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Undergraduate Research Program

The Undergraduate Research Program (URP) at CSHL provides an opportunity for undergraduate scientists from around the world to conduct first-rate research. Students learn the scientific process, technical methods and theoretical principles, and communicate their discoveries to other scientists. Approximately 20 students come to CSHL each summer for the 10-week program, living and working in the exciting Laboratory environment.

URP participants work on an ongoing research project in one of CSHL’s expert labs. Research at CSHL focuses on:

  • Molecular Biology & Cancer
  • Genetics & Genomics
  • Neuroscience
  • Plant Biology
  • Quantitative Biology

In addition to doing research in the lab, URP participants attend a series of specially designed workshops, seminars and collegial events.  Workshops focus on learning particular skills, such as Python programming, while seminars cover research topics, responsible conduct of research, and career development. At the URP Symposium at the end of each summer, students present their research to the entire CSHL community.

URP participants live and work among CSHL scientists. They are invited to all Laboratory social activities, including an exclusive dinner with CSHL President Bruce Stillman. On weekends, students are free to explore nearby New York City or the sandy beaches of Long Island.

By the end of the summer, URP participants have first-hand experience of a career in scientific research.

Former URP participants share their summer experience

The 2021 URP Program will be held Monday, June 7–Saturday, August 7, 2021.

Scientific Research

All URP students undertake an original research project, mentored by one of CSHL’s outstanding research faculty. Students have access to the Lab’s state-of-the-art research facilities, including extensive resources for genomics and microscopy. At the end of the Program, students write a scientific manuscript about their summer work. Some of these become part of peer-reviewed scientific publications.

Bioinformatics and Computational Neuroscience Workshop

CSHL’s URP presents students with a two-part workshop in Bioinformatics and Computational Neuroscience.

Hands-on programming workshops

These workshops (1 per week) train students to use Python and R programming: Python course and R course

Lecture series

The lecture series consists of sessions focused on important topics in bioinformatics and computational neuroscience. Sessions include:

  • Genomics in the cell
  • Small RNA transcriptomics in Zea mays
  • Quantitative principles of the nervous system

Training in Scientific Communication

The Program offers lectures on how to give a scientific talk. In the course of the summer Program, students prepare a research abstract and a scientific report, and present two research talks for the entire CSHL scientific community.

Career Development

URP participants attend a series of lectures and panel discussions aimed at informing them about the process of pursuing a research career or a variety of non-research scientific careers. Sessions include:

  • Faculty perspectives on research careers
  • Graduate school and fellowship applications
  • Non-research career panel

Responsible Conduct of Research

Before starting work in their laboratories, URP participants attend a Responsible Conduct of Research workshop, which covers ethical issues in biological research. Students are also instructed in laboratory safety.

Current sophomores and juniors are eligible. Applications must be submitted online by January 15.

Online Application

  • All applicants must complete an URP application form with a personal statement online.
  • Faxed, mailed, or emailed applications are not accepted.
  • You may submit your application before the recommendation letters have been uploaded by your referees.
  • Once an application has been submitted, changes cannot be made. Please review your application carefully before submitting.
  • To use the online application system, you must first register as a user. On the main login page, there is a link that says “New User? Register Here” to the right of the “Go” button. If you do not see this option, make sure your internet browser is up-to-date and/or try a different browser (Chrome, Firefox, Safari). If you continue to experience problems, please contact Embark, the application manager at

Personal Statement

  • Your personal statement is limited to a single page – approximately 600 words or 3,250 characters (including spaces), single-spaced. You should use a minimum of 1-inch margins.
  • You should ensure that your statement is legible. We would appreciate a minimum of 11-point font, preferably sans serif (such as Helvetica). Other traditional fonts, such as Times New Roman, are also acceptable.

Dates and Deadlines

  • The deadline for receipt of completed applications, including letters of recommendation, is January 15 at 11:59 pm (23:59) Pacific Standard Time (equivalent to January 16, 07:59 UTC/GMT). Applications will not be reviewed if they are received after the deadline.
  • Recommendation letters will not be accepted after the application deadline. Please make sure your referees are aware of the January 15 deadline when you ask them to write a recommendation. Most referees need at least a month to complete a letter. If your referee has any problems uploading the letter to the online application system, they should contact directly.
  • Notification of application status will be sent by the end of March.


  • Students of any nationality are eligible for the program.
  • Students should have a strong academic background in a science. Although the Program emphasizes the biological sciences, students with engineering, chemistry, computer science, math, or physics backgrounds are also encouraged to apply.
  • Students must be returning to an undergraduate degree program following their URP summer research experience; current sophomores and juniors, or the equivalent, are eligible. Only in exceptional cases will first-year undergraduate students, with prior independent research experience, be considered.
  • Previous laboratory research experience will help your application but is not required.
  • If your academic semester conflicts with the dates of the URP program, you are still eligible to apply. If you are accepted into the Program, we will discuss how your academic schedule can be accommodated. For instance, in past years, some students have arranged with their professors at their home university to take one or more final exam at CSHL. But please note that all URP researchers are expected to participate in the program as a single group and must therefore plan to be at CSHL during the dates of the program.

Grades & Transcripts

  • Official transcripts are not required.
  • There is no minimum GPA required. Successful applicants generally have GPAs around 3.5 or higher in their science and math courses.
  • If your GPA is not on a 4.0 scale, then please convert your grade to a 4.0 scale. If your institution does not have a standard scaling, then calculate by dividing your average mark by the maximum possible mark and multiplying by 4.0.

International Applicants

  • Students of any nationality are eligible for the program.
  • TOEFL or IELTS scores are not required for admission to the URP program.
  • If your grades are not based on a 4.0 scale, please note your institution’s grading scale and the actual class mark you received on the application. Also indicate the best possible mark. For example, if your university scale is 1 to 5, then note your grade as X/5, 1=best.

Recommendation Letters

  • Applicants must arrange for two recommendation letters from professors – preferably in math or science – to be submitted online. We do not accept more than two recommendation letters.
  • If you have previous research experience, recommendation letters from professors with whom you have worked in a lab are especially encouraged. Letters from graduate students or postdocs in the lab are less effective.
  • Faxed, mailed, or emailed recommendation letters are not accepted.
  • Your referees will upload their recommendation letters directly to the online application system manager. When you fill in the application, you will submit the email addresses of your referees. Your referees will receive an email with instructions on how to upload their recommendation letter online. Please tell your referee that they will receive an email from the Embark application system so this notification email does not end up in spam.
  • You may submit your application before recommendation letters have been uploaded by your referees.
  • Recommendation letters will not be accepted after the application deadline. Please make sure your referees are aware of the January 15 deadline when you ask them to write a recommendation. Most referees need at least a month to complete a letter. If your referee has any problems uploading the letter to the online application system, they should contact directly.


Students receive a stipend of $5500. All room & board expenses will be covered. Travel costs are not reimbursed.

Housing Environment

URP students reside in new “cabins” on the Cold Spring Harbor Laboratory campus. Each cabin provides single-gender housing for eight individuals with two students per room, and two full bathrooms. All linens and towels are provided, along with full housekeeping services. Lamps, desks, dressers, and small refrigerators will be available in each cabin. One phone with voicemail option is available in each room in the cabin. The cabins are also equipped with Wi-Fi internet access. All cabins are fully air-conditioned.

Meals are served three times a day, seven days a week in the Blackford Dining Hall. Vegetarian and Vegan options are available at all times and our kitchen will make every effort to accommodate any special needs.

Gym equipment and weights are available in the exercise room located in the lower level of the Dolan Hall. Also, washer and dryer facilities are available in Dolan.

The Laboratory owns canoes and kayaks, available for URP student use. All participants are free to use our tennis and volleyball courts, running and hiking trails, swimming pool and private beach.

CSHL holds volleyball tournaments during the summer where different laboratory buildings square off against each other. URP students are invited to join these teams, compete against the graduate students throughout the summer and the faculty at annual URP vs. PI (Principal Investigator/Lab Head) tournament, held at the end of the summer.

What past URP participants said about their summer at CSHL.

Ahmet Doymaz with Dr. Leemor Joshua-Tor

Ahmet Doymaz
Ahmet Doymaz

The most important things I learned at Cold Spring Harbor were the core principles in carrying out a scientific project. The principal investigator with whom I worked, Leemor, taught me during our early meetings what mattered most when embarking on a scientific journey: asking a tangible scientific question and choosing the right method to tackle the problem. Working in her lab helped me grow and boost my confidence as a scientist, and while the expectations of high-level research were daunting at first, I quickly grew comfortable with exploring my project and arguing for what I found important.

This summer I was fortunate enough to be able to work with scientists who viewed and respected me as a fellow scientist, and who worked together with me to realize and refine the questions I had. I was lucky to have a great mentor that facilitated my structural biology journey, a field that was very new to me. I had a wonderful time at CSHL as an URP, and I would recommend the program to anyone who loves biology and who would like to experience the rigor of top-tier research. The program has a long history, and the various amenities offered, such as the housing, catering, planned activities, access to all of CSHL’s resources, and the stipend, reduce the hassles involved in moving to a new place and allow you to focus on what really matters—the science.

Owen Hughes with Dr. Tatiana Engel

Owen Hughes URP 2019
Owen Hughes

When I decided to come to Cold Spring Harbor Laboratory’s Undergraduate Research Program (URP), I did so fearing that, having minimal experience with bench biology, I would be wildly out of my depth and this would make me an outsider in the program. Upon arriving at the lab, I discovered that the former was true, but the latter was not. In my first conversation with a fellow URP participant—URP for short—I came to understand that 90% of what I thought I knew to be true about RNA was simplistic at best. After repeating this process in every area of biological research from healthy plant cells to cancerous human cells, I was worried that the other URPs would regard me as a freak (or at least an ignoramus). This couldn’t have been more misguided. I had the pleasure of working in Tatiana Engel’s lab to develop an uncannily elegant method of inferring neural dynamics from spike data, and the mathematical nature of our lab made it easy for me to integrate into the scientific community there. More surprisingly, the seminars that were organized by the URP directors allowed me to gradually broaden my bench-biology horizons, and chance meetings with bench scientists during my daily coffee break would often lead to a lengthy discussion about the methods that they use in their research. Gradually I was able to speak to the other URPs about what they were doing, and even ask them questions—occasionally even intelligent ones!

This program is one of the most formative experiences in my research career to date. By working in close quarters with academically productive post-docs and savvy professors, I got an honest view of what scientific research looks like. Through seminars, socials, and late-night debates with scientists from biological fields macro and micro, I got a vivid picture of the brilliance and altruism as well as the intense ambition and competition that are central to the way that modern science operates. Working in a burgeoning field like computational neuroscience comes with certain sources of anxiety; the invaluable mentorship that I received over the course of this summer exposed me to and helped me deal with these stressors, and my constant exposure to other labs helped me to see a broad picture of computational neuroscience. Although I reach the end of the summer believing that I’m not well suited for the field, the URP program trusted me with an unfiltered view of what scientific research looks like at a prestigious institution such as Cold Spring Harbor; I’m unable to overstate how useful this experience was to me and to the other URPs I worked and lived with.

The URP program at Cold Spring Harbor Laboratory provided me and the other URPs with an opportunity to practice crucial skills in research–presenting, learning to manage a relationship with an advisor, and how to network with scientific peers. They also selected an impeccable group of peers to help each other cope with the endemic intensity of world-class scientific research, and for these reasons, I will be forever grateful to the program for the time I was able to spend there.

Samantha Rothberg with Dr. Doreen Ware

Samantha Rothberg URP 2019
Samantha Rothberg

Cold Spring Harbor is like a summer camp for scientists. From petri dish relay races to biology-themed art installations to post-work volleyball tournaments, the CSHL community combines science and classic summer fun in the best, quirkiest way possible. My summer in the URP program was one of the most memorable I have ever had. Everyone I worked with was so supportive of my experience as an “URP,” willing to both meet me where I was and push me to improve my skills, hard and soft. This group included my PI and my mentor. I was grateful for the way my mentor gave me a mix of guidance and freedom in my work, allowing me to grow more independent as the summer progressed. My academic support base at CSHL also extended past my designated mentors. It included other faculty in my lab and in neighboring labs, who all contributed to my education even though I was not their student.

My learning as an URP did not stop once I left my lab for the day. My fellow URPs were the most engaged, inquisitive, and knowledgeable group of students I have ever been lucky enough to be a part of. We spent many meals and nights talking about science/math (often over a game of Catan)—about each other’s projects, cool recently published papers, or weird debates such as the one over whether we should bring back the wooly mammoth. These conversations made me more sure of my desire to pursue a career in research, and also just made my summer all the more enjoyable. So, to any student who is passionate about science and, even more so, about learning in a rigorous and immersive, yet fun environment, I cannot recommend the CSHL URP program highly enough.

Yin Yaun with Dr. Christopher Vakoc

Yin Yaun URP 2019
Yin Yaun

Participating in this Undergraduate Research Program at Cold Spring Harbor Laboratory over this summer provided me with a fantastic opportunity to immerse into a world which exposed me to the leading edge of biological sciences. I enjoyed the environment of living in this relatively small community in which I could work closely with both my mentor and my principal investigator as well as form close relationships with my fellow undergraduates and people at CSHL. It is tremendously inspiring for me to work with my outstanding and dedicated mentor and principal investigator who offered me invaluable guidance and support throughout the program, leading me through the process of carrying out independent scientific research. There were also chances to attend various courses, meetings and conferences that are incredibly helpful for me to develop a comprehensive understanding about the latest topics in biological sciences. Not need to mention the unique Python programming workshops and Alumni talks at lunchtime offered me skills and insights with lifelong benefits.

Additionally, I learned a lot along with my fellow undergraduates by joining a casual discussion about our experimental updates and results over lunch and dinner as well as presenting at the final symposium about our individual projects. It was definitely a pleasure for me to play frisbee and volleyball after dinner, enjoy the sunset and BBQ at the beach in CSHL and hangout at NYC or Huntington town over weekends with my fellow undergraduates. I entirely enjoyed this exceptional and rewarding summer research experience at CSHL which equipped me with essential techniques and critical thinking skills that both will be significant for my future research career.

2018 and earlier Student Perspectives

Since 1959, the URP Program has been offering undergraduate students a unique opportunity to study with CSHL’s renowned scientists. Some of our notable alumni include Nobel laureate Dr. David Baltimore (California Institute of Technology), Dr. Gerry Rubin (HHMI, Janelia Farm Research Campus), Dr. Alfred Goldberg (Harvard Medical School), Dr. Geraldine Seydoux (Johns Hopkins), and Dr. Charles Gilbert (Rockefeller University), among many others.

Undergraduate Research Program URP Alumni 2019
The CSHL Undergraduate Research Program (URP) participants, Summer 2019

Previous alumni by year

2019  |  2018  |  2017  |  2016  |  2015  |  2014  |  2013  |  2012  |  2011  |  2010  |  2009  |  2008  |  2007  |  2006  |  2005  |  2004  |  2003  |  2002  |  2001  |  2000  |  All URP Alumni PDF icon

URP Alumni Update

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NSF Sponsored REU in Bioinformatics and Computational Biology

CSHL’s REU program in Bioinformatics and Computational Biology was supported by the NSF 2005 – 2014 and 2016 – present.

The technological advances in this century open a new realm of biological questions that can be addressed experimentally. Large genomic sequence or image datasets are routinely and quickly acquired, but the resources and expertise to analyze this data present a challenge to researchers. CSHL’s unique NSF REU program in Bioinformatics and Computational Biology addresses this need by providing early training to undergraduate students who might not otherwise pursue quantitative approaches. CSHL’s URP/REU students learn theory and techniques from an applied perspective, investigating an important biological problem rather than from the abstract perspective of computer science. Students are mentored by expert CSHL researchers, who combine biology, information theory and sophisticated computational techniques to address questions at the frontiers of modern genomics, bioinformatics, and neuroscience. In the past ten years, CSHL’s URP/REU program has recruited and trained a diverse group of students, many of whom are still working in bioinformatics or computational fields. Almost all URP/REU participants have continued in scientific careers and/or advanced degree programs at competitive institutions. The program provides students with a modern quantitative biology training program that aims to inspire young scientists to become active participants in modern biological research with its demands for quantitative and computational skills.

Prospective REU Project Mentors

  • Dinu F. Albeanu – Neuronal circuits; sensory coding and synaptic plasticity; neuronal correlates of behavior; olfactory processing
  • Gurinder Atwal – Population genetics; bioinformatics; cancer; stochastic processes; statistical mechanics and information theory
  • Anne Churchland – Decision-making; electrophysiology; sensory processing; vision; audition; neural computation; modeling; behavior
  • Alexander Dobin – Computational genomics; transcriptomics; epigenomics; gene regulation; big data; precision medicine
  • Tatiana Engel – Neural dynamics and computation; neural circuit models; machine learning; stochastic processes; dynamical systems theory; decision-making; attention
  • Hiro Furukawa – Membrane proteins; x-ray crystallography; electrophysiology
  • Thomas Gingeras – Genome-wide organization of transcription and the functional roles of non-protein coding RNAs
  • Molly Hammell – Gene regulatory networks; integrated genomic analysis; bioinformatics; RNA biology; small RNAs
  • Ivan Iossifov – Computational biology; molecular networks; human genetics; human disease; applied statistical and machine learning; biomedical text-mining; molecular evolution
  • David Jackson – Plant development; stem cell signaling; genomics and imaging
  • Leemor Joshua-Tor– Structural biology; nucleic acid regulation; RNAi
  • Adam Kepecs – Decision-making; theoretical neuroscience; neuroeconomics
  • Justin Kinney – Sequence-function relationships; biophysics; deep sequencing; machine learning; transcriptional regulation; DNA replication
  • Alexei Koulakov – Theoretical neurobiology; quantitative principles of cortical design; computer science; applied mathematics
  • Alexander Krasnitz – Genomics of cancer; machine learning for biology; inference from noisy biological data; large-scale numerical computing.
  • Je H. Lee – Single-cell; in situ RNA-seq; non-coding RNA; spatial genomics; cancer microenvironment; pancreatic cancer
  • Zachary Lippman – Plant development, genetics; molecular mechanisms of phase transitions for flowering time and inflorescence branching; heterosis
  • Rob Martienssen – Epigenetics; DNA methylation; chromatin and chromosome biology; transposable elements; RNA interference; stem cells; germline specification; plant genomics; plant evolution; aquatic plants
  • David McCandlish – Computational biology; sequence-function relationships; population genetics; protein evolution; machine learning
  • W. Richard McCombie – Genomics of psychiatric disorders; genomics of cancer; computational genomics; plant genomics
  • Partha P. Mitra – Neuroinformatics; theoretical engineering; animal communications; neural prostheses; brain mapping; developmental linguistics
  • Pavel Osten – Anatomical mapping of brain connectivity; neurological diseases
  • Ullas Pedmale – Plant growth; signaling; genomics; development; plant-environment interactions
  • Adam Siepel – Biological statistics; population genomics; evolution; transcriptional regulation
  • David L. Spector – Cell biology; gene expression; nuclear structure; microscopy
  • Doreen Ware – Computational biology; comparative genomics; genome evolution; diversity; gene regulation; plant biology
  • Michael Wigler – Human genetic disorders; population genetics; cancer genomics
  • Anthony Zador – Cortical mechanisms of auditory attention; neural computation; connectomics


All URP participants may take part in the Bioinformatics and Computational Biology program. NSF-supported REU participants are selected from among the URP participants. Students supported by NSF must be citizens or permanent residents of the United States or its possessions. If you are interested in bioinformatics and computational neuroscience, including research in any of the labs listed above, but are not a US citizen or permanent resident, you are eligible for the program through sponsorship from non-restricted URP fellowships.

As for all URP participants, NSF-supported students must be currently enrolled as undergraduates. An undergraduate student is a student who is enrolled in a degree program (part-time or full-time) leading to a baccalaureate or associate degree. Students who will have graduated before the program starts in June are not eligible.

Participants must be “returning to an undergraduate program” after the summer REU program. (See NSF eligibility requirements).

REU Program Alumni