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.
The immune system protects organisms from pathogens. It is characterized by functional heterogeneity at the molecular and cellular levels and operates across time scales. Both innate and adaptive branches of immunity consist of a continuum of cellular phenotypes driven by a complex network of intracellular regulators and extracellular signaling molecules. Immune cells interact with each other and with other cell types across tissues and organs. Adaptive immunity is further characterized by diversity of receptor repertoires enabling heterogeneity of specificities and responses.
Novel high-throughput technologies, such as sequencing, genomic, epigenomic, proteomic, genome editing, spatial, and imaging technologies, are increasingly being adopted to generate massive amounts of data for studies of fundamental features of the immune system in health and disease. However, computational processing, analysis, integration, interpretation of such data presents major challenges. This includes computational problems specific for immunological studies, as well as general ones, but in application to the domain of immunology.
In this special session, we will discuss computational methods that address challenges typical in analysis of multi-dimensional data in immunology, as well as data-driven studies leading to exciting new fundamental and translational discoveries.
Jennifer L. Clarke, University of Nebraska-Lincoln, United States Noah Fahlgren, The Donald Danforth Plant Science Center, United States Camilo Valdes, University of Nebraska-Lincoln, United States
The Special Session on Digital Agriculture will highlight the latest advances in the field at the intersection with computational biology. This includes basic and applied research, from cellular pathways and genetics to AI and machine learning to biotechnology. As such topics relevant for this Special Session include, but are not restricted to, genetics and genomics of agriculturally relevant species; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and FAIR data standards; biotechnology; and soil sciences. This Session will include scientific research talks as well as panel discussions and introductory presentations on relevant, nationwide collaborative projects.
The Special Session on Digital Agriculture supported in part by:
This Special Session on Genome Privacy and Security looks at methods related to the protection of individualized genomic and medical information; privacy models.
Thomas Lengauer, Max Planck Institute for Informatics, Germany Shoshana Wodak, VIB‐VUB Center for Structural Biology, Belgium
This is the third and final edition of a series of sessions on the pandemic that started at ISMB 2020. The session will feature talks that provide insight into the knowledge on the pandemic and the virus causing it that we have gained with strong support of bioinformatics and computational biology and open the topic up to perspectives regarding possible future pandemics.
Corteva Agriscience is a global pure-play agriculture company that provides farmers around the world with the most complete portfolio in the industry - including a balanced and diverse mix of seed, crop protection and digital solutions focused on maximizing productivity to enhance yield and profitability. With some of the most recognized brands in agriculture and an industry-leading product and technology pipeline well positioned to drive growth, the company is committed to working with stakeholders throughout the food system as it fulfills its promise to enrich the lives of those who produce and those who consume, ensuring progress for generations to come. More information can be found at www.corteva.com
The Office of Data Science Strategy (ODSS) leads implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH. The office was formed in 2018 within the Division of Program Coordination, Planning, and Strategic Initiatives, which plans and coordinates trans-NIH initiatives and research supported by the NIH Common Fund.
Akamai Technologies, Inc. is an American content delivery network, a cybersecurity, and cloud service company, providing web and Internet security services. Akamai's Intelligent Edge Platform is one of the world's largest distributed computing platforms.
At Janssen Immunology, we are relentlessly dissatisfied with the status quo, and are working to create a future where autoimmune diseases are a thing of the past. Our Immunology team is focused on redefining care by delivering transformational therapies and regimens to address unmet need in patients and restore balance in the immune system for those living with autoimmune disease. For more information or to learn about career opportunities, please visit https://www.janssen.com/immunology
With 3,000+ researchers in 12 labs on six continents focused on Accelerated Discovery and Exploratory Sciences, IBM Research pioneers the most promising and disruptive technologies in hybrid cloud, AI and quantum computing. The combination of increasingly powerful computers and AI offers the possibility to be able to detect, diagnose, understand and cure diseases like never before. At IBM Research, we’re working on creating software and AI systems that can convert reams of health data into useable information for researchers and clinicians the world over. Scientific discovery is driven by two forces: the development of new capabilities and the relentless tenacity of the world’s sharpest minds. We see it as our duty to accelerate scientific progress by developing cutting-edge technologies, demonstrating scalable processes, and deploying new models of collaborative innovation.
As the world's enterprises accelerate their digital transformations, they discover that next-generation applications must deal with data that are bigger and faster at the same time, outstripping the capabilities of today's infrastructure. MemVerge's mission is to deliver a new architecture, called Big Memory Computing, that converges memory and storage, thereby removing the storage I/O bottleneck once and for all. MemVerge's Memory Machine™ Software virtualizes heterogeneous memory hardware into a software-defined memory service that has both high capacity and high performance. MemVerge ZeroIO™ In-Memory Snapshot technology captures the state of running applications, and can be used for application roll-back, cloning and high availability. The results are new levels of productivity, performance, availability, and mobility for today's data-centric applications, both on-premises and in the cloud.
Terabyte Sponsors
The Jackson Laboratory is an independent, nonprofit biomedical research institution with more than 2,400 employees. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.
Overleaf is a free, collaborative, cloud-based LaTeX editor which makes the process of writing, editing and publishing scientific documents quicker and easier. This intuitive online platform has seen rapid adoption across science and research, and Overleaf's award-winning collaboration technology is now in use by over 9 million researchers, students and technical writers in institutions, labs and industry worldwide. It’s simple and intuitive to use – all you need is a web browser – try it out and use it for free at www.overleaf.com.
The Harvard Medical School Department of Biomedical Informatics offers a variety of opportunities to increase your knowledge base and skill set in the application of quantitative principles to biomedical discovery. Come learn about our educational programs which include a Master’s, PhD, and Summer Institute and hear about our postdoctoral fellowships, faculty positions and other career opportunities.
Visit our booth to learn more about educational and career opportunities. For more information please visit: http://dbmi.hms.harvard.edu
Gigabyte Sponsors
F1000Research is an Open Research publishing platform for scientists, scholars and clinicians across all disciplines offering rapid publication of articles and other research outputs without editorial bias. We publish research across all academic disciplines and in multiple formats, including original articles, data notes, software tool articles and method articles.
Syngenta plays a vital role in enabling the food chain to feed the world safely and take care of our planet. Our ambition is to be the most collaborative and trusted team in agriculture, providing leading seeds and crop protection innovations to enhance the prosperity of farmers, wherever they are.
Oxford University Press publishes a range of computational biology journals, including Bioinformatics, Bioinformatics Advances, GigaScience, Nucleic Acids Research, NAR Genomics and Bioinformatics, Database, Briefings in Bioinformatics, Briefings in Functional Genomics, and more. Bioinformatics publishes the highest quality scientific papers and review articles with its main focus is on new developments in genome bioinformatics and computational biology.
Life is an international, peer-reviewed, open access journal of scientific studies related to fundamental themes in life sciences, published monthly online by MDPI. It publishes topics include, but are not limited to biomolecular design, activation and function; molecular evolution; biomolecular trafficking, and networks; membranes, and molecular organization in cells. We encourage the submission of manuscripts that fall in the broad areas of: Structural biology Computational biology Biochemistry and biophysics of subcellular and molecular processes
Fulgent Genetics is a global leader in next-generation sequencing with a focus on developing flexible and affordable genetic testing panels. By merging the fields of genetics, molecular biology, and computer science, we pursue excellence in genetic sequencing, scalability, and data analysis. We offer an unrivaled catalog of genetic testing covering over 18,000+ single genes, 800+ rare disease tests, whole-genome sequencing, whole-genome copy number variation analysis, mitochondrial sequencing, and CLIA/CAP quality sequencing services.
Biomedical Data Science (BDS) encompasses the study and pursuit of the effective uses of biomedical data, information, and knowledge for scientific inquiry, problem-solving, and decision-making, driven by efforts to improve human health. The graduate programs in BDS blend the best of statistics, computer sciences, biostatistics and biomedical informatics and train students to develop computational and mathematical approaches to analyze large-scale biomedical data and to lead collaborative, interdisciplinary team science efforts.
Recruiter
We are a technology company that has built the world’s largest library of clinical and molecular data and an operating system to make that data accessible and useful, starting with cancer. Our goal is for each patient to benefit from the treatment of others who came before.
We’re looking for people who can help us change the world. Who question the status quo and don’t shy away from tough problems. For the builders who are never done building and the learners who are never done learning. We’re looking for passionate people with undying curiosity. Those who want to attack one of the most challenging problems ever faced… head on.
At St. Jude, we have one common goal: find cures for children with cancer and other life-threatening diseases through research and treatment. As both a world class research institute and a specialized children’s hospital, St. Jude provides an unparalleled opportunity to advance your scientific training and launch your career.
Special Session Sponsors
Monona Terrace Community and Convention Center Coronavirus (COVID-19) Information:
The ISMB 2022 facility follows CDC cleaning and disinfecting guidelines and have enhanced all cleaning and disinfecting procedures to include:
Touch-free hand sanitizer dispensers are located at key points throughout the building.
All frequent touch-points are disinfected multiple times per day with EPA approved sanitizers. Touch-points include stair and escalator handrails, door handles, door push bars, elevator and ATM buttons, house phones, counters, toilets, public area tables and chairs and vending machines.
Restrooms are regularly and thoroughly cleaned and disinfected during event hours and overnight. Facility restrooms have touch-free soap dispensers, water faucets and paper towel dispensers.
Audiovisual equipment will be cleaned and disinfected after each use.
The Monona Terrace cleaning staff has received COVID-19 hygiene and safe practices training and are certified Global Biorisk Advisory Council ® (GBAC) technicians. All employees at our facility wear face coverings and are instructed to stay home if they don’t feel well or if they may have been in contact with someone with COVID-19. Signs are posted to remind staff of hygiene and safety protocols.
We invite abstracts for research that is topical to bioinformatics and computational biology, which is in progress (unpublished, formerly Late-Breaking Research) or previously published within the last 18 months (previously Highlights Track) for consideration for oral and/or poster presentation.
Your abstract should be submitted to the Communities of Special Interest (COSI) Track that most accuratelyreflects the area of the work. (You will have the option to identify two other COSI tracks that may also be suited to your research area during your submission). You can learn more about COSIs here.
Talks and posters are organized according to scientific topics which are covered by the COSIs listed below. Please note, abstracts are not limited to COSI topics and if the topic of your submission falls outside the listed COSIs 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. Multiple talks: The same talk is not permitted to be given more than once as an oral presentation at ISMB 2022. Research may presented as both a talk and poster. Having the same person deliver two (or more) different talks is possible (and not prohibited), but it is not encouraged. This allows for many people from one lab to present the work of the lab. A presenting author may present more than oneposter although not in the same Poster session we encourage labs to involve multiple attendees.
All presentations for ISMB 2022 will presented live regardless if you are participating in-person from Madison or virtually. While many presenters will be in-person in Madison, those unable to travel will be presented live stream (zoom) and presented live through the conference platform and streamed into the Madison presentation room.
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.
Abstract Submission Key Dates (last update May 31)
Monday, January 24, 2022
Call for Abstracts Opens
Thursday, April 21, 2022
Abstracts Submission Deadline (closes at 11:59 p.m. April 21, Any Time Zone)
Monday, April 25, 2022
Late Posters Submissions Open
Thursday, May 12, 2022
Talk and/or Poster Acceptance Notifications
Friday, May 20, 2022
CAMDA Extended Abstracts Deadline (updated May 11)
Thursday, May 19, 2022
Late Posters Submissions Deadline (closes at 11:59 p.m. May 19, Any Time Zone)
Thursday, May 26, 2022
Late Posters Acceptance Notifications
Thursday, May 26, 2022
CAMDA Acceptance Notification
Monday, June 13
Last day for Presenters to have completed release forms, confirmation of participation (form sent by ISMB)
Monday, June 13
Last day for Presenting Authors and Poster Authors registration to be completed
Thursday, June 30, 2022
Speaker to upload videos through delegate profile on conference platform beginning June 30 and no later than July 5. Videos become part of the conference library.
Presentations not uploaded in advance will not be guaranteed to be part of the conference on-demand library.
Thursday, June 30, 2022
Poster presentations videos and details uploaded through accepted poster delegate profile on conference platform beginning June 30 and no later than July 5.
3DSIG: Structural Bioinformatics and Computational Biophysics
Abstract Area Chairs: Douglas Pires, The University of Melbourne, Australia Rafael Najmanovich, Université de Montreal, Canada
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.
Bio-Ontologies
Abstract Area Chairs: Tiffany Callahan, Columbia University, United States Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia
Bio-Ontologies Community of Special Interest Group (COSI) covers the latest and most innovative research in the application of ontologies, the organisation and dissemination of knowledge, and the development and application of knowledge-based methods in biomedicine and life sciences.
Bio-Ontologies provides a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The informal nature of the COSI offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA) and the W3C’s Healthcare and Life Sciences interest group (HCLSIG), thereby increasing impact through broader dissemination and enabling new and exceptional collaborations.
BIOINFO-CORE
Abstract Area Chairs:
Madelaine Gogol, Stowers Institute, United States
Rodrigo Ortega Polo, Agriculture and Agri-Food Canada Alberto Riva, University of Florida, United States
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas.
The major goal of this COSI is to offer a community to people who manage and staff bioinformatics cores around the world. Topics of interest to this group for our ISMB workshop include topics that core members would find interesting or useful. This includes but is not limited to: management topics relevant to cores, core formation and setup, workflow development, reproducibility, best practices, training, or exploring analysis of new types of data.
BOSC: Bioinformatics Open Source Conference
Abstract Area Chairs: Nomi L. Harris (Chair), Lawrence Berkeley National Laboratory, United States Karsten Hokamp, Trinity College Dublin, Ireland Hervé Ménager, Institut Pasteur, France Monica Munoz-Torres, University of Colorado Anschutz Medical Campus, United States Deepak Unni, European Molecular Biology Laboratory, Heidelberg, Germany Nicole Vasilevsky, University of Colorado Anschutz Medical Campus, United States Jason Williams, Cold Spring Harbor Laboratory, United States Peter Cock (ex officio, Open Bioinformatics Foundation (OBF), United Kingdom
BOSC covers all aspects of open science / open source bioinformatics, including standards and ontologies; approaches that promote open science and sharing of data, results and software; bioinformatics tools and libraries; and ways to grow open source communities while promoting diversity within them.
Launched in 2000 and held yearly since then, BOSC is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Keywords: Open source; Open science; Open data; Reproducible research; Interoperability; Data science; Workflows; Translational bioinformatics; Diversifying bioinformatics communities You can learn more about the BOSC COSI here.
BioVis: Biological Data Visualization
Abstract Area Chairs:
Jan Byska, Masaryk University, Czech Republic and University of Bergen, Norway
The BioVis track aims to educate, inspire, and engage bioinformatics and biology researchers in state-of-the-art visualization research and visualization researchers in problems in biological data visualization.
The rapid adoption of data-intensive biology approaches creates enormous challenges for computational visualization techniques, which are needed to enable researchers to gain insight from their large and highly complex data sets. The goal of this session is to bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging bioinformatics and biology researchers in state-of-the-art visualization research, as well as visualization researchers in problems in biological data visualization.
CAMDA: Critical Assessment of Massive Data Analysis
Abstract Area Chairs: Joaquin Dopazo, Fundación Progreso y Salud, Spain David Kreil, Boku University Vienna, Austria Paweł P Łabaj, Austrian Academy of Sciences, and Jagiellonian University, Poland Wenzhong Xiao, Harvard Medical School, United States
(PLEASE note: CAMDA submitters should include a 3-5 page long abstract PDF)
The large, complex data sets for the Critical Assessment of Massive Data Analysis (CAMDA) contest include built-in truths for calibration. In an open-ended competition, however, both seasoned researchers and cunning students push the boundaries of our field, with unexpected questions or angles of approach often bringing the most impressive advances.
The CAMDA track highlights and compares the latest methods and results in an international data analysis contest, with this year's topics including: (1) a cancer prognosis data-integration challenge, now with RNA-seq reads for multiple cancer types introducing 300Mb of new human genomic sequence, (2) a CMap drug safety challenge of comparing / integrating multi-track responses of multiple cell lines for predicting the severity of drug induced liver injury in humans from a range of cell line assays, and (3) a meta-genomics geolocation challenge of constructing multi-source microbiome fingerprints in the context of climate data and predicting the geographical origin or ecological niche of mystery samples.
CompMS: Computational Mass Spectrometry
Abstract Area Chairs: Wout Bittremieux, University of California San Diego, United States Isabell Bludau, Max Planck Institute of Biochemistry, Germany Lindsay Pino, Talus Bio, United States Timo Sachsenberg, University of Tübingen, Germany
The CompMS group promotes the efficient, high quality analysis of mass spectrometry data. The CompMS initiative covers various computational mass spectrometry application domains, including proteomics, metabolomics, and lipidomics.
Education: Computational Biology Education
Abstract Area Chair: Wai Keat Yam, International Medical University, Malaysia
Education-COSI focuses on bioinformatics and computational biology education and training across the life sciences.
A major goal of this COSI is to foster a mutually supportive, collaborative community in which bioscientists can share bioinformatics education and training resources and experiences, and facilitate the development of education programs, courses, curricula, etc., and teaching tools and methods. Keywords: education, training, training resources, curricula, competencies
Evolution and Comparative Genomics
Abstract Area Chairs: Edward Braun, University of Florida, United States Wataru Iwasaki, University of Tokyo, Japan Giltae Song, Pusan National University, Korea
Evolution and comparative genomics are deeply intertwined with computational biology. Computational evolutionary methods, such as phylogenetic inference methods or multiple sequence alignment are widely used, yet remain far from “solved” and are indeed intense areas of research.
At the same time, evolutionary and comparative genomics are inherently “transversal” disciplines in that work in many other biological areas of research have some evolutionary component (e.g. cancer genomics, epidemiology, toxicology, population genetics, functional genomics, structural biology just to name a few). The scope of this COSI is intentionally kept broad. The track will feature a mix of proceedings, highlight, and invited talks. Priority will be given to contributions which are relevant to more than a single area of application, or to contributions which are not covered by more specialised COSIs.
Abstract Area Chairs: Dukka KC, Michigan Technological University, United States Iddo Friedberg, Iowa State University, United States Kim Reynolds, University of Texas Southwestern Medical Center, United States Mark Wass, University of Kent, United Kingdom
The mission of the Function Community of Special Interest (Function-COSI) is to bring together computational biologists, experimental biologists, biocurators, and others who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
The Function COSI features the Critical Assessment of Function Annotation, an ongoing community challenge aimed at improving methods for protein function prediction. The Function-COSI holds annual meetings alongside ISMB. Also, we are conducting the multi-year Critical Assessment of protein Function Annotation, or CAFA, experiment.
Keywords: Protein function prediction, machine learning, performance assessment,
HitSeq: High-throughput Sequencing
Abstract Area Chairs: Can Alkan, Bilkent University, Turkey Christina Boucher, University of Florida, United States Ana Conesa, University of Florida, United States Francisco M. De La Vega, Stanford University, United States Dirk Evers, Dr. Dirk Evers Consulting, Germany Birte Kehr, Universitätsklinikum Regensburg, Germany Kjong Lehmann, ETH-Zürich, Switzerland
HiTSeq is a community of special interest devoted to the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) data. Sessions will be devoted to discussing the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) datasets and will provide a forum for in-depth presentations of the methods and discussions among the academic and industry scientists working in this field.
We seek contributions on any topic involving HTS data analysis including: genome assembly and haplotype phasing; transcriptome analysis; genetics and epigenetics variation; metagenomics and microbiome analysis; and new HTS platform data analysis (e.g. synthetic reads, long reads, nanopore). In addition to general sessions, we propose to have two specialized sessions to focus on current hot topics: a) long sequencing and mapping techniques, b) single cell sequencing applications, c) non-linear genome representations. Both of these topics have generated an enormous amount of interest recently.
Keywords: sequencing, next generation, high throughput, algorithms, assembly, phasing, variation discovery, genotyping, metagenomics, microbiome, long reads, short reads, nanopre, pan-genomes, graph genomes
iRNA: Integrative RNA Biology
Abstract Area Chairs: Yoseph Barash, University of Pennsylvania, United States Klemens Hertel, UC Irvine, United States Athma Pai, University of Massachusetts Medical School, United States Michelle Scott, University of Sherbrooke, Canada
iRNA track covers the full range of research topics in the field of RNA Biology, from computational and high-throughput experimental methods development to their application in different aspects of RNA processing, structure, and function.
The goal of the Integrative RNA Biology session is to bring together experts in computational and experimental aspects of research in RNA Biology to cover new developments across this broad field of research. The meeting focuses on two major areas: (1) the development of computational and high-throughput experimental methods, and (2) the application of such methods to break new grounds in the study of RNA biology and disease. We aim to educate and inspire researchers in the field, novice and seasoned alike, by meshing together different aspects of Computational RNA Biology, and promoting cross-disciplinary collaborative research.
Keywords: Transcriptomics, RNA processing, post-transcriptional regulation, non-coding RNA, RNA 2D/3D structure, alternative-splicing, alternative polyadenylation, RNA translation degragation and localization, genetic variants effect on RNA processing, RNA and disease.
MLCSB: Machine Learning in Computational and Systems Biology
Abstract Area Chairs: Catalina Vallejos, The University of Edinburgh, United Kingdom Marinka Zitnik, Harvard University, United States
Systems Biology and Machine Learning meet in the MLCSB COSI. The community is the place for researchers of these areas to exchange ideas, interact and collaborate.
Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines and tools sharing the -omics suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. Taking advantage of this wealth of genomic information has become a conditio sine qua non for whoever has the ambition to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time, bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms.
Keywords: Machine Learning, Data Mining, Deep Learning, Artificial Intelligence in Bioinformatics and Computational Biology
MICROBIOME
Abstract Area Chair: Zhong Wang, Lawrence Berkeley National Laboratory, United States
The MICROBIOME Community of Special Interest aims at the advancement and evaluation of computational methods in microbiome research, especially metaomic approaches. Based on the Critical Assessment of Metagenome Interpretation (CAMI), the COSI supplies users and developers with exhaustive quantitative data about the performance of methods in relevant scenarios.
It therefore guides users in the selection and application of methods and in their proper interpretation. Furthermore, the COSI provides a platform for exchange and networking between method developers, and provides valuable information allowing them to identify promising directions for their future work.
The MICROBIOME Community of Special Interest aims at the advancement and evaluation of computational methods in microbiome research, especially metaomic approaches.
As large scale, systems-level data are becoming increasingly available, modeling and analyzing them as networks is widespread. Network Biology Community serves to introduce novel methods and tools, identify best practices and highlight the latest research in the growing and interdisciplinary field of network biology.
Abstract Area Chairs: Shaun Mahony, Penn State University, United States Anthony Mathelier, University of Oslo, Norway Alejandra Medina-Rivera, National Autonomous University of Mexico
Regulatory genomics involves the study of the genomic control system, which determines how, when and where to activate the blueprint encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the RegSys COSI meeting focuses on bioinformatics for regulatory genomics.
An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics.
Keywords: 1. Genomic and epigenomic regulatory elements (transcription factors, enhancers, histones, gene promoters, regulatory motifs, non-coding RNAs, etc.) 2. NGS methods in regulatory genomics (e.g., ChIP-seq, RNA-seq, ATAC-seq) 3. Epigenetics and epitranscriptomics 4. Alternative splicing 5. Regulatory networks and pathway analysis 6. Genetic, molecular, and phenotypic variation in human disease 7. DNA shape 8. Single-cell transcriptomics (and other single cell assays) 9. 3D genomics (e.g., Hi-C and ChIA-PET) 10. Regulatory evolution or comparative regulatory genomics
SysMod: Computational Modeling of Biological Systems
Abstract Area Chairs: Andreas Dräger, University of Tübingen, Germany Reihaneh Mostolizadeh, University of Tübingen, Germany Anna Niaraki, Université d’Évery, France
Bhanwar Puniya, University of Nebraska-Lincoln, United States
The Computational Modeling of Biological Systems (SysMod) aims to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. The session will focus on the conjoint use of mathematical modeling and bioinformatics to understand biological systems functions and dysfunctions.
The meeting 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.
Text Mining: Text Mining for Healthcare and Biology
Abstract Area Chairs: Cecilia Arighi, University of Delaware, United States Lars Juhl Jensen, University of Copenhagen, DenmarkRobert Leaman, NCBI/NLM/NIH, United States Zhiyong Lu, NCBI/NLM/NIH, United States
The Text Mining COSI brings together researchers that create text mining tools with researchers who use text mining tools to make new discoveries. Our community discussions include both text mining use cases - concrete problems and applications in the biological/biomedical domain - and methodology development.
TransMed: Translational Medical Informatics
Abstract Area Chairs: Sanne Abeln, Vrije Universiteit Amsterdam, Netherlands Irina Balaur, University of Luxembourg Wei Gu, University of Luxembourg
TransMed covers the current developments in the field of clinical and translational medicine informatics. Analysis of large amounts of multi-omics, imaging (medical and molecular), mobile sensor, clinical and health records data is paving the way for precision medicine. In the TransMed track, we will explore the current status of computational biology and advance machine learning approaches within the field of clinical and translational medicine.
This opens the debate on current state-of-the-art data infrastructures for translational medicine data integration and analysis. A variety of computational approaches are currently being used to harmonize and relate molecular data to clinical outcomes in order to better understand disease conditions. These methods also have the potential to discover biomarkers for early detection of disease, and targets for drug discovery, and to be used predictively to help to suggest personalised therapeutic strategies for patients. In this session we will bring scientists from both academia and industry to exchange knowledge and foster networking, to help in building up of the translational medicine community. .
Keywords: Translational medicine; clinical and ‘omics data integration; curation and harmonization; stratification of patients; informatics for integrating biology and the bedside; medical informatics; ontology-driven data representation; patient centered outcomes research; cohort data; deep learning
VarI: Variant Interpretation
Abstract Area Chairs: Emidio Capriotti, University of Bologna, Italy Hannah Carter, University of California, San Diego, United States Antonio Rausell, Imagine Institute for Genetic Diseases, France
The VarI COSI meeting is dedicated to the recent advances in the analysis and interpretation of the genetic variants.
The meeting aims to organize a research network (VarI-COSI) facilitating the exchange of ideas and the establishment of new collaborations between researchers with different expertise. The VarI-COSI meeting is broadly divided in two sessions (“Genetic variants as markers: evolution, populations, GWAS” and “Genetic variants as effectors: function, structure, and regulation”) that encompass the four major research topics of the field: 1) Databases, data mining algorithms and visualization tools for variants analysis. 2) Methods for predicting regulatory/structural/functional impacts of SNVs. 3) Personal Genomics, GWAS studies and SNV prioritization. 4) Population genomics and phylogenetic analysis.
General Computational Biology Abstract Area Chairs: Xin Gao, King Abdullah University of Science and Technology, Saudi Arabia Sara Mostafavi, University of Washington, United States
(If all other areas are insufficiently descriptive of your work, please submit to the area below. Please note that the submissions in this area can be moved, subject to chairs’ considerations.)
Novel techniques in emerging areas of computational biology, including intersections with other fields.
Equity-focused Research (New for 2022)
Abstract Area 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.
Special Session: Computational Immunology – Posters Only
Special Session Chair: Yuri Pritykin, Princeton University, United States
The Special Session on Computational Immunology invites abstracts for poster presentations in all areas of computational immunology, including both development of computational methods for analysis of multi-dimensional data in immunology and data-driven studies addressing specific immunological questions of fundamental or translational importance. Topics could include but are not limited to: single-cell multi-omics to characterize immune cell heterogeneity and regulatory mechanisms of immune cell function; receptor-ligand interaction analysis; spatial genomics for studies of immune microenvironments and immune cell interactions; trajectory inference and lineage tracing in immune cells; T cell and B cell receptor repertoire profiling, reconstruction and analysis.
Special Session: Digital Agriculture – Posters Only
Special Session Chairs: Jennifer L. Clarke, University of Nebraska-Lincoln, United States Noah Fahlgren The Donald Danforth Plant Science Center, United States Camilo Valdes, University of Nebraska-Lincoln, United States
The Special Session on Digital Agriculture invites abstracts for research that is topical to the field of digital agriculture, from basic to applied sciences and including intersections with other fields. As such topics relevant for this Special Session include, but are not restricted to, genetics and genomics of agriculturally relevant species; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and FAIR data standards; biotechnology; and soil sciences.
Special Session: Genome Privacy and Security
Special Session Chairs:
Bonnie Berger, Massachusetts Institute of Technology, United States
Hyunghoon Cho, Broad Institute of MIT and Harvard, United States
This Special Session on Genome Privacy and Security looks at methods related to the protection of individualized genomic and medical information; privacy models.
Sustainability research in computational biology - Posters Only
Session Chair: Ana Conesa, Spanish National Research Council (CSIC), Spain
We encourage poster submissions in the area of sustainability research in computational biology. This could cover ways to reduce carbon emissions in computational biology, or describe tools and techniques to improve sustainability. Analyses of sustainability in our field would also be in scope.
Abstracts: Deadlines
Any recent research, published or unpublished is eligible for submission and should be received by April 21, 2022. Acceptance notifications will be sent no later than Thursday, May 12, 2022. The conference will accept late posters abstracts beginning April 25, 2022.
Poster only submissions DO NOT require any materials to be uploaded. Submissions are evaluated on the 200 word text abstract provided during submission.
Abstracts: Submission Guidelines
The presenter should be identified during the submission process. Presenters of accepted abstracts are required to make the presentation themselves, and must register and pay to attend the conference.
Submitters may choose to have their submission reviewed for: talk and poster or poster only. If you select talk and poster and are unsuccessful for a talk your abstract will automatically be considered for a poster presentation. Submissions must be received by April 21, 2022.
During submission you will submit to the COSI track that most reflects your research area. You will have the option to identify two other COSI tracks that may also be suited to your research area during your submission.
All abstracts must be submitted using the conference submission site by the abstract deadline: April 21, 2022 (You have until 11:59 p.m. Any Time Zone).
Accepted abstracts (maximum 200 words) will be posted on the conference web site. For authors requesting a talk you should upload a long abstract of up to two (2) pages in PDF format during the submission process. *Do not submit more than two pages* It is best to check individual COSI websites for specific information regarding program goals and guidelines.
PLEASE note: CAMDA submitters should include a 3-5 page long abstract PDF
The 200 word abstract should be a brief and concise summary of the background/motivation for the study, method and result(s), as well as conclusion/statement of significance. The abstract is submitted through the EasyChair submission system. If you are submitting for a talk a PDF (2 pages maximum) can be uploaded to provide additional details including figures and graphics that support the main points of the abstract.
Your abstract must not contain your title/position or any personal information (e.g. affiliation). These details will be collected through the EasyChair submission system.
Selected Abstract talks will be presented in tracks that run in parallel at the conference. The length of a talk is determined by individual COSI tracks. Oral presentation schedules for abstracts will be announced after acceptance notifications directly by the COSI track organizers.
Abstracts: Review Criteria
All submissions will be evaluated by a program committee. Submitters may choose to have their submission reviewed for talk and poster or poster only. If you select talk and poster and are unsuccessful for a talk your abstract will automatically be considered for a poster.
Posters advertising commercial software will be rejected from this poster session and/or removed from the conference without notice. There is a separate space for such posters in the exhibition area. If you have an industry poster, contact This email address is being protected from spambots. You need JavaScript enabled to view it..
Poster Details for ISMB 2022
Scientific Research Exchange - Posters Presentation Hours July 11 - 13, 2022 (Central Time Zone)
Monday, July 11, 2022
BioInfo-Core CAMDA CompMS
Function General Computational Biology iRNA
Special Session: Computational Immunology SysMod Text Mining
Tuesday, July 12, 2022
CAMDA Education HiTSeq
iRNA NetBio Special Session: Digital Agriculture
Special Session: Genome Privacy TransMed VarI
Wednesday, July 13, 2022
3D-SIG Bio-Ontologies BioVis
BOSC EvolCompGen HiTSeq
Microbiome MLCSB RegSys
Attention Poster Authors:
Recommended poster size is 46" (116.84cm) wide x 45" (114.3cm) high. View an Example.
Late Posters
The Call for Late Posters (opens April 25, 2022). Call for Late Posters closes May 19, 2022, 11:59 p.m. Any Time Zone.
Institutional Research
Not-for profit research institutes and universities are able to submit their research findings as part of the call for posters. This will be displayed with in the topic area of Institutional Research.
Reviews of fields or techniques
Individuals may choose to submit a poster presenting a review of a specific field or technique. These submissions do not need to contain original work from the author and are intended to be an introduction for individuals not familiar with the field or technique. These review are not meant to be advertisements (e.g. it is not acceptable that the poster is an advertisement for a book or other type of commercial publication)
FAQ
Q: Can I submit more than one abstract? A: Yes, but although having the same person deliver more than one talk is permitted, it is not encouraged. Also, although a poster presenter offer may present two posters (one in Poster Session A and one in Poster Session B), we encourage labs to involve multiple presenters.
Q: Should I submit a PDF of my poster when completing my submission? A: No, please only submit the poster abstract. In addition, all poster presenters will upload a Poster PDF and short 5-7 minute MP4 talk to the virtual conference platform beginning June 30, 2022.
Q: Can previously accepted work be considered for a poster? A: Yes, we do ask that you note the year the work was published and provide the Digital Object Identifier (DOI) during the submission process.
Tanya Berger-Wolf
Director, Translational Data Analytics Institute Professor, Computer Science and Engineering; Electrical and Computer Engineering; Evolution, Ecology, and Organismal Biology, The Ohio State University Director, Wild Me United States
Introduced by: Iddo Friedberg, Conference Co-chair; Iowa State University, United States Time: Sunday July 10, 2022 at 6:30 PM - 7:30 PM CDT Room: Madison Ballroom ABCD (Level Four, Monona Terrace) Presentation Title:Imageomics: Images as the Source of Information about Life
Abstract
Introducing the new field of imageomics: from images to biological traits using biology-structured computational approaches.
Images are the most abundant, readily available source for documenting life on the planet. Coming from natural history collections, laboratory scans, field studies, camera traps, wildlife surveys, autonomous vehicles on the land, water, and in the air, as well as tourists’ cameras, citizen scientists’ platforms, and posts on social media, there are millions of images of living organisms. But their power is yet to be harnessed for science and conservation. Even the traits of organisms cannot be readily extracted from images. The analysis of traits, the integrated products of genes and environment, is critical for biologists to predict effects of environmental change or genetic manipulation and to understand the significance of patterns in the four billion year evolutionary history of life.
I will show how data science and machine learning can turn massive collections of images into high resolution information database about wildlife, enabling scientific inquiry, conservation, and policy decisions. I will share our vision of the new scientific field of imageomics.
Biography
Dr. Tanya Berger-Wolf is a Professor of Computer Science Engineering, Electrical and Computer Engineering, and Evolution, Ecology, and Organismal Biology at the Ohio State University, where she is also the Director of the Translational Data Analytics Institute. As a computational ecologist, her research is at the unique intersection of computer science, wildlife biology, and social sciences. Berger-Wolf is also a director and co-founder of the AI for wildlife conservation non-profit Wild Me, home of the Wildbook project. It has been recently chosen by UNSECO as one of the top AI 100 projects worldwide supporting the UN Sustainable Development Goals.
Berger-Wolf has given hundreds of talks about her work, including at TED/TEDx and UN/UNESCO AI for the Planet. She has received numerous awards for her research, innovation, and mentoring.
Aïda Ouangraoua
Canada Research Chair, Computational and Biological Complexity; Full Professor, Department of Computer Science, Université de Sherbrooke, Canada
Introduced by: Keith Dunker, Honorary Conference Chair; Professor Emeritus, Indiana University School of Medicine, United States Time: Tuesday July 12, 2022 at 8:45 AM - 9:45 AM CDT Room: Madison Ballroom ABCD (Level Four, Monona Terrace) Presentation Title:Gene evolution at transcript level: challenges and existing solutions
Abstract
Alternative splicing is a ubiquitous process in eukaryotes which allows a single gene to be transcribed into several different transcripts. Transcript evolution focuses on the evolution of gene products at transcript level. The study of the evolution of homologous gene transcripts provides additional information on gene evolution such as the identification of conserved isoforms, the history of isoforms gains and losses along gene phylogenies, and the evolution of alternative splicing. In this talk, I provide a unified view of various models of transcript evolution constrained by gene phylogenies with underlying transcript phylogeny reconstruction problems. I describe existing solutions, including a set of methods and a database we have developed to study transcript evolution.
Biography
Aïda earned her Ph.D. in Computer Science in 2007 from University of Bordeaux (FR) where she also received her Master’s degree in Computer Science, and a Master's degree in Computer Engineering from ENSEIRB-MATMECA in 2004. After a postdoc at Simon Fraser University and Université du Québec à Montréal (CA), she joined INRIA Lille (FR) as researcher in 2009, and then Université de Sherbrooke (CA) in 2014. She is currently full professor at Université de Sherbrooke where she holds the Canada Research Chair in Computational and Biological Complexity. Her research group focuses on the development of models and algorithms in comparative genomics to understand the intertwined evolution of genomes, genes and RNA transcripts. Aïda is also actively engaged in community service, including currently as associate editor for Bioinformatics Advances, Journal of Computational Biology, and Molecular Biology and Evolution. She also regularly serves as PC member, and she has served as Organization, PC and Area Chairs in top conferences of her field — RECOMB-CG, GLBIO, and ISMB.
Director, Translational Data Analytics Institute Professor, Computer Science and Engineering; Electrical and Computer Engineering; Evolution, Ecology, and Organismal Biology, The Ohio State University Director, Wild Me, United States
Presentation Title:Imageomics: Images as the Source of Information about Life
Assistant Professor, Division of Genetics and Center for Data Sciences, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School Associate Member, Broad Institute of MIT and Harvard United States
Presentation Title:Haplotype-informed discovery of hidden genetic variants influencing human traits
Group Leader (ICREA Research Professor), Biomedical Genomics Group, Institute for Research in Biomedicine Spain
Presentation Title: Comprehensive identification of cancer driver mutations
Thursday, July 14, 2022 at 8:30 AM - 9:30 AM CDT
ISMB 2022 - About Us
The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the flagship meeting of the International Society for Computational Biology (ISCB). The 2022 conference is the 30th ISMB conference, which has grown to become the world's largest bioinformatics/computational biology conference.
ISMB 2022 will offer both in-person and virtual attendance. We will welcome you to join us in Madison, Wisconsin, July 10-14 at Monona Terrace Convention Center or virtually in our state of the art virtual interface.
ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems.
Participants will have the opportunity to enjoy:
Training workshops and tutorials
Student Council Symposium
Live and on-demand sessions to benefit attendees from all time zones
500+ expected scientific talks
Live question and answer feature to engage with the speaker during sessions
Live chat feature to engage with other participants within your virtual session room
Dedicated time for research presentation within the Research Exchange Forum (formerly Poster Hall) both face to face and via the virtual platform
Speaker meet ups for our virtual audience
Face to face networking events for our in-person audience
Ability to serendipitously make new connections when utilizing the attendee profile and match maker features within the virtual platform
Schedule one-on-one time with speakers, poster presenters, exhibitors, and sponsors to learn more about their work, products, or services
Exclusive access to the ISMB 2022 on-demand repository of talks and poster presentations for viewing at your leisure after conference dates
ISMB provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology, fostering fresh dialogues and perspectives to learn about and shape the future of the field. In response to the increasing interest in the activities of the ISCB’s Communities of Special Interest (COSIs) the conference is organized with the active participation of the COSIs in the development of the program and highlights emerging or "hot" research areas providing an outstanding scientifically effective program.
ISMB enables intensified community involvement and bolsters its reputation as the leading conference in the field, with the strongest scientific and technical program that showcases the best international developments in bioinformatics and computational biology.
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;
Bio-Ontologies Community of Special Interest Group (COSI) covers the
BOSC covers all aspects of open science / open source bioinformatics, including standards and ontologies; approaches that promote open science and sharing of data, results and software; bioinformatics tools and libraries; and ways to grow open source communities while promoting diversity within them.
The large, complex data sets for the Critical Assessment of Massive Data Analysis (CAMDA) contest include built-in truths for calibration. In an open-ended competition, however, both seasoned researchers and cunning students push the boundaries of our field, with unexpected questions or angles of approach often bringing the most impressive advances.
The CompMS group promotes the efficient, high quality analysis of mass spectrometry data. The CompMS initiative covers various computational mass spectrometry application domains, including proteomics, metabolomics, and lipidomics.
Education-COSI focuses on bioinformatics and computational biology education and training across the life sciences.
Evolution and comparative genomics are deeply intertwined with computational biology. Computational evolutionary methods, such as phylogenetic inference methods or multiple sequence alignment are widely used, yet remain far from “solved” and are indeed intense areas of research.
The mission of the Function Community of Special Interest (Function-COSI) is to bring together computational biologists, experimental biologists, biocurators, and others who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
HiTSeq is a community of special interest devoted to the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) data. Sessions will be devoted to discussing the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) datasets and will provide a forum for in-depth presentations of the methods and discussions among the academic and industry scientists working in this field.
iRNA track covers the full range of research topics in the field of RNA Biology, from computational and high-throughput experimental methods development to their application in different aspects of RNA processing, structure, and function.
Systems Biology and Machine Learning meet in the MLCSB COSI. The community is the place for researchers of these areas to exchange ideas, interact and collaborate.
The MICROBIOME Community of Special Interest aims at the advancement and evaluation of computational methods in microbiome research, especially metaomic approaches. Based on the Critical Assessment of Metagenome Interpretation (CAMI), the COSI supplies users and developers with exhaustive quantitative data about the performance of methods in relevant scenarios.
As large scale, systems-level data are becoming increasingly available, modeling and analyzing them as networks is widespread. Network Biology Community serves to introduce novel methods and tools, identify best practices and highlight the latest research in the growing and interdisciplinary field of network biology.
Regulatory genomics involves the study of the genomic control system, which determines how, when and where to activate the blueprint encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the RegSys COSI meeting focuses on bioinformatics for regulatory genomics.
The Computational Modeling of Biological Systems (SysMod) aims to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. The session will focus on the conjoint use of mathematical modeling and bioinformatics to understand biological systems functions and dysfunctions.
The Text Mining COSI brings together researchers that create text mining tools with researchers who use text mining tools to make new discoveries. Our community discussions include both text mining use cases - concrete problems and applications in the biological/biomedical domain - and methodology development.
TransMed covers the current developments in the field of clinical and translational medicine informatics. Analysis of large amounts of multi-omics, imaging (medical and molecular), mobile sensor, clinical and health records data is paving the way for precision medicine. In the TransMed track, we will explore the current status of computational biology and advance machine learning approaches within the field of clinical and translational medicine.
The VarI COSI meeting is dedicated to the recent advances in the analysis and interpretation of the genetic variants.
Tanya Berger-Wolf
Aïda Ouangraoua
