Funded Research

Real-Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed) RFA-RM-20-003
PI Name Institution Name Title
BELMONT, ANDREW STEVEN (contact) 
HAN, KYU YOUNG
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN Identification of the active nuclear niche(s) using novel proteomic, genomic, transgenic, and live-cell microscopy technologies
BINTU, LACRAMIOARA (contact) 
BOETTIGER, ALISTAIR
STANFORD UNIVERSITY Live-cell multiplex super-resolution imaging of chromatin state transitions
CAI, LONG (contact)
ELOWITZ, MICHAEL B
GUTTMAN, MITCHELL
CALIFORNIA INSTITUTE OF TECHNOLOGY Dynamics of chromosome organization and chromatin states in single cells
GREGOR, THOMAS (contact) 
LEVINE, MICHAEL STEVEN
TOETTCHER, JARED E
PRINCETON UNIVERSITY Control of the 4D chromatin landscape underlying gene activity during development
HA, TAEKJIP (contact)
JOHNSON, MARGARET ELLEN
WU, CARL
JOHNS HOPKINS UNIVERSITY Chromatin 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 FRANCISCO Modulation and functional characterization of protein condensation in chromatin organization
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact)
BLOBEL, GERD A
QI, LEI STANLEY
RAJ, ARJUN
UNIVERSITY OF PENNSYLVANIA Engineering and Imaging 3D genome structure-function dynamics across time scales
TORRES PADILLA, MARIA ELENA HELMHOLTZ ZENTRUM MUENCHEN - GMBH Establishment 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 Name Institution Name Title
DEKKER, JOB (contact)
MIRNY, LEONID A
UNIV OF MASSACHUSETTS MED SCH WORCESTER Center for 3D Structure and Physics of the Genome
MA, JIAN (contact)
ALBER, FRANK
BELMONT, ANDREW STEVEN
WU, CHAO-TING
CARNEGIE-MELLON UNIVERSITY Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data Integration
NOBLE, WILLIAM STAFFORD (contact)
DISTECHE, CHRISTINE M.
SHENDURE, JAY ASHOK
UNIVERSITY OF WASHINGTON UW 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 DIEGO Center 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 Name Institution Name Title
BRUNEAU, BENOIT GAETAN (contact)
POLLARD, KATHERINE S.
J. DAVID GLADSTONE INSTITUTES Genetic determinants of 4D genome folding in human cardiac development
DIXON, JESSE R SALK INSTITUTE FOR BIOLOGICAL STUDIES Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes

HAWKINS, RAYMOND DAVID

UNIVERSITY OF WASHINGTON Three-dimensional conformation changes associated with T cell memory and autoimmunity
HUANGFU, DANWEI (contact)
APOSTOLOU, EFFIE
LESLIE, CHRISTINA S
SLOAN-KETTERING INST CAN RESEARCH Discovery 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 WORCESTER The role of the nucleolus in human genome organization in normal and disease states 
LOMVARDAS, STAVROS COLUMBIA UNIVERSITY HEALTH SCIENCES Interrogating genome folding trajectories in health and disease 
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact)
JAIN, RAJAN
JOYCE, ERIC F.
LAKADAMYALI, MELIKE
VAHEDI, GOLNAZ
UNIVERSITY OF PENNSYLVANIA Single-cell dissection of chromatin architecture mechanisms connecting pathologic instability and transcriptional silencing
SCHATZ, DAVID G. (contact)
WANG, SIYUAN
YALE UNIVERSITY Genome Architecture in Human Germinal Center B Cell Development, Malignancy, and Somatic Hypermutation
SHEN, YIN (contact)
KRIEGSTEIN, ARNOLD
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Charting the 3D epigenome in human brain development and diseases
XU, XIANGMIN (contact)
COTMAN, CARL WAYNE
REN, BING
UNIVERSITY OF CALIFORNIA-IRVINE Single-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 Name Institution Name Title
DIAO, YARUI DUKE UNIVERSITY The 4D nucleome of muscle regeneration in ischemia-induced tissue damage and repair
KALHOR, REZA JOHNS HOPKINS UNIVERSITY Dynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbations
LI, WENBO UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON Beyond Gene Dosage: Understanding Down Syndrome via 4D Genome Organization
SATPATHY, ANSUMAN STANFORD UNIVERSITY 4DN Interrogation of T Cell Exhaustion in Cancer
YAMADA, TOMOKO NORTHWESTERN UNIVERSITY Mechanisms of Genome Organization in Brain Development and Behavior
ZHANG, HUAIYING CARNEGIE-MELLON UNIVERSITY Phase separation-induced nuclear organization in ALT Cancer

 

Limited Competition: 4DN Organizational Hub (U01 Clinical Trial Not Allowed) RFA-RM-20-007
PI Name Institution Name Title
ZHONG, SHENG UNIVERSITY OF CALIFORNIA, SAN DIEGO The 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 Name Institution Name Title
PARK, PETER J HARVARD MEDICAL SCHOOL 4D Nucleome Network Data Coordination and Integration Center

 

NIH Support for Conferences and Scientific Meetings (Parent R13 Clinical Trial Not Allowed) PA-18-648
PI Name Institution Name Title
JARVIS, THALE CROSS KEYSTONE SYMPOSIA 3D Genome: Gene Regulation and Disease

 

Nuclear Organization and Function Interdisciplinary Consortium (NOFIC) (U54) RFA-RM-14-030
PI Name Institution Name Title
ALBER, FRANK (contact) 
CHEN, LIN
UNIVERSITY OF SOUTHERN CALIFORNIA Mapping the 3D Genome Landscape
BELMONT, ANDREW STEVEN UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN Combined Cytological, Genomic, and Functional Mapping of Nuclear Genome Organization
DEKKER, JOB (contact) 
MIRNY, LEONID A
UNIV OF MASSACHUSETTS MED SCH WORCESTER Center for 3D Structure and Physics of the Genome
REN, BING (contact) 
MURRE, CORNELIS
LUDWIG INSTITUTE FOR CANCER RESEARCH LTD San Diego Center for 4D Nucleome Research
RUAN, YIJUN JACKSON LABORATORY Nucleome Positioning System for Spatiotemporal Genome Organization and Regulation
SHENDURE, JAY ASHOK (contact) 
NOBLE, WILLIAM STAFFORD
UNIVERSITY OF WASHINGTON University of Washington Center for Nuclear Organization and Function

 

4D Nucleome Imaging Tools (U01) RFA-RM-14-009
PI Name Institution Name Title
BEWERSDORF, JOERG (contact) 
BADDELEY, DAVID
YALE UNIVERSITY An Integrated Imaging System for High-throughput Nanoscopy of the 4D Nucleome
CAI, LONG (contact) 
QI, LEI STANLEY
CALIFORNIA INSTITUTE OF TECHNOLOGY Hi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISH
ELLENBERG, JAN EUROPEAN MOLECULAR BIOLOGY LABORATORY Reconstructing the dynamic 3D architecture of the human genome by superresolution microscopy and DNA sequence modelling
GREGOR, THOMAS (contact) 
LEVINE, MICHAEL S.
PRINCETON UNIVERSITY Imaging chromosome dynamics and measuring its impact on transcriptional activity
GRUNWALD, DAVID UNIV OF MASSACHUSETTS MED SCH WORCESTER Visualizing 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 DAVIS Genetically Encoded Small Illuminants for 4D nucleome imaging
LIPHARDT, JAN T. STANFORD UNIVERSITY Deep Super-localization Microscopy and Effectively Unbleachable Labeling for 4D Nucleomics
O'SHEA, CLODAGH (contact) 
ELLISMAN, MARK H 
SALK INSTITUTE FOR BIOLOGICAL STUDIES Imaging local and global chromatin structure as a 3D continuum within the nucleus
SINGER, ROBERT H. (contact) 
DARZACQ, XAVIER 
ALBERT EINSTEIN COLLEGE OF MEDICINE Tools For Imaging the Functional Genome in Living Cells and Tissues

 

4D Nucleome Network Data Coordination and Integration Center (U01) RFA-RM-14-011
PI Name Institution Name Title
PARK, PETER J HARVARD MEDICAL SCHOOL 4D Nucleome Network Data Coordination and Integration Center
WANG, TING (contact)  WASHINGTON UNIVERSITY The WashU 4DN Network Data Coordination and Integration Center

 

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

 

Study of Nuclear Bodies and Compartments (U01) RFA-RM-14-008
PI Name Institution Name Title
BRANGWYNNE, CLIFFORD P PRINCETON UNIVERSITY Optogenetic Droplets: Using Light to Control Nucleoplasmic Phase Separation
GERACE, LARRY R. SCRIPPS RESEARCH INSTITUTE Mapping the organization of the peripheral nuclear compartment
GROUDINE, MARK T FRED HUTCHINSON CANCER RES CENTER A toolkit to reversibly disrupt nuclear bodies and move genes among compartments
GUTTMAN, MITCHELL (contact) 
HESS, SONJA  
RINN, JOHN LOUIS
CALIFORNIA INSTITUTE OF TECHNOLOGY Deciphering the function and mechanisms of lncRNA-mediated organization of nuclear compartments
KAUFMAN, PAUL D. (contact) 
DEKKER, JOB  
PEDERSON, THORU
UNIV OF MASSACHUSETTS MED SCH WORCESTER Nucleolar Genomics During Early Mammalian Development
LOMVARDAS, STAVROS (contact) 
BROWN, LEWIS M.
COLUMBIA UNIVERSITY HEALTH SCIENCES Deciphering nuclear bodies and compartments that govern singular olfactory receptor expression

 

Nucleomics Tools (U01) RFA-RM-14-007
PI Name Institution Name Title
FRASER, PETER J (contact) 
TANAY, AMOS      
THE BABRAHAM INSTITUTE New 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 TECHNOLOGY Novel tools to comprehensively map dynamic organization of RNA and DNA in higher-order nuclear structures within single cells
LIEBERMAN-AIDEN, EREZ BAYLOR COLLEGE OF MEDICINE Beyond 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 UNIVERSITY Distance-Hi-C: Creating Photo Activated X-linkers To Define Nuclear Architecture

RAJ, ARJUN (contact) 
BLOBEL, GERD A 

PHILLIPS-CREMINS, JENNIFER

 

UNIVERSITY OF PENNSYLVANIA Engineering and visualizing genome folding at high spatiotemporal resolution

This page last reviewed on October 2, 2020