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URECA Bulletin Board

* Note: The list below is only a small sampling of the opportunities available at Stony Brook. Many students find opportunities by contacting faculty directly by email.

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Posted 8/24/20 - POSITION FILLED

Computational analysis of cancer genomes at Cold Spring Harbor Laboratory

The Sheltzer Lab at Cold Spring Harbor Laboratory is seeking undergraduate researchers for a
computational project analyzing the genomic aberrations found in cancer. The position can pay
hourly or provide course credit, depending on the student’s preference.
Human tumors exhibit an exceptionally wide range of clinical behaviors. Some cancers remain
dormant for years, never threatening a patient’s life or wellbeing, while other cancers rapidly grow
and metastasize despite systematic treatment. The Sheltzer Lab is interested in discovering and
characterizing the genomic changes in cancer cells associated with patient outcome. By studying
clinical genomic data, we seek to identify aberrations found specifically in patients with lethal
tumors. These aberrations may serve as targets for therapeutic development, or as biomarkers
to identify the patients most likely to benefit from aggressive treatment. More information on this
project can be found in one of our previous publications:
Smith, J.C., and Sheltzer, J.M. (2018). Systematic identification of mutations and copy number
alterations associated with cancer patient prognosis. eLife, e39217.
The student will develop and implement software to analyze genomic and transcriptomic data
from human cancers. These projects involve creating new software systems for analysis, as well
as running and expanding upon existing systems for novel experiments.

Position Requirements

 Ability to work at least 12 hours a week (which could include evenings and weekends).
 Experience in Python.
 Familiarity with Linux and command line tools.
 Experience with git (or other VCSs), pandas, or software engineering best practices are
preferred but not mandatory.
It is possible to work on this project remotely – living on Long Island for the 2020-21 academic
year is not a requirement.

More information can be found on the Sheltzer lab website: http://www.sheltzerlab.org. Interested
students should send a CV and cover letter to Dr. Sheltzer at sheltzer@cshl.edu.

 




Posted 12/20/19 

Abigail Nishimura is a PhD candidate in the Functional Morphology Laboratory (Department of Anthropology). She is looking for undergraduate researchers to assist with a project exploring human and primate evolution. The research focuses on neck and spine evolution in primates and other mammals. The ultimate goal of the project is to learn about how the neck relates to the evolution of bipedalism in the human lineage. Abigail has gathered a large comparative sample of animal skeleton micro-CT scans. Undergraduate researchers will be trained to use Amira software to process these three-dimensional CT scans in order to isolate and examine individual bones in the scans. Undergraduate researchers are also invited to join Functional Morphology Lab meetings led by Dr. Gabrielle Russo. 
Position requirements: 
-Interested undergraduates must be detail-oriented, patient, and eager to work in a collaborative environment. Some experience with anatomy or osteology is a bonus but is not required. Non-senior applicants are preferred, as it is hoped that the researchers will be interested in working for two or more semesters. 
-Undergraduates should be prepared to work for at least 3-4 hours per week, but more time can be accommodated if requested. 
-One volunteer semester is required before positions will be offered for course credit. 
Interested undergraduates should submit application materials to abigail.nishimura@stonybrook.edu. Application instructions can be found here:  https://abigailnishimura.weebly.com/undergraduate-researchers.html.

 




Posted 2/26/19 - POSITION FILLED

The Lynch Lab for Quantitative Ecology (Ecology & Evolution Dept.) is looking for two undergraduate researchers to assist with a project using photo-identification to track Weddell seals around Antarctica. Our field team has collected hundreds of photos of Weddell seals and we have recently begun scraping the web for more photographs. We use the unique markings on each seal to identify individuals when they show up in different locations. The research assistant will assist primarily in our matching program - looking through our catalog of individuals to determine whether a seal has been previously sighted or is new to our database.

Interested undergrads should have an interest in ecology and a fine attention to visual detail, as this work relies on visual pattern matching between seals that are in different positions, lighting conditions, etc. Some experience with statistics and/or GIS a plus if interested in developing an independent student project out of the work. Students should be prepared to work 6-10 hrs per week during the term and are welcome to join our weekly lab meetings as well.

Have a look at  www.lynchlab.com for information about the lab and our research. If interested please submit a cover letter describing your academic interests and any research experience (or interest in research if no prior experience!) and a CV (including relevant coursework).



Posted 2/8/19

The Preall Lab at Cold Spring Harbor Laboratory is seeking a motivated undergraduate summer intern to participate in a research project. The student will work within the Single Cell Analysis Core Facility at Cold Spring Harbor where they will learn to use laboratory techniques such as mammalian cell culture, molecular cloning, microfluidic encapsulation, and next-generation sequencing and apply these tools towards the characterization of clonally expanding immune cell populations in the tumor microenvironment. The student will also learn about lab techniques such as flow cytometry and single cell transcriptomics, and computational data analysis.  The ideal candidate will be highly self-motivated, and will contribute to the design and troubleshooting of a technically challenging, but highly rewarding project.

Requirements: 

  • Must be at least a junior in college 
  • Must have taken organic chemistry or completed an upper level biology lab class 
  • Excellent communication skills and willing to work as part of a team 
  • Available to work between 9-5 at least three days a week between May and August with flexible start and end dates 
  • Enthusiasm to tackle new challenges 
  • A car or ability to commute to the Woodbury campus at Cold Spring Harbor Laboratory (A CSHL shuttle is available from Syosset train station)
  • Lab experience preferred

Applicants should send materials to Jon Preall via email at jpreall@cshl.edu and should include: A cover letter; Resume; List of relevant coursework

 


 

The Turner Lab in the Department of Anatomical Sciences is seeking undergraduate researchers for a project examining large-scale patterns of neuro-sensory evolution in living and fossil crocodiles. This paleontological research relies on a growing dataset of conventional CT and microCT scans of fossil crocodylomorph skulls. Undergraduate researchers will be responsible for digital segmentation of these CT datasets and creation of digital 3D models of brain, inner ear, and trigeminal nerve endocasts.

Crocodylomorpha is reptile group that includes living crocodylians and their close extinct relatives. Crocodylomorph evolution spans over 230 million years and multiple mass extinction events. The group has evolved over four orders of magnitude in body size and into ecological and phenotypic diversity paralleling those of Cenozoic mammals. Due to their taxonomic and ecological diversity, crocodylomorphs are a model system for studying how the demands of major habitat and ecological shifts result in large-scale evolutionary transformations. Crocodylomorphs have undergone several transitions from terrestrial predators into pelagic (open ocean marine), semi-aquatic (near-shore and river), and herbivorous niches. Overall brain shape and the positional sensing system of the inner ear are two of many systems expected to change across these ecological shifts.

Position Requirements. Ability to work in the lab at least 6-10 hours a week (more lab time can be accommodated if desired). No prior lab experience necessary, but experience in comparative anatomy or vertebrate biology is a plus. Student researchers will be trained on the use of VGStudio and/or Avizo software. Strong communication, organization, and data analysis skills. Additional Info: Possibility for course credit exists, as does the potential for independent student projects.

More information can be found on the Turner Lab website: http://theturnerlab.org/.
Interested students should send a CV and cover letter to Dr. Turner at alan.turner@stonybrook.edu.

Posted 12/19/17