Call for Proceedings - CLOSED Thursday, January 13, 2022

Proceedings Submission Site


Proceedings Co-chairs:

Christophe Dessimoz, University of Lausanne; University College London; Swiss Institute for Bioinformatics, Switzerland
Sushmita Roy, University of Wisconsin Madison, United States


ISMB 2022 invites submissions of full papers (not abstracts) consisting of new, unpublished work, reporting theoretical, computational, and statistical advances in computational biology and its intersections with other fields.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) first select your "Area" (list below) and 2) select the COSI(s) most suited for presentation of your research from within the area. (learn more about COSIs here).

All presenters 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 available shortly after the live presentation to provide faster and more seamless access to the conference content for virtual participants.

ISMB Proceedings Publication Fee


ISCB introduced publishing fees for ISMB Conference Proceedings beginning with ISMB/ECCB 2021. Authors of accepted Proceedings papers are required to cover the publication fee for their accepted paper if they are able to do so. For this purpose, we have negotiated a publication fee of $700 for ISMB 2022. This is a very substantial reduction from the publication fees customary for OUP journals.

Publication fee payments are due by April 18, 2022. The online proceedings payment system will open March 4, 2022 and can be paid at: https://iscb.swoogo.com/ISCBPublishingFees

Authors are responsible for the publication fee of $700 USD. 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 publications 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 2022 Publications Fee Waiver Request.

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/ECCB 2021 for an example of online-only publication by Oxford University Press.

Areas:  

Bioinformatics Education
(COSIs within this area include: Education)

Chair: Nicola Mulder, University of Cape Town, South Africa

 Systematic examination and analysis of learning models, outcomes, and educational programs.

Bioinformatics of Microbes and Microbiomes
(COSIs within this area include: BioVis, CAMDA, HiTSeq, MICROBIOME, MLCSB, NetBio, Text Mining)

Chairs:
Hélène Touzet, CNRS, CRIStAL, France
Robert Beiko, Dalhousie University, Canada

 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)

Chairs:
Maria Secrier, University College London, United Kingdom
Barbara Engelhardt, Princeton University, United States

3DSIG focuses on structural bioinformatics and computational biophysics. It is impossible to fully understand biological systems without understanding the 3D structure of their constituting parts and their interactions. As such the topics relevant for 3DSIG are wide and include, but are not restricted to Structure-based drug discovery including polypharmacology and network pharmacology; Structure representation, classification and prediction; Structure-based function prediction; Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic-acid; Protein dynamics and disorder; Evolution studied through structures; Application of structure to systems biology; Macromolecular assemblies; Structural genomics; 3D databases and data mining; Molecular visualization; Relevant methods of structure determination particularly hybrid methods; Prediction and analysis of protein domains; Membrane protein structure analysis and prediction; The structural basis of immunology.

Keywords: Drug-discovery; Structure representation/classification/prediction; Structural basis of macromolecular function; Prediction and simulation of biomolecular interactions; Dynamics of biological macromolecules; Evolution studied through structures; Structural systems biology/pharmacology; 3D visualisation/data mining/databases; Structure-based protein engineering; Structural basis of human diseases

 Computational approaches to clinical and medical problems, including disease predisposition, diagnostic, progression, and treatment. Pharmacogenomics.

Evolutionary, Comparative and Population Genomics
(COSIs within this area include: BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, VarI)

Chairs:
Céline Scornavacca, CNRS; Université de Montpellier, France
Lars Arvestad, Stockholm University, Sweden

 Phylogeny estimation, and modelling variation and change under the influence of evolutionary processes. Selection and adapatation. Multi-species analyses.

Genome Privacy and Security
(COSIs within this area include: HiTSeq, MLCSB, TransMed)

Chair:
Hyunghoon Cho, Broad Institute of MIT and Harvard, United States

 Methods related to the protection of individualized genomic and medical information; privacy models.

Genome Sequence Analysis
(COSIs within this area include: BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, NetBio, RegSys, TransMed, VarI)

Chairs:
Carl Kingsford, Carnegie Mellon University, United States
Rob Patro, University of Maryland, United States

 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)

Chairs:
Yann Ponty, CNRS/LIX, Polytechnique, France
Jérôme Waldispühl, McGill University, Canada

 Analysis and annotation of DNA, RNA, and proteins to predict, characterize, and understand their structure, function, and evolution. Includes imaging techniques for macromolecules.

Regulatory and Functional Genomics
(COSIs within this area include: Bio-Ontologies, BioVis, Evolution and Comparative Genomics, Function, HiTSeq, iRNA, MICROBIOME, MLCSB, NetBio, RegSys)

Chairs:
Jian Ma, Carnegie Mellon University, United States
Saurabh Sinha, University of Illinois, United States

Bio-Ontologies Special Interest Group covers the latest and most innovative research in the application of ontologies and more generally the organization, presentation and dissemination of knowledge in biomedicine and the life sciences.
Keywords: Ontology; Knowledge representation; Data integration; Automated reasoning; Text mining: Machine learning; Biocuration; Semantic web; Deep phenotyping; Learning health system
 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)

Chairs:
Marinka Zitnik, Harvard University, United States
Tijana Milenkovic, University of Notre Dame, United States

Network Biology covers new developments across this important and still burgeoning field; focusing on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology and medicine. The session will provide a unique interface between tool developers and users in the field of network biology, and will bring into focus the current state of the field, its future promise and how to get there.
Keywords: Molecular networks; Molecular interactions; Network analysis; Network visualization; Network alignment; Network reconstruction; Heterogeneous networks; Diagnostic networks,: Network tools, Network databases
 Emergent properties and complex multi-component interactions within biological systems, considering genomic, proteomic, metabolomic, and other -omic data; gene regulation and circuit design.

Equity-focused Research  (New for 2022)
(Of interest to all COSIs)

Chair:
Casey Greene, University of Colorado’s Anschutz Medical Campus, United States

 This area is for research that examines issues of equity, representation, diversity, or other elements related to datasets, methods, or the field of computational biology at large.

General Computational Biology*

Chairs:
Mohammed El-Kebir, University of Illinois, United States
Su-in Lee, University of Washington, United States

*You are encouraged to submit to one of the other 10 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.

SysMod aims to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. Focusing on the conjoint use of mathematical modeling and bioinformatics to understand biological systems functions and dysfunctions. SysMod is open to the full range of methods used in systems modeling, including qualitative and quantitative modeling, dynamical and steady-state modeling, as well all applications of systems modeling including basic science, bioengineering, and medicine.
Key words and phrases: Mathematical model; Numerical simulations; Whole genome metabolic models; Signalling pathways; Systems medicine; Quantitative systems pharmacology; Data and model integration; Model parametrization; Multi-scale models; Synthetic biology

Novel techniques in emerging areas of computational biology, including intersections with other fields.

Proceedings Key Dates

Proceedings Submission Key Dates
Monday, November 29, 2021 Call for Proceedings Opens
Thursday, January 13, 2022 
(11:59 PM Any Timezone)		 Proceedings Submission Deadline
*No extensions are granted*
Thursday, March 3, 2022 Conditional Acceptance Notification
Thursday, March 17, 2022 Revised Papers Deadline
Monday, April 4, 2022 Final Acceptance Notification
Thursday, June 30 Speaker presentations upload videos through delegate profile on conference platform beginning June 30 and no later than July 5. Videos become part of the conference library.

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 accepted without a second round of review. 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.

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 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

Authors of submissions will select one of ten areas most suitable for their paper. During submission authors will be able to identify topics (COSI areas) relevant to their submission. 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. 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.

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/ECCB 2021 (here) for an example of online-only publication by Oxford University Press.

ISMB 2022 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.

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. 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), including abstract, figures, tables, and bibliography. In either case, the paper must contain an abstract whose length does not exceed 250 words.

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: http://www.oxfordjournals.org/bioinformatics/for_authors/submission_online.html

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.

For submissions to the Proceedings track, 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.

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 2022, 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, in PDF format only, at the submission site until Thursday, January 13, 2022, 11:59 PM in the time zone of your choice. *No extensions are granted*

Contact

For questions concerning the scientific content of submissions, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..