Keydates

Conference Sponsors

Conference App Sponsor

Lanyard Sponsor

Conference Chairs

Conference Co-chair: Nicola Mulder
University of Cape Town
South Africa

Conference Co-chair: Torsten Schwede
Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Switzerland

ISCB Accomplishments by a Senior Scientist Award Keynote

Bonnie Berger

Simons Professor of Mathematics at MIT; Electrical Engineering and Computer Science
Massachusetts Institute of Technology
Cambridge, United States

Presentation Title: Biomedical Data Sharing and Analysis at Scale
Time: Thursday, July 25, 5:00 pm - 6:00 pm
Room: San Francisco

The ISCB Accomplishments by a Senior Scientist Award recognizes leaders in the fields of computational biology and bioinformatics for their significant research, education, and service contributions. Bonnie Berger is being honored as the 2019 winner of the Accomplishment by a Senior Scientist Award.

Abstact:

Researchers around the globe are gathering biomedical information at a massive scale. However, growing privacy concerns and computational overhead limit researchers' access to these data. In this talk, I will present novel computational approaches that help overcome these barriers to improve the scalability of essential biomedical analysis pipelines. First, I will describe how modern cryptography presents a path toward broader data sharing and collaboration in biomedicine as demonstrated by my recent work on secure genome-wide association studies (GWAS) and pharmacological machine learning. Second, I will build upon our initial introduction of compressive genomics, which capitalized on the growing redundancy and unique structure of biological data, to accelerate and enhance computational data analysis. I will demonstrate how compressive techniques can be used to build compact summaries of rapidly growing single-cell transcriptomic datasets to facilitate their sharing and analysis. These results lay a foundation for more effective and collaborative biomedical research, whereby an unprecedented scale of data can be pooled from individuals and institutes across nations to enable novel life-saving discoveries.

Biography

Many advances in modern biology revolve around automated data collection and the large resulting data sets. I am considered a pioneer in the area of bringing computer algorithms to the study of biological data, and a founder in this community that I have witnessed grow so profoundly over the last 20 years. I have made major contributions to many areas of computational biology and biomedicine, largely, though not exclusively through algorithmic insights, as demonstrated by ten thousand citations to my scientific papers and widely-used software. My research group works on diverse challenges, including and Computational Genomics, Structural Bioinformatics, High-throughput Technology Analysis and Design, Network Inference, and Data Privacy. We collaborate closely with biologists, MDs, and software engineers, implementing these new techniques in order to design experiments to maximally leverage the power of computation for biological exploration. Over the past five years I have been particularly active analyzing large and complex biological data sets; for example, my lab has played integral roles in modENCODE (non-coding RNA analysis), MPEG (biological data compression standard), and the Broad Institute’s sequence analysis efforts.

I continually and actively engage in community service, including recently as Vice President of International Society for Computational Biology, Head of the RECOMB Steering Committee, and member of the NIH NIGMS Advisory Council. I have served as both Proceedings and Conference Chairs for the two top conferences in my field— RECOMB and ISMB. I am also proud to have headed a workshop at ISMB 2016 on Gender Equality and been ISCB Fellows Chair (2015-2019), focusing on minority inclusion. I am an associate editor of Bioinformatics and IEEE/ACM TCBB journals. In addition, I serve on the Executive Editorial Board of Journal of Computational Biology and as member of the editorial boards of Annual Reviews for Biomedical Data Science, Genome Biology, Bioinformatics, IEEE/ACM TCBB, and Cell Systems.

FAQ

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Call for Proceedings - ISMB/ECCB 2019 – Closed

Proceedings Co-chairs:

Yana Bromberg, Rutgers University, United States
Nadia El-Mabrouk, Université de Montréal, Canada
Predrag Radivojac, Northeastern University, United States

ISMB/ECCB 2019 invites submissions of full papers (not abstracts) consisting of new, non-published 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 submission process you will first select your "area" (the list below) and when providing submission details you will also have the opportunity to select your preferred COSI shown as "topics" in EasyChair (learn more about COSIs here).

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 Bioinformatics journal will result in fully citable articles, indexed by Medline and ISI. See the conference proceedings for ISMB 2018 for an example of online-only publication by Oxford University Press.

ISMB/ECCB 2019 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 in the format following the template for author submission to the OUP journal bioinformatics. 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 THESE 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 2019, 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 Monday, January 28, 2019 midnight in the time zone of your choice. *No extensions are granted*

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..

Call for Tutorials - ISMB/ECCB 2019

Chair: Michelle Brazas, Ontario Institute for Cancer Research (OICR), Canada
Co-chair: Patricia M. Palagi, SIB Swiss Institute of Bioinformatics, Switzerland

Opens: November 5, 2018.

Tutorial Submissions

This call is an open invitation to scientists and professionals working in the fields of bioinformatics and computational biology to submit high quality proposals for Tutorials at ISMB/ECCB 2019.

Tutorial Program at ISMB/ECCB

The purpose of the Tutorials program is to build knowledge and provide hands-on training in "cutting-edge" topics relevant to the bioinformatics field and the COSI communities. 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 also serve to bring together people and COSI communities with common interests to discuss, debate and problem-solve defined topics.

Tutorials may include any form of presentation such as brief talks or hands-on exercises or panel discussions. 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. Please note that if you wish to focus your talk on a demo of a specific software package, your proposal should be submitted to the Technology Track.

Tutorials should be designed as half-day (4 hours) or full-day (8 hours) sessions with a 1 hour lunch. (A 15-minute break is scheduled for 11:00 am and 4:00 pm and should be listed in your agenda).

Potential topic areas (a list of Tutorials presented in 2018 is available here) may include but are not limited to the following:

• Analysis tools for long read sequencing
• AI and machine learning for bioinformatics
• GA4GH tools for sequence sharing
• Single-cell RNA or DNA analysis
• Translational informatics: Opportunities for bioinformatics in the clinical realm
• Making your software production ready
• Assembly of genomes in metagenomics
• Data sharing back to the public
• Others?

Compensation

The conference organizers are able to offer full conference complimentary passes for up to 3 tutorial presenters. Tutorial organizers may choose to share the value of the complimentary passes if the tutorial has additional presenters.

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
• 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
• 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: Monday December 17, 2018

Click here to complete a submission for Tutorials. You will also be asked during the submission process to provide a brief description of the tutorial that will be used on the website to promote it to delegates.

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/ECCB attendees and COSI communities
• Completeness, clarity, and quality of the proposal and materials including schedule of tutorial
• Educational value and effectiveness of the proposed presentation approach
• Overlap with tutorials held in 2018

Successful tutorial proposals will be notified by Thursday January 31, 2019.

Tutorial Materials

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

• Copies of the 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.
• Recordings of Tutorials sessions: Tutorials programs will be recorded to serve as online learning tools following the conference. All presenters must agree to allow ISCB to post these recording of the Tutorials program as a requirement of acceptance.

Copyright

The authors will grant copyright to tutorial materials to the ISCB for a period to extend from acceptance through August 1, 2019, and they agree that their materials may be made available for use in perpetuity through ISCB.

Tutorial Contact Information

Correspondence from prospective instructors should be sent to: This email address is being protected from spambots. You need JavaScript enabled to view it.

Call for Special Session Proposals - ISMB/ECCB 2019

Opens: Monday, November 5, 2018.

Special Sessions Submissions

ISMB/ECCB 2019 features a Special Sessions track for emerging research areas that will run throughout the conference in parallel to other tracks (except the keynote presentations). In its structure, each session(s) provides a more in-depth look at the subject matter presented. Proposals for special sessions should be submitted via the online submission system at here by January 31, 2019.

Special Sessions have the purpose of introducing the ISCB community and conference delegates to relevant 'hot' topics that are not already covered in the COSI tracks. Sessions can be considered as mini-symposia on timely topics, or new emerging area presented by top experts.

A wide range of topics is possible, as long as they are of relevance to computational biology and bioinformatics. We also encourage topics that are marginal to computational biology but clearly will need the involvement of such expertise in the near future. The proposed topics for Special Session might, for example, cover emerging themes the conference is not currently approaching with the desired proficiency. Some attractive topics include:

3D genomics
Biological imaging and image analysis
Data compression and storage
Mathematical and computational medicine
New sequencing technologies
RNA structure
Text Mining

In addition we would like to encourage submissions that deal with the Society-Computational Biology interface. Examples might be “Genomic data sharing and privacy”, "Bringing genomic medicine to the clinic”. We encourage you to submit a proposal on an area that you deem as important to the computational biology community and may impact the future of the field.

Proposals should include the following details:

1. Title (up to 20 words, preferably worded to pique delegates' interest)
2. Topic: Describe the field to be covered by the session(s) and its relevance for conference participants (about one page)
3. Meeting details
   1. Duration (time allotments can range from morning: 2 hours 25 minutes, afternoon 3 hours 20 minutes or up to a full day of 5 hours and 45 minutes)
   2. Expected sessions / topics, if possible with an explanatory paragraph about each
   3. A draft schedule showing how the sessions / topics will be organized including placement of keynotes, accepted talks, panel discussions, etc.
   4. How presentations will be selected (invitation, call for submissions, etc.)
   5. Possible speakers. This is not required, but may add weight to the proposal—indicate speakers who have already agreed to participate. NOTE: See Special Session Registration information for more details about compensation.
   6. Previous meetings of this with attendance statistics, if held before
   7. Potential sources of sponsorship for the session(s). ISCB provides session organizers with one-day complimentary registration for the invited speakers (maximum of four (4) per session) for those attending ISMB for the sole purpose of presenting within the Special Session. We encourage the organizers to approach experts from related fields and communities that are not necessarily attending ISMB/ECCB routinely. Organizers will be responsible for raising sponsorship for additional complimentary registrations.
4. Information about the organizers: full name (including title), affiliation, e-­mail and postal addresses, telephone numbers (work and mobile, if available, including country and city codes), URL of home page, and qualifications to organize this meeting.

This call is an invitation for scientists and professionals to submit proposals for Special Sessions for ISMB/ECCB 2019, to take place at the Basel Congress Centre, Switzerland.

Special Session Registration:

Organizers must identify the session speakers designated to receive the complimentary one-day registrations by May 15, 2019 by contacting This email address is being protected from spambots. You need JavaScript enabled to view it. in order to receive special registration instructions. Organizers and presenters within the Special Sessions are responsible for their own travel costs and if attending the full conference are responsible for the full conference registration fee. If needed, organizers are encouraged to seek sponsorships and/or use grant funds available to them to cover their own and their speakers' travel and registration costs.

If you have questions contact This email address is being protected from spambots. You need JavaScript enabled to view it..

Special Sessions Submissions