Bioinformatics

Leverage Computational Tools and Methods to Turn Big Data into Smart Data to Advance Pharma R&D

May 17 - 18, 2023 ALL TIMES EDT

The Bioinformatics track assembles thought leaders who will present case studies using computational resources and tools that take multimodal data analyses across genomics, transcriptomics, proteomics, metabolomics, and other data types (e.g., imaging), 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. Other themes we will explore include new methods of single-cell data analysis, how bioinformatics can leverage tools/methods from data science and AI to advance research, and deep learning approaches to help with applications of bioinformatics to pharma R&D.

Monday, May 15

– 6:00 pm Hackathon*8:00 am

*Separate Complimentary Registration Required, see Hackathon page to submit your project OR register to participate

– 5:00 PM Registration Open – Come Early and Avoid the Lines2:00 pm

Tuesday, May 16

Registration Open7:00 am

Recommended Pre-Conference Workshops and Symposia*8:00 am

On Tuesday, May 16, 2023 Cambridge Healthtech Institute is pleased to offer nine pre-conference workshops scheduled across three time slots (8:00-10:00 am, 10:30 am-12:30 pm, and 1:45-3:45 pm) and two Symposia from 8:25 am-3:45 pm. All 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 Wednesday-Thursday.

*Separate registration required. For details, see Workshop agendas, FAIR Data Symposium agenda, and Knowledge Graphs Symposium agenda.

– 3:45 pm Hackathon*8:00 am

*Separate Complimentary Registration Required, see Hackathon page to submit your project OR register to participate

Refreshment Break and Transition to Plenary Keynote3:45 pm

PLENARY KEYNOTE PROGRAM

4:00 pm

Plenary Keynote Organizer's Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute

4:05 pm

Innovative Practices Awards

Joseph Cerro, Independent Consultant

Chris Dwan, Independent Consultant, Dwan, LLC

Allison Proffitt, Editorial Director, Bio-IT World

The Innovative Practices Awards recognizes and celebrates innovation that advances life sciences research. Bio-IT World is currently accepting entries for the 2023 Innovative Practices Awards, a competition designed to recognize partnerships and projects pushing our industry forward. Winners will be announced in mid-April 2023, recognized during the Tuesday May 16 Plenary Keynote Program, and scheduled to give a 30-minute podium presentation about their project during the conference. The deadline for entry is March 3, 2023. For more details about the Awards and to submit an application, visit the official Bio-IT World Innovative Practices Awards page: https://www.bio-itworld.com/Award/.

4:20 pm Plenary Keynote Introduction

David Gosalvez, PhD, Executive Director, Strategy & Informatics Portfolio, Revvity Signals

4:30 pm PLENARY KEYNOTE PRESENTATION:

The Promise of Data, Analytics, and Technology: Fueling Scientific and Medical Breakthroughs

Anastasia Christianson, PhD, Vice President, Global Head of AI, ML, Analytics, and Data, Pfizer Inc.

Edward Cox, Head & General Manager, Digital Health & Medicines (DHM), Pfizer Inc.

The 21st century has been referred to as the Century of Biology. With 90% of the world’s 97 zettabytes of data generated in the past 2 years and 30% of today’s data being healthcare related, how are we using data technology and advanced analytics (artificial intelligence, machine learning, and deep learning) to advance our understanding of disease and deliver “breakthroughs that change patients' lives?”

Welcome Reception in the Exhibit Hall with Poster Viewing5:45 pm

Close of Day7:00 pm

Wednesday, May 17

Registration and Morning Coffee7:00 am

PLENARY KEYNOTE PROGRAM

8:00 am

Plenary Keynote Organizer's Remarks

Allison Proffitt, Editorial Director, Bio-IT World

8:05 am PLENARY KEYNOTE INTRODUCTION:

Life Science Automation Opportunities – So Many Options, So Little Time

Santanu Sen, Vice President, Healthcare & Life Sciences, Virtusa

The COVID pandemic has demonstrated that therapies and vaccines can be developed in 18 months with a high degree of safety and efficacy. Pioneering work done by companies involved has shed light to archaic processes that have been in existence for decades with little need for change.  In this presentation, we will discuss collaborative efforts, enabling technologies, regulation, and workflow to automate these processes to advance personalized medicine initiatives.

8:15 am PLENARY KEYNOTE PRESENTATION:

Federated Futures: How the Largest Federated Learning Effort in Medicine Will Inform Our Next Steps

Spyridon Bakas, PhD, Assistant Professor, Radiology & Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania

Raymond Y. Huang, MD, PhD, Division Chief, Neuroradiology, Brigham and Women’s Hospital; Associate Professor of Radiology, Harvard Medical School

Jason Martin, Principal Engineer AI Research Science, Security Solutions Lab, Intel Labs

Is a federated learning model sufficient to handle data from 71 institutions and more than 6,000 patients located on six continents? Researchers from Penn Medicine and Intel Labs say yes. An interdisciplinary team created the largest to-date global federated learning effort to develop an accurate and generalizable machine learning model for detecting glioblastoma borders. We will share what we learned about creating and maintaining such a federation, how the software infrastructure evolved over the course of the study, and how this work will empower the future of high-quality, precision clinical care worldwide.

Coffee Break in the Exhibit Hall with Poster Viewing9:30 am

Organizer's Welcome Remarks10:15 am

BIOINFORMATICS FOR PRECISION MEDICINE

10:20 am

Chairperson's Remarks

Jeffrey Rosenfeld, PhD, Executive Director, Bioinformatics & Genomics, Tonix Pharmaceuticals Holding Corporation

10:25 am

Improving Genomic Analysis by Fixing Reference Errors

Sairam Behera, PhD, Postdoctoral Associate, Human Genome Sequencing Center – Informatics, Nex-Gen, Baylor College of Medicine

The GRCh38 human reference genome contains ~9Mbp of falsely duplicated and collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. We present a modified GRCh38 reference that corrects errors while maintaining the same coordinates allowing us to leverage the extensive existing annotations of GRCh38, along with an efficient remapping approach, FixItFelix, that enables quick and efficient re-analysis to gain improved insights from existing data. We showcased improvements over multi-ethnic control samples across short and long-read DNA-, and RNA sequencing by using the fixed reference.

10:45 am

AstraZeneca-TEMPUS Partnership to Interrogate Small Cell Lung Cancer Subpopulations

Jonathan Dry, Vice President, Scientific Discovery, Tempus

Small cell lung cancer (SCLC) is typically detected late, when prognosis is poor.  We assembled a real-world SCLC cohort of >500 US patients, with linked clinical, genetic, transcriptomic and imaging data.  Clinical trial results and published transcriptional subtyping were reproducible when methods were adapted for real-world heterogeneity.  We assess the practicality of biomarker testing in the current patient journey, subtype specificity of molecular targets, prognosis, and signatures of inflammation.

11:05 am

Integration: The New Frontier of (Bio)Informatics for Precision Medicine

Andrea Sboner, PhD, Associate Professor, Pathology & Lab Medicine, Weill Cornell Medicine

Precision Medicine has made significant strides in using sequencing assays to analyze molecular profiles of patients and inform their targeted treatments, particularly in cancer genomics. A new revolution in healthcare is emerging with technologies such as spatial biology, ubiquitous sensors, and powerful AI tools that can further expand molecular profiling and its interpretation. To harness this revolution, (bio)informatics needs to address the challenges of big data by integrating different data sources to create a comprehensive patient profile. At the Englander Institute for Precision Medicine, we have adopted solutions such as micro-services and mixed reality applications to address these challenges.

11:25 am

Achieving Economic Success as an NGS Labs: Strategy and Implementation

Andreas Scherer, PhD, President and CEO, Golden Helix, Inc.

This talk will discuss the key strategies that economically successful NGS deploy to establish a sustainable, growing, and profitable business model. Based on his experience working with hundreds of NGS labs globally, Dr. Andreas Scherer will share strategies and implementation examples that are key for NGS labs to be successful long term.

11:55 am Precision Medicine at Molecular Partners: From Discovery to Early Clinical Development

Ana-Maria Florescu, PhD, Associate Director, Precision Oncology and Virology, Molecular Partners

12:25 pm Strategies for Containing Cloud Computing Costs in Healthcare and Life Sciences

Evan Floden, PhD, CEO, Seqera Labs

Managing cloud spending in life sciences can be uniquely challenging. Researchers and clinicians often use pre-built pipelines developed by others. While curated pipelines such as those found at nf-core provide tremendous value, the result is that resources are often shockingly over-provisioned — in some cases by several orders of magnitude.

Emerging workflow orchestration tools maximize productivity by enabling collaborative data analysis at scale, on-premises, or in any cloud. By simplifying complex tasks and securely sharing both data analysis pipelines and compute environments, researchers can dramatically reduce costs and optimize resources, adding predictability with a clear line of sight on cloud spending

12:40 pm Running the World’s Single Cell Bioinformatics

Iva Babukova, CTO & Co-Founder, Biomage

More than 2000 researchers from around the world have accomplished a high quality single cell RNA-seq data analysis using Cellenics – scalable, cloud-based, open-source software developed at Harvard Medical School.

 

Iva Babukova is a devops engineer who architected Cellenics and maintains the largest deployment of the software. She will share her insights from engineering Cellenics – the most widely used cloud-based system for single cell RNA-seq data analysis.

 

Session Break and Transition to Luncheon Presentation12:55 pm

1:05 pm LUNCHEON PRESENTATION:Accelerating Cancer Research with a Modern Data Platform

Lisa Arbogast, Industry Principal, Life Sciences, Snowflake

Jesse Cugliotta, Global Industry GTM Lead, Healthcare & Life Sciences, Snowflake

Vinay Seth Mohta, CEO & Co-Founder, Manifold.AI

Alpa Patel, PhD, Senior Vice President, Population Science, American Cancer Society

Join a lively discussion on how a modern data platform breaks down data silos. Snowflake customers: American Cancer Society and Manifold will share their journey and joint partnership to accelerate cancer research with the Science Cloud - a research platform for life sciences powered by Snowflake, and the impact this solution is having on the American Cancer Society's research.

Refreshment Break in the Exhibit Hall with Poster Viewing1:50 pm

NON-CODING RNA AND RIBOTHERAPEUTICS FOR POST-GENOMIC PRECISION MEDICINE

2:35 pm

Chairperson's Remarks

Leonard Lipovich, PhD, Professor, Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine & Health Sciences (MBRU)

The first two decades of post-genomic biology have highlighted the formidably diverse functions of the two-thirds of human genes that do not encode proteins. Nevertheless, the bulk of drug development has continued to center on protein-based targets and small-molecule drugs. In this session, we integrate cutting-edge computation with genome-scale experimentation to highlight the inexorable progress of sequence-based precision medicine in targeting non-coding RNA causes of human disease with RNA-based drugs in three key systems: the brain, metabolism, and cancer.

2:40 pm

From the RNA World to the Post-Genomic Era: Primate-Specific Long Non-Coding RNA Genes as Causes of, and Drug Targets in Human Disease

Leonard Lipovich, PhD, Professor, Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine & Health Sciences (MBRU)

Two decades ago, the Human Genome Project revealed that 98% of the human genome was not protein-coding. Long non-coding RNA (lncRNA), the prevalent class of mammalian non-coding genes, is mainly primate-specific in humans. We have characterized estrogen-induced oncogenic lncRNAs in estrogen receptor α positive breast cancer; their suppression points to new cancer treatments. Having discovered, using mass spectrometry in the ENCODE Consortium in 2012, rare translation of short Open Reading Frames in specific lncRNAs, in 2022 we deployed ribosome profiling to show that transcriptional and translational regulation of human estrogen-regulated lncRNAs is unexpectedly discordant. From Genome-Wide Association Studies (GWAS), we have identified a universe of druggable liver-expressed lncRNAs in type 2 diabetes and the metabolic syndrome, which we are pursuing in nonhuman-primate models.

2:55 pm

RNA Patterns and RNA Therapeutics

George A. Calin, MD, PhD, Professor, Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center

MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are involved in all cellular functions and their dysregulation is implicated in the pathogenesis of cancer and many other diseases. Substantial effort has been invested towards the clinical application of RNA-based therapeutics employing mostly mimics and antisense short RNAs, which is now expanding to encompass the larger class of lncRNAs. Despite these efforts, results have been ambivalent, with some trials showing potent effects while in others RNA-based drugs exhibited limited efficacy or were even harmful. In this talk, I will present innovative “out-of-the box” alternative approaches which aim to address the challenges hampering the success of ncRNA therapeutics.

3:20 pm

Integrating Multimodal Human Brain Data to Decipher Roles for lncRNAs in Health and Disease

Jeffrey A. Loeb, MD, PhD, Professor and Chair, Department of Neurology and Rehabilitation; Co-Director, Biomedical Informatics Core, Center for Clinical and Translational Science, University of Illinois at Chicago

Human brain evolution has led to the generation of complex behaviors, but also to diseases.  Because of their human-specific evolution, long-non-coding RNAs (lncRNAs) present major challenge in deciphering their functions in health and disease. We have developed a biomedical informatics platform called INTUITION that takes a multi-systems approach to study human brain tissues linking genomic, proteomic, and molecular differences to quantitative electrical activities, brain imaging studies, and clinical data through a relational database.  In this talk, I will summarize our human brain tissue and data platform as well as recent findings implicating lncRNAs as potential therapeutic targets for human epilepsy.

3:45 pm

Giving Radiosensitivity to Lung Cancers Using Male LncRNAs: Don't Lose Your Maleness!

Ivan Martinez, PhD, Associate Professor, Department of Microbiology, Immunology & Cell Biology, West Virginia University

One of the biggest problems for patients with lung cancer is that after radiation treatment a good percentage of these tumors developed resistance to radiation. We recently discovered a group of lncRNAs, known as lincSPRY3 RNAs, that are expressed from the Y chromosome and give radiation sensitivity to male lung cancers. We found that male lung cancer cells that are resistant to radiation therapy have lost their Y chromosome, losing the expression of these lncRNAs. We are currently developing Artificial Intelligence tools that will predict loss of Y chromosome or linc-SPRY3 RNA expression from images of lung cancer patient tumors.

R&D WORKFLOWS TO ACCELERATE SCIENCE

4:10 pm Current Challenges and Opportunities in Bioinformatics

Mohamed Kassam, Head of Bioinformatics, North America, Zifo Technologies, Inc.

Bioinformatics is a rapidly evolving field in the life sciences, pharmaceutical, and biotech industries, facing challenges in managing big data, integrating/analyzing data, handling data scalability, and in finding the fit- for-purpose resources. However, if harnessed effectively, omics data holds immense potential to revolutionize personalized medicine, spur drug discovery and repurposing, and ultimately enhance healthcare outcomes.

To address these challenges and take advantage of these opportunities, it is crucial to invest in innovative technologies and data management strategies within Bioinformatics.

4:25 pm Lowering NGS Analysis Cost at Lightspeed

Leif Schauser, PhD, Director of Product Management – CLC, QIAGEN Digital Insights

Arguably, the most significant NGS challenges lie within data analysis and interpretation. Many high-speed NGS analysis solutions require purchasing expensive, highly specialized hardware, massive computers, or large cloud computing contracts.  In this presentation we will showcase the QIAGEN CLC LightSpeed module; a flexible software solution which is designed to take your WGS/WES samples and process them in record time while significantly lowering cost, without sacrificing quality.

 

Best of Show Awards Reception in the Exhibit Hall with Poster Viewing4:40 pm

Close of Day6:00 pm

Thursday, May 18

Registration and Morning Coffee7:30 am

PLENARY KEYNOTE PROGRAM

8:00 am

Plenary Keynote Organizer's Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute

Plenary Keynote Sponsor Introduction (Opportunity Available)8:05 am

8:15 am PLENARY PANEL DISCUSSION:

Assessing Innovation: How Pharma Makes Tech Investment Decisions

PANEL MODERATOR:

Aaron Mann, CEO, Clinical Research Data Sharing Alliance

This panel session will assemble senior leaders who evaluate new technology adoption. We will hold an interactive discussion to help provide transparency in the evaluation and decision-making process for assessing and investing in new technologies. Themes we will cover include: 1) process for evaluating, piloting, and scaling new technologies and technology approaches; 2) how an organization evaluates an emerging technology vendor landscape; 3) when and how a formal buying process becomes required, and 4) identifying key stakeholders, decision-makers, and gatekeepers. 

PANELISTS:

April Bingham, Executive Director, Global Medical Compliance and Governance Chapter, Roche

Peter Mesenbrink, PhD, Executive Director, Biostatistics, Novartis Pharmaceuticals

Maria Palombini, Global Practice Leader, Healthcare & Life Sciences, IEEE Standards Association

Laszlo Vasko, Senior Director, Clinical Innovation R&D IT, Janssen Pharmaceuticals, Inc.

Coffee Break in the Exhibit Hall with Poster Viewing9:30 am

Organizer's Remarks10:15 am

BIOINFORMATICS AND DATA-INTENSIVE SCIENCES: BUILDING TECHNOLOGY AND INFRASTRUCTURE FOUNDATIONS FOR GLOBAL GROWTH

10:20 am

Chairperson's Remarks

Ari E. Berman, PhD, CEO, BioTeam, Inc.

10:25 am PANEL DISCUSSION:

African Centers of Excellence in Bioinformatics and Data-Intensive Sciences (ACE): Supporting Novel Science in Africa

PANEL MODERATOR:

Ari E. Berman, PhD, CEO, BioTeam, Inc.

This session will highlight global collaborative efforts in working with the African Centers of Excellence (ACE) in bioinformatics and data-intensive sciences since 2015. Bio-IT World covered this story in February 2021 (https://www.bio-itworld.com/news/2021/02/23/african-centers-of-excellence-in-bioinformatics-and-data-intensive-sciences-building-the-technology-foundations-for-global-growth). Speakers will give us an update about this project and discuss their work to build the technology and infrastructure foundations for sustainable energy systems and constraints involved for achieving global growth.

PANELISTS:

Laura Boykin, PhD, Senior Scientific Consultant, BioTeam, Inc.

Shane Corder, Senior Scientific Consultant, Engineering, BioTeam, Inc.

Daudi Jjingo, PhD, Director, African Center of Excellence in Bioinformatics and Data Science, IDI, Makerere University, Kampala, Uganda

Mike Tartakovsky, CIO, National Institute of Allergy and Infectious Diseases (NIAID)

Christopher J. Whalen, International Program Manager, Cyber Infrastructure & Computational Biology, NIH NIAID

11:55 am Managing the Creative Chaos of the Computational Research Data Lifecycle

Simon Adar, CEO, Code Ocean

Maintaining integrity and traceability of research data through the entire lifecycle of research computation is one of the biggest challenges for R&D teams and the executive level in biopharma. Once primary data leaves the security of a database, the creative scientific process transforms raw data into valuable insights. A new approach guarantees traceability and reproducibility to track the lineage of data and computation from raw data to scientific discovery.

12:25 pm Illumina Complete Long Reads and Population Genotyping at Scale

Jason McCloskey, Amazon Web Services

Rami Mehio, Global Head of Software and Informatics, Illumina

In this session, Rami Mehio, Global Head of Software and Informatics, will discuss two emerging bioinformatics workflows which enable new insights at both the single sample and population scale.

Session Break and Transition to Luncheon Presentation12:55 pm

1:05 pm LUNCHEON PRESENTATION:Investigating Consequences of Nuclear AGO2 in Colon Cancer Model Systems

David Corey, PhD, Professor, Pharmacology & Biochemistry, UT Southwestern Medical Center

We explore Argonaute proteins' binding in human nuclear RNA and its effects on alternative splicing. Our study reveals a novel RNAi mechanism controlling gene expression through splicing, highlighting miRNAs' importance in physiology and disease. Leveraging a state-of-the-art bioinformatics platform, we show how democratizing bioinformatics with reproducible computation, interpretability, and user-friendliness accelerates discovery.

Refreshment Break in the Exhibit Hall with Poster Viewing1:50 pm

STATISTICAL METHODS AND TECHNIQUES TO DEVELOP MEANINGFUL INSIGHTS FROM DATASETS

2:35 pm

Chairperson's Remarks

Matteo Locatelli, Senior Data Analyst, Neurological Clinical Research Institute, Massachusetts General Hospital

2:40 pm

Cost Sensitivity Indexes for Adaptive Platforms in Cancer Care

Christine Huttin, PhD, Professor & CEO, Health Care Technologies & Data Analytics, ENDEPUS Research, Inc. and University Aix Marseille

ENDEPUSresearch, Inc.’s technology specialized in data analytics on economic information interferes with medical decision making processes. For instance, one application leads to the development of cost sensitivity indexes at critical decision points in clinical practices, in conjunction with adaptive platforms, where evidence in development can enhance the decisions. Such decision indexes also need to rely on use of various coding systems especially on diseases (ICD9 codes), drugs (NDC codes), procedures (PCT) and expert coding systems.

3:10 pm

Real-World Data as Control Group

Matteo Locatelli, Senior Data Analyst, Neurological Clinical Research Institute, Massachusetts General Hospital

In clinical research, the gold standard is to use a randomized controlled trial (RCT) to assess the effect of a treatment. Thanks to new technology and the effort of many centers and institutes, the availability of retrospective data about Amyotrophic lateral sclerosis (ALS) is growing. Real World Data and statistics techniques can lead to new ways to assess the effect of medications.

3:40 pm

A Genetic Foundation for Rad-Age Association Supplements a GeroScience Interaction

Nathan Ruprecht, PhD Student, Department of Biomedical Engineering, University of North Dakota

Multiple statistical techniques conducted on publicly available data producing significant findings encompass the intent of bioinformatics. The purpose of our research was to revisit the rad-age associative theory with today’s data availability and computational tools. We explored a radiation-age interaction by combining five different datasets publicly available for secondary analysis by implementing a variety of statistical methods and tests. We used age as a categorical and continuous variable to yield 234 unique genes including 3 that showed statistical differentiation when evaluating lung disease prognosis when including ethnicity and sex. Genes, pathways, and diseases independently associated with radiation exposure and aging processes (such as inflammation, mitochondrial function, and DNA damage/repair) corroborate a dependent association. After attending this presentation, the audience will gain methodology knowledge for employing secondary analysis with varying dataset sizes and platforms, see a genetic foundation for a rad-age association that can indirectly benefit multiple fields of study, and gain statistically significant results that can be used in their own research projects.

Close of Conference4:10 pm






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