes are difficult to study and often lack funding, leading to a research gap. The complexity of cellular processes and the labor-intensive nature of generating relevant datasets have hindered the development of models that can predict how genes affect cell behavior. The initiative is calling for high-throughput methods to accurately annotate these unknown genes, which could significantly advance our understanding of genetics.

    https://www.darpa.mil/ARC/DUF

    https://www.youtube.com/watch?v=AFOPZw8qAJc

    September 16-18, 2024
    Dipartimento di Informatica, Pisa, Italy
    https://biomedinfo.di.unipi.it/cmsb2024/

    CMSB 2024 solicits original research articles, tool papers, posters, and highlight talks on the modelling and analysis of biological systems and networks, as well as the analysis of biological data. The conference brings together researchers from across biological, mathematical, computational, and physical sciences who are interested in the modelling, simulation, analysis, inference, design, and control of biological systems. It covers the broad field of computational methods and tools in systems and synthetic biology and their applications.

    TOPICS

    Topics of interest include, but are not limited to:
    • Formalisms for modelling biological processes
    • Methods and tools for biological system analysis, modelling and simulation
    • Frameworks for model verification, validation, analysis, and simulation of biological systems
    • High-performance methods for computational systems biology
    • Identification of biological systems
    • Applications of machine learning and data analytics in biology
    • Network modelling, analysis, inference
    • Automated parameter and model synthesis
    • Model integration and biological databases
    • Multi-scale modelling and analysis methods
    • Design, analysis, and verification methods for synthetic biology
    • Methods for biomolecular computing and engineered molecular devices
    • Data-based approaches for systems and synthetic biology
    • Optimality and control of biological systems
    • Modelling, analysis and control of microbial communities
    The CMSB 2024 proceedings will be published in the Springer LNCS/LNBI series and indexed by ISI Web of Science, Scopus, ACM Digital Library, DBLP, and Google Scholar.

    Conference organizers:

    Roberta Gori, University of Pisa (Italy)
    Paolo Milazzo, University of Pisa (Italy)
    Mirco Tribastone, IMT School for Advanced Studies Lucca (Italy)

    Invited speakers:

    Juliana Bowles, University of St Andrews, (UK)
    Madalena Chaves, INRIA, Centre Inria d'Université Côte d'Azur (France)
    Karoline Faust, KU Leuven (Belgium)
    Corrado Priami, University of Pisa (Italy)

    IMPORTANT DATES

    Abstract submission (regular/tool papers): April 14, 2024
    Paper submission (regular/tool papers): April 21, 2024
    Notification: June 9, 2024
    Camera ready: June 23, 2024
    Poster/highlight talk: July 9, 2024
    Conference: September 16-18, 2024

    CONTACT

    All questions about the conference should be emailed to cmsb2024[at]easychair.org.

    March 4-8, 2024
    Live online (synchronous), max 18 participants
    Sessions from Monday to Friday, 13:00 to 17:00 (Madrid time zone)
    https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-bayesian-inference-practice/

    INSTRUCTORS

    Dr. Daniele Silvestro (University of Gothenburg, Sweden) and Tobias Andermann (University of Gothenburg, Sweden)

    COURSE OVERVIEW

    This course is based on the assumption that the easiest way to understand the principles of Bayesian inference and the functioning of the main algorithms is to implement these methods yourself.

    The instructors will outline the relevant concepts and basic theory, but the focus of the course will be to learn how to do Bayesian inference in practice. He will show how to implement the most common algorithms to estimate parameters based on posterior probabilities, such as Markov Chain Monte Carlo samplers, and how to build hierarchical models.

    He will also touch upon hypothesis testing using Bayes factors and Bayesian variable selection.

    The course will take a learn-by-doing approach, in which participants will implement their own MCMCs using R or Python (templates for both languages will be provided).

    After completion of the course, the participants will have gained a better understanding of how the main Bayesian methods are implemented in many programs used in biological research work. Participants will also learn how to model at least basic problems using Bayesian statistics and how to implement the necessary algorithms to solve them.

    Participants are expected to have some knowledge of R or Python (each can choose their preferred language), but they will be guided "line-by-line" in writing their script. The aim is that, by the end of the week, each participant will have written their own MCMC – from scratch! Participants are encouraged to bring their own datasets and questions and we will (try to) figure them out during the course and implement scripts to analyze them in a Bayesian framework.

    More information and registration at https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-bayesian-inference-practice/ or writing courses[at]transmittingscience.com

    Best regards,
    Sole
    Soledad De Esteban-Trivigno

    July 15, 2024 - July 18, 2024
    Shanghai, China
    https://ieeeaitest.com/wp-content/uploads/2023/12/CFP-6th-IEEE-AITest-2024.pdf

    CALL FOR PAPERS

    Artificial Intelligence (AI) technologies are widely used in computer applications to perform tasks such as monitoring, forecasting, recommending, predicting, and statistical reporting. They are deployed in a variety of systems, including driverless vehicles, robot-controlled warehouses, financial forecasting applications, and security enforcement and are increasingly integrated with cloud/fog/edge computing, big data analytics, robotics, Internet-of-Things (IoT), mobile computing, smart cities, smart homes, intelligent healthcare, and many more. Despite this dramatic progress, the quality assurance of existing AI application development processes is still far from satisfactory, and the demand for demonstrable levels of confidence in such systems is growing. Software testing is a fundamental, effective, and recognized quality assurance method which has shown its cost-effectiveness to ensure the reliability of many complex software systems. However, the adaptation of software testing to the peculiarities of AI applications remains largely unexplored and needs extensive research to be performed. On the other hand, the availability of AI technologies provides an exciting opportunity to improve existing software testing processes, and recent years have shown that machine learning, data mining, knowledge representation, constraint optimization, planning, scheduling, multi-agent systems, etc. have real potential to positively impact software testing. Recent years have seen a rapid growth of interest in testing AI applications as well as the application of AI techniques to software testing. This conference provides an international forum for researchers and practitioners to exchange novel research results, articulate the problems and challenges from practices, deepen our understanding of the subject area with new theories, methodologies, techniques, process models, impacts, etc., and improve the practices with new tools and resources.

    IMPORTANT DATES

    Abstract Registration Due: March 8, 2024
    Submission Deadline: April 1, 2024
    Notification Due: June 1, 2024
    Final Version Due: June 15, 2024
    Education: Hands-On NGS Data Analysis Workshops 2024
    Submitted by Dr. David Langenberger; posted on Saturday, January 20, 2024

    Submitter

    Check the upcoming hands-on NGS Data Analysis Workshops for 2024:

    February 28-March 1 (Online)
    Online Course - A Practical Introduction to NGS Data Analysis
    Link: https://www.ecseq.com/workshops/workshop_2024-01-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course

    March 11-14 (Berlin, Germany)
    RNA-Seq Data Analysis Workshop
    Link: https://www.ecseq.com/workshops/workshop_2024-02-RNA-Seq-data-analysis

    May 6-8 (Berlin, Germany)
    Single-Cell RNA-Seq Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-03-Single-Cell-RNA-Seq-Data-Analysis

    May 27-29 (Online)
    Online Course - Bioinformatics Pipeline Development with Nextflow
    Link: https://www.ecseq.com/workshops/workshop_2024-04-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course

    June 10-14 (Berlin, Germany)
    8th Berlin Summer School 2024
    Link: https://www.ecseq.com/workshops/workshop_2024-05-8th-Berlin-Summer-School-NGS-Data-Analysis

    September 2-4 (Munich, Germany)
    Next-Generation Sequencing Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-06-NGS-Next-Generation-Sequencing-Data-Analysis-A-Practical-Introduction

    September 25-27 (Leipzig, Germany)
    Single-Cell RNA-Seq Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-07-Single-Cell-RNA-Seq-Data-Analysis

    November 13-15 (Online)
    Online Course - Bioinformatics Pipeline Development with Nextflow
    Link: https://www.ecseq.com/workshops/workshop_2024-08-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course

    December 9-11 (Online)
    Online Course - A Practical Introduction to NGS Data Analysis
    Link: https://www.ecseq.com/workshops/workshop_2024-09-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course

    Link to all courses: https://www.ecseq.com/workshops/ngs-data-analysis-courses
    Software: BIRCH Bioinformatics System v3.90
    Submitted by Brian Fristensky; posted on Monday, January 15, 2024

    Submitter

    BIRCH 3.90 now available for download at http://home.cc.umanitoba.ca/~psgendb/local/public_html/BIRCH3.90announcement.html

    NEW

    • BioLegato 1.1.2
    • New platform: macos-arm64 (eg. M1, M2, Apple Silicon)
    • Many updates to software packages
    • Full Python3 compliance
    BIRCH unifies hundreds of popular bioinformatics tools through the BioLegato family of Object-Oriented applications. BioLegato makes it easy to try out new programs, and to experiment with your data at every step in the analytical process.

    Visit our YouTube Channel at https://www.youtube.com/channel/UC9_3TfH3sjE0YdToVMChq-w?view_as=public

    Submitter

    EXCERPT

    Today, the U.S. Food and Drug Administration approved two milestone treatments, Casgevy and Lyfgenia, representing the first cell-based gene therapies for the treatment of sickle cell disease (SCD) in patients 12 years and older. Additionally, one of these therapies, Casgevy, is the first FDA-approved treatment to utilize a type of novel genome editing technology [CRISPR/Cas9], signaling an innovative advancement in the field of gene therapy.
    Source: https://www.fda.gov/news-events/press-announcements/fda-approves-first-gene-therapies-treat-patients-sickle-cell-disease
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