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.
Presentation Title: Transcription factors and cis-regulatory elements Time: Sunday July 8, 8:30 am - 9:30 am Room: Grand Ballroom C-F
Biography:
Dr. Bulyk received dual undergraduate degrees in Biology and in Mathematics from MIT in 1993. She received her Ph.D. in Biophysics in 2001 from Harvard University, where she worked in Dr. George Church’s group. Shortly thereafter, she began as an Assistant Professor at Harvard. Currently she is a Professor in the Division of Genetics in the Department of Medicine, and also a Professor of Pathology, at Brigham & Women's Hospital and Harvard Medical School. She is also an Associate Member of the Broad Institute of MIT and Harvard, and an Associate Member of the Dana Farber Cancer Institute’s Center for Cancer Systems Biology.
In 2005 Dr. Bulyk was named one of the TR35, MIT Technology Review’s annual competition to select the top 35 young innovators under the age of 35, and in 2007 she was named in Genome Technology’s annual selection of “Tomorrow’s PIs”. She has served on numerous grant review panels and journal editorial boards, and is a Member of Faculty of 1000. Dr. Bulyk has published over 100 scientific articles and book chapters, and has presented over 190 invited seminars. Her group is currently focused on studies of transcription factors and DNA regulatory elements, using a variety of experimental and computational approaches, including new technologies they have developed.
ISMB 2018 - Special Sessions
Attention Presenters - please review the Speaker Information Page available here
3D Genomics: Computational approaches for analyzing the role of three-dimensional chromatin organization in gene regulation.
Room: Grand Ballroom C-FSaturday July 7, 10:15 am - 6:00 pm
Organizer(s):
Ferhat Ay, La Jolla Institute for Allergy and Immunology, United States Sushmita Roy, Biostatistics & Medical Informatics, Wisconsin Institute for Discovery, United States
Presentation Overview:
Long-range gene regulatory interactions are defined as interactions between a region of regulatory DNA sequence and a target gene that can be hundreds of kilobases away. Such interactions are emerging as important determinants of cell type specific expression and the effect of regulatory sequence variants on complex phenotypes including those associated with diseases. The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the availability of chromosome conformation capture (3C) data sets that characterize the 3D organization of chromatin at a genome-wide scale. This organization, also referred to as the 3D nucleome, is not only important for packing the genome into the nucleus, but it also has significant impact on how the genome functions. With the emergence of these new data types, there is an increasingly growing demand for computational tools that can systematically analyze these data. These tools range from data processing issues (e.g. mapping and normalization) to data analysis issues, such as predicting chromosomal organizational units (e.g. TADs), identifying significant interactions between regulatory elements (e.g. enhancer-promoter), examining the interplay of transcription factors, architectural proteins and chromatin states in establishing these interactions, and examining how these interactions are impacted by sequence variants.
Schedule Overview
Invited Speakers
Modeling and predicting the 3D genome William Noble, Genome Sciences & Computer Science University of Washington, United States
High-resolution analysis of chromatin conformation capture data Mathieu Blanchette, Computer Science, McGill University, Canada
Continuous-trait probabilistic model for comparing nuclear genome organization of multiple species Jian Ma, Computational Biology and Machine Learning, Carnegie Mellon University, United States
Impact of structural variants on 3D genome structure in cancer cells Feng Yue, Biochemistry and Molecular Biology, Pennsylvania State University, United States
Connections between the structure and function of 3D genome folding Geoffrey Fudenberg, University of California, United States
Single-particle Cryo-electron Microscopy, Cryo-electron Tomography, and Integrative/Hybrid Methods Studies of Macromolecular Machines: Opportunities and Challenges for the Bioinformatics Community
Room: Columbus EF
Sunday July 8, 10:15 am - 12:40 pm
Organizer(s):
Stephen K. Burley, RCSB Protein Data Bank, United States Jose Duarte, RCSB Protein Data Bank, United States
Presentation Overview:
Among the most exciting of these newly deposited PDB structures are those coming from singleparticle cryo-electron microscopy (EM) and cryo-electron tomography (ET). Recent technical advances in sample preparation, electron optics, direct electron detection, and data processing software have created a perfect storm for the PDB. With these new methods cryo-EM and -ET are producing atomic level structures of macromolecular machines, such as multi-subunit RNA and DNA polymerases, ribosomes, and nuclear pore complexes. The next wave of exciting new structures will come from so-called integrative/hybrid methods, which typically combine cryo-EM or -ET data with data from chemical cross-linking, fluorescence resonance energy transfer, and homology models to produce multi-scale structures of even larger biomolecular machines.
The Special Session will highlight examples of the exciting work going in in these two frontier areas of structural biology from four distinguished speakers, with reference to the manifold challenges and opportunities for the bioinformatics community.
Opening Remarks Speaker: Jose Duarte, RCSB Protein Data Bank, UC San Diego
Cryo-EM visualization of eukaryotic transcription initiation machineries Speaker: Yuan He, Department of Molecular Biosciences, Northwestern
University, United States
Visualizing molecular assemblies inside cells by cryo-electron tomography Speaker: Wei Dai, Department of Cell Biology and Neuroscience, Rutgers
University, United States
Integrative structural biology Speaker: Barak Raveh, Department of Bioengineering and Therapeutic
Sciences, UC San Francisco, United States
Web-based 3D visualization and exploration of cryo-electron microscopy and
integrative/hybrid methods structures Speaker: Alexander Rose, RCSB Protein Data Bank, UC San Diego, United
States
Closing remarks Speaker: Stephen K. Burley, RCSB Protein Data Bank, Rutgers University and
UC San Diego, United States
Omics Data Compression and Storage: Present and Future
Room: Columbus EFSunday July 8, 2:00 pm - 6:00 pm
Organizer(s):
Mikel Hernaez- University of Illinois at Urbana-Champaign, Institute for Genomic Biology, United States Idoia Ochoa, University of Illinois at Urbana-Champaign, Electrical and Computer Engineering, United States
Presentation Overview
In 2003 the first human genome assembly was completed. It was the end of a project that took almost 13 years to complete and cost 3 billion dollars (around $1 per base pair). This milestone ushered in the genomics era, giving rise to personalized or precision medicine. Fortunately, sequencing cost has drastically decreased in recent years. While in 2004 the cost of sequencing a whole human genome was around $20 million, in 2008 it dropped to a million, and in 2017 to a mere $1000. As a result of this decrease in sequencing cost, as well as advancements in sequencing technology, massive amounts of genomic data are being generated. At the current rate of growth (sequencing data is doubling approximately every seven months), more than an exabyte of sequencing data per year will be produced, approaching the zettabytes by 2025 . As an example, the sequencing data generated by the 1000 Genomes Project (www.1000genoms.org) in the first 6 months exceeded the sequence data accumulated during 21 years in the NCBI GenBank database .
In addition, the generation of other types of omics data are also experiencing a rapid growth. For example, DNA methylation data has been found to be important in early detection of tumors and in determining the prognosis of the disease , and as a result it has been the subject of many large-scale projects including MethylomeDB and DiseaseMeth , among others. Proteomics and metabolomics studies are also gaining momentum, as they contribute towards a better understanding of the dynamic processes involved in disease, with direct applications in prediction, diagnosis and prognosis, and several repositories have been created, such as PeptideAtlas/PASSEL and PRIDE.
This situation calls for state-of-the-art, efficient compressed representations of massive biological datasets, that can not only alleviate the storage requirements, but also facilitate the exchange and dissemination of these data. This undertaking is of paramount importance, as the storage and acquisition of the data are becoming the major bottleneck, as evidenced by the recent flourishing of cloud-based solutions enabling processing the data directly on the cloud. For example, companies such as DNAnexus, GenoSpace, Genome Cloud, and Google Genomics, to name a few, offer solutions to perform genome analysis in the cloud.
This sentiment is also reflected by the NIH Big Data to Knowledge (BD2K) initiative launched in 2013, which acknowledged the need of developing innovative and transformative compression schemes to accelerate the integration of big data and data science into biomedical research. In addition, the International Standardization Organization (ISO) is developing, under MPEG (Moving Picture Expert Group), a standard for genomic information representation.
This special session will cover current efforts in this area, as well as future challenges. This is of importance to biologistics and researchers alike that work with omics data, as the developed tools will soon become part of their standard pipelines.
Schedule Overview
Advancing computational biology through critical assessments, community experiments, and crowdsourcing
Room: Columbus GH
Monday July 9, 10:15 am - 4:00 pm
Organizer(s):
Gaia Andreoletti, University of California, Berkeley, United States Steven E Brenner, University of California, Berkeley, United States John Moult, The University of Maryland, United States
Presentation Overview
Current results from a wide range of critical assessment community experiments in computational biology. This session represents a unique and unprecedented gathering of a diverse range of critical assessment organizations.
Community assessment has emerged as an effective framework to evaluate and develop methodologies, especially experiments in which participants are challenged to deduce biological problems such as determining the phenotypic consequences of genomic variation, protein structure, and system perturbations. Some such challenges use community-effort to engage a large community to see how well a certain method can achieve a certain goal. Successful challenge frameworks of this type are able not only to evaluate the effectiveness of methods but also to highlight innovation, progress, and bottlenecks in the field, to guide future research efforts, and to foster strong collaborative communities
Schedule
SCANGEN: Single-cell cancer genomics
Room: Columbus IJ
Tuesday July 10, 8:35 am - 4:40 pm
Organizer(s):
Kieran R Campbell, University of British Columbia & BC Cancer Agency, Canada Sohrab P Shah, University of British Columbia & BC Cancer Agency, Canada
Presentation Overview
In the past five years technological advances have given us the unprecedented ability to measure RNA and DNA at the single-cell level. This now enables us to routinely measure gene expression and genomic alterations across tens of thousands of cells, discovering new cell types, developmental lineages, and cell-specific mutational patterns. This new data has prompted an explosion in statistical and computational methods development (http://www.scrna-tools.org/) with over 150 tools being produced in the past few years.
However, to-date the majority of methods developed have focused on either technical aspects (such as normalization and differential expression) or on applications in developmental biology such as lineage inference, with relatively little attention applied to the huge potential of single-cell data to unveil the complex biology behind cancer inception and progression. As one of the first workshops of its kind, this special session will bring together researchers developing computational and statistical methods for single-cell cancer biology. It will focus around (though not be limited to) four core topics:
1. Modelling cancer evolution As tumors evolve they accumulate both point mutations and large structural rearrangements. The “life-histories” of these tumors are informative of the mutational processes that allow the cancer cells to evade the body’s checkpoints and can be predictive of future evolution and response to therapy. Methods covered under this topic could address: phylogenetic inference from single-cell data; inference of evolutionary processes from single-cell data; identifying singlecell cancer signatures; inference of fitness from single-cell analysis of population dynamics.
2. Integrative analyses of multi-modal data A vast array of measurements can be made at single-cell resolution, including RNA and DNA-sequencing and epigenetic status such as methylation and chromatin accessibility. Methods covered in this topic will include: modelling of joint measurement assays (such as G&T-seq); relating and interpreting measurements from different technologies.
3. Scalable inference at the single-cell level A typical single-cell RNA or DNA-seq dataset now contains around 100x more cells than it did just 5 years ago. As a result, there is a pressing need for computational and statistical methods that scale to “big data” sizes, particularly since fast computation allows iterative analyses by investigators, aiding SCANGEN: Single-cell cancer genomics ISMB 2018 Special Session Proposal biological interpretation. Methods covered in this topic will include: scalable statistical inference for single-cell data using methods such as stochastic optimization; computational tools for dealing with large single-cell datasets.
4. Interactions and perturbations at the single-cell level This broad topic concerns methods to understand how cancer cells react to both their environment and external perturbation. Methods could address: how cells interact with their microenvironment; how cells respond to and resist chemotherapeutic interventions; how transcriptional programming and clonal selection are affected by genomic perturbations such as CRISPR.
Schedule
Call for Abstracts – ISMB 2018 Late-breaking Posters (Closed)
We invite abstracts for research that is topical to bioinformatics and computational biology, which is in progress (unpublished, formally Late-Breaking Research) or has been published after January 1, 2017 (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. (During the submission process you may also select other COSIs where your work may also be suitable for presentation.) 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 2018. 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 only present one poster at ISMB.
3DSIG: Structural Bioinformatics and Computational Biophysics
Chairs: Phil Bourne, University of Virginia, United States Charlotte Deane, Oxford University, United Kingdom Rafael Najmanovich, University of 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
Chairs: Michel Dumontier, Maastricht University, Netherlands Robert Hoehndorf, King Abdullah University of Science & Technology, Saudi Arabia Philippe Rocca-Serra, University of Oxford, United Kingdom Karin Verspoor, University of Melbourne, Australia
Bio-Ontologies Community of Special Interest Group (COSI) covers the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the 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.
BioVis: Biological Data Visualization
Chairs: Thomas Höllt, TU Delft, Netherlands Michael Krone, University of Stuttgart, Germany
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
Chairs: David Kreil, Boku University Vienna, Austria Paweł P Łabaj, Austrian Academy of Sciences, and Jagiellonian University, Poland
Please note: CAMDA requires only a short abstract as intention to submit for April 5, which must be followed by an extended abstract submission May 13, 2018.
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 meta-genomics forensic challenge in constructing urban microbiome fingerprints and identifying the geographical origin of mystery samples (MetaSUB), 2) a CMap drug safety challenge in comparing / integrating responses of multiple cell lines for predicting drug induced liver injury in humans (FDA), and 3) a cancer data-integration challenge in demonstrating a robust analysis approach improving the state of the art for multiple cancer types (FDA SEQC / Metabric.
CompMS: Computational Mass Spectrometry
Viktoria Dorfer, FH Hagenberg, Austria William S Noble, U Washington, United States Oliver Kohlbacher, U of Tübingen, Germany
COSI CompMS promotes the efficient, high-quality analysis of mass spectrometry data through dissemination and training in existing approaches and coordination of new, innovative approaches.
The COSI aims to build a community of scientists working in computational mass spectrometry, to integrate experimental with theoretical research, and to bridge the gap between proteomics, metabolomics, and other MS-driven fields Keyword: computational mass spectrometry, proteomics, metabolomics
Education: Computational Biology Education
Chairs: Russell Schwartz, Carnegie Mellon University, United States Nicola Mulder, University of Cape Town, South Africa
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
Chairs: Lars Arvestad, Stockholm University, Sweden Wataru Iwasaki, University of Tokyo, Japan
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.
Chairs: Iddo Friedberg, Iowa State University, United States Predrag Radivojac, Indiana University Bloomington, United States Mark N 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
Chairs: Can Alkan, Bilkent University,Turkey Ana Conesa, University of Florida, United States Francisco M. De La Vega, Stanford University; Fabric Genomics, United States Dirk J. Evers, Dr. Dirk Evers Consulting, Germany Kjong Lehmann, ETH-Zürich, Switzerland Quaid Morris, University of Toronto, Canada Gunnar Rätsch, 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
MICROBIOME
Chairs: Aaron Darling, University of Technology Sydney, Australia Alice McHardy, Helmholtz Centre for Infection Research, Germany Mihai Pop, University of Maryland, United States Thomas Rattei, University of Vienna, Austria Alexander Sczyrba, Bielefeld University, Germany
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.
MLCSB: Machine Learning in Computational and Systems Biology
Chairs: Florian Markowetz, University of Cambridge, United Kingdom Oliver Stegle, European Bioinformatics Institute, United Kingdom
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
NetBio: Network Biology
Chairs: Alex Pico, Gladstone Institutes, United States Natasa Przulj, University College London, United Kingdom
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.
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
RNA: Computational RNA Biology
Chairs: Yoseph Barash, University of Pennsylvania, United States Eduardo Eyras, Universitat Pompeu Fabra, Spain Klemens Hertel, University of California, Irvine, United States
RNA 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 Computational 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.
SysMod: Computational Modeling of Biological Systems
Chairs: Andreas Draeger, University of Tübingen, Germany Tomas Helikar, University of Nebraska - Lincoln, United States Nicolas Le Novere, Babraham Institute, United Kingdom
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.
Chairs: Wei Gu, Luxembourg Centre For Systems Biomedicine Venkata Satagopam, University of Luxembourg Bissan Al-Lazikani, The Institute of Cancer Research, United Kingdom
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
Chairs: Hannah Carter, UCSD, United States Emidio Capriotti, University of Bologna, Italy Yana Bromberg, Rutgers, United States
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
Chair: Laxmi Parida, IBM T. J. Watson Research Center, 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.
BOSC Open Source Conference
Looking for the BOSC Open Source Conference? More information available here.
Abstracts: Deadlines
Any recent research, published or unpublished is eligible for submission and should be received by April 5, 2018. Acceptance notifications will be sent no later than Thursday, May 3, 2018. The conference will accept late posters abstracts beginning April 9, 2018. Poster submissions DO NOT require a one (1) page PDF and should only provide a 200 word short abstract 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 only; talk and poster; or poster only. If you select talk and poster and are unsuccessful for a talk your poster will automatically be reviewed for a poster presentation.
During submission you will submit to the COSI track that most reflects your research area. You will have the option to identify two other tracks that may also be suited to your research area during the submission process.
If you submit an abstract by the April 5, 2018 deadline, you will be notified whether or not your abstract has been accepted by May 3, 2018 and you may be eligible to apply for a Conference Travel Fellowship.
All abstracts must be submitted using the conference submission site by the abstract deadline: April 5, 2018 (You have until 11:59 p.m. Eastern Time Zone).
Accepted abstracts (maximum 200 words) will be posted on the conference web site. For authors requesting a talk a one (1) page PDF long abstract should also be uploaded during the submission process to provide greater detail on the topic and can include tables and graphics. *Do not submit more than one page*
The 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 additional 1-page pdf can be used to provide additional details, as well as 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).
Selected Abstract talks will be presented in tracks that run in parallel at the conference. The length of a talk is 20 minutes (includes 2-3 minutes for questions). Oral presentation times for abstracts will be announced after acceptance notifications 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 only; talk and poster; or poster only. If you select talk and poster and are unsuccessful for a talk your poster 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
The poster display schedule will be available by May 31, 2018 and will based on the COSI program schedule.
Abstracts submitted and accepted as part of the Call for Late Poster (opens April 9, 2018) are NOT eligible to apply for Conference Travel Fellowship Support. Call for Late Posters closes May 1, 2018 11:59 p.m. Eastern Time Zone
The conference organizers will not offer tables for laptop computer demos during the poster session. If you would like to demonstrate your software, you are encouraged to submit an application for Technology Track. All abstracts will be considered a "personal communication" to the conference attendees. Abstracts will not be published in the proceedings, but will appear on the conference website and app.
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)
Poster Display Size:
Attention Poster Authors: When preparing accepted posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board. One poster will be an odd number and the other will be an even number. View a diagram of the the poster board in pdf format here.
FAQ
Q: Can I submit more than one abstract? A: While you can submit more than one abstract the conference prefers that presenters only present once thus encouraging greater participation. The conference allows only one poster per author for presentation. The acceptance rate for posters is generally very high so there is no need to submit more than one poster.
Q: Should I submit a PDF of my poster when completing my submission? A: No, please only submit the poster abstract. You will bring your physical poster to the conference to present.
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.
ISMB 2018 attracts top international scientists and key decision makers in the life sciences – experts in areas such as computer science, molecular biology and medicine, mathematics and statistics – from the world's largest and most prestigious research institutions and companies.
ISMB 2018 is expected to attract scientific leaders from over 50 countries – that’s 50 markets!
Sponsorship options have been designed for every budget level and customized packages can be arranged as a flexible solution for your marketing requirements.
Join us and take full advantage of this opportunity to enhance your organization's visibility, expand your network of prospects, meet up with your current clients and positively impact your bottom line sales!
Future ISMB Dates
ISMB 2018, July 6-10, Chicago, Illinois, USA
ISMB/ECCB 2019, July 21 - 25, Basel, Switzerland
ISMB 2020, July 12- 16, Montreal, Canada
ISMB/ECCB 2021 TBA
ISMB 2022, July 10 - 14, Madison, Wisconsin, USA
Speakers are requested to review the conference schedules available on the conference website. Please note that minor schedule changes may continue to be made. Schedules are available at: https://www.iscb.org/ismb2018-program
Presentation computer, slides and video release form:
Presentation rooms will have a computer provided - details below. You can use your own computer if you prefer but please ensure that you bring a connecting HDMI adapter or Mini adapter equired to connect to the projector cable. If you prefer you can place slides on the presentation computer - ideally at least 1 hour prior to your talk. We will have AV volunteers in the room to assist you. We suggest the file be labelled as: LastNameTalkCOSI (e.g. JonesTransMed)
Each room will be equipped with a "splitter" so you can use your computer without disconnecting the presentation computer provided.
Many presentations at ISMB 2018 are recorded for the purpose of developing an archival library of ISMB presentations to share the history, growth and development of the science. Selections are published on the ISCB website for viewing. Your permission to allow ISCB to record your presentation for these purposes is required. Please take a moment to either allow or deny permission of the recording by completing the form at: https://www.iscb.org/submissions/permissionForm/
ISMB 2018 Slide Template (blank) and Conference App Slide
Speakers if you are looking for a template for your introduction or last slide feel free to download the below power point template.
Lenovo ThinkPads – Windows 7 Home, Microsoft Office
Don't use "embedded fonts" in PowerPoint especially if there's video/audio or any other linked information in the presentation. Make sure that the Powerpoint file and video / audio-clips are put into the same folder.
Projector Info: 16:9 Ratio / 1280 x 800 resolution
Attention Students, Post Docs and Young Investigators!
Please read these helpful tips on giving a quality talk at the conference.
As you prepare to give an oral presentation the following are some helpful tips for ensuring that both you and the international and interdisciplinary conference audience get the most out of your talk. As some talks will be recorded for viewing by our community for years to come, following these tips can also serve to make certain your best possible presentation serves you well in your future career.
Limit the number of slides to be presented. A common mistake among presenters at all levels of experience is including too many slides for the allotted presentation time. We have all attended talks where the presenter either had to rush through or skip entire sections of slides due to having too many slides for the amount of time allotted to the talk. Worse is the presenter whose talk goes beyond the allotted time, and he or she ignores the session chair and/or session timer in order to give the full presentation detailed in the slides.
A rule of thumb is to have just one robust and informative slide for each minute of the presentation. Two or more slides per minute is sometimes possible, but this typically only works if half of the slides are updates to the slides shown before them, rather than completely new slides of different information. Keep in mind that an oral presentation slot has a time limit, and it will never be enough to fully explain all of your research efforts and results. The goal should be to give enough of an overview, with just enough depth, to make the audience understand your project, believe in your results, and pique their interest to follow up for further information available in your paper, on the web or in a follow up conversation with you after the talk.
ISMB is a conference of many parallel sessions that must all start and stop at the precisely scheduled time, so if some talks go beyond the allotted time limit the entire schedule could be thrown off. With over 500 scheduled talks, one can imagine the havoc that this could create. Therefore, the ISMB schedule is strictly adhered to by the session chairs, and presenters must be cut off if they are unable to finish their presentations on time. Please ensure you are not one of those presenters!
Prepare slides that show well from a distance. There are two important aspects of slide preparation: Visibility and readability.
Regarding readability, the devil is always in the details, and the highly data-driven aspect of computational biology can make this tip hard to follow. But, if a slide has too much data squeezed into it most audience members will not be able to see or decipher the data. If the data is important for the audience to see or follow, such a slide will serve little or no purpose.
So, this tip is intended to encourage you to consider the data included in your slides. Is it essential for the audience to be able to see it to understand it? If yes, go with simple colors and find ways to highlight and feature the most relevant data through the bold and/or color graphics such as arrows, circles, or magnified zoom options available in your presentation software.
It is also to your benefit to give your slides to the technical staff as early as possible and ask to check out how each slide displays under the actual projection display environment. This will give you time to make changes if the layout shifts using the equipment of the venue, and/or if the color washes out and needs to be changed.
Practice, practice, practice. You can never over-rehearse an oral scientific presentation. Although slides will prompt you through each topic, it is important to practice out-loud several times. This will help you develop a suitable pace, attain a natural rhythm, and try out several options of words and phrases to find the ones that best communicate your research. It will also ensure you are able to make it through all of your slides without running out of time. If after a few run-throughs you still cannot meet the time limit, you will need to make adjustments.
Practicing is important for everyone, but it can be even more important if English is not your native language. The conference is expected to have attendees from over 50 countries. Because you will be communicating to many other non-native English speakers your pronunciation should be well exercised. If at all possible, you should ask a family member, friend, colleague from your lab or your advisor to listen to at least one practice session so you can work out the nerves of speaking to a live audience and gain valuable feedback. If possible, self-recording your presentation is another valuable tool.
Practice sessions should start well before you travel to the conference. Please make time the night before your talk to practice again. If you are scheduled to give a 20-minute talk, you should schedule one full hour of practice time that final night to allow yourself at least two or three rehearsals.
Each time you practice you will say things slightly differently, which is fine. When you give the actual conference presentation from the podium, it should sound like you have given this talk before, but not sound like you are reading from a script.
Relax and learn from your presentation experience. Each time you give a talk you will improve your presentation skills and gain confidence in your public speaking abilities. Pay attention to what you did well and where you might have room to improve, and make a note of it for your next talk.
Whether this is the first for fifty-first time you are speaking at a major international conference, you will likely become nervous as the time of your talk approaches (even if you have given this same talk before). These nerves will likely stay with you as you start to give your talk. But, please know that almost everyone experiences this. The audience is interested in your presentation and not nearly as aware of your nerves as you are. Take a deep breath and try to slow down if needed - many speakers talk too fast when they are nervous. If you have rehearsed in advance, the nerves will subside as you hit your stride and you will do very well.
Last but not least, thank you! There are many conference options these days, but none that are as large and internationally diverse in the field of bioinformatics/computational biology as this one. Thank you for choosing to submit your research and congratulations on having your work accepted for presentation. We hope this proves to be a positive experience, and that we will see you again at many more ISMB conferences in the future.
Ian Lawson Van Toch Memorial Award for Outstanding Student Paper
The Outstanding Student Paper Award is given to the student who presents the most thought-provoking or original paper at the Conference, as judged by our panel of experts.
This award is given in memory of Ian Lawson Van Toch, a 23 year old Medical Biophysics graduate student at the University of Toronto who passed away in August 2007. Ian was fortunate to have already discovered his passion for computational biology and how it can - and will - lead to quantum breakthroughs in cancer research. This passion was sparked when Dr Igor Jurisica hired Ian to work in his lab at the Ontario Cancer Institute as a researcher during the summer of 2006. That introduction blossomed into a mentoring relationship that is so vital to helping young students launch their careers.
Our thanks go to the Princess Margaret Hospital Foundation who has sponsored this award since 2008.
Past recipients of this special award include:
ISMB 2018: Rani Powers, University of Colorado, United States
ISMB/ECCB 2017: Kymberleigh Pagel, Indiana University, United States
ISMB 2016: Yaron Orenstein, Massachusetts Institute of Technology, United States
ISMB/ECCB 2015: Farhad Hormozdiari, University of California, Los Angeles, United States
ISMB 2014: Andrey D. Prjibelski, St. Petersburg Academic University, Russia
ISMB/ECCB 2013: Wyatt Clark, Indiana University, United States
ISMB 2012: Deniz Yorukoglu, Massachusetts Institute of Technology, United States
ISMB/ECCB 2011: Sara Berthoumieux, Inria, France
ISMB 2010: Keren Yizhak, Tel Aviv University, Israel
ISMB/ECCB 2009: Manfred Claassen, ETH Zurich, Switzerland
ISMB 2008: Lucas Ward, Columbia University, United States
F1000 Poster Award
F1000 will present six poster awards for outstanding ISMB 2018 poster presentations. Prizes include a one year subscription to F1000Prime and F1000 Workspace, plus a free article submission to F1000Research (value $1000).
RCSB PDB Poster Prize
The RCSB PDB Poster Prize will be awarded for the best student poster presentation in the category of Structure and Function Prediction. The award will consist of a related educational book.
ISCB celebrates another great edition of ISMB. Our deepest gratitude to all of those who put in their own personal time to volunteer to make it a success.
We want to continue to improve your conference experience. Please take our conference survey.
Founder Professor of Engineering; Professor of Bioengineering and Computer Science Member, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign
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; 
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. 
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 Outstanding Student Paper Award is given to the student who presents the most thought-provoking or original paper at the Conference, as judged by our panel of experts.
The RCSB PDB Poster Prize will be awarded for the best student poster presentation in the category of Structure and Function Prediction. The award will consist of a related educational book.
