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.
Are smart robots a threat?
August 23, 2019
In a Q&A, Neuroscientist Anthony Zador explains how neuroscience can inform machine learning, and why he’s not worried about a robot apocalypse.
Creature feature quiz
July 31, 2019
Animals have been the muses behind major scientific breakthroughs for ages. See how much you know about the living organisms sharing the Earth with us.
An essay from the President: Biology for the planet
May 16, 2019
CSHL plant scientists are looking for solutions to the biggest questions in agriculture as environments are reshaped by climate change.
Cryptic mutation is cautionary tale for crop gene editing
May 6, 2019
Unexpected interactions between mutations can be a thorn in the side for plant breeders. Scientists unveil what drove one infamous “cryptic” mutation.
Andrea Schorn zooms in on small RNAs in the cell
April 29, 2019
Dr. Andrea Schorn joins CSHL faculty as research assistant professor. Her focus is exploring transposable elements in the genome of mammalian cells.
How much are we learning? Natural selection is science’s best critic
December 17, 2018
Researchers determine that natural selection and our evolutionary history may be the best guides for future research.
Alexander Dobin dives into genomic data
June 8, 2018
Alexander Dobin joins the faculty as its newest assistant professor, working on the computational side of genomics research
A science writer’s quest to understand heredity
May 30, 2018
LabDish spoke with science writer Carl Zimmer about what he learned about heredity as he zig-zagged through CSHL while writing his new book.
CRISPR-based system identifies important new drug targets in a deadly leukemia
March 8, 2018
CRISPR was used to find 2 new druggable targets in a deadly leukemia
The secret to tripling the number of grains in sorghum and perhaps other staple crops
February 26, 2018
A simple genetic modification can triple grain production in sorghum, a drought-tolerant plant that is an important source of food and animal feed.
More rice, please: 13 rice genomes reveal ways to keep up with ever-growing population
February 1, 2018
Rice provides 20% of calories consumed. As the population grows toward 9 billion and the climate shifts, we'll need to grow more rice in more places.
Evolving sets of gene regulators explain some of our differences from other primates
January 29, 2018
What makes us different from our primate relatives? Gene regulation is one important evolutionary factor
Hannon named director of Cancer Research UK Cambridge Institute
November 21, 2017
Dr. Greg Hannon has been named the new director of the Cancer Research UK Cambridge Institute, effective February 1, 2018.
Library of CRISPR targeting sequences increases power and accuracy of the gene-editing method
July 20, 2017
New library of RNA sequences that can be used by researchers to direct the CRISPR-cas9 complex to cut DNA with unprecedented precision.
Newly identified small RNA fragments defend the genome when it’s ‘naked’
June 29, 2017
Fragments snipped from tRNAs protect embryonic stem cells while they’re being epigenetically reprogrammed.
New statistical method finds shared ancestral gene variants involved in autism’s cause
June 21, 2017
Researchers find children with autism are genetically more like other autistic children than their unaffected siblings.
How cool is science? Students use barcoded DNA to identify a weapon against antibiotic resistance
June 14, 2017
Sometimes viruses cause harmful infections, but students in the DNA Learning Center’s Urban Barcode Research Program identified a new virus that could.
Detailed new ‘reference’ genome for maize shows the plant has deep resources for continued adaptation
June 12, 2017
A new, much more detailed reference genome for maize, or corn, as it is called in the U.S., provides new insight into the crop.
What a real-life science test looks like
March 24, 2017
By revealing evidence that contradicts the rationale for a new cancer drug, a pair of student scientists learns firsthand that when you do science.
Dark matter of the genome, part 1
March 15, 2017
This episode of Base Pairs digs into "dark matter" a type of genetic information that could help scientists better understand diseases like
Focus on quiescent cells brings to light the essential role of RNA interference in transcription control
November 9, 2016
RNAi and other epigenetic processes induce changes in where and when specific genes are expressed without altering their genetic code.
How a cold-causing virus and inexplicable experiments helped revolutionize thinking about the genome
September 6, 2016
Nobel laureate Richard Roberts discusses the importance of RNA splicing and how scientists can learn from "failed" experiments.
August 15, 2016
This episode on Base Pairs explores how genetic information to better understand human history.
Riding out of the shadows of ALS, toward better treatments
August 1, 2016
Graduate student Lisa Krug discusses her research and personal connection to ALS, and Ride for Life, a not-for-profit organization for ALS research.
To divide or not: a cellular feedback loop that enables new cells to make a fateful decision
July 21, 2016
Team explains a key mechanism to prevent aberrant cell proliferation
“Amazing protein diversity” is discovered in the maize plant
June 24, 2016
The genome of the corn plant “is a lot more exciting” than scientists have previously believed.
Why is autism more common in boys?
April 29, 2016
Ivan Iossifov talks about some of the reasons why autism disproportionately effects boys on a genetic level.
What do autism “risk genes” do?
April 21, 2016
A discussion with Ivan Iossifov with what exactly the term "risk genes" means and what they do.
How many autism “risk genes” have scientists found?
April 14, 2016
A look at the research which points to the different genes potentially at the root of autism.
Where does autism come from when it doesn’t run in the family?
April 7, 2016
Associate Professor Ivan Iossifov discusses how parents who are not autistic can pass autism onto their children through their genes.
Scientists sequence genome of worm that can regrow body parts, seek stem cell insights
September 21, 2015
Worm’s genome could lead to better understanding of its regenerative prowess and advance stem cell biology.
The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!
July 6, 2015
Scientists work to figure out how to capture, store, process and interpret all that genome-encoded biological information.
A unique partnership
March 24, 2015
The story of a high school student working with Michael Schatz to create an app that analyzes DNA.
In a role reversal, RNAs proofread themselves
January 29, 2015
Molecular photographs of an enzyme bound to RNA reveal a new, inherent quality control mechanism
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Researchers have identified some 6600 genes whose level of expression varies within a comparatively restricted range in humans and mice
New junior faculty join CSHL
November 12, 2014
Interviews with new junior faculty members Jessica Tollkuhn and Je Lee.
Re-learning how to read a genome
November 10, 2014
Study suggests a unified model for how DNA is read, offering insight into how genes evolve
Missing sponge gene is found at ‘ghost’ site, proving our oldest common ancestor was more complex than believed
October 30, 2014
The last common ancestor of all animals, some 600 million years old, was not as primitive as most experts have assumed.
How a molecular Superman protects the genome from damage
October 16, 2014
Scientists find a new role for RNAi protein Dicer in preventing collisions during DNA replication.
Scientists looking across human, fly and worm genomes find shared biology
September 8, 2014
Researchers found that human, fly, and worm genomes have a number of key genomic processes in common, reflecting their shared ancestry.
A shift in the code: New method reveals hidden genetic landscape
August 18, 2014
Scientists develop algorithm to uncover genomic insertions and deletions involved in autism, OCD
Big Data meets DNA
June 17, 2014
Postdoctoral researcher Michael Hübner discusses how big data is being used in genomics and disease research.
The Single Cell Analysis course–at the cutting edge of science
August 20, 2013
A look at the second annual Single Cell Analysis course held as CSHL.
Full genome map of oil palm indicates a way to raise yields and protect rainforest
July 24, 2013
A single gene is identified whose regulation controls oil palm yield.
Two pioneering plant genomics efforts given a funding boost by National Science Foundation
September 5, 2012
New 5-year grant awarded to the Gramene database project to apply Reactome data model supports data integration efforts.
In massive genome analysis ENCODE data suggests ‘gene’ redefinition
August 31, 2012
Potentially far-ranging implications for complex disease.
Knowing thy genome: The science and ethics of personal genome sequencing
July 10, 2012
W. Richard McCombie talks about the ethics of getting one's genome sequenced, and what consequences it may have.
An error-eliminating fix overcomes big problem in ‘3rd-gen’ genome sequencing
June 29, 2012
The next “next-gen” technology in genome sequencing has gotten a major boost.
‘Most comprehensive’ genetic analysis of maize plant will help raise yields, expand its range
June 1, 2012
An international research team involving 17 institutions has published the most comprehensive analysis to date of the maize genome.
2012 “Biology of Genomes” in 140 ch@r@cters
May 25, 2012
CSHL's annual "The Biology of Genomes" meeting continued conversation on genomics through Twitter.
Research reveals how dynamic changes in methylation can determine cell fate
September 26, 2011
Scientists have uncovered intriguing new evidence helping to explain one of the ways in which a stem cell’s fate can be determined.
CSHL’s sequencing power gets a fresh boost
August 12, 2011
W. Richard McCombie discusses the evolution of genomic sequencing technology and the use of new third generation machines.
CSHL to help assemble ‘knowledgebase’ on plants, microbes, to aid US biofuel, environment efforts
July 15, 2011
Investigators at CSHL join initiative by the U.S. Department of Energy (DOE) to address the problem involving plant and microbial life.
Collaboration column: A new gene-hunting strategy locates genetic cause of a rare disease
April 14, 2011
CSHL scientists join collaboration in a new study on hereditary spastic paraparesis, a disease which impairs a person's ability to walk and move.
Collaboration column: SMA therapeutics and potential drug target for schizophrenia
March 11, 2011
CSHL's Adrian Krainer works on treatment for spinal muscular atrophy that reverses the disease's symptoms.
Reference genome of maize, America’s most important crop, is published by team co-led by CSHL scientists
November 19, 2009
Complex sequence and "HapMap" shed light on maize's "wonderful diversity" could help future efforts to adapt the plant to a warming climate.
Cold Spring Harbor Laboratory brings New York’s business elite up to speed on the personal genome
April 28, 2009
The much-heralded era of personalized medicine holds great hope for the future of healthcare in America
CSHL scientists find a new class of small RNAs and define its function
January 27, 2009
Small, stable RNAs clipped from mature protein-coding RNAs can regulate gene expression.
Scientists discover new class of small RNAs that regulate gene expression and protect the genome
May 13, 2008
Researchers published findings on small RNAs, identifying a brand new class and clarifying how a known class acts to regulate gene activity.
Scientists at Cold Spring Harbor Laboratory hone method to selectively target cancer genes and cells
February 21, 2008
Collaboration announced the development of a faster and more affordable method for discovering genes essential to the survival of cancer cell.
Cold Spring Harbor scientists devise novel, low-cost method of sifting genome’s high-value regions
November 6, 2007
Technique opens new horizons for scientists seeking disease-related genes.
Watson genotype viewer now online
June 28, 2007
Cold Spring Harbor Laboratory releases sequence browser.
Psychiatric Genomics Center established at Cold Spring Harbor Laboratory with $25 million gift from the Stanley Medical Research Institute
June 22, 2007
CSHL has received one of the largest gifts in its history from Theodore and Vada Stanley to establish the Stanley Center for Psychiatric Genomics.
CSHL selected for modENCODE Data Coordination Center
May 15, 2007
CSHL researcher Lincoln Stein, M.D., Ph.D. was selected to lead the National Human Genome Research Institute’s (NHGRI) data coordination efforts.
International Consortium launches new web-based tool
June 2, 2004
CSHL release Reactome, a curated database of humans biological processes, in collaboration with the European Bioinformatics Institute.
RNA Interference Library covers entire human genome
March 24, 2004
CSHL scientists created the first library of human RNA interference clones.
Lincoln Stein named 2004 Benjamin Franklin Award in Bioinformatics laureate
February 12, 2004
Lincoln Stein receives the Benjamin Franklin Award from the Bioinformatics Organization.
Genome Technology’s Institute of the Year is “Long Island’s Genomics Gem”
January 14, 2004
Cold Spring Harbor Laboratory was name the most innovative institution in bioinformatics by Genome Technology.
Plotting a course to understanding human health: International HapMap Project begins the cartography of human genome variation
December 17, 2003
CSHL researchers join other scientists across the globe in the HapMap project, hoping to better identify disease-related genes and develop therapies.
Researchers achieve germline transmission of RNAi “gene knockdown” in mice
January 19, 2003
CSHL's Gregory Hannon and his colleague find that inherited RNAi can lower or silence a specific gene, which has implications for disease treatments.
Mouse genome published: Medical research to benefit
December 4, 2002
W. Richard McCombie and colleagues publish a draft sequence of the mouse genome, with a comparative analysis to the human genome.
Top genome researchers gather at Cold Spring Harbor
May 7, 2002
Researchers from around the globe convened at the annual Genome Sequencing & Biology meeting.
Scientists report efficient “gene silencing” strategy
April 14, 2002
Researchers find a method to use a naturally-occurring mechanism to shut down selected genes in mammalian cells.
Finding genes in the human genome
November 28, 2001
Scientists develop new program that finds the on/off switches of pieces of genes.
Scientists report first complete genome sequence of a plant
December 13, 2000
Scientists complete the genome sequence of the mustard plant.
The silence of the clones: new link between DNA replication and ‘silent’ chromosome architecture
November 8, 2000
Researchers detail the intricate mechanism that duplicates the DNA sequence and the silenced parts of chromatin structure
Scientists issue telomerase caution
June 14, 2000
Scientists warn that using telomerase as a means of extending the life-span of human tissue could lead to cancer risks.
Maternal genes rule during early development
March 3, 2000
Scientists find that embryonic development is mostly control by the maternal genome in its early days.
Scientists report first complete DNA sequence of plant chromosomes
December 15, 1999
Scientists have entirely mapped the genome of the mustard plant, the first time feat for a plant species.
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.
The biological landscape is made up of millions of variables that interact in complex and often seemingly random ways. I am applying principles from physical and computational sciences to the study of biology to find patterns in these interactions, to obtain insight into population genetics, human evolution, and diseases including cancer.
Next generation sequencing technologies revolutionized many areas of genetics and molecular biology, enabling quantitative analyses of the entire genomes and paving the way for Personalized Medicine. We develop novel statistical methods and computational algorithms for multi-omics processing and integration, and leverage Big Genomic Data to elucidate various problems in precision health, such as genetic and epigenetic mechanisms of cancer development and progression, and clinical impact of functional variants.
Of the tens of thousand of protein-coding genes in the human genome, only a small portion have an experimentally defined function. For the rest, how can we determine what they do? My lab develops computational predictions based on co-expression networks. We are applying our predictions to understand neuropsychiatric disorders.
Only a small portion of the RNAs encoded in any genome are used to make proteins. My lab investigates what these noncoding RNAs (ncRNAs) do within and outside of cells, where regulators of their expression are located in the genome, and how perturbations of ncRNAs and their regulators contribute to disease.
As organisms develop, genes turn on and off with a precise order and timing, much like the order and duration of notes in a song. My group uses model organisms to understand the molecules that control the tempo of development. We also study how changes in the timing of gene expression contribute to diseases like cancer.
To ensure that cells function normally, tens of thousands of genes must be turned on or off together. To do this, regulatory molecules - transcription factors and non-coding RNAs – simultaneously control hundreds of genes. My group studies how the resulting gene networks function and how they can be compromised in human disease.
Every gene has a job to do, but genes rarely act alone. Biologists have built models of molecular interaction networks that represent the complex relationships between thousands of different genes. I am using computational approaches to help define these relationships, work that is helping us to understand the causes of common diseases including autism, bipolar disorder, and cancer.
My lab studies genes and signals in cells that regulate the growth and shape of plants. We have discovered several genes that control plant architecture by exerting an influence on stem cells. By identifying the genes that control the number of stem cells in corn plants, for example, we’ve discovered a means of boosting the yield of that vital staple.
Many types of cancer display bewildering intra-tumor heterogeneity on a cellular and molecular level, with aggressive malignant cell populations found alongside normal tissue and infiltrating immune cells. I am developing mathematical and statistical tools to disentangle tumor cell population structure, enabling an earlier and more accurate diagnosis of the disease and better-informed clinical decisions.
Cells are amazingly complex, with the ability to sense, and remember timing, location and history. I am exploring how cells store this information, and how their surroundings influence their communication with other cells. I am also developing various imaging and molecular sequencing methods for tracking genes, molecules, and cells to understand how cancer cells arise and evolve.
We have recently come to appreciate that many unrelated diseases, such as autism, congenital heart disease and cancer, are derived from rare and unique mutations, many of which are not inherited but instead occur spontaneously. I am generating algorithms to analyze massive datasets comprising thousands of affected families to identify disease-causing mutations.
My research team studies the genes that determine when and where, and thus how many, flowers are produced on plants. Flowers form on branches called inflorescences, which originate from stem cells. By studying the genes that control how stem cells become inflorescences, we are able to manipulate flower production to improve crop yields.
Chromosomes are covered with chemical modifications that help control gene expression. I study this secondary genetic code - the epigenome - and how it is guided by small mobile RNAs in plants and fission yeast. Our discoveries impact plant breeding and human health, and we use this and other genomic information to improve aquatic plants as a source of bioenergy.
Over the last two decades, revolutionary improvements in DNA sequencing technology have made it faster, more accurate, and much cheaper. We are now able to sequence up to 10 trillion DNA letters in just one month. I harness these technological advancements to assemble genomes for a variety of organisms and probe the genetic basis of neurological disorders, including autism and schizophrenia, better understand cancer progression and understand the complex structures of the genomes of higher plants.
I am a computer scientist who is fascinated by the challenge of making sense of vast quantities of genetic data. My research group focuses in particular on questions involving human evolution and transcriptional regulation.
When we think of evolution, we often think about physical changes, like a plant developing broader leaves to collect more solar energy. Such evolution actually occurs within the plant’s DNA. I am using computational analysis and modeling to visualize how plant genomes have evolved over time, particularly those of staple crops. We are learning from this work to improve the range and yield of modern plants.
Devastating diseases like cancer and autism can be caused by spontaneous changes to our DNA—mutations first appearing in the child, or in our tissues as we age. We are developing methods to discover these changes in individuals, tumors, and even single cells, to promote early detection and treatments