Bioinformatics

The Bioinformatics track assembles thought leaders who will present case studies using computational resources and tools that discuss the problems and challenges of taking data from multiple -omics sources and aligning it with clinical action. Turning big data into smart data can lead to real-time assistance in disease prevention, prognosis, diagnostics, and therapeutics. With the ever-increasing volume of information generated for curing or treating diseases and cancers, bioinformatics technologies, tools, and techniques play a critical role in turning data into actionable knowledge to meet unstated and unmet medical needs. Case studies will be presented on addressing these problems and challenges, including making the jump from prototyping to production code, defining what a "validated" informatics pipeline means, how to balance agility needs with requirements to be consistent/compliant, pipeline and workflow frameworks, containerization for reproducibility, and more. How do your approaches deal with inconsistencies in definitions and meta-data across the multiple datasets that form the basis of big data?

Tuesday, October 6

PLENARY KEYNOTE PROGRAM

10:00 am

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Scott Parker, Director of Product Marketing, Marketing, Sinequa
10:15 am

NIH’s Strategic Vision for Data Science

Susan K. Gregurick, PhD, Associate Director, Data Science (ADDS) and Director, Office of Data Science Strategy (ODSS), National Institutes of Health
Rebecca Baker, PhD, Director, HEAL (Helping to End Addiction Long-term) Initiative, Office of the Director, National Institutes of Health
11:05 am

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Ari E Berman, PhD, CEO, BioTeam Inc
11:25 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Recommended Pre-Conference Workshops*
W1: Data Management for Biologics: Registration and Beyond
W2: A Crash Course in AI: 0-60 in Three
W3: Data Science Driving Better Informed Decisions

*Separate registration required. See workshop page for details.

1:55 pm Refresh Break - View Our Virtual Exhibit Hall
2:15 pm Recommended Pre-Conference Workshops*
W4: Digital Biomarkers and Wearables in Pharma R&D and Clinical Trials
W5: AI-Celerating R&D: Foundational Approaches to How Emerging Technologies Can Create Value
W6: Dealing with Instrument Data at Scale: Challenges and Solutions

*Separate registration required. See workshop page for details.

4:15 pm Close of Day

Wednesday, October 7

PRECISION CANCER MEDICINE

9:00 am

The Human Intelligence Revolution – How Collaboration, Data Sharing, and Human Intelligence Will Create a Healthier Future

Jeffrey G. Reid, PhD, Vice President & Head, Genome Informatics & Data Engineering, Regeneron Pharmaceuticals Inc.

The future of medicine will be enabled by our understanding of genetic disease drivers. As the architects of the world’s largest database of genomic data paired with de-identified health records, the Regeneron Genetics Center (RGC) is aiming to improve human health through data innovation and collaborative knowledge sharing. Dr. Reid discusses initiatives like Project Glow and the RGC-UK Biobank exome consortium, which enable the global scientific community to tap key datasets and identify new, better ways of preventing and treating human disease.

9:20 am

Using Networks to Understand Genetic and Genomic Drivers of Disease

John Quackenbush, PhD, Chair, Biostatistics & Henry Pickering Walcott Professor, Computational Biology & Bioinformatics, Harvard T.H. Chan School of Public Health

This presentation will address the problem of biological complexity in which many factors, each of small effect size, collectively influence disease risk, development, complexity, and response to therapy in cancer and other complex diseases. By using innovative computational methods built around network representations of biological interactions, we can gain insight into the disease process, develop predictive biomarkers, and identify possible avenues of therapeutic intervention.

9:40 am

Precision Cancer Medicine

Jeffrey Rosenfeld, PhD, Manager, Biomedical Informatics Shared Resource and Assistant Professor of Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey; President, Rosenfeld Consulting LLC

This presentation will illustrate the current methods that are used for determining the precise treatment of cancer rather than the standard chemotherapy methods.

10:00 am Coffee Break - View Our Virtual Exhibit Hall

SYSTEMS-LEVEL DATA APPROACHES AND MODELS FOR PRECISION ONCOLOGY

10:20 am

mTOR System: A Database for Systems-Level Biomarker Discovery in Cancer

Iman Tavassoly, PhD, Physician Scientist, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai

mTOR system is a database I have designed for exploring biomarkers and systems-level data related to mTOR pathway in cancer. This database consists of different layers of molecular markers and quantitative parameters assigned to them through a current mathematical model. This database is an example of merging systems-level data with mathematical models for precision oncology.

10:40 am

Building an Artificial Intelligence-Based Vaccine Discovery System: Applications in Infectious Diseases & Personalized Neoantigen-Related Immunotherapy for Treatment of Cancers

Kamal Rawal, PhD, Associate Professor, Bioinformatics & Computational Biology, Amity University

Infectious disease affects several million individuals all over the world, particularly from developing countries. We have built a bioinformatics pipeline, which combines reverse vaccinology tools, network biology system, and text mining algorithms to analyze proteomes of pathogens, and ranks proteins based upon their propensity to be an optimal vaccine candidate. Our system compares various machine learning approaches, such as support vector machines, neural networks, ensemble learning, and decision trees.

Ritu Kamal, Staff Product Manager, Clinical Software, Illumina

Learn how TruSight™ Software Suite offers ready-made infrastructure to analyze and interpret rare disease variants.  Powered by DRAGEN variant-calling, this software platform can evaluate all rare disease variant types within a single interface. Intuitive variant filtering, visualization and curation enable laboratories to perform streamlined interpretation and generate customizable reports.

George Vacek, Sequencing Strategic Development, NVIDIA
Sasha Paegle, Senior Business Development Manager, Dell Technologies

Multiple somatic variant callers have been created to identify variants that tumor cells acquire during their evolution. It is still unclear which variant caller, or combination of callers, is best suited to analyze tumor sequencing data.  Dell Technologies and NVIDIA highlight tools/technologies to maximize opportunities for new methods development.

11:30 am LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Jeffrey Rosenfeld, PhD, Manager, Biomedical Informatics Shared Resource and Assistant Professor of Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey; President, Rosenfeld Consulting LLC
Panelists:
Kamal Rawal, PhD, Associate Professor, Bioinformatics & Computational Biology, Amity University
Jeffrey G. Reid, PhD, Vice President & Head, Genome Informatics & Data Engineering, Regeneron Pharmaceuticals Inc.
John Quackenbush, PhD, Chair, Biostatistics & Henry Pickering Walcott Professor, Computational Biology & Bioinformatics, Harvard T.H. Chan School of Public Health
Iman Tavassoly, PhD, Physician Scientist, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai
Ritu Kamal, Staff Product Manager, Clinical Software, Illumina
Sasha Paegle, Sr. Business Development Manager, Dell Technologies
George Vacek, Sequencing Strategic Development, NVIDIA
Ka Yee Yeung, Professor, School of Engineering and Technology, University of Washington Tacoma; Adjunct Professor, Microbiology, University of Washington Seattle
11:50 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Michael Riener, President, RCH Solutions

Join us for a lively discussion among prominent pharma leaders, and learn:

Why, when & how to implement a public Cloud for your computing needs

Challenges and opportunities when setting and managing stakeholder expectations

Critical keys to success to realize the best outcomes

To learn more about RCH Solutions, visit our Virtual Booth

Joe Donahue, Managing Director, Life Sciences, Accenture

Hosted by Joe Donahue, Managing Director, Life Sciences, Accenture

 

Participants include: 

Andreas Matern, Head of Digital Translational Medicine, Sanofi

John Quackenbush, Professor of Computational Biology and Bioinformatics; Harvard T.H. Chan School of Public Health

Seungtaek Lee, VP, Strategic Partnerships and AI RWE Head of CoE; ConcertAI

Preston Keller, PhD, MBA, President & CCO, PercayAI

Philip Payne, PhD, Becker Professor and Chief Data Scientist, Washington University in St. Louis

 

Jeff Evernham, VP of Customer Solutions, Consulting, Sinequa

Most large scale analysis of clinical trial data only leverages part of the picture, ignoring unstructured data and limiting findability across all the information collected throughout multiple disparate data sources.  This roundtable will discuss leveraging a cognitive platform to combine all data from multiple sources into one unified view using a single entry point to the data.

 

Sasha Paegle, Life Science Business Development, Dell Technologies

Evaluating, optimizing and benchmarking of next generation sequencing (NGS) methods are essential for clinical, commercial and academic NGS pipelines. Optimizations for speed and accuracy often require making trade-offs relative to other constraints. Join this roundtable to discuss benchmarking strategies, trade-offs, and the value of benchmarking genomics tools and applications. 

PLENARY KEYNOTE PROGRAM

Michael Schwartz, Head, Product Marketing, Marketing, Benchling

The life science industry has forged ahead with a new generation of therapeutics. A new R&D paradigm is required to develop scientific platforms, manage data complexity, and orchestrate progress across specialized teams. Digital solutions and data ecosystems are at the heart of this, but require both structure and adaptability to thrive in the modern life science R&D environment.

12:30 pm KEYNOTE PRESENTATION & PANEL DISCUSSION:

Game On: How AI, Citizen Science, and Human Computation Are Facilitating the Next Leap Forward

Allison Proffitt, Editorial Director, Bio-IT World

While the precision medicine movement augurs for better outcomes through targeted prevention and intervention, those ambitions entail a bold new set of data challenges. Various panomic and traditional data streams must be integrated if we are to develop a comprehensive basis for individualized care. However, deriving actionable information requires complex predictive models that depend on the acquisition and integration of patient data on a massive scale. This picture is further complicated by new data streams emerging from quantified self-tracking and health social networks, both of which are driven by experimentation-feedback loops. Tackling these issues may seem insurmountable, but recent advancements in human/AI partnerships and crowdsourcing science adds a new set of capabilities to our analytic toolkit. This session describes recent work in online collective systems that combine human and machine-based information processing to solve biomedical data problems that have been otherwise intractable, and an information processing ecosystem emerging from this work that could transform the landscape of precision medicine for all stakeholders. Pietro will open with a framing talk, followed by short presentations from each panelist, ending with a moderated Q&A discussion by Allison with speakers and attendees. 

Panelists:
Seth Cooper, PhD, Assistant Professor, Khoury College of Computer Sciences, Northeastern University
Lee Lancashire, PhD, CIO, Cohen Veterans Bioscience
Pietro Michelucci, PhD, Director, Human Computation Institute
Jérôme Waldispühl, PhD, Associate Professor, School of Computer Science, McGill University
1:55 pm Refresh Break - View Our Virtual Exhibit Hall

KNOWLEDGE MANAGEMENT AND EXPLORATION TOOLS FOR DRUG DISCOVERY AND DEVELOPMENT

2:10 pm

How to Hold on to Your Knowledge in an Agile World

Etzard Stolte, PhD, Global Head, Knowledge Management PTD, F. Hoffmann-La Roche

As pharma is embracing digital and agile, new challenges for the retention and sharing of information are emerging. While the information standards of a validated environment remain, ad hoc processes and distributed cloud solutions are creating new islands of knowledge. In this presentation, I will present a knowledge strategy based on automated discovery and integration for a development department of several thousand scientists at Roche.

2:30 pm

Powering Question-Driven Problem Solving to Improve the Chances of Finding New Medicines

Samiul Hasan, PhD, Director, Scientific Analytics and Visualization, Data and Computational Sciences, GlaxoSmithKline

Making true “molecule”-“mechanism”-“observation” relationship connections is a time-consuming, iterative and laborious process. In addition, it is very easy to miss critical information that affects key decisions or helps make plausible scientific connections. The current practice for deciphering such relationships frequently involves subject matter experts (SMEs) requesting resources from already constrained data science departments to refine and redo highly similar ad hoc searches. The result of this is impairment of both the pace and quality of scientific reviews. In this presentation, I show how semantic integration can be made to ultimately become part of an integrated learning framework for more informed scientific decision-making. I will take the audience through our pilot journey and highlight practical learnings that should inform subsequent endeavors.

2:50 pm Refresh Break - View Our Virtual Exhibit Hall
3:10 pm

Computational Efforts on Drug Repurposing for Rare Diseases

Bin Li, PhD, Director, Computational Biology & Translational Medicine, Data Science Institute, Millennium, The Takeda Oncology Co.

We conducted in silico screens trying to repurpose >100 compounds for ~4000 rare disease indications. Various data types were utilized (protein-protein interaction network, pathways, disease-driven genes, competitive intelligence, etc.), and different computational methods were implemented and evaluated. Some biologically interesting drug/disease pairs were observed.

4:00 pm LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Etzard Stolte, PhD, Global Head, Knowledge Management PTD, F. Hoffmann-La Roche
Panelists:
Samiul Hasan, PhD, Director, Scientific Analytics and Visualization, Data and Computational Sciences, GlaxoSmithKline
Bin Li, PhD, Director, Computational Biology & Translational Medicine, Data Science Institute, Millennium, The Takeda Oncology Co.
4:20 pm Bio-IT Connects - View Our Virtual Exhibit Hall
5:00 pm Close of Day

Thursday, October 8

SINGLE-CELL RNA-Seq DATA PLATFORMS, TOOLS, AND ANALYSIS

9:00 am

Embedding Single-Cell RNA-Seq Profiles in Non-Euclidean Spaces

Jiarui Ding, PostDoc Associate, Broad Institute

Single-cell RNA-Seq has become an invaluable tool for studying biological systems in health and diseases. We introduced scPhere, a scalable deep generative model to embed cells into low-dimensional hyperspherical or hyperbolic spaces, as a more accurate representation of the data. scPhere resolves cell crowding, corrects multiple, complex batch factors, facilitates interactive visualization of large datasets, and gracefully uncovers pseudotemporal trajectories.

9:20 am

Scaling scRNASeq Visualization to Unlimited Datasets with Cellxgene Gateway

Alok Saldanha, PhD, Technical Associate Director, NIBR Informatics, Novartis Institutes for Biomedical Research

Cellxgene Gateway is an open source tool (https://github.com/Novartis/cellxgene-gateway) which allows you to use the Cellxgene Server provided by the Chan Zuckerberg with multiple datasets. I will introduce this tool in the context of a typical single-cell RNA-Seq analysis workflow, and touch on deployment issues in an enterprise cloud with a budget.

9:40 am Coffee Break - View Our Virtual Exhibit Hall
10:00 am

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Alok Saldanha, PhD, Technical Associate Director, NIBR Informatics, Novartis Institutes for Biomedical Research
Panelists:
Jiarui Ding, PostDoc Associate, Broad Institute

VISUALIZING BUSINESS VALUE WITH VCs

10:20 am PANEL DISCUSSION:

Live Panel Discussion:  Visualizing Business Value with VCs

Panel Moderator:
Annastasiah M. Mhaka, PhD, Co-Founder & Convenor, AAIH; Founder, Mawambo

This panel is useful for startups and young companies to learn what VCs are looking for to invest in new platforms and technology. Topics to be addressed include: 1) Explore trends and lessons learned with regards to how AI and digital health platform developers are strategically partnering with BioPharma to accelerate business and asset value; 2) How to collaborate with pharmaceutical and technology companies when you are a startup; 3) What are VCs looking for?; 4) Discuss how software and platform developers are creating value around tools to secure capital, including key challenges and opportunities, and 5) Examine tangible case studies of what is working and what isn’t within this dynamic of stakeholders.

Panelists:
Navid Alipour, Co-Founder & Managing Partner, Analytics Ventures
Jessica J. Federer, Venture Affiliate Partner, Boston Millennia Partners
Ardy Arianpour, CEO & Co-Founder, Seqster
Sean J. Cheng, PhD, Senior Investment Manager, Philips Ventures
Michael Langer, Head of Search and Evaluation, Pear Therapeutics
10:40 am

BENJAMIN FRANKLIN AWARD ACCEPTANCE SPEECH: Open Access for Computational Biology

Xiaole Shirley Liu, PhD, Prof, Statistics & Biostatistics, Dana Farber Cancer Institute
Jeffrey W. Bizzaro, Managing Partner, Bioinformatics.org
11:30 am Lunch Break - View Our Virtual Exhibit Hall
11:35 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Timothy Gardner, CEO, Riffyn, Inc.

How do you use data / digitization today to drive scientific discovery / product development?

What are you greatest scientific pain points / gaps that are not being met by digitization?

What kinds of outcomes do you believe digital tools could help you achieve?

 

Scott Jeschonek, Principal Program Manager, Microsoft Azure

Welcome to this discussion group on the growth of demand for HPC in scientific research. We are looking forward to a lively forum. We'll start by looking at three related topics:

- What events trigger demand in your organization? How has the current pandemic impacted resources?

- What could make scale and collaboration more accessible to more researchers?

- Share a recent experience of shifting workloads to manage HPC capacity.

Greg DiFraia, General Manager, Americas, Executive Team, Scality
Shailesh Manjrekar, Head of AI and Strategic Alliances, Executive Team, WekaIO

In this session we’ll discuss how to provide researchers with performance and scale in genomics & research analytics, to drive results at a price point that’s economically viable on public & private cloud.

11:35 am

Breakout: NGS Pipeline Optimizations

Tristan J Lubinski, PhD, Sr Scientist, Next Generation Sequencing Informatics, AstraZeneca Pharmaceuticals; Co-organizer, Boston Computational Biology and Bioinformatics (BCBB)
Howard Marks, Technologist Extraordinary and Plenipotentiary, VAST Data

Storage solutions we’ve been using force bioinformaticists to make trade-offs between the capacity and low-cost of disk and the performance of flash. This results in complex tiering configurations that only deliver performance for a small slice of the data. In this session, we will review how advancements in technology enable VAST Data to revolutionize the cost of all-flash and allows bioinformatists faster analysis across larger datasets for deeper insights.

PLENARY KEYNOTE PROGRAM

12:00 pm

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
12:15 pm

Toward Preventive Genomics: Lessons from MedSeq and BabySeq

Robert C. Green, Professor & Director, G2P Research, Genetics & Medicine, Brigham & Womens Hospital
12:40 pm

AI in Pharma: Where We Are Today and How We Will Succeed in the Future

Natalija Z. Jovanovic, PhD, Chief Digital Officer, Sanofi
1:05 pm

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Vivien R. Bonazzi, PhD, Managing Director & Chief Biomedical Data Scientist, Deloitte Consulting LLP
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
1:25 pm Happy Hour - View Our Virtual Exhibit Hall
2:00 pm Close of Conference





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