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Funded Research

Real-Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed) RFA-RM-20-003
PI NameInstitution NameTitle
BELMONT, ANDREW STEVEN (contact) 
HAN, KYU YOUNG
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGNIdentification of the active nuclear niche(s) using novel proteomic, genomic, transgenic, and live-cell microscopy technologies
BINTU, LACRAMIOARA (contact) 
BOETTIGER, ALISTAIR
STANFORD UNIVERSITYLive-cell multiplex super-resolution imaging of chromatin state transitions
CAI, LONG (contact)
ELOWITZ, MICHAEL B
GUTTMAN, MITCHELL
CALIFORNIA INSTITUTE OF TECHNOLOGYDynamics of chromosome organization and chromatin states in single cells
GREGOR, THOMAS (contact) 
LEVINE, MICHAEL STEVEN
TOETTCHER, JARED E
PRINCETON UNIVERSITYControl of the 4D chromatin landscape underlying gene activity during development
HA, TAEKJIP (contact)
JOHNSON, MARGARET ELLEN
WU, CARL
JOHNS HOPKINS UNIVERSITYChromatin Function During Transcription and DNA Repair at Single Molecule Resolution in Living Cells
HUANG, BO (contact) 
NARLIKAR, GEETA J
SHU, XIAOKUN
UNIVERSITY OF CALIFORNIA, SAN FRANCISCOModulation and functional characterization of protein condensation in chromatin organization
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact)
BLOBEL, GERD A
QI, LEI STANLEY
RAJ, ARJUN
UNIVERSITY OF PENNSYLVANIAEngineering and Imaging 3D genome structure-function dynamics across time scales
TORRES PADILLA, MARIA ELENAHELMHOLTZ ZENTRUM MUENCHEN - GMBHEstablishment and visualization of nuclear architecture at the onset of mammalian development

 

4DN Centers for Data Integration, Modeling and Visualization (UM1 Clinical Trial Not Allowed) RFA-RM-20-004
PI NameInstitution NameTitle
DEKKER, JOB (contact)
MIRNY, LEONID A
UNIV OF MASSACHUSETTS MED SCH WORCESTERCenter for 3D Structure and Physics of the Genome
MA, JIAN (contact)
ALBER, FRANK
BELMONT, ANDREW STEVEN
WU, CHAO-TING
CARNEGIE-MELLON UNIVERSITYMultiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data Integration
NOBLE, WILLIAM STAFFORD (contact)
DISTECHE, CHRISTINE M.
SHENDURE, JAY ASHOK
UNIVERSITY OF WASHINGTONUW 4-Dimensional Genomic Organization of Mammalian Embryogenesis Center
REN, BING (contact)
DULAC, CATHERINE G
LEIN, ED
NICODEMI, MARIO
POMBO, ANA
WANG, TING
ZHUANG, XIAOWEI
UNIVERSITY OF CALIFORNIA, SAN DIEGOCenter for Integrated Multi-modal and Multi-scale Nucleome Research

 

4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed) RFA-RM-20-005
PI NameInstitution NameTitle
BRUNEAU, BENOIT GAETAN (contact)
POLLARD, KATHERINE S.
J. DAVID GLADSTONE INSTITUTESGenetic determinants of 4D genome folding in human cardiac development
DIXON, JESSE RSALK INSTITUTE FOR BIOLOGICAL STUDIESInvestigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes
HAWKINS, RAYMOND DAVIDUNIVERSITY OF WASHINGTONThree-dimensional conformation changes associated with T cell memory and autoimmunity
HUANGFU, DANWEI (contact)
APOSTOLOU, EFFIE
LESLIE, CHRISTINA S
SLOAN-KETTERING INST CAN RESEARCHDiscovery of diabetes-relevant β cell enhancers through 4D enhancer mapping, integrative analysis, and large-scale CRISPRi perturbation screens
KAUFMAN, PAUL D. (contact)
FOLTZ, DANIEL RICHARD
HUANG, SUI
UNIV OF MASSACHUSETTS MED SCH WORCESTERThe role of the nucleolus in human genome organization in normal and disease states 
LOMVARDAS, STAVROSCOLUMBIA UNIVERSITY HEALTH SCIENCESInterrogating genome folding trajectories in health and disease 
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact)
JAIN, RAJAN
JOYCE, ERIC F.
LAKADAMYALI, MELIKE
VAHEDI, GOLNAZ
UNIVERSITY OF PENNSYLVANIASingle-cell dissection of chromatin architecture mechanisms connecting pathologic instability and transcriptional silencing
SCHATZ, DAVID G. (contact)
WANG, SIYUAN
YALE UNIVERSITYGenome Architecture in Human Germinal Center B Cell Development, Malignancy, and Somatic Hypermutation
SHEN, YIN (contact)
KRIEGSTEIN, ARNOLD
UNIVERSITY OF CALIFORNIA, SAN FRANCISCOCharting the 3D epigenome in human brain development and diseases
XU, XIANGMIN (contact)
COTMAN, CARL WAYNE
REN, BING
UNIVERSITY OF CALIFORNIA-IRVINESingle-Cell Analysis of Aging-Associated 4D Nucleome in the Human Hippocampus

 

New Investigator Projects on 4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed) RFA-RM-20-006
PI NameInstitution NameTitle
DIAO, YARUIDUKE UNIVERSITYThe 4D nucleome of muscle regeneration in ischemia-induced tissue damage and repair
KALHOR, REZAJOHNS HOPKINS UNIVERSITYDynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbations
LI, WENBOUNIVERSITY OF TEXAS HLTH SCI CTR HOUSTONBeyond Gene Dosage: Understanding Down Syndrome via 4D Genome Organization
SATPATHY, ANSUMANSTANFORD UNIVERSITY4DN Interrogation of T Cell Exhaustion in Cancer
YAMADA, TOMOKONORTHWESTERN UNIVERSITYMechanisms of Genome Organization in Brain Development and Behavior
ZHANG, HUAIYINGCARNEGIE-MELLON UNIVERSITYPhase separation-induced nuclear organization in ALT Cancer

 

Limited Competition: 4DN Organizational Hub (U01 Clinical Trial Not Allowed) RFA-RM-20-007
PI NameInstitution NameTitle
ZHONG, SHENGUNIVERSITY OF CALIFORNIA, SAN DIEGOThe second phase of NIH Common Fund 4D Nucleome Network Organizational Hub

 

Limited Competition 4DN Data Coordination & Integration Center (U01 Clinical Trial Not Allowed) RFA-RM-20-008
PI NameInstitution NameTitle
PARK, PETER JHARVARD MEDICAL SCHOOL4D Nucleome Network Data Coordination and Integration Center

 

NIH Support for Conferences and Scientific Meetings (Parent R13 Clinical Trial Not Allowed) PA-18-648
PI NameInstitution NameTitle
JARVIS, THALE CROSSKEYSTONE SYMPOSIA3D Genome: Gene Regulation and Disease

 

Nuclear Organization and Function Interdisciplinary Consortium (NOFIC) (U54) RFA-RM-14-030
PI NameInstitution NameTitle
ALBER, FRANK (contact) 
CHEN, LIN
UNIVERSITY OF SOUTHERN CALIFORNIAMapping the 3D Genome Landscape
BELMONT, ANDREW STEVENUNIVERSITY OF ILLINOIS URBANA-CHAMPAIGNCombined Cytological, Genomic, and Functional Mapping of Nuclear Genome Organization
DEKKER, JOB (contact) 
MIRNY, LEONID A
UNIV OF MASSACHUSETTS MED SCH WORCESTERCenter for 3D Structure and Physics of the Genome
REN, BING (contact) 
MURRE, CORNELIS
LUDWIG INSTITUTE FOR CANCER RESEARCH LTDSan Diego Center for 4D Nucleome Research
RUAN, YIJUNJACKSON LABORATORYNucleome Positioning System for Spatiotemporal Genome Organization and Regulation
SHENDURE, JAY ASHOK (contact) 
NOBLE, WILLIAM STAFFORD
UNIVERSITY OF WASHINGTONUniversity of Washington Center for Nuclear Organization and Function

 

4D Nucleome Imaging Tools (U01) RFA-RM-14-009
PI NameInstitution NameTitle
BEWERSDORF, JOERG (contact) 
BADDELEY, DAVID
YALE UNIVERSITYAn Integrated Imaging System for High-throughput Nanoscopy of the 4D Nucleome
CAI, LONG (contact) 
QI, LEI STANLEY
CALIFORNIA INSTITUTE OF TECHNOLOGYHi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISH
ELLENBERG, JANEUROPEAN MOLECULAR BIOLOGY LABORATORYReconstructing the dynamic 3D architecture of the human genome by superresolution microscopy and DNA sequence modelling
GREGOR, THOMAS (contact) 
LEVINE, MICHAEL S.
PRINCETON UNIVERSITYImaging chromosome dynamics and measuring its impact on transcriptional activity
GRUNWALD, DAVIDUNIV OF MASSACHUSETTS MED SCH WORCESTERVisualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging
LAM, KIT S (contact) 
CHENG, R.HOLLAND
IZUMIYA, YOSHIHIRO 
UNIVERSITY OF CALIFORNIA AT DAVISGenetically Encoded Small Illuminants for 4D nucleome imaging
LIPHARDT, JAN T.STANFORD UNIVERSITYDeep Super-localization Microscopy and Effectively Unbleachable Labeling for 4D Nucleomics
O'SHEA, CLODAGH (contact) 
ELLISMAN, MARK H 
SALK INSTITUTE FOR BIOLOGICAL STUDIESImaging local and global chromatin structure as a 3D continuum within the nucleus
SINGER, ROBERT H. (contact) 
DARZACQ, XAVIER 
ALBERT EINSTEIN COLLEGE OF MEDICINETools For Imaging the Functional Genome in Living Cells and Tissues

 

4D Nucleome Network Data Coordination and Integration Center (U01) RFA-RM-14-011
PI NameInstitution NameTitle
PARK, PETER JHARVARD MEDICAL SCHOOL4D Nucleome Network Data Coordination and Integration Center
WANG, TING (contact) WASHINGTON UNIVERSITYThe WashU 4DN Network Data Coordination and Integration Center

 

4D Nucleome Network Organizational Hub (U01) RFA-RM-14-010
PI NameInstitution NameTitle
ZHONG, SHENG (contact) 
CHIEN, SHU
REN, BING
SUBRAMANIAM, SHANKAR
UNIVERSITY OF CALIFORNIA SAN DIEGOThe Organizational Hub and Web Portal for the 4D Nucleome Network

 

Study of Nuclear Bodies and Compartments (U01) RFA-RM-14-008
PI NameInstitution NameTitle
BRANGWYNNE, CLIFFORD PPRINCETON UNIVERSITYOptogenetic Droplets: Using Light to Control Nucleoplasmic Phase Separation
GERACE, LARRY R.SCRIPPS RESEARCH INSTITUTEMapping the organization of the peripheral nuclear compartment
GROUDINE, MARK TFRED HUTCHINSON CANCER RES CENTERA toolkit to reversibly disrupt nuclear bodies and move genes among compartments
GUTTMAN, MITCHELL (contact) 
HESS, SONJA
RINN, JOHN LOUIS
CALIFORNIA INSTITUTE OF TECHNOLOGYDeciphering the function and mechanisms of lncRNA-mediated organization of nuclear compartments
KAUFMAN, PAUL D. (contact) 
DEKKER, JOB
PEDERSON, THORU
UNIV OF MASSACHUSETTS MED SCH WORCESTERNucleolar Genomics During Early Mammalian Development
LOMVARDAS, STAVROS (contact) 
BROWN, LEWIS M.
COLUMBIA UNIVERSITY HEALTH SCIENCESDeciphering nuclear bodies and compartments that govern singular olfactory receptor expression

 

Nucleomics Tools (U01) RFA-RM-14-007
PI NameInstitution NameTitle
FRASER, PETER J (contact) 
TANAY, AMOS
THE BABRAHAM INSTITUTENew automated experimental and computational pipeline for high coverage single-cell Hi-C and its integration with single cell RNA-seq: enabling 4D Nucleomics at single cell resolution
GUTTMAN, MITCHELL (contact) 
ISMAGILOV, RUSTEM F
CALIFORNIA INSTITUTE OF TECHNOLOGYNovel tools to comprehensively map dynamic organization of RNA and DNA in higher-order nuclear structures within single cells
LIEBERMAN-AIDEN, EREZBAYLOR COLLEGE OF MEDICINEBeyond pairwise DNA contacts: exploring higher-order genome structure using proximity ligation and split pool barcoding
LIS, JOHN T (contact) 
LIN, HENING
ZIPFEL, WARREN R 
CORNELL UNIVERSITYDistance-Hi-C: Creating Photo Activated X-linkers To Define Nuclear Architecture

RAJ, ARJUN (contact) 
BLOBEL, GERD A 

PHILLIPS-CREMINS, JENNIFER

UNIVERSITY OF PENNSYLVANIAEngineering and visualizing genome folding at high spatiotemporal resolution

This page last reviewed on February 29, 2024