Genome Informatics Image

Biological information from genome sequences is derived by the application of computer and statistical techniques. Additionally, protein sequence and structure can be predicted by analyzing DNA sequence information. Tremendous advancements have been made to broaden sequencing applications from research to the clinic, especially as genomics becomes more integrated with precision medicine and AI initiatives. In spite of this, enormous problems still exist with data integration and analysis pipelines and sensitivity to accuracy in diagnosis and/or disease stratification. What is the role of computer science in modeling cells, analyzing and mapping data networks, and incorporating clinical and pathological data to determine how diseases arise from mutations? How do bio-IT approaches help relate SNPs, expression, and disease? What is the role of AI in data curation techniques, text mining approaches, and statistical analytics to discover disease or drug response pathways to identify personalized and focused treatments and cures? Presentations in the Genome Informatics track will explore these issues and how organizations and research teams are implementing computational approaches to understand the biology of genomes for accurate disease diagnosis.

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


4:15 pm Innovative Practices Awards – Winners Spotlight

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. 

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


8:10 am

The Complete Sequence of a Human Genome

Sergey Koren, PhD, Staff Scientist, Genome Informatics, NIH NHGRI

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published initial drafts of the human genome. However, the heterochromatin and many other complex regions were left unfinished or erroneous. The Telomere-to-Telomere (T2T) Consortium has finished the complete sequence of a human genome, including centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome for the first time.

8:40 am

CO-PRESENTATION: COVID & IT: SARS-CoV-2 Genome Analyses and Computational Tools for Infectious Disease Surveillance

Benjamin R. Busby, PhD, Director, Solution Science, DNAnexus
Todd J. Treangen, PhD, Assistant Professor, Computer Science, Rice University

The COVID-19 pandemic has revealed the critical importance of computational approaches for monitoring environmental microbiomes for emerging pathogens, including samples taken from the air, wastewater sites, and built environments. In this workshop we will highlight computational tools that enable rapid and robust global surveillance of infectious disease. The workshop will focus on existing computational approaches for SARS-CoV-2 detection and monitoring, and then address computational strategies for emerging pathogen detection.

9:10 am Coffee Break in the Exhibit Hall with Poster Viewing


10:00 am

WebMeV: An Interactive, Web-Based Bioinformatics Analysis Toolkit

Derrick DeConti, PhD, Research Associate, Biostatistics, Harvard T.H. Chan School of Public Health

WebMeV was designed to address the hurdles present for wet lab scientists using Bioinformatics tools. RNASeq tools and pipelines have become robust and standardized. WebMeV leverages this fact to provide a simple, fully graphical, and interactive web-based solution to Bioinformatic analyses. WebMeV endeavors to be fully transparent and reproducible by having both code and environment open-sourced, portable, and fully reproducible independent of WebMeV with Github and Docker repositories.

George Vacek, PhD, MBA, Global Director, Genomics Alliances, NVIDIA

For precision medicine to become routine, more must be done to understand human genetic variations and how they contribute to diseases and disorders. This requires high-confidence variant catalogues, comprehensive annotations, and approaches to genome-wide analytics that drive new understandings in human biology and medicine. GPU-based parallel processing of sequencing data is now addressing the myriad bottlenecks that occur across the computational workflow. With performance of up to 60x acceleration for state-of-the-art bioinformatics tools and complete end-to-end workflows in under 25 minutes, larger sequencing projects are becoming less expensive, easier to manage, and generating more useful insights than ever before. We will discuss an accelerated analysis solution that includes IT infrastructure requirements to detect and annotate genetic variants.

10:45 am Sponsored Presentation (Opportunity Available)
11:00 am Interactive Discussions (Opportunity Available)
12:15 pm Refreshment Break in the Exhibit Hall with Poster Viewing


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


3:05 pm

Isoform Discovery and Analysis Using PacBio Long-Reads

Frank Zappulla, Systems Analyst, The Jackson Laboratory

We describe the development and maturation of a computational system for using long-read RNA-seq data to first identify novel isoforms in the human genome, then characterize differences in isoform distribution across biological conditions of interest. We focus on architectural features and strategies for enhancing portability, reproducibility, scalability, and reliability. This resource-efficient system maintains substantial flexibility in the way this self-documenting pipeline is executed.

3:35 pm

Micronoma: Using the Microbiome to Detect Early-Stage Cancer (Innovative Practices Awards Winner)

Sandrine Miller-Montgomery, PharmD, PhD, President and CEO, Micronoma Inc.

Micronoma is the only cancer diagnostic company using the microbiome to detect early-stage cancer. As liquid biopsy is fast becoming an important new direction method for cancer diagnostics, early detection remains a challenge that using the cancer microbiome may be able to solve. Micronoma's promising research, published in Nature in 2020, found unique microbial signatures in tissue and blood for most major types of cancer.

4:05 pm Refreshment Break in the Exhibit Hall with Poster Viewing
4:35 pm

Using Probes as a Functional Genomics Tool: Identifying Sources, Comparing Sources, Determining Availability

Christopher Southan, PhD, Competitive Intelligence Analyst, Data Sciences, Medicines Discovery Catapult

There has been a confusing proliferation of probe sources. Probes are increasingly important functional genomics tools but have associated pitfalls. Specific and potent small-molecule chemical probes generate biological insights for understudied proteins and can validate new drug targets. Since the NLP/NIH probes developed between 2005 to 2014 many sources have surfaced new probe structures. However, it has become difficult to know exactly what is available. The Probes & Drugs database (P&D) has collated 4,471 probes from 12 sources, experimentally supported or calculated. This work compares these sources and PubChem intersections. This provides a unique overview of the numbers and highlights unexpected results.

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 (Sponsorship Opportunity) or Morning Coffee

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


9:55 am

Building a Research-Based Bioinformatics Education Program for High School Students

Phillip Compeau, PhD, Associate Teaching Professor, Computational Biology Department, Carnegie Mellon University
Joshua Kangas, PhD, Assistant Teaching Professor, Carnegie Mellon University

The Pre-College Program in Computational Biology ( computational-biology/) is a three-week summer educational program in computational biology designed for students in high school. Students in the program collect water samples from multiple locations in Pittsburgh's three rivers, perform wet-lab experiments to capture data from their samples, and write algorithms to analyze the resulting data. We discuss this program, the results of our students' work, and our pivot to online delivery in 2020 and 2021.

10:25 am

The Metagenomics Education Partnership: Harnessing the Power of Microbial Genome Sequencing and Big Data with High School Students and Teachers

Stephen Koury, PhD, Research Associate Professor, Department of Biotechnical and Clinical Laboratory Sciences, University at Buffalo

The implementation of Oxford Nanopore sequencing by high school students and teachers to determine the composition of the microbial communities present in waterways of Western New York in the NIH SEPA funded Metagenomics Education Partnership will be discussed. Topics covered will include project goals, the development of SOPs by graduate students, and the first implementation of teacher professional development training that took place in the summer of 2021. Included will be water collection methods, DNA extraction from filters for metagenomic sequencing, DNA extraction for whole genome sequencing and initial metagenomic results using Flongle flow cells to perform sequencing.

10:55 am

Broadening Participation in Data Science and Genomics through High School and Undergraduate Internship Programs

David Boone, PhD, Director, Hillman Academy; Assistant Professor of Biomedical Informatics, University of Pittsburgh School of Medicine

The University of Pittsburgh’s Hillman Academy and Internship Program for Biomedical Research, Informatics, and Computer Science (iBRIC) pathway programs have provided 8-10 week authentic and mentored research experiences in data science to hundreds of high school and undergraduate students from underrepresented groups for over a decade. In this talk, we will discuss the structure, student outcomes, and opportunities for collaboration and expansion.

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



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:

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


4:35 pm

Genomics for Preventive Health: Case Studies from Singapore and the UK

Nardev Ramanathan, PhD, Senior Analyst, Lux Research

The promise of genomics in preventive health has often made headlines – yet there have been few practical applications in healthcare delivery to date. In this talk, I will share some early use cases from Singapore and the U.K. that are starting to leverage genomic information to identify risk factors and subsequently recommend early medical intervention. This approach could potentially improve health outcomes and reduce healthcare costs.

5:05 pm

Patient-Centric Precision Genomics

Ardy Arianpour, CEO & Co-Founder, Seqster
5:35 pm Close of Conference

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