Links within this page: Proceedings Overview | Proceedings Publication Fee | Areas | Proceedings Key Dates | Review Process | Transfers to Bioinformatics Advances | Submission Guidelines | Conference Proceedings | Hybrid Format | Contact
Proceedings Chairs:
Karsten Borgwardt, Max Planck Institute of Biochemistry, Germany
Tijana Milenkovic, University of Notre Dame, USA
Proceedings Overview
ISMB/ECCB 2025 invites submissions of full papers (not abstracts) consisting of new, unpublished work, reporting theoretical, computational, and statistical advances in computational biology and its intersections with other fields.
Submissions are encouraged to report on advances in algorithm development and optimization, data structures, data visualization, artificial intelligence/machine learning, text mining, statistical inference, database and ontology development, image analysis, citizen and open science, etc. to analyze all types of biological data.
While we encourage submissions in new and emerging areas, we expect that the majority of submissions addressing topical biological domains will fall into one of the areas below. Please note during the EasyChair submission process you will: 1) select your "Area" (list below) and 2) select one or more of the Communities of Special Interest (COSIs) best suited for the presentation of your research from within the area. (learn more about COSIs here).
For a variety of reasons, ISCB 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 requires notification at the time of acceptance and no later than May 14, 2025. 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 pre-approved virtual presenters will be required to provide a pre-recorded talk for the virtual platform library in advance of the conference as a precaution due to possible technical issues.
ISMB/ECCB 2025 follows the ISCB policy for acceptable use of large language models (https://www.iscb.org/iscb-pol
Proceedings Publication Fee
Authors of accepted Proceedings papers are responsible for the publication fee of $700 USD. This is a substantial reduction from the publication fees customary for OUP journals. ISCB is committed to supporting all of its members, especially those from under-developed nations and/or those without funding. If your manuscript is accepted and you are unable to pay for the publication fees in part or in full, you may submit a fee waiver request to This email address is being protected from spambots. You need JavaScript enabled to view it.. Please provide your name, full institute address, and a short (up to 50 words) justification of why you are unable to cover the publication fee with the subject line of ISMB 2024 Publications Fee Waiver Request.
Publication fee payments are due by May 1, 2025. The online proceedings payment system will open April 9, 2025.
Proceedings publications are part of an online-only special issue of Bioinformatics and are open access (CC-BY), fully citable, and indexed by Medline and ISI. See the conference proceedings for ISMB 2024 for an example of online-only publication by Oxford University Press.
Areas:
| Bioinformatics Education and Citizen Science (COSIs within this area include: Education) Chair(s): Russell Schwartz, Carnegie Mellon University, USA Jérôme Waldispühl, McGill University, Canada |
Systematic examination and analysis of learning models, outcomes, and educational programs. Serious gaming and game-ification. |
| Bioinformatics of Microbes and Microbiomes (COSIs within this area include: BioVis, CAMDA, HiTSeq, MICROBIOME, MLCSB, NetBio, Text Mining) Chair(s): Nicola Mulder, University of Cape Town, South Africa Mihai Pop, University of Maryland, USA |
Computational methods and algorithms for studying microbial organisms, viruses, and their communities from omics and marker data. |
| Biomedical Informatics (COSIs within this area include: Bio-Ontologies, BioVis, CAMDA, Function, HiTSeq, iRNA, MLCSB, NetBio, Text Mining, TransMed, VarI) Chair(s): Niko Beerenwinkel, ETH Zurich, Switzerland Giulio Caravagna, University of Trieste, Italy Jenna Wiens, University of Michigan, USA |
Computational approaches to clinical and medical problems, including disease predisposition, diagnostic, progression, and treatment. Pharmacogenomics. |
| Equity and Diversity in Computational Biology Research (Of interest to all COSIs) Chair(s): Larry Hunter, University of Chicago, USA Alejandra Medina Rivera, Universidad Nacional Autónoma de México, Mexico |
Research that examines issues of equity, representation, diversity, or other elements related to datasets, methods, or the field at large; health policy; fairness in ML; biases in GWAS studies; bias in literature; biology/genomics of traditionally understudied groups. |
| Evolutionary, Comparative and Population Genomics (COSIs within this area include: BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, VarI) Chair(s): Flora Jay, Université Paris-Saclay, France Erin Molloy, University of Maryland, USA |
Phylogeny estimation, and modelling variation and change under the influence of evolutionary processes. Selection and adaptation. Multi-species analyses. |
| Genome Sequence Analysis (COSIs within this area include: BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, NetBio, RegSys, TransMed, VarI) Chair(s): Laurent Jacob, CNRS, Sorbonne Université, France Tobias Marschall, Heinrich Heine University Düsseldorf, Germany |
Assembly and mapping algorithms. Gene prediction and annotation. Detection, qualification, and annotation of genomic variants and their structural and functional effects. |
| Macromolecular Sequence, Structure, and Function (COSIs within this area include: 3DSIG, Bio-Ontologies, BioVis, CompMS, Evolution and Comparative Genomics, Function, iRNA, MLCSB, RegSys, VarI) Chair(s): Jianlin Cheng, University of Missouri, USA Mark Wass, University of Kent, UK |
Analysis and annotation of DNA, RNA, and proteins to predict, characterize, and understand their structure, function, and evolution. Includes protein design and imaging techniques for macromolecules. |
| Privacy and Security for Computational Biology (COSIs within this area include: HiTSeq, MLCSB, TransMed) Chair(s): Michael Baudis, University of Zurich, Switzerland Kana Shimizu, Waseda University, Japan |
Methods related to the protection of individualized molecular and medical information; privacy models; federated learning; GWAS on summary statistics; federated EHR data analysis; new approaches to federated data storage, access, and analysis. |
| Regulatory and Functional Genomics (COSIs within this area include: Bio-Ontologies, BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, NetBio, RegSys) Chair(s): Kimberly Glass, Harvard Medical School, USA Saurabh Sinha, Georgia Institute of Technology, USA |
Transcriptomics, single-cell RNA techniques, non-coding RNA, epigenetics, chromatin structure. |
| Systems Biology and Networks (COSIs within this area include: Bio-Ontologies, BioVis, CompMS, Function, MICROBIOME, MLCSB, NetBio, RegSys, Text Mining, TransMed) Chair(s): Anaïs Baudot, Aix Marseille Université, CNRS, INSERM, France Natasa Przulj, Barcelona Supercomputing Center, Spain |
Emergent properties and complex multi-component interactions within biological systems, considering genomic, proteomic, metabolomic, and other -omic data; gene regulation and circuit design. |
| General Computational Biology* Chair(s): Gary Bader, University of Toronto, Canada Alberto Paccanaro, Fundação Getúlio Vargas, Brazil & Royal Holloway, University of London, UK |
Novel techniques in emerging areas of computational biology not covered by the other areas listed above, including intersections with other fields. |
| *You are encouraged to submit to one of the other thematic areas. If you feel your contribution is at the intersection of many fields, please pick one. If you still want to submit to this area, you will be asked to explain why. Please note that the submissions in this area and others are likely to be moved, subject to chairs’ considerations. | |
Proceedings Key Dates
Review Process
Submissions will be subject to two rounds of reviews, allowing the authors to reply to the reviewer comments. In the first round the submissions will be classified into three categories: (a) accept/minor changes, (b) major changes, and (c) not accepted. Papers in the first category will be considered “conditionally" accepted without a second round of full review; Area Chairs would review the final version and in some cases ask the reviewers if concerns, if any, have been addressed. Authors of submissions in the second category will be given the opportunity to submit revised drafts based on the reviewer comments, with letters of response to the reviewers outlining the main changes and/or giving counter arguments to the reviewer points.
We expect the majority of papers to fall in categories (a) and (c), with category (b) reserved for papers that the reviewers identified as strong but with substantial issues that need to be addressed. Among the resubmitted papers, the second round of review will select the most suitable papers for presentation. All reviews of submitted papers are considered confidential and details are not disclosed outside of the review process. These will be published in the Bioinformatics journal and presented at the conference. All accepted papers are expected to have source code available and linked in the manuscript to ensure reproducibility of results.
Transfers to Bioinformatics Advances
Getting your paper accepted to the ISMB Proceedings is very competitive. For papers which are ranked highly but are not accepted we will be making offers to transfer some manuscripts to the ISCB journal Bioinformatics Advances. Manuscripts and the associated ISMB reviews would only be transferred to the journal upon author agreement. By transferring the reviews rapid decisions can be made by the journal. Papers accepted to Bioinformatics Advances would NOT be a part of the ISMB/ECCB 2025 Proceedings and would NOT be offered a talk. Please also note that Bioinformatics Advances is fully open access and that the normal Open Access Charges for the journal would apply.
Authors may opt out of this transfer process at submission time.
Submission Guidelines
All submission MUST select a presenting author. The presenting author MUST be marked as a corresponding author. Papers can be submitted in either a template-free format or by following the template for author submission to the OUP journal Bioinformatics. You are encouraged to submit in the OUP format. You are encouraged to submit in the OUP format. If the OUP template is used, the paper length must not exceed nine pages. If the template-free format is used the length of the paper must not exceed 12 pages (single space, 12 point font). In either format the page count should include any required abstract, figures, tables, and bibliography. Papers must be submitted as a PDF. If your submission is conditionally accepted, it then MUST be resubmitted as a Word or LaTeX file to adhere to the OUP proxy requirements. In either case, the paper must contain an abstract whose length does not exceed 250 words.
Authors of submissions will need to select 1st choice and 2nd choice areas most suitable for their paper (this is relevant for which Area Chairs/reviewers will review the paper). During submission, authors will be able to identify up to three COSIs most relevant to the topic of their submission (this is relevant for which COSI, i.e. conference track, the talk will be presented at if the paper is accepted). During the review process three reviews will be sought. Papers may be moved between areas as appropriate - this is often necessary for load balance and fit between areas during the review process.
If absolutely necessary, submissions can be accompanied by supplementary material, similar to submissions to scientific journals. The supplementary material should be collected in a separate file that is appropriately marked and uploaded as an attachment on the paper submission page in EasyChair. However, we advise against adding supplementary material, in general. Supplementary material will be published on the proceedings site alongside the online version of the conference paper. We do not support supplementary material presented at any other than the publisher's site. Additionally, OUP does not edit or typeset supplementary data - it is uploaded online exactly as it is received, so authors must ensure its accuracy before submitting.
Papers should be submitted in their final form since the evaluation procedure does not allow for additional rounds of refinement / modification in response to referee criticisms. Poor quality submissions or insufficiently prepared papers are very often rejected. Paper presenters must register and pay to attend and present at the conference.
ISMB does not accept previously published works through peer-reviewed publications. Please note that conference presentations, posting on recognized preprint servers (such as Arxiv, Biorxiv and PeerJ preprints), or posting on a personal or employer's website do not constitute prior publication. In case of doubt, please contact This email address is being protected from spambots. You need JavaScript enabled to view it.
After acceptance papers will have to be formatted according to the layout style required by the OUP Bioinformatics journal and will be limited to 9 pages. Formatting requirements can be found at:
https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript?login=true
Templates are available on OUP’s site for direct download:
http://static.primary.prod.gcms.the-infra.com/static/site/journals/document/oup-authoring-template.zip?node=7987de40f2eea956bc39
Papers not conforming to guidelines will not be reviewed
Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to ISMB/ECCB 2025, and for the entire review period, the paper should not be under review by any other conference or scientific journal.
Papers will be accepted electronically via the submission system, as a PDF, until January 23, 2025, 11:59 PM in the time zone of your choice. *No extension will be granted* If your submission is conditionally accepted, it then MUST be resubmitted as a Word or LaTeX file to adhere to the OUP proxy requirements.
Conference Proceedings
Publication of the proceedings as an online part of the journal Bioinformatics will result in fully citable articles, indexed by Medline and ISI. See the conference proceedings for ISMB 2024 for an example of online-only publication by Oxford University Press.
Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal with an electronic version distributed to conference delegates. The proceedings will be available online approximately one month prior to the conference opening.
ISMB/ECCB 2025 provides authors of accepted papers an oral presentation to provide an oral summary of their work. All presentations should be no longer than 20 minutes including 3-4 minutes for discussion. Paper presenters must register and pay to attend and present at the conference.
Hybrid format
All presenters who have been granted a waiver to present virtually will be required to provide a pre-recorded talk for the virtual platform library in advance of the conference. The pre-recorded talk will be kept on hand in case of any issues that may interfere with the presenters ability to present virtually. If this video is not submitted and an issue arises any delays will be deducted from the allotted presentation time.
Contact
Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for questions concerning the scientific content of submissions.
