Seattle, Washington, United States
Dave is currently a Biotech consultant. Previously, he was at NanoString, and before VP/Head of R&D at Mission Bio, awarded Science fellowships including a Senior Research Fellow at Oxford University and an academic appointment as a Fellow at Worcester College. At Oxford, he developed CRISPR/cas9 strategies, multiomics and single-molecule DNA detection. Dave also provided career/entrepreneurship mentoring to Oxford postdocs/Ph.D students. Before Dave began his research fellowships, he was the global leader and PI/collaboration scientist at Fluidigm. These scientific endeavors innovated and advanced multimodal and chromatin interrogation using single-cell samples and workflows. Prior to Fluidigm, Dave spent 17 years innovating and developing the first qPCR technology (TaqMan/SYBR Green, ABI 7700 platform), human genome/transcriptome discovery, NGS technologies at Applied Biosystems/Life Technologies. He was team leader in single-cell analysis, Ion Torrent Ampliseq &Avalanche, multiomics, qPCR genomic assays/chemistry, multiplex preamplification, protein quantification (Proximity Ligation Assay), NGS library preparation, nucleic acid sample-prep processes for ccf nucleic acids and blood collection tubes. Prior to ABI, he was research scientist at several early-stage/startup Pharma and cell therapy biotech companies in California, including five years when Amgen was beginning. He received his undergraduate instruction in biochemistry at University of California, Riverside and graduate training in molecular biology at Caltech. Dave has coauthored numerous journal articles, book chapters, patents and serves on the Editorial Board of the Elsevier Journal Biomolecular Detection and Quantification. Sampling of Papers (2015-2022) Single-cell chromatin accessibility reveals principles of regulatory variation, Buenrostro Nature 2015 Joint Profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia, Demaree Nature Communications 2021 High throughput single-cell detection of multiplex CRISPR-edited gene modifications, ten Hacken Genome Biology 2020 Concurrent single cell RNA and targeted DNA sequencing on an automated platform for co-measurement of genomic and transcriptomic signatures, Li Kong Clin Chem 2019 Simultaneous DNA, RNA, and Protein Analysis from Single Cells Using a High-Throughput Microfluidic Workflow for Resolution of Genotype-to-Phenotype Modalities, Dhingra Methods Mol Biol 2022 Simultaneous Targeted Detection of Proteins and RNAs in Single Cells, Ooi Single Cell Immunology: Springer Press 2019
Available for Large Multi-Month Projects, Retainer and By-the-Hour for Smaller Projects. Confidential Consulting for: Technology, Science, Research and Leadership Teams, IP Topics and, Investment Strategies and Diligence. Systems Biology, Quantitative Biology, Multimodal and Single-Cell Technologies, Next-generation Proteomics, Epigenomics, Precision Medicine in Cancer and Immunology. Active contributor to global expert network consulting organizations. And Consulting Associate of Business Talent Group, LLC (BTG).
Spatial transcriptomics and spatial multiomic technologies. Team Leader for Nanostring's R&D Innovation Group. Examples of Innovation Team work presented at conferences in 2023: AGBT 2023, Florida USA, February 6-9, 2023 Path to the Holy Grail of Spatial Biology: Spatial Single Cell Whole Transcriptomes using Ultra-High Plex Spatial Molecular Imaging Joseph Beechem, Jose Ceja Navarro, Nathan Dunaway, Ashley Heck, Rustem Khafizov, Andrew Klock, Rachel Liu, Joseph Phan, Erin Piazza, Zachary Reitz, Michael Rhodes, David Ruff, Max Walter, Lidan Wu, Kimberly Young This work describes 6000-plex spatial RNA imaging Single-cell Genomics Conference 2023 (scg2023), Engelberg Switzerland, October 9-11, 2023 Ultra high-plex in situ proteogenomic interrogation of human brain sections with spatial molecular imaging Ashley Heck, Kimberly Young, Alyssa Rosenbloom, Aster Wardhani, Max Walter, Giang Ong, Rustem Khafizov, Mithra Korukonda, Zachary Lewis, Tien Phan-Everson, Shilah A. Bonnett, Claire Williams, Patrick Danaher, Rachel Liu, Jose Ceja Navarro, Christine Kang, Jason Reeves, Gary Geiss, David W. Ruff, Joseph M. Beechem Here, we demonstrate the “proteogenomic” capability of the CosMx™ Spatial Molecular Imager (SMI), a single-cell spatial biology platform that leverages in situ hybridization chemistry to enable ultra high-plex detection of RNAs and proteins at subcellular resolution. In this proteogenomic system, over 60 proteins and 6,000 RNAs are targeted on the same FFPE human brain section, delivering highly quantitative results. The target proteins focus on neural cell typing and neurodegenerative disease pathology (including amyloid precursor protein, amyloid beta, and phosphorylated tau variants).
Primary activities in Next-Generation Proteomics. Also Systems Biology, Quantitative Biology, Multimodal and Single-Cell Technologies, Precision Medicine in Cancer and Immunology. Consulting Associate of Business Talent Group, LLC (BTG).
Updated June 2019 CYTO 2019, June 22-26, Vancouver, Canada Combined high-throughput single-cell DNA genotyping and protein quantification B Demaree, C Delley,D Dhingra,D Ruff,K Jones, D Eastburn,A Abate LifeTime Research Conference, Berlin Germany, May 6-7, 2019 High-throughput Single-cell Targeted DNA Sequencing from Tumor and Metastatic Samples Reveal Spatial Resolution of Routes to Clonal Propagation A Ooi ,P Mendez,D Dhingra,N Li,N Beard,DRUFF Podium Presentations (and conference co-chairperson) qPCR/NGS 2019, Technical University of Munich, Freising, March 18, 2019 High-throughput Single-cell Targeted DNA Sequencing from Tumor and Metastatic Samples Reveal Spatial Resolution of Evolutionary Trajectory Routes to Clonal Propagation AACR, March 31-April 3, 2019 High-throughput single-cell targeted DNA sequencing from frozen, fixed and preserved solid tumor samples reveals complex genomic variation and clonal propagation, Poster #2532 P Mendez,D Mendoza,N Li,A Sciambi,K Gokhale, D Dhingra,K Jones, D Eastburn,D Ruff A complete solution for high throughput single cell targeted multiomic DNA and RNA sequencing for cancer research, Poster #3540 D Dhingra, P Mendez, S Wang, S Sahu, M Manivannan, A Ooi, K Gokhale, N Li, A Sciambi, K Jones, C Silver, D Eastburn, D Ruff Combined high-throughput DNA genotyping and protein quantification in single cancer cells, Poster #3527 B Demaree,C Delley,D Ruff,S Treusch,D Eastburn, K Jones,A Abate AGBT 2019, Marco Island, FL High-throughput universal workflow to prepare single-nuclei provides for high quality precision genomic analysis from cryopreserved tissue samples P Mendez,D Mendoza,N Li,A Sciambi,K Gokhale, A Parikh,H Viernes,K Jones,C Silver, D Ruff Single Cell Biology – Keystone Symposia, January 13-17, 2019 Breckenridge, CO Enabling high-throughput single-nuclei DNA sequencing from cryopreserved tumors with a simple protocol P Mendez,D Mendoza,N Li,A Sciambi,K Gokhale,K Jones,D Eastburn,D Ruff
Led R&D team to develop MagicPrep automated RNA-seq chemistry and move process to a Tecan platform (company was subsequently acquired by Tecan in summer 2018). Innovated novel RNA sample prep for RNA-seq library construction workflows and multiomic NGS sequencing (DNA and RNA). WO Patents filed.