2024 Advances in Genomic Technology Development Annual Meeting

9:30 AM – 12:00 PM: Small BusinessInnovation Research Experiential Learning (In-person only)

• TEM-seq: Ultrasensitive multi-omic platform using epitope-targeted DNA methylation mapping
  EpiCypher, Inc.
   
• The accessible epitranscriptome: how anyone can include RNA modifications in their research
  Alida Biosciences, Inc.

12:00 – 1:00 PM: Lunch and Small Business Innovation Research (SBIR) Expo

1:00 – 2:30 PM: Emerging Technologies for Understanding Human Genome Functions

• Chromatin Structure and Gene Regulation
  Lacra Bintu, Stanford University
   
• Imaging 3D Genome
  Siyuan (Steven) Wang, Yale University
   
• Towards a Comprehensive Functional Map of Human Protein-RNA Interactions 
  Brent Graveley, University of Connecticut 
   
• Scalable investigation of gene functions in vivo
  Xin Jin, Scripps Research 

2:30 – 3:00 PM: Break and SBIR Expo

3:00 – 4:30 PM ET: Emerging Technologies for Making and Sequencing DNA and RNA 

• Expanding studies of genomic diversity with complete, telomere-to-telomere (T2T) assemblies
  Karen Miga, University of California, Santa Cruz 
   
• Synthetic Biology
  Jef Boeke, NYU Langone Medical 
   
• Synthetic Genetic Systems. A New Frontier in Genomic Research 
  Steven Benner, Foundation for Applied Molecular Evolution 
   
• Investigating epitranscriptomes by sequencing
  Tao Pan, University of Chicago 

4:30 – 4:45 PM: Break

4:45 – 5:30 PM: Keynote Address 

Stacey Gabriel
Broad Institute

5:30 PM: Reception and SBIR Expo

9:00 AM: Welcome and Introduction 

Mark Adams, Ph.D., The Jackson Laboratory 
Stephanie Morris, Ph.D., National Human Genome Research Institute

Session 1 – Genome Technologies: Protein Interactions and DNA and RNA

9:15 AM: Photoactivable DNA binding molecules for Protein-DNA crosslinking

Lin Chen, Ph.D.
University of Southern California (Abstract #6)

9:30 AM: ChIP-DIP: A multiplexed method for mapping proteins to DNA uncovers combinatorics controlling gene expression

Andrew Perez
California Institute of Technology (Abstract #13)

9:45 AM: Decoding global RNP topologies in splicing regulation 

Zhipeng Lu, Ph.D.,
University of Southern California (Abstract #19)

10:00 AM: SpliceRUSH: an exon-centric screening platform for proximal and distal splicing-regulatory elements in a native sequence context 

Chaolin Zhang, Ph.D.
Columbia University (Abstract #35)

10:15 AM: INSCRIBE: High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues 

Gene Yeo, Ph.D., MBA 
University of California, San Diego (Abstract #103)

10:30 AM: Break

11:00 AM: Keynote: New genomic methods to study nucleic acids and RNA-binding proteins

Chuan He, Ph.D.
The University of Chicago

12:00 PM: Lunch: Topic-based seating

1:00 PM: Innovative Molecular Analysis Technologies (IMAT) 

Kelly Crotty Ph.D.
Director of IMAT, National Cancer Institute

Session 2 – Spatial 'Omics

1:15 PM: Slide-tags: Single-nucleus high-resolution multi-modal spatial genomics 

Andrew J.C. Russell, Ph.D.
Broad Institute of Harvard and MIT (Abstract #4)

1:30 PM: DNA-optical barcoding technology for spatiotemporal single-cell analysis

Marissa Fahlberg, Ph.D.
LASE Innovation (Abstract #17)

1:45 PM: A multiplex in situ method to study the combinatorial code of epigenetic marks in single cells

Yanbo Chen
Yale University (Abstract #34)

2:00 PM: Development of multi-color 3D super-localization liveFISH and liveFISH PAINT to investigate the chromatin dynamics at any genomic scale

Yanyu Zhu, Ph.D.
Stanford University (Abstract #24)

2:15 PM: A single plasmid system for multiplexed CRISPR gene tagging in induced pluripotent stem cells

Oscar Perez-Leal, M.D.
Temple University (Abstract #22)

2:30 PM: Break

2:50 PM: Flash Talks - 2-minute poster previews from staff/trainee abstracts

Breakout Session - Refer to the pre-meeting survey to select your top 2

4:30 PM: Poster Session 1: Abstracts 1-49

Session 3 – Single-Molecule Protein Sequencing

9:00 AM: Progress towards long-read single-molecule nanopore protein sequencing using unfoldase motors

Jeff Nivala, Ph.D.
University of Washington (Abstract #69)

9:15 AM: Engineered nanopores for single-molecule protein sequencing

Andrea Bonini, Ph.D.
University of Groningen (Abstract #67)

9:30 AM: Molecular determinants of current blockade produced by peptide transport through a nanopore

Jingqian Liu
University of Illinois Urbana Champaign (Abstract #79)

9:45 AM: Nanopore optimization for direct, single-molecule protein sequencing

Eric Peterson, Ph.D.
Electronic Biosciences, Inc. (Abstract #55)

10:00 AM: Chemical tools to uncover hidden proteome

Monika Raj, Ph.D.
Emory University (Abstract #72)

10:15 AM: Photo-fragmentation methods for single-molecule protein sequencing by nanopore mass spectrometry 

Derek Stein, Ph.D.
Brown University (Abstract #77)

10:30 AM: Break

11:00 AM: Commercialization Panel Discussion

Moderators: 

• Ian Nova, Ph.D., NHGRI 
• Mostafa Analoui, Ph.D., Quinnipiac University 

Panelists:

• Evan Macosko, M.D., Ph.D., representing Curio Biosciences 
• Omar Abudayyeh, Ph.D., representing Tome Biosciences 
• Sasha Levy, Ph.D., representing BacStitch DNA, Inc. 
• Anna Marie Pyle, Ph.D., representing RNAConnect, Inc. 
• Shenglong Zhang, Ph.D., representing DirectSeq Biosciences, Inc.

12:30 PM: Buffet Lunch

Session 4 – Synthetic Nucleic Acid Synthesis

1:30 PM: Towards High-throughput BIG DNA Writing

Antonio Vela Gartner
NYU Langone Health (Abstract #2)

1:45 PM: Scalable DNA engineering by mating bacteria in arrays and pools

Sasha Levy, Ph.D.
BacStitch DNA, Inc. (Abstract #18)

2:00 PM: Generating sequence variants by templated gene synthesis

Harris Wang, Ph.D.
Columbia University (Abstract #33)

2:15 PM: Progress towards a low-cost benchtop inkjet enzymatic DNA synthesizer

Damiano Verardo, Ph.D.
DNA Script (Abstract #62)

2:30 PM: Development of Genome-Build as a universal method to synthesize genomes 

Christopher Warren, Ph.D.
Proteovista (Abstract #80)

2:45 PM: Flash Talks – 2-minute poster previews invited from staff/trainee abstracts

3:10 PM: Break

3:30 PM: Keynote: A Tale of 2 Strands: From Genomics to Origami, Vaccines, Data Storage and Back

Mark Bathe, Ph.D.
Massachusetts Institute of Technology

4:30 PM: Poster Session 2: Abstracts 50-98

Session 5 – Sequencing Technology Development

9:00 AM: High accuracy nanopore sequencing

Andrew Laszlo, Ph.D.
University of Washington (Abstract #60)

9:15 AM: Navigating the pitfalls of long-read based DNA modification detection 

Gang Fang, Ph.D.
Icahn School of Medicine at Mount Sinai (Abstract #10)

9:30 AM: Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

Karen Miga, Ph.D.
University of California, Santa Cruz (Abstract #68)

9:45 AM: Measuring the epigenome with nanopore sequencing

Winston Timp, Ph.D.
Johns Hopkins University (Abstract #78)

10:00 AM: Psi modification profiling and dynamics in the human transcriptome 

Sara Rouhanifard Ph.D.
Northeastern University (Abstract #73)

10:15 AM: Break

Session 6 – 2024 Opportunity Fund Previews

10:30 AM: Transfer RNA epitranscriptome by multi-target sequencing and top-down mass spectrometry
Shenglong Zhang, Ph.D., New York Institute of Technology 
Tao Pan, Ph.D., University of Chicago 

High-throughput interrogation of transcription factor binding within the mammalian brain
Bing Ren, Ph.D., University of California, San Diego 
Alejandro Chavez, Ph.D., University of California, San Diego 

Transliteration of a 8 base alphabet into 4 bases in eukaryotic cells
Steven Benner, Ph.D., Foundation for Applied Molecular Evolution 
Jef Boeke, Ph.D., NYU Langone Health 

Imaging-free spatial transcriptomics
Fei Chen, Ph.D., Broad Institute of Harvard and MIT 
Evan Macosko, M.D., Ph.D., Broad Institute of Harvard and MIT

11:00 AM: Keynote: New machine learning models for single-cell and regulatory genomics

Christina Leslie, Ph.D.
Memorial Sloan Kettering Cancer Center

12:00 AM: Buffet Lunch

Session 7 – Single-Cell Genomics and Chromatin Structure

1:00 PM: A novel flexible approach for high-throughput single-cell phenotyping and genotyping

Magali Soumillon Ph.D.
Flexomics (Abstract #29)

1:15 PM: Single-cell massively parallel reporter gene assays (scMPRA)

Barak Cohen, Ph.D.
Washington University in St. Louis (Abstract #7)

1:30 PM: Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development

Xin Jin, Ph.D.
Scripps Research (Abstract #64)

1:45 PM: High-throughput measurements of gene expression and chromatin state changes upon targeted gene activation

Lacra Bintu, Ph.D.
Stanford University (Abstract #1)

2:00 pm TEM-seq: An ultrasensitive, multi-omic method that directly links chromatin features to DNA methylation

Bryan Venters, Ph.D.
EpiCypher, Inc. (Abstract #14)

2:15 PM: Genomic sequence context and histone marks regulate pioneer binding to nucleosomes

Martha Bulyk, Ph.D.
Brigham and Women’s Hospital and Harvard Medical School (Abstract #3)

2:30 PM: Break

Session 8 – Wrap-up and Future Directions

2:50 PM: Breakout session wrap-up and TDCC Future Directions

Mark Adams, Ph.D., The Jackson Laboratory 
Stephanie Morris, Ph.D., NHGRI

3:50 PM: Adjourn