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2023 Advances in Genomic Technology Development Annual Meeting

Event Details

The Advances in Genomic Technology Development (AGTD) 2023 Annual Meeting was hosted by the Technology Development Coordinating Center (TDCC) in-person and virtually from Tuesday, June 6, until Thursday, June 8, at The Sanford Consortium for Regenerative Medicine, La Jolla, CA. The purpose of the meeting was to provide an open forum for NHGRI Genome Technology Development Program grantees to discuss key scientific and technical challenges faced with advanced sequencing, genomic, and synthetic nucleic acid technologies and to promote collaboration.

All times in Pacific Standard Time.

to

Virtual and In-Person
Sanford Consortium for Regenerative Medicine

880 Torrey Pines Scenic Dr.
La Jolla, CA 92037

Tuesday, June 6, 2023

 

Time Topic Speaker
8:30 a.m. Welcome and Introduction

Mark Adams, Ph.D.
The Jackson Laboratory

Carolyn Hutter, Ph.D.
NHGRI

Stephanie Morris, Ph.D.
NHGRI
Genome Technologies: Protein-DNA Interactions
Session Moderators: Michal Rozenwald, University of California, Berkeley and Jingtian Zhou, Salk Institute for Biological Studies
8:45 a.m. STAMPing RNA binding protein-RNA networks Gene Yeo, Ph.D., MBA
University of California, San Diego
9:00 a.m. Single-cell and single-molecule profiling of protein-DNA interactions by MACHA Sebastian Pott, Ph.D.
The University of Chicago
9:15 a.m. Mapping protein-DNA interactions on single molecules with DiMeLo-seq Jeremy Marcus
University of California, Berkeley
Genome Technologies: Genome-wide Methods
Session Moderators: Sonya Rozenblat, University of Michigan and Vishnu Sunitha Kumary, Ph.D., Epicypher, Inc.
9:30 a.m. Opportunity Fund Update: Programmable Eukaryotic Protein Expression with RNA Sensors Omar Abudayyeh, Ph.D. 
Massachusetts Institute of Technology
9:45 a.m. Multiplex Genomic Recording of Enhancer and Signal Transduction Activities in Mammalian Cells Wei Chen, Ph.D.
University of Washington
10:00 a.m. A Novel Approach for Studying RBP-RNA and RBP-RBP Interactions at Isoform and Single-Molecule Resolution Pratibha Jagannatha 
University of California, San Diego
10:30 a.m. Define the Phenotypic Landscape of Essential Human Genes with Image-Based Pooled Genomic Screens Paul Blainey, Ph.D.
Broad Institute of MIT and Harvard
10:45 a.m.

Chromosome conformation mapping using transposable phage Mu

 Peter Freddolino, Ph.D.
University of Michigan
11:00 a.m.

Concomitant DNA/RNA next-sequencing library preparation from low abundance inputs using a single-reaction ligation approach

 Varsha Rao, Ph.D.
Claret Bioscience
11:15 a.m.

Quantitative fate mapping: Reconstructing progenitor field dynamics using lineage barcoding

 Reza Kalhor, Ph.D.
Johns Hopkins University
11:30 a.m.

Versatile, exponentially scalable methods for single cell molecular profiling

 Jean-Benoît Lalanne, Ph.D.,
University of Washington
11:45 a.m. Morning Session Wrap-up and Q&A
12:00 p.m. Buffet Lunch - Topic-Based Seating
1:00 p.m.

Keynote: Enhancing genome and transcriptome engineering: new approaches, new challenges

 Prashant Mali, Ph.D.
University of California, San Diego
2023 Common Fund Previews
2:00 p.m.

Hanna Liao, University of Washington presents:
Jay Shendure, Ph.D., University of Washington; Maksim Royzen, Ph.D., SUNY Albany; Ya-Ming Hou, Ph.D., Thomas Jefferson University; and Marija Drndic, Ph.D., University of Pennsylvania

Hugo Medina-Muñoz, Ph.D., UC, San Diego presents:
Gene Yeo, Ph.D., MBA, University of California, San Diego and Rahul Kohli, M.D., Ph.D., University of Pennsylvania

Joanne Yeakley, Ph.D., BioSpyder Technologies, Inc. presents:
Bruce Seligmann, Ph.D., BioSpyder Technologies, Inc. and Yang Liu, Ph.D., Yale University
2:30 p.m. Coffee Break
Single-Molecule Protein Sequencing
Session Moderator: Keisuke Motone, Ph.D., University of Washington
2:50 p.m.

Towards high accuracy nanopore sequencing of DNA and peptides with MspA

 Jens Gundlach, Ph.D.
University of Washington
3:05 p.m. Going with the flow: Engineering an electroosmotic flow to transport unfolded proteins against an electroosmotic force Giovanni Maglia, Ph.D.
University of Groningen
3:20 p.m. Progress towards long-read single-molecule protein sequencing on an array of unfoldase-coupled nanopores Jeff Nivala, Ph.D.
University of Washington
3:35 p.m. Single molecule oligopeptide fingerprinting based on templated self-assembly of oligonucleotide structures Henry Hess, Ph.D.
Columbia University
3:50 p.m. Structural profiling of native proteins using fluorosequencing, a single molecule protein sequencing technology Jagannath Swaminathan, Ph.D.
University of Texas at Austin, Erisyon, Inc.
Flash Talks and Poster Previews
4:00 p.m.

Evan Boyle, Ph.D., University of California, San Diego
Qishan (Lisa) Liang, University of California, San Diego
Christopher Thomas, University of Washington
Jonathan Craig, Ph.D., University of Washington
Amr Makamreh, Northeastern University
Hyeon-Jin Kim, University of Washington
Daphne Kontogiorgos-Heintz, University of Washington
Allison Hickman, Ph.D., EpiCypher, Inc.
Qi Qiu, Ph.D., University of Pennsylvania
Yue (May) Wu, Salk Institute for Biological Studies
Ignas Mazelis, Harvard University
Autum Koenigs, Harvard University
4:35 p.m. Poster Session
6:00 p.m. Group Dinner

Wednesday, June 7, 2023

 

Time Topic Speaker
8:30 a.m.

Keynote: Global insights into RNA nucleotide variants, isoforms and stability

 Xinshu (Grace) Xiao, Ph.D.,
University of California, Los Angeles
Flash Talks and Poster Previews
9:30 a.m.

Hope Eden, Johns Hopkins University
Min Cheol Kim, University of California, San Francisco
Po-Hsiang Hung, Ph.D., Stanford University
Raeline Valbuena, Stanford University
Caroline McCormick, Northeastern University
Oleksandra Fanari, Northeastern University
Han Wan, Yale University
Miao Liu, Yale University
Paul Hook, Ph.D., Johns Hopkins University
Antonio Vela Gärtner, New York University Langone Health
Zhuoyu Zhang, Northeastern University
10:00 a.m. Coffee Break
Local Experts Introduction and Discussion
Session Moderators: Mark Adams, Ph.D., The Jackson Laboratory and Gene Yeo, Ph.D., MBA, University of California, San Diego
10:30 a.m.

Fernando Aleman, Ph.D., Navega Therapeutics
Aaron Parker, Ph.D., J.D., Bristol Myers Squibb
Ranjan Batra, Ph.D., Locanabio, Inc.
Holly Chrzanowski Winter, MS, Locanabio, Inc.              
Stephanie Dusaban Gonzales, Ph.D., Goodwin
Katannya Kapeli, Ph.D., Trotana Therapeutics
aclyn Einstein, Ph.D., Trotana Therapeutics
Sergio Duron Ph.D., Enlaza Therapeutics
Adam Mullick, Ph.D., Ionis Pharmaceuticals, Inc.
12:10 p.m. Buffet Lunch
1:15 p.m. Poster Session
Genome Technologies
Session Moderators: Pratibha Jagannatha, University of California, San Diego Shawn Cai, Stanford University
2:45 p.m.

High-throughput identification and characterization of human and viral transcriptional activation and repression domains

 Lacramioara Bintu, Ph.D.
Stanford University
3:00 p.m. Harnessing the template switching activity of MarathonRT for quantitative detection of low abundance RNA in RNA-seq and single-cell applications | Li-Tao Guo, Ph.D.
Yale University
3:15 p.m. Finding Clipped Tails: Developing an innovative NGS approach to discover the specific loci targeted for histone H3 N-terminal tail proteolysis Benjamin Weekley
University of Southern California
3:30 p.m. A genome-integrated reporter assay for systemic interrogation of long-range enhancer-promoter interactions Yawei Wu
Washington University in St. Louis
3:45 p.m.

Targets and functions of the mammalian snoRNAome

 Tao Pan, Ph.D.
University of Chicago
4:00 p.m.

Rapid exploration of combinatorial protein design to identify enhanced CRISPR activators

 Marley Giddens
Columbia University
4:15 p.m. Coffee Break
4:30 p.m.

Keynote: Protein design using deep learning

 David Baker, Ph.D.
University of Washington
Panel Discussion: Strategies for Commercialization
3:10 p.m. Jenny Rooke, Ph.D., Genoa Ventures
Michael Keogh, Ph.D., EpiCypher
Eric Ervin, Ph.D., Electronic Biosciences
Winston Timp, Ph.D., Johns Hopkins University
4:30 p.m. Poster Session
6:00 p.m. Group Dinner

 

Thursday, June 8, 2023

 

Time Topic Speaker
Sequencing Technology Development
Session Moderator: Joonwon Kim, Ph.D., University of California, San Diego
8:30 a.m.

Electro-optical zero-mode waveguides

 Meni Wanunu, Ph.D.
Northeastern University
8:45 a.m.

Controlled Translocation Through Biological Nanopore Readers

 Anna Schibel, Ph.D.
Electronic Biosciences
9:00 a.m.

Improving biological nanopores for precision nucleic acid sequencing using a computational microscope

 Jingqian Liu
University of Illinois Urbana-Champaign
9:15 a.m. Single molecule DNA/RNA sequencing technology based on parallel Raman scattering readout in a coupled nanochannel/nanopore system Steven Brueck, Ph.D.
Armonica Technologies
Synthetic Nucleic Acid Synthesis Technology
Session Moderator: Beatrice Adelizzi, Ph.D., DNA Script
9:30 a.m. EChemical synthesis and non-chromatographic purification of long RNA oligonucleotides containing naturally occuring modifications Maksim Royzen, Ph.D.
SUNY Albany
10:30 a.m.

Architect Directed DNA Synthesis

 Adim Moreb, Ph.D.
Duke University
10:30 a.m. Coffee Break
GREGoR Consortium
10:45 a.m. GREGoR Presentation Matt Wheeler, M.D., Ph.D.
Stanford University
NHGRI Programs
Session Moderators: Vishnu Udayakumaran Nair Sunitha Kumary, Ph.D., EpiCypher and Clarice Hong, Washington University in St. Louis
11:00 a.m.

Carolyn Hutter, Ph.D., NHGRI
Stephanie Morris, Ph.D., NHGRI
Temesgen Fufa, Ph.D., NHGRI
Katie Bardsley, NHGRI
12:00 p.m. Buffet Lunch

Sequencing: DNA and RNA Modifications
Session Moderators: Sepideh Tavakoli, Northeastern University and Yvonne Yee, Northeastern University
1:00 p.m.

Novel chemical probes for sequencing multiple DNA modifications                       

 Linlin Zhao, Ph.D.
University of California, Riverside
1:15 p.m.

METHYL-SENTRY: Feasibility study of a nanopore diagnostic tool to detect hypermethylated biomarkers

 Ariel Pearson
Goeppert, LLC.
1:30 p.m. Multiplexed Detection of RNA Modifications Gudrun Stengel, Ph.D.
Alida Biosciences
1:45 p.m. Single RNA-level analysis of full-length HIV-1 RNAs reveals functional redundancy of N6-methyladenosine modifications Sanggu Kim, Ph.D.
Ohio State University
2:00 p.m. Progress toward large-scale de novo direct RNA sequencing using mass spectrometry Shenglong Zhang, Ph.D.
New York Institute of Technology
2:15 p.m.

Single-molecule detection and quantification of pseudouridine in the human transcriptome

 Sara Rouhanifard, Ph.D.
Northeastern University
2:30 p.m. Morning and Afternoon Session Wrap-up and Q&A
2:45 p.m. Coffee Break
Wrap-up and Future Directions
3:00 p.m. Feedback and Future Directions
4:00 p.m. Closing Remarks Mark Adams, Ph.D.
The Jackson Laboratory

Last updated: August 17, 2023