computational biology phd mit

Evolutionary and Computational Biology

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Research in Evolutionary and Computational Biology leverages large-scale genomic, transcriptomic and related data across diverse species to unlock the molecular mechanisms of life.

Sinisa Hrvatin

Scientists track evolution of microbes on the skin’s surface.

A new analysis reveals how Staphylococcus aureus gains mutations that allow it to colonize eczema patches .

Brandon (Brady ) Weissbourd

Jörn dunkel, uncovering how cells control their protein output.

Gene-Wei Li investigates the rules that cells use to maintain the correct ratio of the proteins they need to survive.

A typical bacterial genome contains more than 4,000 genes, which encode all of the proteins that the cells need to survive. How do cells know just how much of each protein they need for their everyday functions?

Hernandez Moura Silva

A new way to regulate gene expression.

Biologists uncover an evolutionary trick to control gene expression that reverses the flow of genetic information from RNA splicing back to transcription.

Computational and Systems Biology Ph.D. Program (CSB)

Principal Investigator Christopher Burge

Co-investigators Joel Voldman , Forest White , Jacob White , Ron Weiss , Alan Grossman , Amy Keating , B L Whang , Eric Alm , Mark Bathe , Ernest Fraenkel , Mehmet Fatih Yanik

Project Website http://csbi.mit.edu/education/phd.html

The Computational and Systems Biology (CSB) Ph.D. Program prepares students to become independent, interdisciplinary researchers in post-genomic biology and related fields. There is a strong focus on quantitative methods and modeling, experimental design, and device development. This unique program integrates MIT's world-class research and educational opportunities in biology, engineering, and computer science.

The emerging field of systems biology represents an integration of concepts and ideas from the biological sciences, engineering disciplines, and computer science. Recent advances in biology, including the Human Genome Project and massively parallel approaches to probing biological samples, have created new opportunities to understand biological problems from a systems perspective. Systems modeling and design are well established in engineering disciplines but are relatively new to biology. Microsystems has been fundamental to advances in electronics and computing, but now has the potential to revolutionize biology as well. Advances in systems biology will require multidisciplinary teams to apply principles and tools from engineering and computer science to solve problems in biology and medicine.

To provide training in this emerging field, MIT offers a Ph.D. Program in Computational and Systems Biology (the CSB Ph.D. Program). Spanning the School of Engineering and the School of Science, the program integrates coursework and research opportunities in biology, engineering, mathematics, microsystems, and computer science with interdisciplinary courses in computational and systems biology developed for this program. Graduates of the program will be uniquely prepared to develop original methods, make discoveries, and establish new paradigms. They will also be well-positioned to assume critical leadership roles in academia and industry, where this new research area is of growing importance.

MIT Department of Biological Engineering

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David Gifford, PhD

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David received his BS from MIT in 1976, and PhD from Stanford University in 1981.   He joined the MIT faculty in 1982, where he is Professor of Computer Science and Engineering and Professor of Biological Engineering.

Research: 

Our group develops combined computational and experimental approaches to the discovery of novel biology and human therapeutics.    We create interpretable computational models that we train and validate with experimental evidence.   With collaborators, we apply these models to problems in experiment design, developmental biology, gene regulation, immunology, genomics, and human therapeutics.   We typically evaluate our models and discover new biology with multiplexed high-throughput experimental studies that produce data from populations of cells and single cells.

A continuing challenge is our incomplete knowledge of biological systems that leads to model uncertainty.   An active area of study in our group is the generation of appropriate uncertainty metrics for models, and how they can guide experiment design to improve model accuracy.   We use conventional large scale linear and non-linear models, Bayesian methods, and deep learning approaches in our computational thinking.

Our current specific biology focus areas include motor neuron development, single-cell perturbation studies, the regulation of chromatin accessibility, the regulatory genome, antibody design, and peptide presentation by major histocompatibility complex (MHC) proteins.

Research Areas: 

• Computational Modeling
• Neurobiological
• Systems Biology

Honors & Awards: 

Publications: .

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Rachel S. (MechE)

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Exploring the brain's blueprint

Talya Kramer was given some advice when she started graduate school. “I had been told to pick your grad lab based on the mentorship you're going to get,” Kramer, now in her sixth year working toward a PhD in biology, recalled. “The research question matters, but having a good advisor is going to make a huge difference, too. ” She took that guidance, and found a place for herself in the lab of Associate Professor of Brain and Cognitive Sciences Steven Flavell at The Picower Institute for Learning and Memory . “The lab environment is really excellent. It’s a mix of people who do more computational work and do more experimental work, and it really runs the spectrum. There are people whose expertise is in coding, and people whose expertise is in the wet lab, and they are coming together around the same questions,” Kramer said. “Steve is a fantastic mentor with exceptional scientific knowledge, and his approach plays a big part in the culture in the lab.” What was the journey that brought you to the Flavell Lab?

I majored in neuroscience and did neuroscience research all throughout my time as an undergrad. I tried a psychology lab one summer to see if that was what I was interested in, but I really felt like looking at the molecular and systems sides of neuroscience appealed to me most. When I started as a graduate student in biology here, I wanted to keep doing neuroscience research. I'm really drawn to research questions that have a larger picture to them, and I think neuroscience research has the ability to address some really fundamental questions. How do brains work? What is it that makes us human? You're going at these very fundamental truths. I ended up joining Steve’s lab and it has been a really fantastic home for the past few years. What is the focus of your research?

We work with C. elegans, which are microscopic worms, and they're a perfect mix of complexity and simplicity. They are see-through, which is practically useful because it lets you image them without doing anything invasive, but they also have complex behavioral repertoires. You can look at their sensory responses, you can look at their mating behavior, you can look at their sleep behavior, but they only have 300 brain cells driving all of that behavior. This means they're using very few nodes to direct these complex behaviors, which allows you to look at everything at once. It is a neuroscientist’s dream. My project is looking at their olfactory responses. Worms mostly move about their world by smelling. We have a good understanding from past work about  neurons that respond to smell. The question I am trying to answer is: how do networks of neurons act together to direct behavioral changes based on smell? What are some of the potential future benefits of this research?

Research in C. elegans has the potential to discover neural circuits that can be found in higher organisms and serve as a basis for answering fundamental questions about how the brain works. The ability to do whole brain imaging is relatively new in neuroscience. We’re able to look at relatively complex processes and understand how it is that not just one cell does one thing, but an ensemble of cells that acts together to produce important behaviors To be here and to be able to use these techniques is really wonderful and exciting. How are the skills you are learning now preparing you for the future?

One of my goals when I started graduate school was to gain computational skills, and now my project relies on  generating and analyzing large data sets, which is really exciting. It’s just one example of the numerous things I’ve learned here, there are so many things I have been able to try over the course of this project. There are practical skills, like how to use a unique type of microscope, or how to use different image tracking software, and there are more big picture skills about how to approach questions and obstacles in the research process. Everything I’m learning is preparing and inspiring me to continue with my research.

Kramer was among the presenters at Brains on Brains, the Department of Brain and Cognitive Sciences' biennial symposium.  

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Boehringer Ingelheim Corporation

Computational biology and digital sciences – co-op – remote.

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Boehringer Ingelheim is currently seeking a talented and innovative Co-Op to remotely join our global Computational Biology and Digital Sciences (gCBDS) department. As a Co-Op, you will contribute to data analysis that will help us discover new therapies for pulmonary fibrosis. Progressive pulmonary fibrosis involves the gradual exchange of normal lung parenchyma with fibrotic tissue, leading to lung function decline and death within 3-5 years of diagnosis. There currently is no cure and treatment options to slow disease progression are limited. Under the guidance of a Senior Scientist, you will assist with the analysis and integration of large multi-omics datasets such as bulk RNA-seq, single cell RNA-seq or proteomics to improve our understanding of disease mechanisms and to identify potential novel targets that may lead to the development of better treatments.

As an employee of Boehringer Ingelheim, you will actively contribute to the discovery, development and delivery of our products to our patients and customers. Our global presence provides opportunity for all employees to collaborate internationally, offering visibility and opportunity to directly contribute to the companies´ success. We realize that our strength and competitive advantage lie with our people. We support our employees in a number of ways to foster a healthy working environment, meaningful work, diversity and inclusion, mobility, networking and work-life balance. Our competitive compensation and benefit programs reflect Boehringer Ingelheim´s high regard for our employees.

Remote*: This position is considered remote based

Duties & Responsibilities

• Assist with data cleanup and processing
• Use computational methods and tools to analyze and integrate transcriptomic, proteomic and other omic data from human subjects to further characterize disease mechanisms
• Assist with interpretation of results
• Communicate results within the gCBDS department and to biologists in the therapeutic area

Requirements

• Must be a current undergraduate, graduate or advanced degree student in good academic standing.
• Student must be enrolled at a college or university for the duration of the internship.
• Overall cumulative minimum GPA from last completed quarter/semester 3.0 GPA (on a 4.0 scale) preferred.
• Major or minor in related field of internship
• Undergraduate students must have completed at least 12 credit hours at current college or university.
• Graduate and advanced degree students must have completed at least 9 credit hours at current college or university.

Desired Experience, Skills and Abilities:

• Experience programming in R and Python, including the ability to write your own scripts
• Completed coursework in biology, especially molecular biology or bioinformatics
• Experience with Unix/command line tools
• Experience dealing with large amounts of data
• Good communication skills
• Ability to work independently and as part of a team
• Good work ethic, ability to think creatively, and enjoyment of problem solving

Compensation Data

This position offers an hourly rate of $20.00 – $33.00 USD commensurate to the level of degree program in which an applicant is actively enrolled. For an overview of our benefits please click here .

Eligibility Requirements

Must be legally authorized to work in the United States without restriction. Must be willing to take a drug test and post-offer physical (if required). Must be 18 years of age or older.

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Science communication competition brings research into the real world

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Laurence Willemet remembers countless family dinners where curious faces turned to her with shades of the same question: “What is it, exactly, that you do with robots?”

It’s a familiar scenario for MIT students exploring topics outside of their family’s scope of knowledge — distilling complex concepts without slides or jargon, plumbing the depths with nothing but lay terms. “It was during these moments,” Willemet says, “that I realized the importance of clear communication and the power of storytelling.”

Participating in the MIT Research Slam, then, felt like one of her family dinners.

The finalists in the 2024 MIT Research Slam competition met head-to-head on Wednesday, April 17 at a live, in-person showcase event. Four PhD candidates and four postdoc finalists demonstrated their topic mastery and storytelling skills by conveying complex ideas in only 180 seconds to an educated audience unfamiliar with the field or project at hand.

The Research Slam follows the format of the 3-Minute Thesis competition, which takes place annually at over 200 universities around the world. Both an exciting competition and a rigorous professional development training opportunity, the event serves an opportunity to learn for everyone involved.

One of this year’s competitors, Bhavish Dinakar, explains it this way: “Participating in the Research Slam was a fantastic opportunity to bring my research from the lab into the real world. In addition to being a helpful exercise in public speaking and communication, the three-minute time limit forces us to learn the art of distilling years of detailed experiments into a digestible story that non-experts can understand.”

Leading up to the event, participants joined training workshops on pitch content and delivery, and had the opportunity to work one-on-one with educators from the Writing and Communication Center, English Language Studies, Career Advising and Professional Development, and the Engineering Communication Labs, all of which co-sponsored and co-produced the event. This interdepartmental team offered support for the full arc of the competition, from early story development to one-on-one practice sessions.

The showcase was jovially emceed by Eric Grunwald, director of English language learning. He shared his thoughts on the night: “I was thrilled with the enthusiasm and skill shown by all the presenters in sharing their work in this context. I was also delighted by the crowd’s enthusiasm and their many insightful questions. All in all, another very successful slam.”

A panel of accomplished judges with distinct perspectives on research communication gave feedback after each of the talks: Deborah Blum, director of the Knight Science Journalism Program at MIT; Denzil Streete, senior associate dean and director of graduate education; and Emma Yee, scientific editor at the journal Cell .

Deborah Blum aptly summed up her experience: “It was a pleasure as a science journalist to be a judge and to listen to this smart group of MIT grad students and postdocs explain their research with such style, humor, and intelligence. It was a reminder of the importance the university places on the value of scientists who communicate. And this matters. We need more scientists who can explain their work clearly, explain science to the public, and help us build a science-literate world.”

After all the talks, the judges provided constructive and substantive feedback for the contestants. It was a close competition, but in the end, Bhavish Dinakar was the judges’ choice for first place, and the audience agreed, awarding him the Audience Choice award. Omar Rutledge’s strong performance earned him the runner-up position. Among the postdoc competitors, Laurence Willemet won first place and Audience Choice, with Most Kaniz Moriam earning the runner-up award.

Postdoc Kaniz Mariam noted that she felt privileged to participate in the showcase. “This experience has enhanced my ability to communicate research effectively and boosted my confidence in sharing my work with a broader audience. I am eager to apply the lessons learned from this enriching experience to future endeavors and continue contributing to MIT's dynamic research community. The MIT Research Slam Showcase wasn't just about winning; it was about the thrill of sharing knowledge and inspiring others. Special thanks to Chris Featherman and Elena Kallestinova from the MIT Communication Lab for their guidance in practical communication skills. ”

Double winner Laurence Willemet related the competition to experiences in her daily life. Her interest in the Research Slam was rooted in countless family dinners filled with curiosity. “‘What is it exactly that you do with robots?’ they would ask, prompting me to unravel the complexities of my research in layman’s terms. Each time, I found myself grappling with the task of distilling intricate concepts into digestible nuggets of information, relying solely on words to convey the depth of my work. It was during these moments, stripped of slides and scientific jargon, that I realized the importance of clear communication and the power of storytelling. And so, when the opportunity arose to participate in the Research Slam, it felt akin to one of those family dinners for me.”

The first place finishers received a $600 cash prize, while the runners-up and audience choice winners each received $300.

Last year’s winner in the PhD category, Neha Bokil, candidate in biology working on her dissertation in the lab of David Page, is set to represent MIT at the Three Minute Thesis Northeast Regional Competition later this month, which is organized by the Northeastern Association of Graduate Schools.

A full list of slam finalists and the titles of their talks is below.

  PhD Contestants: 

• Pradeep Natarajan, Chemical Engineering (ChemE), “What can coffee-brewing teach us about brain disease?”
• Omar Rutledge, Brain and Cognitive Sciences, “Investigating the effects of cannabidiol (CBD) on social anxiety disorder”
• Bhavish Dinakar, ChemE, “A boost from batteries: making chemical reactions faster”
• Sydney Dolan, Aeronautics and Astronautics, “Creating traffic signals for space”

  Postdocs: 

• Augusto Gandia, Architecture and Planning, “Cyber modeling — computational morphogenesis via ‘smart’ models”
• Laurence Willemet, Computer Science and Artificial Intelligence Laboratory, “Remote touch for teleoperation”
• Most Kaniz Moriam, Mechanical Engineering, “Improving recyclability of cellulose-based textile wastes”
• Mohammed Aatif Shahab, ChemE, “Eye-based human engineering for enhanced industrial safety” 

Research Slam organizers included Diana Chien, director of MIT School of Engineering Communication Lab ; Elena Kallestinova, director of MIT Writing and Communication Center ; Alexis Boyer, assistant director, Graduate Career Services, Career Advising and Professional Development (CAPD); Amanda Cornwall, associate director, Graduate Student Professional Development, CAPD; and Eric Grunwald, director of English Language Studies. This event was sponsored by the Office of Graduate Education, the Office of Postdoctoral Services, the Writing and Communication Center, MIT Career Advising and Professional Development , English Language Studies, and the MIT School of Engineering Communication Labs.

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Related links.

• MIT Research Slam
• Research Slam YouTube channel
• MIT Career Advising and Professional Development (CAPD)
• Graduate Student Professional Development
• Writing and Communication Center
• MIT School of Engineering Communication Lab
• MIT English Language Studies

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• Contests and academic competitions
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Related Articles

Third annual MIT Research Slam showcase highlights PhD and postdoc communication skills

MIT Research Slam showcases postdoc and PhD communication skills

Third annual Science Slam becomes first virtual Research Slam

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MIT Postdoctoral Associate, Cancer Biology, Nano-Cybernetic Biotrek

by Jordan Madrid

April 30, 2024

Share this job

Job description.

There is an opening in Prof.  Deblina Sarkar’s research group at MIT for a Postdoctoral Associate with experience in studying the molecular mechanisms underlying cancer development, progression,  and post-treatment profiling with a particular emphasis on the analysis of various genome sequencing data for cancer both in vitro and in vivo models.  Background in brain tumor or glioblastoma is preferred but not required.  For details, see the Qualifications and Skills sections.

For details, visit:  https://web.mit.edu/deblina-sarkar/

Responsibilities

• Study the effect of novel therapeutics for cancer both in vitro and in vivo cancer models;
• Conduct in-depth analysis of RNA sequencing, DNA sequencing, whole-genome;
• sequencing, and single-cell sequencing data to identify key genetic and transcriptomic alterations in cancer;
• Develop and apply advanced bioinformatics and computational biology techniques to interrogate complex sequencing datasets;
• Design and execute in vitro and in vivo experiments to validate the functional significance of identified molecular targets and pathways;
• Collaborate with multidisciplinary teams of clinicians, biologists, and computational scientists to integrate diverse data sources and drive translational research;
• Contribute to the preparation of research manuscripts, grant proposals, and presentations at scientific conferences;
• Mentor and train junior researchers, such as graduate students and research assistants.

Qualifications

 Required:

• PhD in cancer biology, molecular biology, bioinformatics, bioengineering, neuroscience, materials science, electrical/electronics engineering or relevant field;
• Experience in creating orthotopic and heterotopic PDX cancer mouse models;
• Experience in studying the effect of therapeutics (chemotherapy/immunotherapy/radiation etc) for cancer both in vitro and in vivo transcriptome, and proteome including stemness, invasiveness, migration, autophagy, tumor promotino, inflation, cancer immunity, and related cancer pathways;
• Experience with techniques such as gene sequencing, PCR, Western blot, immunofluorescence, IHC, flow cytometry, transfection, transduction, and transformation etc.;
• Experience with in vivo methods such as MRI, IVIS;
• Proficiency in computers and the use of bioinformatics tools and software for data analysis and visualization;
• Extensive experience in the design and execution of in vitro and in vivo cancer biology experiments, including cell culture, animal models, and molecular biology techniques;
• Strong publication record in high-impact peer-reviewed journals.
• Excellent communication and collaboration skills, with the ability to work effectively in a multidisciplinary team.
• Commitment to advancing the field of cancer research and a passion for scientific discovery.
• Expertise in the integration and interpretation of multi-omics data (e.g., genomics, transcriptomics, proteomics, metabolomics).
• Experience in PDX models;
• Experience in neuro oncology;
• Experience in immune engineering;
• Experience with cancer stem cells/neural progenitors;
• Experience with neurospheres or organoids or other 3D cultures
• Experience in study of electric field in tumor;
• Experience in recording electrical/ionic signaling from cells;
• Experience in drug delivery;
• Experience with statistical analysis;
• Experience with genetic manipulation (cell line engineering, GEVIs, etc.);
• Experience in single cell sequencing and spatial transcriptomics.

This is a one-year appointment with the possibility of extension based on funding and course of research.

To apply, please visit  MIT's careers at   https://hr.mit.edu/careers    and search for job ID number  #23979.

MIT Postdoctoral Associate, Transcranial Direct Current Stimulation (tDCS) in large animals or humans, Nano-Cybernetic Biotrek

Administrative assistant, camera culture, real talk systems lead, mit center for constructive communication.

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