Funded Research

The Single Cell Analysis Program (SCAP) has transitioned from Common Fund support in 2017. For more information, please visit https://commonfund.nih.gov/singlecell/. Please note that since SCAP is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.

Development of Highly Innovative Tools and Technology for Analysis of Single Cells (SBIR) (R43/R44) PA-13-140
PI Name	Institution Name	Title
BELL, CALEB B (contact) RUTT, BRIAN KEITH	BELL BIOSYSTEMS, INC.	Single Cell Spatiotemporal and Functional Reporting using Magneto-Endosymbionts
DOBES, NICHOLAS CARL	CELL MICROSYSTEMS, INC.	CellRaft Arrays for Single-cell PCR
HEYMAN, JOHN A	SPHEREBIO, INC.	Droplet-based Analysis of Secretion and Sorting (DASS) for characterization and selection of individual immune cells
HUANG, CHANGJIN	INFINITESIMAL, LLC	High-Throughput Microdevice for Temporal Single-Cell Analysis
SCOUTEN, CHARLES WILLIAM (contact) SCHWEIZER, FELIX SUN, YING	ROKHAN, LLC	Cellular Capacitance Monitoring Integration into Digital Patch Clamp Amplifier
YEAKLEY, JOANNE MULLIGAN	BIOSPYDER TECHNOLOGIES, INC.	Multiplexed mRNA and miRNA Profiling of Single Cells

Revisions to Add Single Cell Analysis to Active Research Projects (U01) RFA-RM-13-023
PI Name	Institution Name	Title
FRAZER, KELLY A (contact) CHI, NEIL C EVANS, SYLVIA M YEO, EUGENE WEI-MING ZHANG, KUN	UNIVERSITY OF CALIFORNIA SAN DIEGO	Regulatory Genomic Studies in a Cohort of IPS Cell Derived Cardiomyocytes

Revisions to Add Single Cell Analysis to Active Research Projects (R01) RFA-RM-13-022
PI Name	Institution Name	Title
CHANG, JOHN T	UNIVERSITY OF CALIFORNIA SAN DIEGO	Regulation and Function of Polarity and Asymmetric Cell Division in Immunity
CHEN, C CASEY	UNIVERSITY OF SOUTHERN CALIFORNIA	Novel clone-specific virulence determinants of A. actinomycetemcomitans
KRAUSE, DIANE S	YALE UNIVERSITY	Mechanisms of megakaryocyte maturation
RAO, DINESH S	UNIVERSITY OF CALIFORNIA LOS ANGELES	Characterizing tumor suppressive functions of microRNAs in B-cell neoplasia
ROTHENBERG, ELLEN V. (contact) CAI, LONG	CALIFORNIA INSTITUTE OF TECHNOLOGY	Genomic site binding rules and regulatory factor function in developing T cells
SHIVDASANI, RAMESH A	DANA-FARBER CANCER INST	Multidimensional characterization of RNAs and signals in single intestinal cells
TENEN, DANIEL G	BETH ISRAEL DEACONESS MEDICAL CENTER	Molecular biology of myeloid differentiation
WU, CATHERINE JU-YING	DANA-FARBER CANCER INST	Personal tumor neoantigens for immunity against chronic lymphocytic leukemia

Exceptionally Innovative Tools and Technologies for Single Cell Analysis (R21) RFA-RM-13-021
PI Name	Institution Name	Title
CAI, DAWEN (contact) YE, BING	UNIVERSITY OF MICHIGAN	MACS: A genetic labeling tool to depict the complete neuroblast lineage of all neurons in individual Drosophila brains
CHENG, JI-XIN	PURDUE UNIVERSITY WEST LAFAYETTE	Microsecond Raman spectroscopy: Assessing single cell metabolism in a vital organism
GARTNER, ZEV JORDAN	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	Identifying the intercellular networks regulating estrogen receptor expression with a high definition single cell printer
NEMES, PETER	GEORGE WASHINGTON UNIVERSITY	In Situ Optoguided Microsampling Single-cell Mass Spectrometry for Elucidating Cell Heterogeneity
PARANT, JOHN M	UNIVERSITY OF ALABAMA AT BIRMINGHAM	Light-Induced Genetic Alterations within Single Cell of a Live Vertebrate Animal
PERRIMON, NORBERT	HARVARD MEDICAL SCHOOL	Innovative reporters to characterize heterogeneous states among cells
PRATX, GUILLEM	STANFORD UNIVERSITY	Real-time tracking of single cells in live animals
ZARE, RICHARD N	STANFORD UNIVERSITY	High Spatiotemporal Resolution Mass Spectrometry for Single Cell Analysis

Validation and Advanced Development of Technologies for the Study of Biological Properties of Single Cells (R33) RFA-RM-13-020
PI Name	Institution Name	Title
HOLLEY, SCOTT A	YALE UNIVERSITY	Quantification and modeling of the emergence of tissue-level mechanics from individual cell heterogeneity
HUANG, BO	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	Analyzing genomic elements in live animals by CRISPR imaging
HUANG, TONY JUN	PENNSYLVANIA STATE UNIVERSITY-UNIV PARK	Validation of acoustic tweezers for single-cell analyses of purine metabolism
NORRIS, JEREMY L	VANDERBILT UNIVERSITY	Laser-Based Mass Spectrometry Analysis of Single Cells
RAJ, ARJUN	UNIVERSITY OF PENNSYLVANIA	Validation and development of single nucleotide variant RNA FISH in single cells in culture and tissue
SOUSA-NEVES, RUI (contact) MIZUTANI, CLAUDIA	CASE WESTERN RESERVE UNIVERSITY	Multidimensional analysis of cell lineages
SUL, JAI-YOON	UNIVERSITY OF PENNSYLVANIA	Nuclear pre-mRNA analysis of single cells in brain slice
YOUNG-PEARSE, TRACY L	BRIGHAM AND WOMEN'S HOSPITAL	Detection of cell type specific effects of pathway manipulation in neural cells

Accelerating the Integration and Translation of Technologies to Characterize Biological Processes at the Single Cell Level (R01) RFA-RM-11-015
PI Name	Institution Name	Title
BAO, ZHIRONG	SLOAN-KETTERING INSTITUTE FOR CANCER RES	An integrated system to monitor complex tissues at single-cell resolution
BOYDEN, EDWARD S. (contact) FOREST, CRAIG ZENG, HONGKUI	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	High-throughput robotic analysis of integrated neuronal phenotypes
BUSHKIN, YURI (contact) GENNARO, MARIA LAURA TYAGI, SANJAY	UNIV OF MED/DENT OF NJ-NJ MEDICAL SCHOOL	Rapid Analysis of Single T Cell Immunity Signatures in Tuberculosis
CAI, LONG (contact) SOMLO, GEORGE	CALIFORNIA INSTITUTE OF TECHNOLOGY	Multiplex RNA imaging in single cells by superresolution microscopy& barcode FISH
GERDES, MICHAEL (contact) COFFEY, ROBERT J. SHAIKH, KASHAN	GENERAL ELECTRIC GLOBAL RESEARCH CTR	Validation of a single cell multiplexed in-situ biomarker analysis platform for p
LOVE, JOHN CHRISTOPHER	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	Nanowell-based single-cell technology for characterizing clinical samples ex vivo
MAYFORD, MARK R.	SCRIPPS RESEARCH INSTITUTE	Activity Based Tagging of Neurons
VARADARAJAN, NAVIN (contact) COOPER, LAURENCE J.N.	UNIVERSITY OF HOUSTON	Quantitative single-cell biomarkers of T-cells to optimize tumor immunotherapy
WIRTZ, DENIS	JOHNS HOPKINS UNIVERSITY	Single-cell phenotyping for therapeutic stratification in pancreatic cancer

Exceptionally Innovative Tools and Technologies for Single Cell Analysis (R21) RFA-RM-11-014
PI Name	Institution Name	Title
COVERT, MARKUS W	STANFORD UNIVERSITY	New methods for monitoring the immune system, in individual cells and in vivo
DENISENKO, OLEG N	UNIVERSITY OF WASHINGTON	Single cell analysis of chromatin changes at individual genes
KARTALOV, EMIL P	UNIVERSITY OF SOUTHERN CALIFORNIA	High-Throughput Single-Cell-PCR Technique for Tissue Analysis of Genetic Heteroge
KIRSCHNER, MARC WALLACE	HARVARD UNIVERSITY (MEDICAL SCHOOL)	A high-throughput method for simultaneous profiling of mRNA and protein levels in
KONRY, TALI TANIA	MASSACHUSETTS GENERAL HOSPITAL	Development of Microfluidic Nano-Liter Platform for Single Cell Dynamic Monitorin
LEVY, MATTHEW (contact) SNAPP, ERIK L.	ALBERT EINSTEIN COL OF MED YESHIVA UNIV	Fluorescent probes for quantitation of secretory protein levels in single cells
LOVE, JOHN CHRISTOPHER	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	Highly Multiplexed Single-cell Transcript Analysis Using DNA-barcoded Nanowells
MELDRUM, DEIRDRE R.	ARIZONA STATE UNIVERSITY-TEMPE CAMPUS	In Situ Single Cell Laser Lysis and Downstream qRT-PCR Profiling
MIZUTANI, CLAUDIA (contact) GUO, WEIHONG SOUSA-NEVES, RUI	CASE WESTERN RESERVE UNIVERSITY	Real-time visualization of neural stem cell transcriptome
MURRAY, KERMIT KING	LOUISIANA STATE UNIV A&M COL BATON ROUGE	Nanoscale Laser Ablation Capture Mass Spectrometry for Single Cell Proteomics
NAVIN, NICHOLAS	UNIVERSITY OF TEXAS MD ANDERSON CAN CTR	Developing a whole-genome sequencing method for single human cells
NEU, COREY P	PURDUE UNIVERSITY WEST LAFAYETTE	Combined Biophysical and Biochemical Study of Single Cells
RESHETNYAK, YANA K. (contact) ANDREEV, OLEG A	UNIVERSITY OF RHODE ISLAND	Mapping pH at the surface of individual cell
SIMS, PETER ALAN	COLUMBIA UNIVERSITY HEALTH SCIENCES	Multiplexed, Single Molecule Protein Identification for Single Cell Proteomics
WANG, YINGXIAO	UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN	A Systematic Approach to Engineer Fyn Kinase Biosensor

Studies to evaluate cellular heterogeneity using transcriptional profiling of single cells (U01) RFA-RM-11-013
PI Name	Institution Name	Title
EBERWINE, JAMES H (contact) KIM, JUNHYONG	UNIVERSITY OF PENNSYLVANIA	Role of Single Cell mRNA Variation in Systems Associated Electrically Excitable C
KNOWLES, JAMES A (contact) CHOW, ROBERT HSIU-PING	UNIVERSITY OF SOUTHERN CALIFORNIA	Evaluation of Cellular Heterogeneity Using Patchclamp and RNA-Seq of Single Cells
ZHANG, KUN	UNIVERSITY OF CALIFORNIA SAN DIEGO	Single-cell sequencing and in situ mapping of RNA transcripts in human brains