Bioinformatics Image

The Bioinformatics track assembles thought leaders who will present case studies using computational resources and tools that take data from multiple -omics sources and align 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.

Monday, September 20

7:30 am Registration Open
8:00 am Recommended Pre-Conference Workshops*

Cambridge Healthtech Institute is pleased to offer morning and afternoon pre-conference workshops on Monday, September 20, 2021. They are designed to be instructional, interactive and provide in-depth information on a specific topic. They allow for one-on-one interaction and provide a great way to explain more technical aspects that would otherwise not be covered during the main conference tracks that take place Tuesday-Wednesday. 

*Separate registration required. See Workshop page for details.

9:30 am Break
9:45 am Recommended Pre-Conference Workshops*
11:15 am Enjoy Lunch on Your Own
12:45 pm Recommended Pre-Conference Workshops*
2:15 pm Break
2:30 pm Recommended Pre-Conference Workshops*
4:00 pm Session Break and Transition to Plenary Keynote

PLENARY KEYNOTE PROGRAM

4:15 pm Innovative Practices Awards – Winners Spotlight
4:20 pm PANEL DISCUSSION:

Pharma Executive Roundtable: Broadening the Data Ecosystem

Panel Moderator:
Lita Sands, Head, Life Sciences, Amazon Web Services

The Bio-IT World community employed creativity, problem solving, and technical ingenuity to weather 2020 and never was the work more important. Meanwhile, digitization has been broadening the horizons of new possibilities and initiatives that are driving innovation in the life sciences sector. While over the past year many pharmaceutical companies have seen an acceleration of digital transformation, there are still many that are unsure what to expect going forward. Digital transformation is now a strategic imperative, not a buzzword. Join our Pharma Executive Roundtable to discover how biopharma companies are broadening their digital strategies and capabilities to develop products and services to scale, streamline operations, and drive innovation in life sciences R&D. 

Panelists:
Ramesh V. Durvasula, PhD, Vice President & Information Officer, Research Labs, Eli Lilly & Co.
Michael Montello, Senior Vice President, R&D Tech, GlaxoSmithKline
Bryn Roberts, PhD, Senior Vice President & Global Head of Data Services, Roche
Holly Soares, PhD, Vice President & Head, Precision Medicine, Pfizer Inc.
Lihua Yu, Chief Data Officer, FogPharma
5:45 pm Welcome Reception in the Exhibit Hall with Poster Viewing
7:00 pm Close of Day

Tuesday, September 21

7:00 am Registration Open and Morning Coffee

ROLE OF COMPUTATIONAL METHODS TO UNDERSTAND DISEASE AND IDENTIFY THERAPEUTIC INTERVENTIONS

8:10 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.

8:40 am

Bringing the Power of Synthetic Biology to Medicine

Aoife M Brennan, President & CEO, Synlogic

Synlogic is delivering the power of synthetic biology to medicine, combining the precision of engineering with rational drug development. With a premiere synthetic biology platform, we design Synthetic Biotic medicines to treat disease in new ways. Synthetic biology brings engineering principles to science enabling the design of new biological systems, genetic circuits and molecular components that can create medicines that can have a potentially meaningful impact for patients.

9:10 am Coffee Break in the Exhibit Hall with Poster Viewing
Juergen Klenk, Principal, Precision Medicine Leader, Deloitte Consulting
Vivien Bonazzi, Managing Director, Deloitte Consulting LLC

Patient privacy requires the removal of Protected Health Information before public sharing of clinical images. An automated de-identification tool, tested on a limited collection, independently prepared by The Cancer Imaging Archive of the National Cancer Institute, yielded 99.8% accuracy. We’ll discuss how the cloud-based tool allows scalable de-identification and public sharing of imaging data for development and validation of AI tools, some of which may find their way into clinical workflows.

Alexandr Ishkin, Senior Science Analyst, Clarivate

Quality bioinformatics pipelines are indispensable for getting insights out of molecular data, potentially leading to breakthroughs in drug development. However, it is difficult to identify the best tools for these pipelines. Recently launched Algorithm Benchmarking Consortium is an attempt at a pre-competitive effort to systematically evaluate bioinformatics tools. This talk will focus on how the consortium was conceived, how it operates, and what insights it brings to the members.

11:00 am Interactive Discussions (Opportunity Available)
12:15 pm Refreshment Break in the Exhibit Hall with Poster Viewing

PLENARY KEYNOTE PROGRAM

Michael Stapleton, PhD, Managing Director, Life Sciences, Accenture
1:15 pm

How Digital Evolution and an Attitudinal Revolution are Re-Shaping the Future of the Life Sciences Industry

Nimita Limaye, PhD, Research Vice President, Life Sciences R&D Strategy and Technology, IDC

The world has rapidly transitioned to a model of disaggregated care and decentralized clinical trials, with a heightened focus on patient-centricity. Digital resiliency has become the priority and discretionary spend on R&D platforms has been delayed. Federated-learning models are fueling co-innovation and GPU-powered transformer models are accelerating drug discovery. Technology is enabling access and equity. The borders between healthcare and life sciences are blurring and real-world data is being leveraged to drive a precision medicine strategy.

1:50 pm

All of Us Research Program – Seeking To Advance Precision Health for All Populations

Joshua Denny, MD, MS, CEO, All of Us Research Program, National Institutes of Health

The All of Us Research Program launched May 6, 2018 and currently has over 375,000 participants who have contributed biospecimens, health surveys, and a willingness to share their EHR. Participants are partners in the program and receive research results from data they contribute, including genetic ancestry and traits. In the future, participants will also receive health-related genomic results from whole genome sequencing. In May 2020, the program launched the beta version of the Researcher Workbench. Once researchers register and are approved to use the workbench, they can access individual-level data and a suite of tools to analyze these data. All of Us is committed to catalyzing a robust ecosystem of researchers and providing a rich dataset that drives discovery and improves health.

2:30 pm Refreshment Break in the Exhibit Hall with Poster Viewing

USING ADVANCED ALGORITHMS FOR VARIANT CALLING

3:05 pm

Analysis of Cancer Genome Variation Using Advanced Techniques

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

There have been many recent advances in algorithms and tools for analyzing cancer genomes and making them useful in a research and clinical context. I will discuss how these developments are improving care including the use of a new advanced genome reference.

3:35 pm

PRINCESS: Comprehensive Detection of Haplotype Resolved SNVs, SVs, and Methylation

Medhat Mahmoud, PhD, Postdoctoral Associate, Human Genome Sequencing Center, Baylor College of Medicine

Long-read sequencing became widely adopted due to its improvements for Structural Variation detection and methylation calling. But, it is hard to fully utilize the generated data and thus many studies focus either on SV, methylation, or phasing of SNVs. We developed PRINCESS, PRINCESS starts with a raw sequence and provides within hours a fully phased SNV, SV, and methylation call set. This allows a comprehensive study of the sample at scale and for a wide number of scientists. PRINCESS achieves high accuracy (SNVs: 96.21%-97.92%, SVs: 85.60%-90.91%) and long phasing 821,907 bp (N50).

4:05 pm Refreshment Break in the Exhibit Hall with Poster Viewing

MODELS AND TOOLS FOR DATA PROCESSING AND RESEARCH WORKFLOW

4:35 pm

Bringing Operational Machine Learning in Research Workflows

Christophe Chabbert, PhD, Senior Scientist, Data Integration and ML Ops, Roche

Machine learning and deep learning models are rapidly being adopted throughout the entire drug discovery value chain. Deploying them productively in business processes is a critical step towards generating business value and transforming pharma research. Handling these productive deployments and managing them throughout their life cycle requires dedicated and collaborative efforts across the organization.

Richard Lee, Director of Core Technology, ACD/Labs

Systems that execute enterprise level automated data transfer are often black boxes with limited configurability and access. This leaves R&D organizations reliant on vendor services for even simple workflow changes. To address this, we introduce a framework that allows for the admin-level user to configure and design an analytical data marshalling system. This framework can incorporate source monitoring, data transfer, data processing, databasing, and measure system performance metrics.

5:35 pm Networking Reception in the Exhibit Hall with Poster Viewing
6:35 pm Close of Day

Wednesday, September 22

7:30 am Registration Open
8:00 am Interactive Discussions

Interactive Discussions are informal, moderated discussions, allowing participants to exchange ideas and experiences and develop future collaborations around a focused topic. Each discussion will be led by a facilitator who keeps the discussion on track and the group engaged. For in-person events, the facilitator will lead from the front of the room while attendees remain seated. For virtual attendees, the format will be in an online networking platform. To get the most out of this format, please come prepared to share examples from your work, be a part of a collective, problem-solving session, and participate in active idea sharing. Please visit the website's Interactive Discussions page for a complete listing of topics and descriptions.

9:00 am Coffee Break in the Exhibit Hall with Poster Viewing

MODELS AND TOOLS FOR DATA PROCESSING AND RESEARCH WORKFLOW

9:55 am

Regeneron Deva Computational Biology Pipeline for Cryo-EM (Innovative Practices Awards Winner)

Quan Yang, PhD, Executive Director Research & Pre-clinical Development IT, Information Systems & Technology, Regeneron Pharmaceuticals
Srinivasan Sadanandhamurthy, Director IT Digital and Data Engineering, Information Systems & Technology, Regeneron Pharmaceuticals

We will present a new computational data process pipeline which enables the end-to-end data flow based on a complete cloud-based platform to support a high-throughput data processing and computational services. As a result, the researchers have at the ready, the ability to transfer an average of 2TB transfer in under 2 hours, and can analyze the data using GPU computation. It enabled the resolution of REGEN-COV2 antibody cocktails binding structure to COVID-19 Spike protein and allowed us to provide an effective therapeutic medicine to fight against the current pandemic in a timely fashion.

10:25 am

Turbocharging Research Workflows: Case Studies Involving Open Chemical Data

Evan E Bolton, PhD, Head, Information Engineering, NIH NLM

This talk will help you understand some of the opportunities to use open and free-to-use chemical data available from resources such as PubChem, which I manage at the National Center for Biotechnology Information (NCBI).  By the end of this talk, you should have some sense of the ways you can access open chemical information content from within your workflows and how it might help you or your colleagues improve the science that you do.

10:55 am

Accurate COVID-19 Health Outcome Prediction and VHA/PrecisionFDA Modeling Challenge

Alice Feng, Senior, Harker School

We developed a supervised machine learning pipeline using longitudinal Electronic Health Records (EHR) to accurately predict COVID-19 related health outcomes. In particular, we developed unique and effective data processing algorithms, then trained models using state-of-the-art machine learning strategies combined with different parameter settings and feature selection. In addition, we identified top COVID-19 risk factors, which are consistent with epidemiologic findings. This pipeline achieved top performance at VHA/precisionFDA COVID-19 modeling challenge.

Mehdi Keddache, PhD, Executive Specialist, Informatics, Illumina
The Illumina informatics portfolio includes some the most accurate and advanced tools for analysis, interpretation, and data aggregation. Our comprehensive solutions are integrated with Illumina sequencers to offer cloud computing, storage, and variant alignment detection. This presentation will introduce updates on Illumina Connected Analytics (ICA), the capabilities on BaseSpaces' custom pipeline development, including DRAGEN tools, secure and scalable data warehousing and our cloud-based Clarity LIMS for managing library preparation workflows.
Ken Berta, BME, MBA, Global Lead, Life Sciences - UDS, Dell Technologies
Christopher Bouton, PhD, CEO, Vyasa Analytics

During this session, colleagues from Vyasa and Dell Technologies will discuss the scientific and technical aspects involved in creating data fabric architectures. This discussion will address how to overcome the complexity and dimensionality of biomedical data including content types beyond databases such as unstructured documents and images. We will explore how best to connect the dots between internal and external data sources, how to enable organizations to ask complex questions across their data silos using novel deep learning A.I. text analytics. We will demonstrate how to gain critical insights to make better decisions, while highlighting best practices in hybrid compute deployment strategies that scale along with your organization.

 

11:55 am Interactive Discussions (Opportunity Available)
1:10 pm Refreshment Break in the Exhibit Hall with Poster Viewing

PLENARY KEYNOTE PROGRAM

2:10 pm PANEL DISCUSSION:

Trends from the Trenches

Panel Moderator:
Kevin Davies, PhD, Executive Editor, The CRISPR Journal; Founding Editor, Bio-IT World

Since 2010, the “Trends from the Trenches” presentation, given by Chris Dagdigian, has been one of the most popular annual traditions on the Bio-IT Program. The intent of the talk is to deliver a candid (and occasionally blunt) assessment of the best, the worthwhile, and the most overhyped information technologies (IT) for life sciences. The presentation has helped scientists, leadership, and IT professionals understand the basic topics related to computing, storage, data transfer, networks, cloud, data science, and machine learning that are involved in supporting data-intensive science. In 2021, Chris will give the “Trends from the Trenches” presentation in its original “state-of-the-state address” followed by guest speakers giving podium talks on relevant topics. An interactive Q&A moderated discussion with the audience follows. Come prepared with your questions and commentary for this informative and lively session. To stay connected with Trends from the Trenches updates after today and all year, sign up for BioTeam's newsletter here: https://bit.ly/33uO0OY

Panelists:
Chris Dagdigian, Senior Director, BioTeam, Inc.
Fernanda S. Foertter, PhD, Director of Applications, NextSilicon
Karl Gutwin, PhD, Director, Software Engineering Services, BioTeam, Inc.
Adam Kraut, Director Infrastructure & Cloud Architecture, BioTeam, Inc.
3:30 pm Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 pm

PANEL SESSION: Inclusion and Diversity in Life Sciences: Producing Stronger Research and Sparking Innovation

Panel Moderator:
Allison Proffitt, Editorial Director, Bio-IT World
Panelists:
Ari E Berman, PhD, CEO, BioTeam Inc
Stephanie Hintzen-Matoian, Senior Associate Data Scientist II, bluebird bio
Kevin M Ileka, PhD, Chemist, Process Chemistry, Bristol Myers Squibb Co
Annastasiah M. Mhaka, PhD, Co-Founder & Convenor, AAIH; Founder, Mawambo
5:35 pm Close of Conference





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