Research Menu

cancer geneticsThe Cancer Genetics Program is focused on revealing the structure and landscape of cancer genomes. Such information provides insight into how cancer develops, progresses, and responds to therapy. The Program includes a diverse collection of faculty who are developing new technology that is changing how researchers across the globe study cancer. The Program currently has three main focus areas: experimental technology, bioinformatics, and cancer progression.

Program Co-leaders

cancer geneticsIn the Cancer Genetics Program, research is driven by the desire to innovate, developing new strategies that will allow researchers to rapidly interrogate, analyze, or model cancer risk, tumor development and progression, or cancer therapies. This innovative spirit is bolstered by an interactive environment, with numerous partnerships both within the CSHL Cancer Center and with other collaborators around the world. Research in the Cancer Genetics Program has had a broad impact on the cancer community, providing tools and strategies that facilitate bench research while offering new technologies to better diagnose, monitor, and treat cancer in the clinic.

The Cancer Genetics Program continues to make discoveries that have an impact on our understanding of cancer and on the lives of patients. Members of this program are focused on both the genetics and epigenetics of cancer—studying changes in bulk tissue and, increasingly, in single cells. The Program is also expanding their preclinical and clinical research, taking advantage of the close partnership between CSHL and Northwell Health to explore the genomics of patient samples. In addition, this Program benefits from significant strengths in computational research that have a broad impact on research, from helping to identify driver mutations in cancer population to improving cancer diagnostics in the clinic.

    New method to determine <em>before</em> surgery which prostate tumors pose a lethal threat

    New method to determine before surgery which prostate tumors pose a lethal threat

    December 1, 2017

    Prostate cancer is common and largely nonlethal. But for some 21,000 men—a small percentage of the total, but a nonetheless substantial number—the disease is fatal. For earlier and more accurate detection, the Krasnitz and Wigler labs have devised a new method to analyze tumor biopsies to identify the most lethal forms of prostate cancer.


    Next-gen cancer test

    Next-gen cancer test

    November 24, 2017

    Knowing that cancers become lethal when they spread, investigators at Cold Spring Harbor Laboratory (CSHL) seek a way of detecting tumors much earlier than now possible—when they’re more likely to be curable. Fleshing out an idea Professor Michael Wigler had years ago—before there was technology to act on it—research led by Associate Professor Alexander Krasnitz...


    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...


    Relationship between incorrect chromosome number and cancer is reassessed after surprising experiments

    Relationship between incorrect chromosome number and cancer is reassessed after surprising experiments

    January 12, 2017

    Copy number variation is a hallmark of most cancers, and it often serves as a driver of cell proliferation. Surprisingly, new research from the Sheltzer lab suggests that an extra chromosome alone is not enough to initially spur tumor growth. Rather, prolonged changes in chromosome number lead to genetic instability that ultimately causes uncontrolled cell proliferation.


    A theoretical physicist’s approach to breast cancer

    A theoretical physicist’s approach to breast cancer

    October 21, 2016

    LabDish blog Written by Gurinder “Mickey” Atwal Ideas borrowed from physics could help scientists improve treatments for breast cancer. Associate Professor Mickey Atwal explains in this guest blog post. Breast cancer is more than a group of rogue cells. They exist within an intricate battleground inside patients, which scientists call the “microenvironment.”  This consists not only of...


    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    April 12, 2016

    Cold Spring Harbor, NY – Two scientists, both leaders of research labs at Cold Spring Harbor Laboratory (CSHL), are among 25 teams that have won Human Frontier Science Program (HFSP) Research Program Grants for 2016. The awards were announced by the International Human Frontier Science Program Organization (HFSPO), based in Strasbourg, France. The two CSHL...


    Introducing the mighty Panoramix–defender of genomes!

    Introducing the mighty Panoramix–defender of genomes!

    October 15, 2015

    Protein named for comic book hero is no joke: it guides gene-silencing machinery to sites of havoc-causing transposons Cold Spring Harbor, NY — Organisms from bacteria to humans must defend themselves against parasitic genetic elements called transposons, and the stakes are high. These pieces of DNA, which disrupt genes by jumping around  in the genome,...


    CSHL Fellow wins 2015 NIH Early Independence Award for cancer research

    CSHL Fellow wins 2015 NIH Early Independence Award for cancer research

    October 6, 2015

    Cold Spring Harbor, NY — Cold Spring Harbor Laboratory (CSHL) today congratulates CSHL Fellow Jason Sheltzer, Ph.D. on receiving the 2015 Early Independence Award from the National Institutes of Health (NIH) High Risk, High Reward Research Program. With a Ph.D. in Biology from MIT, Sheltzer joined CSHL in August 2015 to pursue cancer research. Sheltzer,...


    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,...


    Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases

    Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases

    September 4, 2015

    The Schatz lab, in collaboration with the Wigler and Atwal labs, has developed a new interactive, open-source analysis program called Gingko that can be used to reduce the uncertainty of single-cell analysis and visualize patterns in copy number mutations across populations of cells.


    12th annual LI2DAY Walk raises over $400,000

    12th annual LI2DAY Walk raises over $400,000

    September 1, 2015

    Cold Spring Harbor, NY – Cold Spring Harbor Laboratory (CSHL) is among 17 Long Island-based organizations to receive funding from the 2015 Long Island 2 Day Walk to Fight Breast Cancer.  This year’s walk raised over $400,000 for outreach services, educational programs and research to benefit women and their families affected by breast and other...


    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...


    Scientists show the mammary gland ‘remembers’ prior pregnancy, spurring milk production

    Scientists show the mammary gland ‘remembers’ prior pregnancy, spurring milk production

    May 7, 2015

    Camila dos Santos, as a postdoctoral researcher in the Hannon lab, identified the epigenetic changes that occur after pregnancy in the mouse mammary gland. The work offers insight into how pregnancy early in life may protect against breast cancer later.


    Tumor cells that mimic blood vessels could help breast cancer spread to other sites

    Tumor cells that mimic blood vessels could help breast cancer spread to other sites

    April 8, 2015

    The Hannon lab developed a novel mouse model for breast cancer heterogeneity and used it to identify clones that were highly metastatic. The team found that these cells formed tube-like structures that mimic blood vessels, and identified two genes that drive vascular mimicry, which is likely promote growth of the primary tumor as well as metastasis.


    Cold Spring Harbor Laboratory engages Hairpin Technologies Inc. to license its short hairpin RNA (shRNA) technology

    Cold Spring Harbor Laboratory engages Hairpin Technologies Inc. to license its short hairpin RNA (shRNA) technology

    March 31, 2015

    Cold Spring Harbor, NY — Cold Spring Harbor Laboratory (CSHL) has engaged Hairpin Technologies Inc. to expand the commercial distribution and research use of short hairpin RNA (shRNA) technology.  Hairpin Technologies will serve as CSHL’s exclusive agent for negotiating and executing new license agreements with potential licensees of CSHL’s U.S. and international patents covering the...


    CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship

    CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship

    February 20, 2015

    Cold Spring Harbor, NY — Associate Professor Michael Schatz of Cold Spring Harbor Laboratory (CSHL) will receive a 2015 Alfred P. Sloan Foundation Research Fellowship. This prestigious research award has been issued since 1955. Schatz is one of 126 outstanding early-career scientists from the U.S. and Canada recognized by the Foundation this year. Past honorees...


    Harnessing data from Nature’s great evolutionary experiment

    Harnessing data from Nature’s great evolutionary experiment

    January 21, 2015

    Scientists develop a computational method to estimate the importance of each letter in the human genome Cold Spring Harbor, NY — There are 3 billion letters in the human genome, and scientists have endlessly debated how many of them serve a functional purpose. There are those letters that encode genes, our hereditary information, and those...


Building publication list.
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.

Kenneth Chang

Kenneth Chang

Currently the Director of the Functional Genomics Shared Resource at CSHL. His studies focus on shRNA, microRNA, RNA interference, and siRNA. The lab has studied cancer proliferation gene discovery through functional genomics.

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.

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.

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.

Scott Lyons

Scott Lyons

Applies non-invasive imaging methods and develops new imaging reagents to facilitate the use of genetically engineered mouse models of cancer in pre-clinical and basic cancer research. As Director of Animal Imaging, he provides collaborative research support to investigators at both CSHL and neighboring institutions and will an important role in the pre-clinical research facility at CSHL.

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.

Alea A. Mills

Alea A. Mills

Cells employ stringent controls to ensure that genes are turned on and off at the correct time and place. Accurate gene expression relies on several levels of regulation, including how DNA and its associated molecules are packed together. I study the diseases arising from defects in these control systems, such as aging and cancer.

Jon Preall

Jon Preall

Developing single-cell genomics technologies for applications related to cancer progression, immune surveillance, and discovery of rare novel cell types and transcriptional programs.

Jason Sheltzer

Jason Sheltzer

Nearly all tumors exhibit a condition known as aneuploidy – their cells contain the wrong number of chromosomes. We’re working to understand how aneuploidy impacts cancer progression, in hopes of developing therapies that can specifically eliminate aneuploid cancers while leaving normal cells unharmed.

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.

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