Research Menu

DNA chipGenomics 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.

    Public Lecture – Genetic privacy: friend or foe?

    Public Lecture – Genetic privacy: friend or foe?

    August 13, 2018

    Please join us for the 2018 Lorraine Grace lectureship on societal issues of biomedical research… GENETIC PRIVACY: Friend or foe? Yaniv Erlich, Ph.D. Chief Science Officer, MyHeritage Associate Professor of Computer Science, Columbia University [Leave Of Absence] Adjunct Core Member, New York Genome Center Q&A and coffee reception to follow


    Alexander Dobin dives into genomic data

    Alexander Dobin dives into genomic data

    June 8, 2018

    The development of analytical tools and algorithms is crucial in an era in which studies are producing more data than researchers know what to do with. Alexander Dobin, who joins the CSHL faculty as its newest assistant professor, does just that, developing new ways to analyze DNA sequencing data in the hope of fully annotating...


    A science writer’s quest to understand heredity

    A science writer’s quest to understand heredity

    May 30, 2018

    LabDish Blog At this very moment, there is more Neanderthal DNA on Earth than there was when Neanderthals were alive. Bits of their DNA, inherited tens of thousands of years ago, persist in many of our genomes today. This astounding legacy is one of many revelations that renowned science writer Carl Zimmer uses to burst...


    CRISPR-based system identifies important new drug targets in a deadly leukemia

    CRISPR-based system identifies important new drug targets in a deadly leukemia

    March 8, 2018

    Cold Spring Harbor, NY — Scientists at Cold Spring Harbor Laboratory (CSHL) have discovered a way to rein in an overactive protein that drives some aggressive leukemias. The renegade molecule, MEF2C, belongs to a class of proteins that is notoriously difficult to manipulate with drugs. But the new research suggests an opportunity to develop therapies...


    The secret to tripling the number of grains in sorghum and perhaps other staple crops

    The secret to tripling the number of grains in sorghum and perhaps other staple crops

    February 26, 2018

    Cold Spring Harbor, NY — A simple genetic modification can triple the grain number of sorghum, a drought-tolerant plant that is an important source of food, animal feed, and biofuel in many parts of the world. In new research reported today in Nature Communications, scientists at Cold Spring Harbor Laboratory (CSHL) have figured out how...


    More rice, please: 13 rice genomes reveal ways to keep up with ever-growing population

    More rice, please: 13 rice genomes reveal ways to keep up with ever-growing population

    February 1, 2018

    Cold Spring Harbor, NY — Billions of people around the world rely on rice as a mainstay of their diet. The grain provides about 20 percent of the calories consumed by humans worldwide. Rice production is critical for global food security, and demand will only grow as the world’s population expands by an estimated 2-3...


    Evolving sets of gene regulators explain some of our differences from other primates

    Evolving sets of gene regulators explain some of our differences from other primates

    January 29, 2018

    Cold Spring Harbor, NY – Today, biologists add an important discovery to a growing body of data explaining why we’re different from chimps and other primate relatives, despite the remarkable similarity of our genes. The new evidence has to do with the way genes are regulated. It’s the result of a comprehensive genome-wide computational analysis...


    Hannon named director of Cancer Research UK Cambridge Institute

    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. Currently an adjunct professor and HHMI Investigator at Cold Spring Harbor Laboratory, Hannon was a mainstay of the CSHL faculty for over 20 years, and one of several people at the Lab who helped design the...


    Library of CRISPR targeting sequences increases power and accuracy of the gene-editing method

    Library of CRISPR targeting sequences increases power and accuracy of the gene-editing method

    July 20, 2017

    Cold Spring Harbor, NY — CRISPR, the gene-editing technology that has taken biology by storm, is now more powerful than ever. Scientists have assembled a library of RNA sequences that can be used by researchers to direct the CRISPR-cas9 complex to cut DNA with exquisite, unprecedented precision. Among other advantages, the new tool greatly increases...


    Newly identified small RNA fragments defend the genome when it’s ‘naked’

    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 Cold Spring Harbor, NY — Our genomes are minefields, studded with potentially damaging DNA sequences over which hundreds of thousands of sentries stand guard. These sentries, called epigenetic marks, attach to the double helix at such spots and prevent the underlying DNA...


    New statistical method finds shared ancestral gene variants involved in autism’s cause

    New statistical method finds shared ancestral gene variants involved in autism’s cause

    June 21, 2017

    Cold Spring Harbor, NY — The way you measure things has a lot to do with the value of the results you get. If you want to know how much a blueberry weighs, don’t use a bathroom scale; it isn’t sensitive enough to register a meaningful result. While much more is at stake, the same...


    How cool is science? Students use barcoded DNA to identify a weapon against antibiotic resistance

    How cool is science? Students use barcoded DNA to identify a weapon against antibiotic resistance

    June 14, 2017

    LabDish blog Sometimes viruses cause harmful infections, but students in the DNA Learning Center’s Urban Barcode Research Program identified a new virus that could help fight dangerous infections. Viruses have a pretty bad reputation, but high schoolers Tony Valencia and Isabel Abonitalla are now determined to spread the idea that viruses can be our friends....


    Detailed new ‘reference’ genome for maize shows the plant has deep resources for continued adaptation

    Detailed new ‘reference’ genome for maize shows the plant has deep resources for continued adaptation

    June 12, 2017

    ‘Phenotypic plasticity’ traced to maize’s regulatory flexibility bodes well for expanding the staple’s growing range as the planet warms Cold Spring Harbor, NY — A new, much more detailed reference genome for maize, or corn, as it is called in the U.S., will be published in Nature today. In its accounting of the sequence of DNA letters in...


    What a real-life science test looks like

    What a real-life science test looks like

    March 24, 2017

    LabDish blog By revealing evidence that contradicts the rationale for a new cancer drug, a pair of student scientists learns firsthand that when you do science, you must ultimately treat everything as a hypothesis. At first, Ann Lin and Chris Giuliano thought, “we must have done something wrong.” The two Stony Brook undergrads are cancer...


    Dark matter of the genome, part 1

    Dark matter of the genome, part 1

    March 15, 2017

    Base Pairs podcast Could “genome” be a misnomer? The name implies that our genetic information is mainly genes, yet when the Human Genome Project was completed in 2003, it revealed that genes comprise a tiny minority. About 98 percent of the genome is something else—a kind of genomic dark matter. We’re kicking off the second...


    Focus on quiescent cells brings to light the essential role of RNA interference in transcription control

    Focus on quiescent cells brings to light the essential role of RNA interference in transcription control

    November 9, 2016

    Cancer forms when quiescent cells begin dividing and proliferating. New research from the Martienssen lab demonstrates that the RNAi machinery—which is often mutated in cancers—plays a key role in this transition, holding cells in quiescence.


    The “secret” science center where openness is everything

    The “secret” science center where openness is everything

    October 27, 2016

    LabDish blog What appears to be a few elegant houses tucked in the woods by the harbor is actually an epicenter of ideas in biology, from the iconic Human Genome Project in the late 1980s to the more down-to-earth subject of Lyme disease at this recent meeting. Maybe it’s no surprise that the Banbury Center has gained...


    How a cold-causing virus and inexplicable experiments helped revolutionize thinking about the genome

    How a cold-causing virus and inexplicable experiments helped revolutionize thinking about the genome

    September 6, 2016

    LabDish blog Nobel laureate Richard Roberts explains the importance of adenovirus in the landmark discovery of RNA splicing and his love for ‘failed’ experiments. Adenoviruses are best known for their role in causing illness. They may have been to blame for some of the colds and sore throats you’ve suffered through. But around CSHL, the...


    Non-modern family

    Non-modern family

    August 15, 2016

    Base Pairs podcast Few people today would take kindly to being called a Neanderthal. The name of this extinct human species has become synonymous with “stupid and rude,” and it’s not hard to see why. When we stand in front of museum dioramas depicting Neanderthals wearing little or no clothing, their hairy bodies crouched in...


    Riding out of the shadows of ALS, toward better treatments

    Riding out of the shadows of ALS, toward better treatments

    August 1, 2016

    LabDish blog Written by Lisa Krug Watson School graduate Lisa Krug studied ALS in flies, but the human element of this research always remained present for her. She explains in this guest blog post. ALS is a disease that makes itself nearly invisible. Although each year 6,400 Americans are diagnosed with Amyotrophic Lateral Sclerosis, often called...


    To divide or not: a cellular feedback loop that enables new cells to make a fateful decision

    To divide or not: a cellular feedback loop that enables new cells to make a fateful decision

    July 21, 2016

    New research from the Stillman lab has revealed that key components of the DNA replication machinery participate in a feedback loop to control cell proliferation. The proteins—which are often mutated in cancer—provide a direct link between replication and proliferation.


    “Amazing protein diversity” is discovered in the maize plant

    “Amazing protein diversity” is discovered in the maize plant

    June 24, 2016

    Cold Spring Harbor, NY — The genome of the corn plant—or maize, as it’s called almost everywhere except the US—“is a lot more exciting” than scientists have previously believed. So says the lead scientist in a new effort to analyze and annotate the depth of the plant’s genetic resources. “Our new research establishes the amazing...


    Why is autism more common in boys?

    Why is autism more common in boys?

    April 29, 2016

    LabDish blog Boys diagnosed with autism far outnumber their female counterparts. Autism genetics researcher Ivan Iossifov lays out what research into the disorder’s genetic basis reveals about the reasons for this striking pattern. Many of the numbers pegged to autism are staggering. By some estimates, as many as 1 in 68 children lies somewhere along...


    What do autism “risk genes” do?

    What do autism “risk genes” do?

    April 21, 2016

    LabDish blog Autism’s genetic roots are notoriously tricky to untangle, but researchers are beginning to understand how particular genes may contribute to the disorder. Among those researchers is CSHL’s Ivan Iossifov. For some disorders, genetics explains everything. Hemophilia is a good example: the abnormally profuse bleeding associated with it is neatly accounted for by a...


    How many autism “risk genes” have scientists found?

    How many autism “risk genes” have scientists found?

    April 14, 2016

    LabDish blog Autism genetics researchers are building up a list of autism “risk genes” by looking into the genomes of families affected by the disorder. CSHL’s Ivan Iossifov is one of the researchers leading the charge. “We actually have a list of genes about which we are very confident,” says Iossifov. “To be able produce...


    Where does autism come from when it doesn’t run in the family?

    Where does autism come from when it doesn’t run in the family?

    April 7, 2016

    LabDish blog Autism genetics expert Ivan Iossifov breaks down recent research that sheds light on how unaffected parents can pass autism onto their child. Parents with no history of autism in their families have a child who is diagnosed with the disorder. It’s a common and upsetting story. A quick Google search for “autism causes” is...


    Scientists sequence genome of worm that can regrow body parts, seek stem cell insights

    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 Cold Spring Harbor, NY — Tourists spending a recuperative holiday on the Italian coast may be envious of the regenerative abilities of locally found flatworm Macrostomum lignano. Named for its discovery near the Italian beach town of Lignano Sabbiadoro,...


    The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!

    The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!

    July 6, 2015

    Cold Spring Harbor, NY — Who’s about to become the biggest beast in the Big Data forest? A group of math and computing experts have arrived at what they say is a clear answer. It’s not YouTube or Twitter, social media sites that gobble up awesome quantities of bandwidth and generate hard-to-grasp numbers of electronic...


    A unique partnership

    A unique partnership

    March 24, 2015

    LabDish blog Written by Skyler Palatnick This post was written by Skyler Palatnick, a junior at Cold Spring Harbor High School with a penchant for writing about scientists. His first contribution to LabDish was about CSHL Director of Research David L. Spector. In this post, he introduces us to someone closer to home. A 14-year-old...


    Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues

    Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues

    November 19, 2014

    Results are part of a comprehensive view of the mouse genome that emerges from the Mouse ENCODE project Cold Spring Harbor, NY — An international team of researchers led by Professor Thomas R. Gingeras of Cold Spring Harbor Laboratory (CSHL) and Roderic Guigo, of the Centre For Genomic Regulation, Barcelona, have identified some 6600 genes...


    New junior faculty join CSHL

    New junior faculty join CSHL

    November 12, 2014

    LabDish blog This fall, the Lab welcomes six new faculty members. They’re a diverse group—a mix of junior and senior investigators, with research spanning across Biology. Want to know a little more? We are featuring brief profiles all week. So check back for more! Assistant Professor Je Lee, Genomics Where are you from? George Church’s...


    Re-learning how to read a genome

    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 Cold Spring Harbor, NY — There are roughly 20,000 genes and thousands of other regulatory “elements” stored within the three billion letters of the human genome. Genes encode information that is used to create proteins, while other genomic elements...


    Missing sponge gene is found at ‘ghost’ site, proving our oldest common ancestor was more complex than believed

    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—a creature that lived some 600 million years ago—was not as primitive as most experts have assumed. Cold Spring Harbor, NY — The last common ancestor of all animals—a creature that lived some 600 million years ago—was not as primitive as most experts have assumed. This is the fascinating implication...


    How a molecular Superman protects the genome from damage

    How a molecular Superman protects the genome from damage

    October 16, 2014

    The Martienssen lab found that Dicer, a canonical RNAi protein, facilitates the release of transcription machinery from DNA during replication, thereby preventing collisions and protecting the genome from damage.


    Scientists looking across human, fly and worm genomes find shared biology

    Scientists looking across human, fly and worm genomes find shared biology

    September 8, 2014

    Washington, DC and Cold Spring Harbor, NY — Researchers analyzing human, fly, and worm genomes have found that these species have a number of key genomic processes in common, reflecting their shared ancestry. The findings, appearing in the journal Nature, offer fresh insights into embryonic development, gene regulation and other biological processes vital to understanding...


    Big Data meets DNA

    Big Data meets DNA

    June 17, 2014

    LabDish blog Written by Michael Hübner, Postdoctoral researcher in Spector Lab Today, we welcome guest blogger Michael Hübner, a postdoctoral researcher in Professor David Spector’s lab. Dr. Hübner co-founded the Bioscience Enterprise Club, a resource for students and postdocs to explore science careers outside of academia. 300,000,000 sequence fragments. 20,000 megabytes of data. That is...


    The Single Cell Analysis course–at the cutting edge of science

    The Single Cell Analysis course–at the cutting edge of science

    August 20, 2013

    LabDish blog In June I had the chance to sit down and talk with Professors Jim Eberwine (University of Pennsylvania) and Cynthia McMurray (University of California, Berkeley/Lawrence Berkeley National Laboratory) about the Single Cell Analysis course they co-direct, held here at Cold Spring Harbor Laboratory (CSHL).The course, currently in only its second year, was a...


    In massive genome analysis ENCODE data suggests ‘gene’ redefinition

    In massive genome analysis ENCODE data suggests ‘gene’ redefinition

    August 31, 2012

    Cold Spring Harbor, NY — Most people understand genes to bespecific segments of DNA that determine traits or diseases that are inherited. Textbooks suggest that genes are copied (“transcribed”) into RNA molecules, which are then used as templates for making protein—the highly diverse set of molecules that act as building blocks and engines of our...


    Knowing thy genome: The science and ethics of personal genome sequencing

    Knowing thy genome: The science and ethics of personal genome sequencing

    July 10, 2012

    LabDish blog Until not too long ago, asking “Who am I?” of oneself often meant undertaking a voyage of self-discovery either through travel to a faraway land or through time-limited visits to a therapist’s couch. We now live in an era that offers a third, possibly cheaper armchair option. For less than the price of...


    An error-eliminating fix overcomes big problem in ‘3rd-gen’ genome sequencing

    An error-eliminating fix overcomes big problem in ‘3rd-gen’ genome sequencing

    June 29, 2012

    Michael Schatz and colleagues devised a method to correct errors in single molecule sequences, by combining long PacBio reads with shorter read sequencing data for > 99.9 percent base-call accuracy.


    ‘Most comprehensive’ genetic analysis of maize plant will help raise yields, expand its range

    ‘Most comprehensive’ genetic analysis of maize plant will help raise yields, expand its range

    June 1, 2012

    Cold Spring Harbor, NY and Washington, DC — An international  research team involving 17 institutions including Cold Spring Harbor Laboratory has published the most comprehensive analysis to date of the maize genome.  It is an achievement that substantially increases scientists’ understanding of differences across related but different species of the plant, which most North Americans call...


    2012 “Biology of Genomes” in 140 ch@r@cters

    2012 “Biology of Genomes” in 140 ch@r@cters

    May 25, 2012

    LabDish blog CSHL’s annual “The Biology of Genomes” meeting, held May 8-12 this year, has come to be known as the yearly shindig for researchers working in the vast and rapidly growing field of genomics. Named one of the top scientific conferences based on many criteria such as the quality of speakers, networking opportunities, etc.,...


    Research reveals how dynamic changes in methylation can determine cell fate

    Research reveals how dynamic changes in methylation can determine cell fate

    September 26, 2011

    Scientists at Cold Spring Harbor Laboratory (CSHL) and the University of Southern California (USC) have uncovered intriguing new evidence helping to explain one of the ways in which a stem cell’s fate can be determined. Cold Spring Harbor, NY — Scientists at Cold Spring Harbor Laboratory (CSHL) and the University of Southern California (USC) have...


    CSHL’s sequencing power gets a fresh boost

    CSHL’s sequencing power gets a fresh boost

    August 12, 2011

    LabDish blog At CSHL’s Woodbury Genome Center a decade ago, it took 12 technicians working in two shifts and six “first generation” sequencing machines to sequence 70 million bases of DNA—repeats of A, T, G, C—in a single month. By 2007, as the Center began to acquire “second generation” machines, the output jumped up to...


    CSHL to help assemble ‘knowledgebase’ on plants, microbes, to aid US biofuel, environment efforts

    CSHL to help assemble ‘knowledgebase’ on plants, microbes, to aid US biofuel, environment efforts

    July 15, 2011

    In Kbase, cloud computing brings disparate data streams into focus Cold Spring Harbor, NY — In the decade that has passed since the completion of the first draft sequence of the human genome, biologists have grown increasingly aware of a problem ironically generated by the success of their work.  Biological experiments in the age of...


    Collaboration column: A new gene-hunting strategy locates genetic cause of a rare disease

    Collaboration column: A new gene-hunting strategy locates genetic cause of a rare disease

    April 14, 2011

    LabDish blog With an ingenious combination of next-generation sequencing, conventional gene mapping and bioinformatics detective work, an Israel-led collaboration that includes CSHL scientists has helped a Palestinian family to confront the genetic culprit behind a rare, hereditary neurological disease that afflicts some of its members. The study appears in the April 12 online issue of...


    Collaboration column: SMA therapeutics and potential drug target for schizophrenia

    Collaboration column: SMA therapeutics and potential drug target for schizophrenia

    March 11, 2011

    LabDish blog CSHL researchers are part of two highly successful, multi-institutional collaborations that report exciting advances in developing therapeutics for a devastating neuromuscular disorder and in finding a ‘druggable’ target for schizophrenia. For several years now, CSHL’s Adrian Krainer has devoted his expertise in alternative splicing—a cellular process for editing RNA—towards fixing the genetic glitch that underlies...


    Podcast: CSHL Prof. Thomas Gingeras on new findings about the fly genome and why they are important

    Podcast: CSHL Prof. Thomas Gingeras on new findings about the fly genome and why they are important

    December 23, 2010

    CSHL Professor Thomas Gingeras, Ph.D., is a widely recognized genome investigator and developer of pioneering technologies used to probe it, including DNA microarrays. He is a co-principal investigator of ENCODE, The Encyclopedia of DNA Elements, a project launched by the National Genome Research Institute. Its aim: to compile a comprehensive list of functional elements across...


    CSHL scientists find a new class of small RNAs and define its function

    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 Cold Spring Harbor, NY — Researchers at Cold Spring Harbor Laboratory (CSHL) announced today the discovery of a new class of small RNAs. At the same time, they reported that their discovery suggests the presence of a strikingly novel biochemical pathway for RNA...


    Scientists discover new class of small RNAs that regulate gene expression and protect the genome

    Scientists discover new class of small RNAs that regulate gene expression and protect the genome

    May 13, 2008

    The list of short RNAs grows longer Cold Spring Harbor, NY — RNA is best known as a working copy of the DNA sequence of genes.  In this role, it’s a carrier of the genes’ instructions to the cell, which manufactures proteins according to information in the RNA molecule. But molecular biologists have increasingly realized...


    Scientists at Cold Spring Harbor Laboratory hone method to selectively target cancer genes and cells

    Scientists at Cold Spring Harbor Laboratory hone method to selectively target cancer genes and cells

    February 21, 2008

    A Genetic Cancer Genome Project is envisioned to identify new targets for cancer treatments Cold Spring Harbor, NY — Medicine’s cancer-fighting arsenal is not as accurate as many patients might wish. Chemotherapy and radiation treatments often cause serious side effects because they damage normal cells as well as cancerous ones. Scientists at Cold Spring Harbor...


    Cold Spring Harbor scientists devise novel, low-cost method of sifting genome’s high-value regions

    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 Cold Spring Harbor, NY — Scientists at Cold Spring Harbor Laboratory (CSHL) have developed a new means of extracting and interpreting data from the human genome that is more powerful and more economical than methods currently employed.  The new technology, called selective resequencing, promises to be...


    Watson genotype viewer now on line

    Watson genotype viewer now on line

    June 28, 2007

    Cold Spring Harbor Laboratory Releases Sequence Browser Nobel Laureate James D. Watson’s personal genome sequence is now publicly available on Cold Spring Harbor Laboratory’s (CSHL) web site. “I am putting my genome sequence on line to encourage the development of an era of personalized medicine, in which information contained our genomes can be used to...


    Psychiatric Genomics Center established at Cold Spring Harbor Laboratory with $25 million gift from the Stanley Medical Research Institute

    Psychiatric Genomics Center established at Cold Spring Harbor Laboratory with $25 million gift from the Stanley Medical Research Institute

    June 22, 2007

    Cold Spring Harbor Laboratory (CSHL) has received one of the largest gifts in its history from Theodore and Vada Stanley to establish the Stanley Center for Psychiatric Genomics on its Long Island campus. The goal of the Center is to unambiguously diagnose patients with psychiatric disorders based on their DNA sequence in 10 years time....


    CSHL selected for modENCODE Data Coordination Center

    CSHL selected for modENCODE Data Coordination Center

    May 15, 2007

    Setting the Paradigm for Organizing All Knowledge of Human Biology CSHL researcher Lincoln Stein, M.D., Ph.D. has been selected to lead the National Human Genome Research Institute’s (NHGRI) data coordination efforts in a $57 million initiative to identify all functional elements in the genomes of the fruit fly and roundworm. “This will open an unprecedented...


    International Consortium launches new web-based tool

    International Consortium launches new web-based tool

    June 2, 2004

    Joint Press Release European Bioinformatics Institute Cold Spring Harbor Laboratory Reactome Provides Map of Human Biological Pathways New York/Hinxton — A partnership between Cold Spring Harbor Laboratory (CSHL) and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EBI) has publicly released Reactome, a curated database of biological processes in humans. This database, available at www.reactome.org,...


    RNA Interference Library covers entire human genome

    RNA Interference Library covers entire human genome

    March 24, 2004

    Provides Biotech & Pharma Industry Powerful New Tool Cold Spring Harbor, NY — In a paper published this week in the journal Nature (March 25), scientists at Cold Spring Harbor Laboratory announced the creation of the first library of human RNA interference (RNAi) clones, which will eventually provide users the ability to shut off virtually...


    Lincoln Stein named 2004 Benjamin Franklin Award in Bioinformatics laureate

    Lincoln Stein named 2004 Benjamin Franklin Award in Bioinformatics laureate

    February 12, 2004

    Scientist, inventor and statesman, Benjamin Franklin once said, “As we enjoy great Advantages from the Inventions of others, we should be glad of an Opportunity to serve others by any Invention of ours; and this we should do freely and generously.” In his spirit, the Bioinformatics Organization, Inc. (Bioinformatics.org) established the Benjamin Franklin Award in...


    Genome Technology’s Institute of the Year is “Long Island’s Genomics Gem”

    Genome Technology’s Institute of the Year is “Long Island’s Genomics Gem”

    January 14, 2004

    Cold Spring Harbor Laboratory Researcher Named Most Innovative in Bioinformatics Cold Spring Harbor Laboratory, was named “Institute of the Year” in the November/December issue of Genome Technology, which called the Laurel Hollow research and educational powerhouse “Long Island’s Genomics Gem.” Cold Spring Harbor Laboratory Associate Professor Lincoln Stein was named “Most Innovative in Bioinformatics,” in...


    Plotting a course to understanding human health: International HapMap Project begins the cartography of human genome variation

    Plotting a course to understanding human health: International HapMap Project begins the cartography of human genome variation

    December 17, 2003

    Tracking down genes involved in health and disease and the response of patients to therapies is a principal goal of contemporary biomedical research. In the December 18 issue of Nature, the International HapMap Consortium describes the new tools and approaches it has developed that will enhance the ability of scientists to identify disease-related genes and...


    Researchers achieve germline transmission of RNAi “gene knockdown” in mice

    Researchers achieve germline transmission of RNAi “gene knockdown” in mice

    January 19, 2003

    RNA interference (RNAi) has emerged as an extremely versatile and powerful tool in biomedical research. A new study published in the February issue of Nature Structural Biology reports the creation of transgenic mice in which inherited RNAi lowers or silences the expression of a target gene, producing a stable “gene knockdown.” This finding extends the...


    Mouse genome published: Medical research to benefit

    Mouse genome published: Medical research to benefit

    December 4, 2002

    Cold Spring Harbor Laboratory scientist W. Richard McCombie and his colleagues in the international Mouse Genome Sequencing Consortium have published a high quality draft sequence of the mouse genome, along with a comparative analysis of the mouse and human genomes describing insights gleaned from the two sequences. This landmark study appears in the December 5...


    Top genome researchers gather at Cold Spring Harbor

    Top genome researchers gather at Cold Spring Harbor

    May 7, 2002

    Some 500 of the top genome scientists from around the world meet at Cold Spring Harbor Laboratory this week for the annual Genome Sequencing & Biology meeting. The researchers will exchange their latest findings in the burgeoning field of genome science. Sessions on Bioinformatics, Comparative Genomics, and High Throughput Biology (among others) will comprise more...


    Scientists report efficient “gene silencing” strategy

    Scientists report efficient “gene silencing” strategy

    April 14, 2002

    Genome Research and Medical Applications Expected to Flourish Treatments for cancer, AIDS and a host of other diseases may lie in scraps of hairpin-shaped RNA. Researchers at Cold Spring Harbor Laboratory have successfully co-opted a natural cellular mechanism to shut down the activity of specific genes in mammalian cells cheaply and efficiently. The new technique...


    Finding genes in the human genome

    Finding genes in the human genome

    November 28, 2001

    New Computer Program Detects Overlooked Gene Segments In order to study genes for a wide variety of research, diagnostic, or therapeutic purposes, scientists use computer programs that analyze DNA sequences. These programs indicate where pieces of genes are located within what is frequently a vast and complex genetic landscape. Although conventional programs detect many parts...


    Scientists report first complete genome sequence of a plant

    Scientists report first complete genome sequence of a plant

    December 13, 2000

    Cold Spring Harbor, NY — An international effort to sequence the entire genome of the plant species Arabidopsis thaliana is now complete. This first-ever complete genome sequence from a plant has many implications for biology, medicine, agriculture, and the environment because it will enable detailed studies of the entire genetic structure of plants to be...


    The silence of the clones: new link between DNA replication and ‘silent’ chromosome architecture

    The silence of the clones: new link between DNA replication and ‘silent’ chromosome architecture

    November 8, 2000

    Cold Spring Harbor, NY — As genetically identical cells (such as those in an embryo) multiply, different sets of genes are switched on, and others off, giving rise to cells and tissues with distinctive properties (e.g. liver versus muscle). Such differential gene expression is determined in part by the large-scale architecture or chromatin structure of...


    Scientists issue telomerase caution

    Scientists issue telomerase caution

    June 14, 2000

    Cold Spring Harbor, NY — The enzyme telomerase has received a great deal of attention since 1998 when researchers showed that expressing this enzyme in human tissue culture cells significantly extended the life-span of the cells. Telomerase expression was immediately recognized as a useful strategy for growing the large number of cells required for cell-based...


    Maternal genes rule during early development

    Maternal genes rule during early development

    March 3, 2000

    Possible Mechanism to Filter Deleterious Mutations Cold Spring Harbor, NY — For many years, scientists studying gene expression in plants assumed that genes inherited from both male and female parental sources contribute equally to development after fertilization. A new study by scientists working at Cold Spring Harbor Laboratory challenges this view, and instead indicates that...


    Scientists report first complete DNA sequence of plant chromosomes

    Scientists report first complete DNA sequence of plant chromosomes

    December 15, 1999

    In the midst of a heated public debate about genetically modified food, scientists have quietly reached a significant milestone in plant biology analogous to the recent sequencing of an entire human chromosome. Despite its status as a diminutive relative of the mustard plant, Arabidopsis thaliana has emerged as a powerful tool in plant molecular biology...


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

Gurinder Atwal

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.

Alexander Dobin

Alexander Dobin

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.

Jesse Gillis

Jesse Gillis

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.

Thomas Gingeras

Thomas Gingeras

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.

Christopher Hammell

Christopher Hammell

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.

Molly Hammell

Molly Hammell

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.

Ivan Iossifov

Ivan Iossifov

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.

David Jackson

David Jackson

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.

Alexander Krasnitz

Alexander Krasnitz

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.

Je H. Lee

Je H. Lee

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.

Dan Levy

Dan Levy

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.

Zachary Lippman

Zachary Lippman

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.

Rob Martienssen

Rob Martienssen

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.

W. Richard McCombie

W. Richard McCombie

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.

Adam Siepel

Adam Siepel

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.

Doreen Ware

Doreen Ware

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.

Michael Wigler

Michael Wigler

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