Center for Genome Imaging (CGI)



The goal of the CGI is to develop, implement, and disseminate imaging, analysis, and modeling technologies that will elucidate how genomes, in their entirety, are organized and function in three dimensions (3D).

Develop strategies to massively scale imaging methods.

Develop strategies for distinguishing maternal and paternal homologs as well as visualizing repeated sequences.

Produce computational pipelines to increase the power and speed of image analysis and genome 3D modeling. 

Support the community through a CGI incubator, internships, and courses.

The Team

Jumana AlHaj Abed


I want to understand the relationship between homologous chromosome shapes, epigenetic marks, and transcriptional programs in extreme scenarios using homolog-specific super-resolution imaging and chromatin conformation capture technologies. In Drosophila, homologous pairing events are genome-wide, abundant, and extensive and, in mammals, they are rare and stochastic. What are the common or different principles governing functional trans-homologous contact events in different contexts and organisms?

Sarah Aufmkolk



Imaging the structural organization of the whole human genome is an adventure. Being able to visualize with nanometer resolution this information-rich origami masterpiece is daunting, especially if you take it one molecule localization at a time. I’m thankful for being in the midst of what I would call an expedition team, which is joining forces of biological conceptualization, photo-physical finesse, and computational analytics. Let’s climb this mountain!

Laura Breimann



Laura is a biochemist with a background in gene regulation, microscopy and image analysis. She is interested in understanding whole-genome organization in health and disease using diffraction-limited and super-resolution microscopy. For this goal, she also works on new imaging technologies and image analysis methods. 

Audrey Dalgarno



Audrey Dalgarno in PhD candidate in the Neretti lab at Brown University in the Molecular Biology, Cell Biology, and Biochemistry program. Her research focuses on the role of genomic architecture in cellular senescence. For her project, she will combine spatial multi-omic microscopy with machine learning to determine the ability of local chromatin structure to predict transcriptional status at senescence-associated loci.

Gabrielle Dewson


I am a second-year Ph.D. student at University of Texas Medical Branch Galveston Texas under the mentorship of Dr. Guy Nir. In Dr. Nir’s lab, I am studying the genome organization of leukemia cells that have the Philadelphia Chromosome. The Philadelphia Chromosome is a translocated chromosome between chromosomes 9 and 22 that create an oncogene BCR-ABL1 at the fusion point.  Prior to starting at UTMB, I was a research assistant at Oregon Health and Science University, studying metabolic convergence on the lipogenesis pathway in lymphomas. 

My current interest rests in understanding the genome organization in different cancers. I hope to continue to study this topic and connect varying genomic organization in minority populations. My goal after getting my Ph.D. is to get a postdoctoral position and to continue to work and teach in an academic setting. Outside of lab, I love reading, walking along the beach, and walking my German Shepard Apollo.

Olga Dudchenko



Olga Dudchenko has extensive experience with data analysis involving Hi-C, a method for probing the 3D structure of genomes through proximity ligation and high-throughput sequencing, specifically those involving genome assembly, phasing and structural rearrangement analysis. She is the author of several widely used bioinformatics tools for Hi-C based genome assembly including 3D-DNA, the pipeline for automatic assembly of chromosomes using Hi-C data, and Juicebox Assembly Tools or JBAT, an interactive tools for manual polishing of genome assemblies. She will contribute, among other efforts, to creating new tools and computational pipelines that utilize 3D imaging for structural variability and extended homolog resolution.

Eunice Fabian-Morales


Eunice is a biologist with expertise in human cytogenetics and a background in super-resolution microscopy. Her research is centered on unraveling the intricate relationship between 3D genome organization, cell functions, and genome stability, employing advanced super-resolution imaging techniques.

Irene Farabella



Over the years, as a computational structural biologist, I have leveraged the integration of experimental data (mainly obtained using imaging techniques) and computational methods to learn more about the mechanisms by which chromatin is organized within nuclei. My goal is to develop and apply transformative tools for the genome-wide analysis and modelling of super-resolution genome images. This will significantly facilitate the investigation of spatial genome organization at an unprecedented scale and resolution.

Anat Galis Vivante


I am a biophysicist with a background in chromatin dynamics, live-cell imaging, microscopy, and image analysis. I am currently working as a postdoctoral researcher in the laboratory of Dr. Guy Nir at the University of Texas Medical Branch (UTMB). My research explores how rigidity sensing impacts genome organization and cell fate decisions from ensemble-level to single-cell-level methods. We aim to determine whether regulation of gene expression through rigidity sensing is facilitated by alternation of genome organization and repositioning Lamina-Associated Domains (LADs).


Dimos Gkountaroulis


Being a computational knot theorist, I am interested in understanding the topology of genomes from a mathematical point of view. Are there any mathematical/topological mechanisms that drive their organization in 3D-space? If yes, how are they relevant to biology? These are some of the questions that drive my research. Currently, I am focused on applying imaging methods like OligoSTORM to visualize genomes and then using original mathematical and computational methods to infer their topology. 

Conor Herlihy



Coming from a background in centromere biology, chromosome segregation, and genome instability, I am interested in visualizing the genome-wide structural arrangement of chromosomes in order to understand how structure impacts genome integrity. To this end, I am utilizing OligoFISSEQ and developing new imaging methods in cells as well as in tissues and organisms.

Peter Hoboth


I am a molecular cell biologist by training and passion. My interest is in the functional organization of the cell nucleus, which I previously studied in Prague by quantitative super-resolution microscopy of the nuclear proteins (RNA polymerase II, nuclear speckle components...) and also the intranuclear lipids, whose roles just start to emerge. In Marc A. Marti-Renom's group at CNAG in Barcelona I'm specialised technician / microscopist and I'm implementing and optimizing chromatin imaging techniques, such as oligoSTORM, and I collaborate with the image analysts, for the needs of the projects within our group and the whole CGI. I also have my postdoc project, where we aim to test if the cellular memory is encoded, at least in part, in the 3D genome architecture. 

Jeremy Horrell



Jeremy Horrell is a PhD candidate in the Neretti laboratory as part of the Molecular Biology, Cell Biology, and Biochemistry Graduate Program at Brown University. His research interests center around interrogating the hierarchical nature of chromosome architecture of normal and aging human genomes through the combined use of Oligopaints, diffraction-limited, and super-resolution microscopy.

S. Dean Lee



I am interested in the structural interplay between the maternal and paternal genomes in diploid organisms. To that end, I am developing a genome-wide imaging technology to identify the maternal and paternal chromosomes at conventional as well as super resolution. Integrating images representing both resolutions, I seek to elucidate the potential implications of intracellular variability in chromatin packaging between the maternal and paternal chromosomes.

Antonios Lioutas



Understanding the vastness of information behind genome organization that leads to cell function is what drives my research. Thus, I am actively developing and implementing new imaging and computational tools to tackle this gigantic effort of imaging whole genomes.

Iago Maceda Porto


I'm a postdoctoral researcher in the Structural Genomics group at CNAG. I am developing a pipeline to easily asses the quality of microscopy models with the scope of using them in integrative modelling. The aim of the integrative modelling part is to have a combination of the best of both worlds: physical information from the microscopy experiments with the sequence accuracy of the HiC. In this way we can project different signals on the microscopy model and possibly get new insights

John Markahm


I am a bioinformatician in the Structural Genomics group at CNAG-CRG. I am developing analysis pipelines for multiplexed DNA-labelling techniques such as OligoFISSEQ and OligoSTORM. I use a combination of modelling and Bayesian techniques to find genome-wide 3D DNA structure from microscopy data. the goal is to improve inference by incorporating prior knowledge of the system and data from other experimental modalities.

Nuno Martins



I apply the technologies of Oligopaints and OligoSTORM to the development of experimental pipelines for tackling biological questions at the level of the chromosome. This goal has led me to develop tools such as MART (Multiple-Alignment Repeat-Targeting) probes. The focus of my work has been on complex genomic regions, such as centromeres, on which the inheritance of entire genomes rests.

Guy Nir


My lab studies how physical and chemical stress restructure the three-dimensional genome organization to reprogram the genomic output of an organism, thus supporting its adaptation to the changing environment. Since the cells’ response is heterogenous, we develop and employ single-cell technologies, including sequential OligoSTORM, which harnesses single-molecule localization microscopy with barcoded oligos (specifically, ‘Oligopaints’) to visualize the structure of many loci within the same cells. Then, either by developing or through collaborations, such as the CGI, we utilize a set of tools to analyze genomes structurally and functionally.

Meritxell Novillo


I am a PhD student in the Structural Genomics group at CNAG-CRG. My research is focused on the identification of differential "3D enhancer hubs" in organoids derived from colorectal cancer patients, with respect to healthy tissue. To get a detailed picture of the genes involved in colorectal cancer, we will combine computational modelling with Next-Generation Sequencing technologies, and we will further adapt the newly developed imaging methods OligoFISSEQ and OligoSTORM to visualize the entire genome on organoids.

Ada Olins


Ada Olins is a Visiting Scientist in Erez’s group and a Research Professor at the University of New England.  Her preferred research tool is the microscope with strong interests in the 3-D structure of chromatin and nuclei.  Confocal imaging of the immunostained preparations, deconvolution and analysis in 2- and 3-D are routine.  The role of LBR in nuclear shape, the surface of interphase nuclei (epichromatin) and macrophage differentiation are current subjects of investigation.

Donald Olins


Donald Olins is a Visiting Scientist in Erez’s group and a Research Professor at the University of New England.  His principal research interest is the 3-D structure of chromatin and nuclei from the perspective of a cell biologist.  Major research pleasures include cell culture, immunostaining and immunoblotting of nuclear antigens.  Current research projects include myeloid cell differentiation; the role of LBR in nuclear shape; the structure of interphase epichromatin (i.e., chromatin adjacent to the nuclear envelope).

Ivan Piacere


I apply my computer science and data science knowledge in the development of computational tools for the inference of 3D genome architecture from Single-Molecule Localization Microscopy data. On the one hand I'm trying to model the way in which super-resolution images are obtained from chromatin segments, on the other I search for algorithms that best reconstruct chromatin segments from super-resolution images.

Azucena Rocha



Azucena Rocha is a PhD candidate in the Molecular and Cellular Biology program at Brown University. Her research focuses on investigating the association of cyclic GMP-AMP synthase (cGAS) with repetitive elements in the nucleus, with a particular interest in cellular senescence and aging.

Miiko Jaakkima Sokka



Miiko is a molecular and cell biologist at Brown University in Providence, RI, USA, with a background in DNA replication and DNA damage response. His research aims to better understand cell cycle, proliferation and senescence in human cells and how the genome is structurally organized in these different states. Currently, his main goal is to use Oligopaint FISH to visualize chromosome territories of the entire genome in normal and senescent human cells.

Johannes Stein


As a physicist by training, I took the turn toward biology during my PhD developing both tools and instrumentation for DNA-based super-resolution microscopy (SR). I will be bringing my SR-background in DNA-PAINT to the CGI as we work toward imaging entire genomes at the single-cell level.

Douglass Turner


Douglass Turner is a software developer. He has over 15 years of experience in software development services for data visualization and 3D graphics. He specializes in front-end Web Development, software development, and training services. He will work on the spacewalk system for microscopy data visualization. 

David Weisz


David Weisz is a computer scientist in the Aiden lab with expertise in Hi-C data flows, cloud computing, and high performance computation (HPC). His wok in the lab focuses on the development of pipelines, adapting and optimizing them to HPC Clusters, monitoring and analysis of data. Within the Center for Genome Imaging (CGI) CEGS project he will be able to contribute by using the extensive experience with technologies in the computational field of bioinformatics. 

Fei Zhao


My research interest is to use OligoSTORM and OligoFISSEQ to achieve whole genome imaging in super resolution. With a background in chemistry and microscopy, I am hoping also to contribute to the development of new technologies, from fluidics to imaging.

Conflict of Interest Statement: The Wu laboratory holds or has patent filings pertaining to imaging and has held a sponsored research agreement with Bruker Inc. TW is a non-equity-holding co-founder of Acuity Spatial Genomics and, through personal connections to George Church, has equity in companies associated with him, including 10x Genomics and Twist.

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