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ISMB 2018 - Special Sessions

Schedule subject to change


SST01: 3D Genomics: Computational approaches for analyzing the role of three-dimensional chromatin organization in gene regulation.

Saturday July 7, 10:15 am - 6:00 pm


Ferhat Ay, La Jolla Institute for Allergy and Immunology, United States
Sushmita Roy, Biostatistics & Medical Informatics, Wisconsin Institute for Discovery, United States


There is currently a call for contributed talks. Click the button below for more details.

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.

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

SST02: Single-particle Cryo-electron Microscopy, Cryo-electron Tomography, and Integrative/Hybrid Methods Studies of Macromolecular Machines: Opportunities and Challenges for the Bioinformatics Community

Sunday July 8, 10:15 am - 12:40 pm


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 Andrej Sali, 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

SST03: Omics Data Compression and Storage: Present and Future

Sunday July 8, 2:00 pm - 6:00 pm


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
2:00 pm - 3:00 pm Keynote: Gene Robinson, Carl R. Woese Institute for Genomic Biology Swanlund Chair of Entomology University of Illinois at Urbana-Champaign
3:00 - 3:30 pm Tsachy Weissman, Electrical Engineering Department, Stanford University
3:30 - 4:00 pm Christian Iseli, Swiss Bioinformatics Institute
4:00 pm - 4:15 pm Coffee Break
4:15 pm - 4:45 pm Cenk Sahinalp, Center for Genomics and Bioinformatics Indiana University
4:45 pm - 5:15 pm Claudio Alberti, Genomsys, Switzerland
5:15 pm - 5:45 pm Jörn Ostermann, Electrical Engineering Department, Leibniz Universität Hannover
SST04: Advancing computational biology through critical assessments, community experiments, and crowdsourcing

Monday July 9, 10:15 am - 4:00 pm


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


10:15 am - 10:20 amGaia Andreoletti (UC Berkeley)
10:20 am - 10:40 amCASP: Critical Assessment of protein Structure Prediction
John Moult University of Maryland
10:40 am - 11:00 amCAPRI: Critical Assessment of Prediction of Interactions
Ilya Vakser (University of Kansas) and Michael Sternberg (Imperial College)
11:00 am - 11:10 amCAMEO: Continuous Automated Model Evaluation
Torsten Schwede (University of Basel)
11:10 am - 11:20 ampFDA: Precision FDA
David Litwack (FDA) Elaine Johanson (FDA)
11:20 am - 11:40 amCAGI: Critical Assessment of Genome Interpretation
Steven E Brenner (UC Berkeley)
11:40 am - 12:00 pm GAW: Genetic Analysis Workshop
Laura Almasy (University of Pennsylvania), Jean MacCluer (Texas Biomedical Research Institute)
12:00 pm - 12:20 pm DREAM: Dialogue for Reverse Engineering Assessment and Methods
Jim Costello (Department of Pharmacology, UC Denver)
12:20 pm - 12:40 pm CAMI, Alice Mchard (Helmholtz Centre for Infection Research)
Alexander Sczyrba (Bielefeld University )
2:00 pm - 2:20 pm European Infrastructure of Bioinformatics
Alfonso Valencia (Life Science Department, Barcelona Supercomputing Centre (BSC pm - CNS), & Institució Catalana de Recerca i Estudis Avançats (ICREA))
2:20 pm - 2:40 pm CAFA: Critical Assessment of Functional Annotation
Iddo Friedberg (Iowa State University), Predrag Radivojac (Indiana University)
2:40 pm - 2:50 pm Critical Assessment of Information Extraction in Biology
Lynnette Hirschmann (MITRE Corporation)
2:50 pm - 3:00 pm Integrating Data for Analysis, Anonymization and SHaring (iDASH)
Haixu Tang (Indiana University)
3:00 pm - 3:20 pm CAMDA: Critical Assessment of Massive Data Analysis
David Kreil (University of Warwick), Joaquin Dopazo (National Institute of Bioinformatics)
3:20 pm - 3:30 pm sbv-IMPROVER: Systems Biology Verification combined with Industrial Methodology for Process Verification in Research
Julia Hoeng (Philip Morris International Science)
3:30 pm - 3:40 pm PLoS Comput Biol – Benchmarking
Papin, Jason A. (University of Virginia)

SST05: Building an academia-industry bridge to bring precision medicine to the clinic ** (This Special Session is Championed by the ISCB Industry Advisory Council)

Monday July 9, 2:00 pm - 6:00 pm


Benjamin Glicksberg- University of California, San Francisco, Institute for Computational Health Sciences, United States
Kipp Johnson- Icahn School of Medicine at Mount Sinai, Institute for Next Generation Healthcare, United States
Aparna Divaraniya- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, United States
Garima Kushwaha- Roche, Sequencing Solutions, United States
David Stark- Icahn School of Medicine at Mount Sinai, Institute for Computational Health Sciences, United States
Shameer Khader- Northwell Health, Healthcare Data Science and Bioinformatics, United States
Joel Dudley- Icahn School of Medicine at Mount Sinai, Institute for Computational Health Sciences, United States

Presentation Overview

Academia-industry collaboration is a principal vector for the translation of research discoveries from life sciences into pharma, the clinic and the public at large. The pharmaceutical, diagnostics, and healthcare technology industry have a long history of successful collaboration with academia, both in the form of clinical trials as well as basic, applied, and translational research. As a newer industry, biotechnology and bioinformatics companies have less history and often-different objectives than the pharmaceutical industry. Furthermore, as recent academic publications by companies such as Regeneron and 23andMe have demonstrated, academia-industry partnerships with strong bioinformatics focus can be well suited to add to the existing body of scientific knowledge. As the popularity of wearable devices, direct-to-consumer testing services, and real-time health monitoring continues to increase, we expect this trend to likewise progress and touch various layers of modern biological findings, the pharmaceutical industry, and healthcare overall. However, academia-industry partnerships exist in many forms such as consulting, contracted research, bilateral partnerships, public-private partnerships, start-ups, etc. These many forms of collaboration invite several nuances that make project outcomes highly variable. We propose to (1) Highlight significant research produced by successful academia-industry partnerships that have resulted in a change in healthcare practices, and (2) Focus on the elements of the partnerships that enabled success in the context of value-driven bioinformatics enterprise.

When incentives are aligned, the complementarity of aims from academic and industrial research are well suited to enable significant research advances. Biotech and bioinformatics companies can offer resources and scalability options that are often unfeasible in the typical academic environment, while academics are able to offer innovative analyses, disease expertise, and access to samples and patients. A great number of successful collaborations in the biotech space have recently resulted in high-impact work. For example, Regeneron recently partnered with Geisinger Health System and Penn State University to sequence the exomes of over 50,000 patients, nearly equaling the total number of exomes currently available in the ExAC database. 23andMe recently leveraged its massive database of patient data to detect 15 new genetic loci associated with depression. The public-private collaboration opentargets.org is a forward-thinking partnership which has the potential to discover innovative therapies and pharmaceuticals. The Institute for Next Generation Healthcare (INGH) at Mount Sinai has itself participated in several impactful research efforts in collaboration with industry partners. For example, INGH worked with the artificial intelligence company Ayasdi to perform precision subtyping of Type II Diabetes Mellitus, work that was eventually covered in Francis Collin’s NIH blog as an example of the potential of big data. INGH has also collaborated with Saffron Technology (recently acquired by Intel) to use its cognitive computing platform to enable accurate diagnosis from cardiovascular imaging in challenging clinical scenarios. Thus, collaboration between industry and academia has the potential to massively expand the currently available body of scientific knowledge and improve healthcare delivery.

At the same time, important questions must be answered such as the nature of the collaboration, how the partnership can be made worthwhile for all sides, compensation strategies, etc. Another important issue is how promising technology can be commercialized from within a laboratory, instead of initially partnering with an outside entity. In this vein, another important aspect of this session will be how start-ups, particularly those born from academia, fit into this landscape. Specifically, we hope to tailor part of our session to highlight how these start-ups can enable changing clinical practice as well through a venue different from even academic-industry partnerships. We plan to illustrate a successful example of this in our session where a start-up founder in this space will give a keynote on his or her experiences from idea to inception and foundation. Furthermore, as part of our session, we also plan to host a special platform for students/post-docs to pitch start-up/entrepreneurship ideas to these esteemed panelists. These short pitches, in the form of 10 minute talks, will provide experience for these students/post-docs and could hopefully form a connection with these panelists.

We believe that these key note talks and panels will be of broad interest to the audience of ISMB, which brings together biologists, computer scientists, statisticians, medical doctors, startups, and industry professionals. Healthcare practice is now being influenced by a myriad of features and players that reflect a deviation from the past; not just academics and pharma/biotech but also start-ups and other industries like the recent announcements from Apple (http://www.businessinsider.com/why-apples-moving-into-the-health-records-market2018-1) and Amazon (https://www.beckershospitalreview.com/healthcare-informationtechnology/amazon-adds-top-iora-health-physician-to-healthcare-team.html), as well as combinations of all the above. We also believe that the pitch platform will be of great interest to students and post-docs who have start-up ideas of their own that would like to receive feedback and make connections.

Schedule Overview
2:00 pm - 2:45 pm Academic-industry partnerships that have changed clinical practice.
2:45 pm - 3:30 pm Panel: Discussion of current challenges and opportunities for academic-industry partnerships and ways in which they can encourage personalized medicine. Panelists will have academic or industry affiliation and experience in a collaborative project across these lines.
3:30 pm - 4:15 pm Panel: Academic-initiated start-ups that enable precision medicine.
4:15 pm - 5:00 pm Discussion of current barriers and opportunities for start-ups to affect the life science, pharma and healthcare landscape. Panelists will be those that have led a start-up or academics that have spun-off their work.
5:00 pm - 6:00pm Student start-up pitches  
SST06: SCANGEN: Single-cell cancer genomics

Tuesday July 10, 10:15 am - 4:40 pm


Kieran R Campbell, University of British Columbia & BC Cancer Agency, Canada
Sohrab P Shah, University of British Columbia & BC Cancer Agency, Canada


There is currently a call for contributed talks and posters. Click the button below for more details.

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.

Invited Talks

Inferring cellular networks from single cell RNA - seq profiles after CRISPR perturbations
Speaker: Florian Markowetz (Cancer Research UK Cambridge Institute)

Scalable Bayesian Tensor Factorization for single - cell Genomics
Speaker: Christopher Yau (Center for Computational Biology, University of Birmingham)

Modelling tumour evolution from single - cell sequencing data
Speaker: Katharina Jahn (ETH Zürich)

An approach to studying clonal cell populations using bulk exome and single - cell RNA sequencing data
Speaker: Davis McCarthy (EMBL-EBI)

Integrated genetic and transcriptional analysis at the single - cell level
Speaker: Jean Fan (Harvard University)