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Genomics is the study of individual genomes, both at the sequence level and at the structural level. Technological advances have made genomic approaches critical for understanding basic biological processes, so that genomic research now impacts all areas of life science research.
The CSHL Genomics Program includes faculty working across disciplines and research areas. Their main interests are genomic organization, structural variation of the human genome as related to disease, computational genomics, small RNA biology, transcriptional modeling, and sequencing technology. Genomics research at CSHL benefits from state-of-the-art technology and innovative software development, with researchers both on the main CSHL campus and at the nearby CSHL Woodbury Genome Center.
Broadly, genomics research falls into three categories with significant overlap: Cognitive Genomics, Cancer Genomics and Plant Genomics. In addition, Genomics researchers works closely with researchers in other CSHL programs, particularly the Simon Center for Quantitative Biology.
CSHL is one of the founding members of the New York Genome Center, an independent, non-profit organization that is leveraging the collaborative resources of leading medical and research institutions to transform medical research and clinical care in New York.
The CSHL Cancer Genomics group seeks to understand how the cancer genome differs from the normal genome, how these differences lead to the growth and development of cancer, and how biomarkers can be used for diagnosis and prognosis. Researchers in this area are members of the CSHL Cancer Center.
Much of the research focuses on the genomic changes that occur in numerous cancer types, such as breast, prostate, lung and pancreatic cancers, as well as leukemia, glioma and melanoma. Researchers have also focused on the development and application of sophisticated tools for genome analysis that permit high resolution mapping of deletions, amplifications and changes in the sequence or epigenetic status of chromosomal loci.
Another focus area is the development and application of genomic methods in cell culture and animal models. These include sophisticated chromosome engineering techniques as well as applications of large-scale RNAi and CRISPR screens to identify both driver genes and tumor-cell-specific dependencies, as well as single cell sequencing approaches. These genetic tools/approaches allow biological validation of loci discovered by analysis of cancer genomes.
A third area of focus centers on developing tools and software that can harness large scale genomic datasets that are available to the community. Examples include the study of allelic variation in the human genome and the development of computational methods for the discovery of cancer-associated genes and diagnostic cancer markers using genomic profiles derived from different tumor types. Many of these researchers are also part of the Simons Center for Quantitative Biology at CSHL.
Schizophrenia, bipolar disorder, and major recurrent depression are cognitive disorders that create an enormous burden on patients, their families and our health care system. These disorders tend to run in families and likely have a genetic component but little is known about the genetic basis of the diseases.
With recent advances in genomic technologies, CSHL is now poised to unravel the genetic complexity of cognitive disorders. Simultaneously, advanced technologies in Neuroscience research are allowing CSHL researchers to understand how the brain assembles neural circuits to control behaviors and cognitive processes like attention and decision-making. Much of this research occurs within the CSHL Stanley Institute for Cognitive Genomics, where approaches from genomics and neuroscience are integrated to improve the diagnosis and treatment of cognitive disorders. 
The CSHL Plant Genomics group is using genomic approaches with the ultimate goal of improving access to food and fuel in the future. As part of Plant Biology research at CSHL, scientists are using genomic approaches to understand everything from plant evolution to how plants grow, develop, and reproduce.
This research is challenging because many plant genomes are very large. CSHL scientists have taken part in numerous plant genome sequencing projects including Arabidopsis, rice, sorghum and maize. In addition, CSHL plant scientists have participated in epigenomic sequencing and profiling. CSHL is also part of the iPlant Cyberinfrastructure consortium and the Long Island Biofuels Alliance.
Current research projects include sequencing the wheat genome through a combination of Illumina short read sequencing and long sequence reads using the new Pacific Biosciences sequencers. The latest results for this project can be found on the CSHL wheat genome sequencing project page.
Gurinder Atwal - Associate Professor

Applies insights from the physical and computational sciences to the study of population genetics, evolution, and disease. Recent work on the evolution of genetic variants identified a role of p53 tumor suppressor in female fertility. The lab also analyzes comparative genomics and physical organization of cancer related genes, and their role in mediating tumorigenesis across numerous tissue types. 
Jesse Gillis - Associate Professor

Developing meta-analysis methods that allows systematic investigation of gene networks at a very sophisticated level. This will allow researchers to find commonalities among disease genes in neuropsychiatric disorders.
Thomas Gingeras - Professor

Examines how functional information encoded in genomes is organized and regulated using high-throughput technologies and computational approaches, focusing primarily on the roles of non-coding RNAs. These efforts help explain the origins of the biological characteristics exhibited by cells during and after their development and whose perturbations are the underlying causes of the human disease.
Christopher Hammell - Associate Professor

Studies the gene regulatory processes that give rise to robust phenotypes associated with normal development, and examines the alterations in these pathways that give rise to diseases such as cancer. The Hammell lab uses a variety of model systems to investigate this, including c. elegans and patient-derived cancer cell lines.
Molly Hammell - Assistant Professor

Uses computational and experimental approaches to study gene regulatory networks and how they adapt to changes. Current work focuses on identifying mechanisms underlying acquired resistance to BRAF-targeted therapies in melanoma and investigating the processes underlying neuronal cell death in amyotrophic lateral sclerosis (ALS), including with a possible role for non-coding RNA genes.
Ivan Iossifov - Associate Professor

Applies computational methods to improve conventional genetic analyses to detect correlations between specific alleles and common complex hereditary disorders such as schizophrenia, bipolar disorder and autism.
David Jackson - Professor

Studies stem cells and morphogenesis in plants, using maize and Arabidopsis as model systems.  Recent work has identified new signaling pathways for cell-to-cell communication and their positive effects on crop yields.
Alexander Krasnitz - Associate Professor

Develops and applies statistical methods to understand how cancers evolve. His lab has designed a novel, comprehensive methodology to discover recurrent genomic aberrations in cancer genomes and has used it to analyze multiple data sets in breast, liver, ovarian, and prostate cancer. More recently, he used his computational tools to reveal how genomically distinct cell populations evolve in individual malignancies.
Je Lee - Assistant Professor

Studies how cells interact with their microenvironment to regulate gene expression during development. Currently focusing on the role of non-coding RNA in chromatin remodeling and tumor progression using mouse and organoid models of human cancer. In situ sequencing, cell lineage tracing, and single-cell profiling are used, with a long-term goal, to develop better tumor classification tools and anti-cancer therapeutics.
Dan Levy - Assistant Professor

Develops algorithms to identify mutations associated with various diseases, including cancers and autism, from large, complex data sets. His work focuses on using targeted sequence data to identify copy number variants and multiscale genomic rearrangements, including most recently analysis of data obtained from single cells.
Zachary Lippman - Professor

Combines genetic, genomic, and molecular approaches to study the mechanisms controlling flowering and reproductive fitness in plants, with tomato as a model system. By identifying the genes that control flowering, the lab aims to manipulate flower production and improve crop yields.
Gholson Lyon - Assistant Professor

Studies the pathophysiology of severe neurodevelopmental disorders. Uses next generation sequencing, induced pluripotent stem cells and mouse models to perform detailed functional studies of rare genetic mutations in families with increased prevalence of facial dysmorphology, intellectual disability, and/or autism.
Rob Martienssen - Professor & HHMI Investigator

Uses plants and yeast as model organisms to investigate the epigenetic mechanisms that control gene expression, transposon silencing, and germ cell fate. Currently employing methods in functional genomics and developmental genetics to gain insight into how defects in the epigenome cause disease.
W. Richard
W. Richard McCombie - Professor

Develops methods and strategies that use the new generation of sequencing instruments to determine variation in the genomes, transcriptomes, and epigenomes of animals and plants. The lab is currently applying this technology to understand genetic variation in different types of cancer, schizophrenia, bipolar disorder and major depression. 
Adam Siepel - Professor

Uses mathematical analysis and computer science to study evolution of populations, species, and individual genes. Employs these methods to understand transcriptional regulation and evolution.
Marja Timmermans - Professor

Uses Arabidopsis and maize as model organisms to study the role of small regulatory RNAs as positional signals regulating plant development. Recently demonstrated that dorsoventral polarity in leaves is specified through a novel patterning mechanism involving opposing small RNA gradients with morphogen-like activities.
Doreen Ware - Adjunct Associate Professor

Focuses on understanding genome organization and evolution in plants by combining computational analysis, modeling and prediction with experimental verification. 
Michael Wigler - Professor

Works in the areas of cancer and autism genetics, applying and developing tools for genomic analysis, such as detection of de novo mutation, sequence assembly, and single cell RNA and DNA analysis. The biological focus is on genetic causation, early detection and outcome analysis.