Undergraduates: Open Research Positions & Projects

Current Harvard Undergraduates: contact Dr. Logan McCarty​​​​​, Director of Science Education, for advice on applying for reearch positions. If you find a position below that looks interesting, please contact the lab directly.

Faculty: if you are interested in posting your open research position, please contact Dr. Logan McCarty​​​​​.

Consult HUROS Abstract booklet for the Spring/Summer opportunities. If you need a copy, email Dr. Logan McCarty​​​​​.

 

Posted in Fall 2022

Metabolism, Harvard Chan School of Public Health, Kory Lab, Posted Sept 22, 2022

Neuroscience research, Orefice Lab at MGH, Posted Sept 22, 2022

Research Opportunities for Undergraduates in the Ramanathan Lab, Posted Sept 2, 2022

Remote Undergraduate Research Opportunities in Computational and Systems Biology at Zomorrodi Lab (MGH/HMS), Posted Sept 2, 2022

Full-time (30 hrs/week) Funded Research Opportunity, Dana-Farber Cancer Institute/Harvard Medical School, Posted August 19, 2022

 

Posted in Spring 2022 (for Spring and Summer) 

Undergraduate Research Opportunity, Dr. Rashidian, Dana-Farber Cancer Institute/Harvard Medical School, Posted June 21, 2022

Undergraduate research opportunity—Weitz laboratory—remote possible, Posted May 23, 2022

Undergraduate research opportunity—Ressler Laboratory, Neurobiology of Fear, Posted May 17, 2022

Undergraduate research opportunity at Surgical Planning Lab (BWH, Harvard Medical School) - Remote possible (2 positions open), Posted May 17, 2022

Undergraduate Volunteer Research Opportunity in Neuroimaging & Psychology, Golby Lab | Brigham and Women's Hospital, Posted May 6, 2022

Unrdergraduate Researcher, Dr, Loparo Group, HMS, Posted Apr 11, 2022

Detection of fetal anatomy in in-utero magnetic resonance images (MRI) using artificial intelligence and deep learning, Posted Mar 22, 2022

Research technician position (Research Assistant I) in Angiogenesis/Immunology/Wound healing at Harvard/MGH, Posted Mar 17, 2022

Mapping the functional transitions of proteins using DNA springs , Posted Feb 28, 2022

Summer Research Analyst, MGH, Posted Feb 22, 2022

Summer Research Assistant, MGH, Posted Feb 22, 2022

Undergraduate Research Opportunity, Danial lab, Dana-Farber Cancer Institute, HMS, Posted Jan 28, 2022

Undergraduate Research Intern, Strominger Lab, HSCRB, Posted Jan 28, 2022

Undergraduate Research Intern, Gaab Lab, HGSE, Posted Jan 14, 2022

Remote Undergraduate Research Opportunity in Thoracic Surgery Research at Dr. Yang’s lab, MGH/HMS, Posted Jan 7, 2022

 

September 22, 2022

Metabolism, Harvard Chan School of Public Health, Kory Lab, Posted Sept 22, 2022

Contact information: Nora Kory, Harvard T.H. Chan School of Public Health. Department of Molecular Metabolism. Email: nkory@hsph.harvard.edu, 655 Huntington Ave, Boston MA 02115

Project description and duties:

The Kory lab in the Department of Molecular Metabolism at the Harvard T.H. Chan School of Public Health focuses on mitochondria, critical organelles in metabolism that generate both energy and precursors for biosynthesis. Beyond their metabolic roles, mitochondria are being recognized as important signaling hubs and mitochondrial dysfunction is one of the hallmarks of aging and age-associated diseases including neurodegeneration, cancer, and diabetes. For mitochondria to function properly metabolites must be efficiently exchanged with the rest of the cell in a regulated manner. While metabolites can diffuse through pores in the outer membrane, the inner mitochondrial membrane is impermeable to most metabolites and separates two chemically contrasting environments. We want to understand how mitochondria achieve efficient metabolite exchange and at the same time maintain the unique chemical environment of the mitochondrial matrix.

 

Our goal is to use mitochondrial transport proteins as tools to interrogate metabolic and signaling pathways to understand how mitochondria perform their multifaceted functions.

 

Current projects address:

• How is mitochondrial metabolite flux adjusted to proliferative demand and cell function?

• What role does the mitochondrial NAD pool play in the development of aging and age-associated disease?

• How are metabolic processes inside mitochondria, such as TCA cycle, electron transport chain and one-carbon metabolism coordinated with cytosolic metabolism?

• What are the roles of mitochondrial metabolites in metabolic signaling, quality control, communication and regulation of physiology?

• How can dietary modifications be harnessed to improve mitochondrial health in aging?

 

The student will be working closely with Dr. Kory, postdoctoral fellows and research scientists and in the lab to conduct experiments, prepare reagents, discuss research and analyze and present data.

Skills required: Students with basic biology lab experience motivated to contribute to cutting edge research relevant to human health are encouraged to apply.

Learning outcomes: This position offers a stimulating environment to work closely with an international group of scientists with backgrounds from biochemistry to neuroscience.

Students will learn research skills such as study design, data analysis methods, presentations, and scientific writing, as well as lab skillsets such as cell culture, CRISPR techniques, molecular cloning, protein expression and purification, running SDS-PAGE, mass-spec, and western blot analyses, mouse experiments and working with instruments such as FPLC, LC-MS, microscopy and flow cytometry. The candidate will also gain the possibility for co-authorship on publications.

Number of hours: We require a minimum time commitment of 18 hours per week and enrollment in relevant FAS courses. Priority is given to students who aim to commit to long-term research and perform their thesis research in the lab.

Mentoring: Students will be mentored by Dr. Kory, a postdoctoral fellow and research Scientist in the group. Students can also attend weekly group meetings / talks and can connect with other members of the group. Students will also get regular feedback from Professor Kory and have the opportunity to participate in department events, such as research seminars, retreats and social events.

Student stipend: Students may receive academic credit or a stipend. Students interested in receiving academic credit should reach out to their concentration department or Director of Undergraduate Study for information about registering for the course. Students can receive funding through programs like the Harvard College Research Program (HCRP).

 

Application information: Please email your resume to Dr. Nora Kory at nkory@hsph.harvard.edu.

 

 

 

Neuroscience research, Orefice Lab at MGH, Posted Sept 22, 2022

The Orefice Lab, located at Massachusetts General Hospital (MGH), is seeking 2 undergraduate research assistants to participate in ongoing projects exploring somatosensory and viscerosensory neural circuits. Students from underrepresented groups are especially encouraged to apply to this position.

Each student would work with a graduate student or postdoc in the lab. Project A aims to understand how the gut microbiome influences the development of sensory neurons in the gastrointestinal tract. Project B investigates the neural mechanisms underlying altered taste, texture, and feeding behaviors in mouse models for autism spectrum disorder. Students working on these projects would have the opportunity to perform mouse behavior, mouse husbandry, tissue processing, histology, and imaging, as well as various data analysis methods. Prior experience with rodent models is a plus, but is not required.

This position will begin ASAP. Interested students should be willing to commute to MGH (185 Cambridge St, Boston) and to commit to a minimum of 10 hours a week in the lab during the school year. The position is paid hourly. Ideal applicants will be willing to make a long-term commitment to this project (a year or more), provided that the lab is a good fit for the student.

If interested in Project A, please send your CV to Lyuba Bolkhovitinov at lbolkhovitinov@g.harvard.edu.

If interested in Project B, please send your CV to Yao Zhou at yzhou51@mgh.harvard.edu.

If interested in both projects, you may email both individuals. In your email please specify:

  1. your research interests and why you are interested in joining our laboratory
  2. why you are interested in Project A and/or B
  3. your previous research laboratory experience, if any
  4. current year, major, and courses you may be taking
  5. the approximate days and times you may be able to work in the lab (e.g., Monday mornings from 8-12pm; Friday afternoons from 12-5pm)
  6. career or post-graduate plans (if known)

Student training will be tailored to the applicant’s skill set and interests, with the aim of nurturing independence and scientific proficiency. In addition to developing technical lab skills, the student will have the opportunity to enhance their scientific knowledge by participating in lab meetings, journal clubs, and seminars as schedules allow. We are committed to providing a mentorship-focused research environment that will help prepare students for future careers in medicine and biomedical research. Students showing strong dedication may have the opportunity to perform an independent research project. Students who contribute significantly to a research project may be included as co-authors on publications resulting from the project.

The Orefice Lab is committed to building and sustaining an equitable and inclusive laboratory environment, where diversity is celebrated and valued. We believe diversity benefits and enriches the development of our science. We support an environment where lab members of different backgrounds and experiences, including socio-economic origins, nationalities, immigration statuses, races, religions, gender identities or expressions, sexual orientations, genetics, disabilities, ages, and veteran statuses, feel a sense of belonging.

For further questions, please contact lbolkhovitinov@g.harvard.edu and yzhou51@mgh.harvard.edu. For more information on the lab, visit https://www.oreficelab.org/.

 

 

September 2, 2022

 

Research Opportunities for Undergraduates in the Ramanathan Lab

 

We have been working on human development using human embryonic stem cells. The goal is to recapitulate the morphogenesis of tissues during human development, and use such robust systems to both understand the underlying mechanisms and disease focusing on the central nervous system. The lab has a team of biologists, bioengineers, physicists and applied mathematicians. Part of the lab also works on computational approaches to make inferences from large data sets in order to guide our experiments.

 

We are looking to recruit and work with undergraduate students in the lab again, now that we are done with COVID! Students in the past have started in our lab their junior year and continued to work on their thesis. All of them have gone on to MD PhD, MD and PhD programs at the best of places.

 

The most recent papers and sample papers from the lab can be found by following the links below

 

https://www.biorxiv.org/content/10.1101/2022.05.10.491358v1

https://www.biorxiv.org/content/10.1101/2022.05.10.491359v1

https://pubmed.ncbi.nlm.nih.gov/30573831/

https://pubmed.ncbi.nlm.nih.gov/30573831/

https://www.cell.com/fulltext/S0092-8674(11)00543-5

 

Please contact PI Sharad Ramanathan if interested: sharad@cgr.harvard.edu 

 

 

 

Remote Undergraduate Research Opportunities in Computational and Systems Biology at Zomorrodi Lab (MGH/HMS)

 

Contact information:

Ali R. Zomorrodi

Mucosal Immunology and Biology Research Center

Massachusetts General Hospital for Children

44 Fruit St, Boston, MA 02114

E-mail: azomorrodi@mgh.harvard.edu

Zomorrodi lab website

 

Project description and duties:

Zomorrodi lab integrates biological networks, mathematical/statistical/physical models and engineering tools to develop computational mechanistic models of the microbiome and the host. These models are used to advance our understanding of disease pathogenesis and to streamline the design of personalized treatments.

 

We are recruiting undergraduate researchers to work on a projects

  1. Integrate metabolic and genetic networks for immune cells

The goal of this project is to construct integrated biological network models for immune cells. More specifically, in this project we will integrate genome-scale computational models of metabolism with gene expression models for macrophages (an important innate immune cell type).

Skills required: Familiarity with a programming language (preferably Python).

  1. Develop machine learning tools to analyze longitudinal microbiome data

The goal of this project is to develop new machine learning methods that use longitudinal microbiome data to predict disease progression or onset.

Skills required: Familiarity or prior experience in machine learning. Familiarity with a programming language (preferably Python or R).

  1. Develop statistical tools to analyze longitudinal multi-omics data.

The goal of this project is to develop efficient statistical analysis approaches for the integrated analysis of longitudinal multi-omics data from the human host and microbiome.

Skills required: Background in statistical hypothesis testing and generalized linear models, bility to program in R or Python. This project is rather suitable for stat/biostat majors.

Learning outcomes:

Students will learn how computational simulations and biological network models can be used to address translational problems. More broadly, students gain experience in essential research skills including data analysis, interpretation of results, presentations, and scientific writing.

 

Time commitment:

Negotiable. The PI is flexible to accommodate students’ schedules or other time demands although students who plan to stay in the lab for longer time periods (two semesters or so) are preferred. These projects can be extended further upon mutual interest.

 

Mentoring:

Students will be directly mentored by Dr. Zomorrodi and have the opportunity to (remotely) interact with other lab members and attend group meetings. Mentorship Zoom meetings are held once a week on a regular basis.

 

Student stipend:

These are volunteer research positions. Students are encouraged to apply for undergraduate research fellowships such as HCRP or to register for a research course credit.

 

Application information:

Interested candidates should email a CV to Dr. Zomorrodi at azomorrodi@mgh.harvard.edu and briefly explain what their interests are. Please use “Remote Undergraduate Research Opportunities” as the subject of your email.

 

 

August 19, 2022

 

Full-time (30 hrs/week) Funded Research Opportunity, Dana-Farber Cancer Institute/Harvard Medical School

 

Contact information: Mohammad Rashidian, Ph.D.

Assistant Professor, Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute

Assistant Professor of Radiology, Harvard Medical School

 

Project description and duties: Developing novel methods to treat cancer

 

Immunotherapy has revolutionized cancer treatment, however, a significant fraction of patients fail to respond to therapy and may suffer serious side effects. Our lab studies cancer immunology using expertise in chemical biology, molecular biology, and immunology. We are focused on understanding the underlying mechanisms of how the tumor microenvironment is shaped and continuously changed in response to cancer immunotherapies. We aim to develop new and improved diagnostic, prognostic, and therapeutic tools to detect, diagnose, characterize, treat, and prevent cancer.

 

Our research aims are: (1) to develop methods for non-invasive monitoring of immune responses; (2) to investigate changes in the tumor microenvironment (TME) in response to treatment; (3) to explore how to reshape the TME to a more pronounced anti-tumor status and develop tools to realize this possibility; and (4) to develop precision therapeutics for cancer. In the long term, our goals are to help better understand the dynamics of immune responses, and to investigate what is behind the heterogeneous response to cancer immunotherapy. These are essential for developing more effective therapies, more effective methods for early detection of cancer, and new prognostic modalities.

 

Student stipend: This is a funded position and requires ~30-40 hours of commitment per week, ideal for students who are wrapping up their studies or would like to spend a year working in a lab before applying for graduate studies or MD programs.

 

Skills required: students with biology lab skillsets are encouraged to apply. Prior experience with mice models is a plus as the job requires working with animal models.

 

Learning outcomes: research skills such as study design, data analysis methods, presentations, and scientific writing, as well as lab skillsets such as cell culture, protein engineering, protein expression, and purification, ELISA analysis, running SDS-PAGE, mass-spec, and western blot analyses, protein labeling, animal handling, and working with instruments such as FPLC, LC-MS, microscopy, and flow cytometry.

 

The number of hours students are expected to work, and the length of the project: at least 30 h per week for one year.

 

Mentoring: senior graduate students and postdocs in the lab will be mentoring students. The PI will have regular weekly meetings with students as well.

 

Application information: motivated students should contact Dr. Rashidian at mohammad_rashidian@dfci.harvard.edu

 

 

June 21, 2022

 

Undergraduate Research Opportunity, Dr. Rashidian, Dana-Farber Cancer Institute/Harvard Medical School

 

Contact information: Mohammad Rashidian, Ph.D.

Assistant Professor, Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute

Assistant Professor of Radiology, Harvard Medical School

 

Project description and duties: Developing novel methods to treat cancer

Immunotherapy has revolutionized cancer treatment, however, a significant fraction of patients fail to respond to therapy and may suffer serious side effects. Our lab studies cancer immunology using expertise in chemical biology, molecular biology, and immunology. We are focused on understanding the underlying mechanisms of how the tumor microenvironment is shaped and continuously changed in response to cancer immunotherapies. We aim to develop new and improved diagnostic, prognostic, and therapeutic tools to detect, diagnose, characterize, treat, and prevent cancer.

 

Our research aims are: (1) to develop methods for non-invasive monitoring of immune responses; (2) to investigate changes in the tumor microenvironment (TME) in response to treatment; (3) to explore how to reshape the TME to a more pronounced anti-tumor status and develop tools to realize this possibility; and (4) to develop precision therapeutics for cancer. In the long term, our goals are to help better understand the dynamics of immune responses, and to investigate what is behind the heterogeneous response to cancer immunotherapy. These are essential for developing more effective therapies, more effective methods for early detection of cancer, and new prognostic modalities.

 

Skills required: students with basic biology lab skillsets are encouraged to apply. Students will have the opportunity to work with senior scientists in the lab and be trained for lab techniques. Priority is given to students who aim to commit to long-term research and perform their thesis on cancer immunology research in the lab.

 

Learning outcomes: research skills such as study design, data analysis methods, presentations, and scientific writing, as well as lab skillsets such as cell culture, protein engineering, protein expression and purification, ELISA analysis, running SDS-PAGE, mass-spec, and western blot analyses, protein labeling, and working with instruments such as FPLC, LC-MS, microscopy and flow cytometry.

 

Number of hours students are expected to work, length of the project: at least 30 h per week for the summer.

 

Mentoring: senior graduate students and postdocs in the lab will be mentoring students. The PI will have regular weekly meetings with students as well.

 

Student stipend: positions are volunteer positions, however the PI will work with students to apply for available fellowship programs (HCRP, PRISE, etc.).

 

Application information: motivated students should contact Dr. Rashidian at mohammad_rashidian@dfci.harvard.edu

 

 

May 23, 2022

Undergraduate research opportunity—Weitz laboratory—remote possible

 

Title: iDROP: a smartphone app for accurate and rapid digital PCR-based diagnostics

PI – Prof. David Weitz;
Postdoctoral Fellow – Jean Carlos Serrano – jeancs@seas.harvard.edu -
Gordon McKay Laboratory, Harvard University -
https://weitzlab.seas.harvard.edu/

Description of the project and duties:

PCR-based diagnostics is one of the main clinical tools in our ongoing efforts against the COVID-19 pandemic. While it became the standard diagnostic assay to confirm molecular signatures specific to SARS-COV-2 in patient samples, it still lacks the ability to identify the presence of the virus in low-abundance samples correspondingly to early-stage infections. Thus, resulting in numerous false-negative cases. We seek to improve upon this technology by converting it into a digital assay where we partition the initial sample into millions of micron-sized droplets, each serving as its own PCR reaction chamber which results in an increased sensitivity. Once we perform PCR amplification, we need to quickly quantify the population of positive and negative droplets, via fluorescence, to deliver diagnostic readout to the patient and clinicians as soon as possible.

The main responsibility of the student will be to facilitate this final quantification step by developing image-based processing algorithms that can rapidly and accurately analyze fluorescent images taken by a smartphone camera. Ultimately, we want to develop a user-friendly app that will translate digital PCR into a widely accessible diagnostics platform, all the way from the clinical bench to at-home tests.

Skills required:

Familiarity with a programming language (preferably Python or any other language amenable for App development).

 

Funding:

The lab does not directly provide student stipends, but the mentor can assist in finding and applying for potential funding opportunities. Students are encouraged to apply to the HCRP and other fellowships (https://uraf.harvard.edu/uraf-opportunities), REUs, or register for a research course credit.

 

Working Requirements:

Students can be located in the Boston area or work remotely. Time commitment is flexible, but a minimum of 15 hours a week. They would be actively mentor by the postdoctoral fellow for the purpose of this project and any additional academic opportunities the student is interested in pursuing.

 

Applying:

Please send a brief email (introduce yourself, detail your interest in the lab/project, state your future career aspirations) with your CV/resume to jeancs@seas.harvard.edu.

 

 

May 17, 2022

Undergraduate research opportunity—Ressler Laboratory, Neurobiology of Fear

The Ressler Laboratory on the Neurobiology of Fear, in the Harvard Medical School Psychiatry Department at McLean Hospital, is seeking a highly motivated and enthusiastic individual who wishes to contribute to cutting-edge translational neuroscience research in a dynamic and collaborative environment. The ideal applicant will be highly motivated to pursue a future career in neuroscience and will use this job opportunity to both contribute to ongoing NIMH-funded research projects and to take advantage of training opportunities to gain skills in behavioral and molecular neuroscience techniques. We will consider any individual who meets these criteria, though preference will be given to those with animal research and/or wet lab experience.

This is a a full-time research assistant to help with ongoing studies that use transcriptomics, single-cell 1p calcium imaging, real-time pose estimation, and all-optical closed-loop approaches to study fear and aggression in mice.

To Apply: Job Number 3199028 at

https://partners.taleo.net/careersection/ex/jobsearch.ftl

 

 

Undergraduate research opportunity at Surgical Planning Lab (BWH, Harvard Medical School) - Remote possible (2 positions open)

Contact information: Nazim Haouchine, Harvard Medical School. Radiology Department. Email: nhaouchine@bwh.harvard.edu, 75 Francis Street, Boston MA 02115

Project description and duties:

The Surgical Planning Laboratory (SPL) is a computer science oriented laboratory in the Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School. The SPL is looking for motivated students for two projects:

Project 1: Develop a deep learning model for vessel segmentation of the brain surface. Data will first need to be collected from a public repository and manually labeled. Open source tools are already available.

Project 2: Develop a deep learning model to decompose 2D XRay images of the brain vessels into 3 phases: arterial, capillary and venous. Data and open source tools are already available

The candidate will be working with computer scientists and neurosurgeons from the department of Radiology and Neurosurgery.

Skills required: Experience in programming in Python and ability to quickly prototype algorithms but it’s not necessary. Understanding of image processing. Basic knowledge in Machine learning is a plus. Motivation !

Learning outcomes:

This position provides an excellent opportunity to be involved in cutting-edge research in surgical navigation, and offers a stimulating environment to work closely with engineers, computer scientists, radiologists and surgeons. The position also offers the opportunity of observing surgical procedures in our state-of-the-art operating room using intraoperative imaging. The candidate will also gain valuable written and oral communication skills, and the possibility for co-authorship on publications.

Number of hours: Minimal commitment of 10 hours per week. 12 to 16 weeks. Flexible.

Mentoring:

Students will be mentored by a Faculty Researcher in the group and meet with the mentor 1-2 times per week via zoom. Students can also attend weekly group meetings / talks and can connect with other members of the group. Students will also get regular feedback from neurosurgeons.

Student stipend: The position is a volunteer position. However, a stipend could be offered.

Application information: Please email your resume to Dr. Nazim Haouchine at nhaouchine@bwh.harvard.edu.

 

May 6, 2022

Undergraduate Volunteer Research Opportunity in Neuroimaging & Psychology: The Image Guided Neurosurgery Laboratory at Brigham and Women's Hospital has an undergraduate research volunteer position open to an interested and self-motivated student.  This position is well suited for an individual interested in psychology, linguistics, social development, cognitive science, or a similar field.  Experience in neuroimaging and behavioral research is not required, but some interest in these fields is expected. The student researcher would be responsible for conducting a thorough literature search that would serve as the basis for an introductory section of an upcoming paper.  Significant contributions may be reflected in co-authorship of the eventual manuscript.  Expected skills include strong reading, writing and critical thinking, with an opportunity to develop scientific writing. Students can be located in the Boston area or work remotely.  Time commitments are flexible, but a minimum of 14 hours a week.  They would work closely with a graduate student in the lab, and meet periodically throughout the course of the project.  There are additional opportunities to learn about neurosurgery and neuroimaging advances, and develop their own projects.  Please send your CV to zekelman@g.harvard.edu and suggest a couple of available times for an interview.
 

 

Apr 11, 2022

Unrdergraduate Researcher, Dr, Loparo Group, HMS

The laboratory of Professor Joseph Loparo at Harvard Medical School is looking for an enthusiastic undergraduate researcher to join us as early as summer 2022. Ideally candidates would be interested in continuing to work with the lab during the semester. The Loparo lab is a collaborative and diverse group of molecular biologists, protein biochemists and biophysicists interested in understanding the molecular mechanisms of genome maintenance.

Project description:

Undergraduate researchers will work closely with a postdoctoral researcher to dissect the molecular mechanisms of microhomology mediated end joining (MMEJ), a recently discovered DNA double strand break repair pathway.  The MMEJ pathway is emerging as a promising therapeutic target for certain types of cancers including hereditary breast and ovarian cancer syndrome. There is also an increasing effort to employ MMEJ as an alternative strategy for CRISPR-based precise genome editing.

Major skills and techniques:

In the short term, interested students will learn how to prepare recombinant proteins and DNA substrates and use these reagents in biochemical assays. Techniques include plasmid mutagenesis and PCR; bacteria and insect cell cultures; protein chromatography using the ÄKTA system and various blotting and gel electrophoresis techniques. In the longer term, students will be introduced to biophysical/microscopy-based assays - fluorophore labeling of proteins/DNAs, single-molecule microscopy and data analysis with Matlab/Python.

Interested students should send a brief email explaining their interest to Joseph_Loparo@hms.harvard.edu.

 

Mar 22, 2022

Detection of fetal anatomy in in-utero magnetic resonance images (MRI) using artificial intelligence and deep learning

Dr. Malte Hoffmann, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital

mhoffmann@mgh.harvard.edu

149 13th St, Suite 2301, Charlestown, MA 02129  https://www.nmr.mgh.harvard.edu/lab/lcn

Description of the project and duties 

The goal of this project is to leverage deep learning to detect fetal anatomy such as the brain and eyes in three-dimensional (3D) magnetic resonance images (MRI) acquired during pregnancy. We are pursuing these developments to inform fetal-MRI analysis algorithms (similar to https://arxiv.org/abs/2203.09974 for adult brains) and to detect the fetal-head pose for automating MRI sessions (these applications are listed for completeness and out of scope for the project offered).

The student will train deep convolutional neural networks (CNNs) to delineate structures of interest based on acquired data paired with existing manual annotations and also based on diverse synthetic data generated from label maps. The student will learn to manually annotate 3D MRI data using FreeSurfer/FreeView and have the opportunity to present their work to the research group.

Skills required. High motivation and some prior experience with Python programming and the Unix shell are needed. Deep learning experience will be helpful but is not required. The project will be most suitable for a 3rd or 4th year student (or beyond). Prior research experience is not required.

Learning outcome: Research skills including deep-learning algorithm development, image segmentation, manual labelling of 3D data, presentations, and potentially scientific writing.

Hours per week: project requires a minimum of 3 months of full-time effort at 35 hours per week but can extend to up to 1 year depending on mutual agreement and availability/need for funding, in which case a thesis could be conducted in the lab. The project work can be completed remotely or on site.

Mentoring: The student will be mentored by Dr. Hoffmann, during 1 weekly meeting and informal discussions/feedback via Microsoft Teams chat as needed.

Funding is available for three months of full-time effort.

Please email your resume and a brief cover letter explaining your motivation and prior experience to Dr. Hoffmann at mhoffmann@mgh.harvard.edu.

 

 

Mar 17, 2022

Research technician position (Research Assistant I) in Angiogenesis/Immunology/Wound healing at Harvard/MGH

Laboratory of Angiogenesis and Inflammation, Dr. Alexander G. Marneros, Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital/Harvard Medical School, Boston

lab website: https://www.massgeneral.org/dermatology/research/cutaneous-biology-resea...

Our laboratory is investigating molecular mechanisms involved in wound healing, angiogenesis and inflammation.

Project 1: We are investigating molecular mechanisms that control macrophage activation and the role that activated macrophages play for inflammation and pathological angiogenesis. We have established in vitro assays to identify regulators of macrophage polarization. In chemical screens we could identify pharmacologic inhibitors of alternative macrophage polarization (M2-type macrophages) and could show in vivo that these inhibitors can block macrophage-induced angiogenesis (Cell Reports, 2013; JBC, 2014; Cell Reports 2021). This project aims to define molecular pathways that are critical for macrophage polarization and that influence the ability of activated macrophages to induce pathological angiogenesis in conditions such as age-related macular degeneration, cancer or wound healing.

Project 2: We investigate the role of proangiogenic factors for wound healing and age-related diseases. We could show that the proangiogenic factor VEGF-A induces oxidative stress and NLRP3 inflammasome activation to promote age-related diseases (Cell Reports, 2013; FASEB J, 2014; EMBO Mol Med, 2016; FASEB J, 2018, eLife, 2020). We use a variety of in vivo and in vitro approaches to investigate a novel pathogenic link between VEGF-A and NLRP3 inflammasome activation.

Project 3: We identified a novel pathway that is critical for epithelial differentiation, especially in the kidney. This AP-2b/KCTD1 pathway plays a critical role in kidney development and for renal function in the adult. We use mouse genetics to elucidate the role of this pathway for kidney functions (Dev Cell, 2020; Cell Reports, 2021).

In summary, our laboratory uses a large number of diverse experimental approaches (human genetics, mouse genetics, chemical screens, in vitro assays, cutting-edge imaging technology) to define novel mechanisms in angiogenesis, wound healing and inflammation. All of our projects have strong translational clinical relevance. Our laboratory is embedded in a highly productive and well-equipped environment at the Cutaneous Biology Research Center of Massachusetts General Hospital/Harvard Medical School. Cutting-edge technologies are available within our Department and the MGH/Harvard research community.

Skills required:

- Passionate about science and commitment for ~1 year required

- prior laboratory experience, especially working with mice, preferred

- applicants must be reliable, well organized and have good log-keeping abilities

Student will learn how to address scientific questions using mainly mouse genetics approaches.

Number of hours students are expected to work, length of the project (if it is negotiable, state so):

ideally full-time, 40hrs/week for 1 year; negotiable

Mentoring: Daily mentoring by PI and other students in the lab

Salaried position.

Interested candidates should send the CV and references to Alexander G. Marneros, M.D., Ph.D.,

Email: amarneros@mgh.harvard.edu

 

 

Feb 28, 2022

Mapping the functional transitions of proteins using DNA springs

Contact information:

Doeke Hekstra, Dept of Molecular & Cellular Biology, and Applied Physics, School of Engineering and Applied Sciences,

doeke_hekstra@harvard.edu, Northwest Lab 311, https://hekstralab.fas.harvard.edu/

Project description and duties:

To perform their many functions in the human body, proteins constantly need to undergo internal motions to interconvert between different states. The nature of these motions is often hard to study. Work by the Zocchi group at UCLA shows that one can use double-stranded DNA springs to put force across pairs of surface sites and see an effect on protein activity. How this works on the atomic scale is not known. To address this gap, we have developed a protocol to prepare enough of these protein-DNA “chimeras” to perform nuclear magnetic resonance (NMR) spectroscopy measurements. We’d like your help with preparing such chimeras and performing and interpreting NMR studies of their structure and dynamics. The project can be extended to include a molecular dynamics simulation component if the student is interested.

Skills required: Experience with chromatographic methods and an understanding of basic physical chemistry and organic chemistry concepts is important.

Learning outcomes: The student gets an opportunity to join a project when it is just starting to work, and can improve their ability to collaborate and present their work.

Number of hours: Students are expected to work around 10 hours per week on the project, with a minimal commitment of one semester or summer (an intent to stay longer is a plus).

Mentoring: A research assistant will mentor the student daily, with, weekly meetings with the PI. The student is strongly encouraged to participate in all lab activities, including group meetings.

Student stipend:

If the student applies for summer research funding (e.g. PRISE), the lab can provide a spring semester stipend.

Application information:

Interested students should send a short introductory email to Dr. Hekstra, describing their interests and referencing any relevant experience they already have. A resume or CV is optional.

 

 

Feb 22, 2022

Summer Research Analyst, MGH

The Mongan Institute’s Health Policy Research Center (HPRC) is seeking a full-time Research Analyst for Summer 2022.

Founded in 1998 and an affiliate of the Mass General Brigham Healthcare System, Mongan is a leading institute conducting policy and clinical research designed to inform policy decisions at the national, state, and local levels.

The Research Analyst will be joining HPRC’s Program for Clinical Economics and Policy Analysis (CEPA), led by John Hsu MD, MBA, MSCE and Vicki Fung PhD and collaborating with economists, clinicians, and statisticians across Harvard Medical School and Mass General Brigham.

The Research Assistant will play a key role in conducting research that examines the clinical and economic effects of health care policy changes in the United States, including insurance coverage expansion, payment reform, and delivery system change. These studies have informed and led to changes in national and state policies or decisions by health care organizations. The work will lead to presentations in scientific conferences, peer-reviewed publications, and presentations to policy makers and organizational decision-maker, among other dissemination venues. Summer interns often continue work with CEPA throughout undergraduate and graduate/medical education.

Responsibilities may include the following:

  • Evaluating the impact of health policies on health care access, use, quality, and spending
  • Assisting in devising sophisticated empirical methodologies across the social and health sciences
  • Assisting in the implementation of sophisticated statistical techniques for data analysis including in the following areas:
    • Machine-learning based disease prediction
    • Causal inference and comparative effectiveness research
    • Trial emulation
  • Assisting in data visualization and presentation of results
  • Disseminating findings through presentation and manuscript publication
  • Assisting the in the preparation of grant proposals

Applicants should be pursuing a Bachelor’s or Master’s Degree in statistics, mathematics, computer science, economics, or related fields. Candidates must have strong technical/quantitative skills, including experience with statistical programs (e.g., Stata, SAS, R), and should enjoy working with large datasets.

Candidates should also have excellent analytic, communication, and organizational skills, the ability to work both independently and in a team setting, and an enthusiasm for learning about health policy and new methodologies related to the research.

If you are interested in joining our team, please send your CV/resume and cover letter to Max Weiss mrweiss@mgh.harvard.edu. Be sure to highlight your relevant coursework and/or experience. Applications will be reviewed on a rolling basis.

 

 

Summer Research Assistant, MGH

The Mongan Institute’s Health Policy Research Center (HPRC) is seeking a full-time Research Assistant for Summer 2022.

Founded in 1998 and an affiliate of the Mass General Brigham Healthcare System, Mongan is a leading institute conducting policy and clinical research designed to inform policy decisions at the national, state, and local levels.

The Research Assistant will be joining HPRC’s Program for Clinical Economics and Policy Analysis (CEPA), led by John Hsu MD, MBA, MSCE and Vicki Fung PhD and collaborating with economists, clinicians, and statisticians across Harvard Medical School and Mass General Brigham.

The Research Assistant will play a key role in conducting research that examines the clinical and economic effects of health care policy changes in the United States, including insurance coverage expansion, payment reform, and delivery system change. These studies have informed and led to changes in national and state policies or decisions by health care organizations. The work will lead to presentations in scientific conferences, peer-reviewed publications, and presentations to policy makers and organizational decision-maker, among other dissemination venues. Summer interns often continue work with CEPA throughout undergraduate and graduate/medical education.

Responsibilities may include the following:

  • Reviewing policy changes at the national and state levels
  • Evaluating the impact of health policies on health care access, use, quality, and spending
  • Assisting in data visualization and data analysis
  • Evaluating and exploring novel data sources
  • Disseminating findings through presentation and manuscript publication
  • Managing IRB applications, protocols, and continuing reviews
  • Assisting the in the preparation of grant proposals
  • Coordinating collaborations across government agencies, universities, and health providers

Candidates must have excellent analytic, communication, and organizational skills, the ability to work both independently and in a team setting, and an enthusiasm for learning about health policy and new methodologies related to the research. Prior experience with statistical programs (e.g., Excel, Stata, SAS, R) and the research process is preferred, though not required.

If you are interested in joining our team, please send your CV/resume and cover letter to Max Weiss mrweiss@mgh.harvard.edu. Be sure to highlight your relevant coursework and/or experience. Applications will be reviewed on a rolling basis.

 

Posted Jan 28, 2022

Undergraduate Research Opportunity, Danial lab, Dana-Farber Cancer Institute, HMS

Contact information: Nika Danial, PhD, Department of Cancer Biology, Dana-Farber Cancer Institute
450 Brookline Avenue, CLS 11-143, Boston, MA 02215 nika_danial@dfci.harvard.edu, https://www.daniallab-dana-farber.org/

Project description and duties: We are looking for a motivated student interested in studying metabolic regulation of biologic processes in cancer cells. The project involves opportunities to learn research techniques relevant to the study of metabolism and nutrient signaling such as cell culture, biochemical investigation of nutrient utilization and processing, metabolic tracing studies, analyses of large genomic, proteomic and metabolomics datasets, as well as genetic gain- and loss-of-function approaches using gene knockdown and CRISPR technologies, and quantification of cellular proliferation and survival.

Skills required: No prior research experience is required. A background in computer science or bioinformatics (R programming/ MATLAB) is a plus but not mandatory.

Learning outcomes: Research skills including experimental design, basic cell and molecular biology techniques, critical evaluation of scientific literature and data analysis and communication.

Time commitment: Flexible

Mentoring: Will be mentored by postdoctoral researcher on day-to-day basis, with regular meetings with the PI and the opportunity to present and receive feedback in lab meetings, as well as participation in ongoing collaborations.

Student stipend: Students are encouraged to apply for support from HCRP, PRISE and other fellowships, or register for a research course credit

Application information: Interested candidates should email a CV and Cover letter to nika_danial@dfci.harvard.edu

 

 

Undergraduate Research Intern, Strominger Lab, HSCRB

Contact information:

Dr. Jack Strominger, Higgins Professor of Biochemistry.

Email address: jlstrom@fas.harvard.edu, bowengu@fas.harvard.edu

Project description and duties:

Our laboratory’s research interest lies in understanding how tolerance and immunity is established at the maternal-fetal interface. Current projects are 1) working with extravillous trophoblast (EVT) cell lines to explore the specific role of transcription factors in regulating the expression of HLA-C (a human leukocyte antigen I (HLA-I) molecule which is essential for immune tolerance as well as resolving infections during pregnancy). 2) investigating a novel signaling pathway for progesterone - a hormone important during implantation and throughout pregnancy - in regulating trophoblast function at the maternal-fetal interface. 3) Using genome-wide CRISPR screens to identify novel factors in regulating the non-canonical HLA-I molecules (HLA-E and -G) expressed in EVT. Ultimately, we aim to explore the mechanism how EVT escape from cytotoxic immune cells and thus establishing fetal tolerance by the maternal immune system.

Skills required: Previous lab experience in molecular biology and tissue culture is a plus but not required.

Learning outcome: This internship experience will provide the student with the opportunity to learn research skills in genome editing by CRISPR-Cas9 and tissue culture of EVT.  Moreover, the student will gain research experiences in maternal-fetal immunology.

Number of hours students are expected to work: Ideally, we are looking to establish a long-term relationship with a student for the duration of 1-2 years, that should result in the completion of a senior research thesis. We can work with the student and their schedule to decide on the number of hours per week during the school year but expect a full-time commitment of 2-3 months for at least one summer to allow for completion of an independent research project. The lab is located at the Sherman Fairchild Building, 7 Divinity Ave., Cambridge, MA 02138

Mentoring: Student will be mentored by a postdoctoral fellow, Dr. Bowen Gu.

Student stipend: This is a volunteer position.
Application information

Please e-mail your resume/CV along with a one-page cover letter including a brief outline of your previous experiences, interests, goals, and anticipated time availability to Dr. Strominger (jlstrom@fas.harvard.edu) and Dr. Gu (bowengu@fas.harvard.edu).

 

 

Posted Jan 14, 2022

Undergraduate Research Intern, Gaab Lab, HGSE

PI name, department, contact information, location, lab website

Dr. Nadine Gaab, Harvard Graduate School of Education, gaablab@gse.harvard.edu, 50 Church St., Cambridge, MA, https://www.gaablab.com/

Description of the project and duties (link to published manuscripts describing the work)

The Gaab Lab at the Graduate School of Education is seeking semester-long undergraduate research interns. Our lab works at the intersection of neuroscience, education, EdTech, and policy. We focus on typical/atypical learning trajectories with a special focus on language and reading development and the role of the environment in shaping these trajectories.

As an intern, you will gain experience in data entry and analysis, participant recruitment, and data collection. Data collection can include helping with behavioral testing and/or scanning young children in an MRI scanner. We are looking for someone who can dedicate at least 8 hours a week to the lab, split between 1-2 days a week. Availability to work over the weekend occasionally is a plus. The ideal candidate will be detail-oriented, careful, self-motivated, and interested in our lab's work, and have a background in neuroscience, psychology, linguistics, education, computer science, or a related field.

For publication listings please visit https://www.gaablab.com/

Skills required. Previous lab experience is a plus but not required.

Learning outcome:  Laboratory and research skills including data entry and analysis, participant recruitment, and data collection. Data collection can include helping with behavioral testing and/or scanning young children in an MRI scanner.

Number of hours students are expected to work: Semester internship, at least 8 hours per week, split between 1-2 days a week.

Mentoring:  Student will be mentored by PI Dr. Nadine Gaab and/or by a postdoc.

Currently, this is an unpaid position, but students are encouraged to apply to HCRP funding

To apply: Interested applicants please send a cover letter and CV to gaablab@gse.harvard.edu by January 20, 2022

 

Posted Jan 7, 2022

 

Remote Undergraduate Research Opportunity in Thoracic Surgery Research at Dr. Yang’s lab, MGH/HMS

 

Contact information: Dr. Chi-Fu Jeffrey Yang, Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital.  cjyang@mgh.harvard.edu

 

Project description and duties: Our program is an opportunity to work with physicians and medical students on cutting-edge clinical surgical research. In addition, we will teach students how to raise awareness about lung cancer screening in the community. Our program is meant to be more than an assistantship: this is a unique opportunity to work directly alongside talented physicians and researchers in the field. We want to develop your research and leadership skills and allow you the opportunity to create and lead innovation that may potentially improve the lives of patients.

Responsibilities include:

• Learning how to perform clinical research in thoracic oncology with physicians and medical students
• Collaborating with team members to raise awareness about lung cancer screening
• Programs development

Skills required:

• Proficiency with Microsoft Word, Excel, and Outlook. Familiarity with statistical programs such as R or STATA are a plus but not required. Video-editing and familiarity with web design are a plus, but not required

• Commitment to research and public service
• Previous leadership experience and demonstrated individual initiative are key criteria that will be considered when reviewing applicants for this position

 

 

Learning outcomes: By the end of their training, the trainee should be able to:

  1. Learn how to perform cutting-edge clinical research in thoracic surgery
  2. Read papers in any major medical journal and understand the strengths and weaknesses of the study
  3. Be fluent in medical vocabulary and understand the diagnosis and treatment of lung cancer
  4. Learn how to effectively engage with the public to raise awareness about lung cancer
  5. If warranted based on their contributions, students will be co-authors on scientific manuscripts.

 

Number of hours: The project will require at least 8-10 hours/week of commitment.  At the same time, we recognize that students have many commitments, including studying for finals and spending time with family and friends, and we will work around the student’s schedule to make this a fun and engaging learning experience.

 

Mentoring: Dr. Yang is a thoracic surgeon at Massachusetts General Hospital.  He graduated from Harvard College and Harvard Medical School.  He lived in Matthews as a first-year and then Leverett House.  He has over 9 years of experience teaching and mentoring undergraduate students, many of whom are now in medical school.  He has built a team that cares deeply about the undergraduate research experience and really wants to help students achieve their dreams. 

These are his publications: https://www.ncbi.nlm.nih.gov/myncbi/chi-fu.yang.1/bibliography/public/

Student stipend: Volunteer position. The Laboratory does not have funds to pay student stipends, but students are encouraged to apply to the HCRP and other fellowships (https://lifesciences.fas.harvard.edu/research-opportunities)

 

Application information: Please e-mail your resume/CV along with a cover letter including a brief outline of your interests, goals, and anticipated time availability

to Dr. Chi-Fu Jeffrey Yang at cjyang@mgh.harvard.edu