Bioinformatics
The Hybrid Science
The potential of science in a data-driven world just keeps growing.
Data and analytics applied to science give rise to more rapid discoveries, swifter technological advances, and most importantly, more immediate impacts on the human condition.
Integrated knowledge from biological, computational and mathematical disciplines creates a unique professional perspective preparing graduates to play pivotal roles in today’s cutting-edge life sciences, biotechnology and pharmaceutical industries.
Students take classes in a range of disciplines including molecular biology, biochemistry, statistics, ethics, data mining and machine learning, giving them a competitive edge in the ever-expanding life sciences sector.
This is so much more than crunching numbers. It’s changing lives.
Degree Options
Introduces the concepts of probability and statistics used in bioinformatics applications, particularly the analysis of microarray data. Uses statistical computation using the open-source R program. Topics include maximum likelihood; Monte Carlo simulations; false discovery rate adjustment; nonparametric methods, including bootstrap and permutation tests; correlation, regression, ANOVA, and generalized linear models; preprocessing of microarray data and gene filtering; visualization of multivariate data; and machine-learning techniques, such as clustering, principal components analysis, support vector machine, neural networks, and regression tree.
Covers various aspects of data mining, including classification, prediction, ensemble methods, association rules, sequence mining, and cluster analysis. The class project involves hands-on practice of mining useful knowledge from a large data set.
Intended for those familiar with the basics of genetics, molecular and cellular biology, and biochemistry, all of which are required to appreciate the beauty, power, and importance of modern genomic approaches. Introduces the latest sequencing methods, array technology, genomic databases, whole genome analysis, functional genomics, and more.
Fall
- 6/1 International
- 8/15 Domestic
Spring
- 10/1 International
- 12/1 Domestic
- Bioinformatics and Chemoinformatics
- Bioinformatics Enterprise
- Biotechnology
- Data Analytics
- Health Informatics
- Medical Health Informatics
- Omics
5-9% expected national job growth for bioinformatic scientists by 2026 (US Department of Labor)
Real World Experience
Northeastern’s bioinformatics students benefit from Northeastern’s extensive network of industry partners in Boston, the San Francisco Bay Area, and around the globe. Masters degree students complete either a 4-8 month co-op work experience or participate in an industry-based independent project, providing an invaluable opportunity to gain professional training within the commercial sector.
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Biology and Bioinformatics With Julian Stanley
What motivated you to pursue a PlusOne master’s degree?
I joined Northeastern in the biochemistry program on a 5-year, 3-co-op plan. I already had an interest in bioinformatics, but the Bioinformatics PlusOne program had not been approved yet. During my third year, I wanted to learn more technical skills, so I briefly switched to the “Biology and Computer Science” combined program.By the beginning of my fourth year, I learned that the Bioinformatics PlusOne had been approved. I also learned that I could finish the BS Biology/MS Bioinformatics PlusOne in the same amount of time and credits as my 5-year undergraduate program.
My choice to join the program came after consultation with a variety of members of the faculty and staff. Professor Steve Vollmer initially told me about the program, and I also received thoughtful advice and guidance from Professors Veronica Godoy-Carter and Erin Cram, academic advisors Amy Carmack and Mark Bresnihan, and program assistant Melisa Brown, among others.
Can you tell me about your overall experience as a participant in the PlusOne program?
The two biggest benefits for me were in teaching and co-op. I spent my PlusOne year as a TA for BINF6308 and BINF6309, the two core introductory courses in the Bioinformatics curriculum. As a graduate TA, I was given much more independence and responsibility than as an undergraduate TA. I felt really lucky to be able to practice teaching and curriculum development, and that experience solidified my interest in continuing to teach after finishing the program.
I also completed a 6-month co-op through the PlusOne program, where I worked as a student in the Silver Lab at Harvard Medical School. In the Silver Lab, I was given a lot more freedom and independence as a graduate student than as an undergraduate. My experience during my co-op helped to convince me that I was ready to join a Ph.D. program and further develop my ability to conduct research independently.
Would you recommend PlusOne to other students?
For me, the PlusOne program was a relatively clear choice because it took the same amount of time and money as a 5-year undergraduate degree program. Since I knew that I was interested in Bioinformatics (and not, for example, software development), and there was no undergraduate Bioinformatics program, the PlusOne program also meshed very well with my academic and professional interests.
Other students may have a more complex decision to make, especially since the PlusOne program usually requires additional tuition costs. In broad terms, the PlusOne Bioinformatics program is likely a good investment for students looking to immediately join the workforce as bioinformaticians. Students who prefer software development or intend to complete a Ph.D. are less likely to benefit from the program. I highly recommend that any student considering the program weigh their options carefully with help from family, academic advisors, and faculty mentors.
How did PlusOne and COS help shape your interests and/or prepare you for your future?
COS as a whole has played a huge role in shaping my interests and plans.
My research in COS, advised by Professor Javier Apfeld and supported by the Honors Program and Undergraduate Office of Research and Fellowships, was undoubtedly the activity that had the largest impact on my interests and future. In conjunction, advice and mentorship that I received from faculty and staff like Professors Sue Powers-Lee, Erin Cram, and Veronica Godoy-Carter (to name just a few), academic advisors like Danielle Massey, and my friends and classmates were invaluable.
The PlusOne program itself also helped to shape my interests. It gave me a year to focus on my skills in bioinformatics and computational biology and to hone my specific research interests before beginning my Ph.D. Through the program, I spent a year splitting my time between learning, teaching, and conducting research, which helped convince me that I would be comfortable continuing to learn, teach, and conduct research during my Ph.D. and beyond.
What do you plan on doing post-graduation?
Right now (Summer 2020), I am working as a software engineering intern for the R Project for Statistical Computing (funded by Google Summer of Code). In the fall, I will join the Biology Ph.D. program at the Massachusetts Institute of Technology. I hope to continue teaching and conducting increasingly-independent research professionally.
Best of luck in your future endeavors, Julian, from everyone at the College of Science! We can’t wait to see what you accomplish next.
Iron: The Swiss Army Knife for Bacteria
Biofilms are the name of the game in the Chai Lab at Northeastern University, and iron is shaking up the rules.
Dr. Yunrong Chai and his team recently published an article in Nature Communications on their novel discoveries surrounding biofilm formation. Biofilms are communities of bacteria, that are tougher to kill with antibiotics than free bacterial colonies. That’s because of the protective coating that makes up the spaces between cells. The way that a biofilm forms and operates is still a question — one that Chai hopes to answer.
The team noticed that their model bacteria, Bacillus subtilis, requires hundreds of times more iron when growing as part of a biofilm than it needs to grow outside of a biofilm. This observation sparked the questions that started Chai and his team on their two-and-a-half-year-long project. Where is all that iron going, and what is it for?
Dr. Yunrong Chai with graduate student in the Chai lab.
“Iron is very important, there’s lots of biological processes that need iron,” Chai said. “Bacteria will need iron to grow, and they will also need iron to build these biofilms.” Without all that extra iron, a robust biofilm will never form.
Through a collaboration with the Larese-Casanova Research Group at Northeastern University, the team found that 99 percent of the iron needed for biofilm formation wasn’t used by the cells to grow and replicate. High iron concentrations induce transcription of genes that code for the precursor of a siderophore protein, called bacillobactin. Siderophores are a group of proteins that bacteria use to scavenge iron from their environments. The precursor, 2,3-Dihydroxybenzoate (DHB), solves a key problem with iron, its insolubility. DHB binds to iron and helps it dissolve in the aqueous environment of a biofilm. The theory is that iron then acts as an extracellular electron acceptor.
The implications of that discovery are powerful, as it means that bacteria might be communicating in ways that we hadn’t previously realized.
Communication is key for biofilm formation. That’s because biofilms are complex, genetically identical bacteria that can differentiate into specialized, phenotypically diverse forms that carry out unique functions.
If that sounds familiar, its because a biofilm is eerily similar to a multicellular organism. It was thought that chemical messengers were responsible for cell to cell communication.
“Chemicals are the language of bacteria,” Chai said, but DHB changes things. Iron could act as part of a bacterial circuit that allows cells to communicate through electrical as well as chemical signals. That discovery isn’t the only conclusion to the biofilm story, however. A second use for extracellular iron could change what we’ve been taught about cellular respiration.
The electron transport chain (ETC) is the essential final step for aerobic respiration. Electrons are passed down a chain of membrane-bound proteins until they are deposited on an oxygen molecule, forming water. Iron can also act as the final electron acceptor instead of oxygen for energy production.
It might not be as efficient as oxygen, but in the anaerobic depths of a biofilm, iron can be a valuable alternative. “The textbook always tells you that this always happens on the membrane,” Chai said. “They will never tell you that these electrons could leak and get into an extracellular space.” That is still electron transfer, according to Chai, even if it isn’t happening in a conventional way.
Extracellular electrical signaling and electron transfer for respiration aren’t two competing theories. According to Chai, these two processes are likely happening simultaneously. The Chai Lab found that disrupting these processes by preventing cells from producing DHB disrupted the whole biofilm.
Biofilms are found everywhere, from the bottom of the ocean to the driest deserts and even inside of our bodies. It’s theorized that biofilms in human and other eukaryotic microbiota might communicate directly with their hosts, potentially through Chai’s electronic mechanism. The Chai Lab’s paper represents a huge step towards a deeper understanding of how and why biofilms form, how they interact with their environments, and how they interact with their human hosts.
Student Spotlight: Nareh Sahakian
Why did you choose to attend Northeastern?
While I originally chose to do my undergrad at Northeastern for the co-op program, coming to Northeastern ended up being one of the best decisions of my life for so many reasons. Not only did I have the opportunity to work full time in my field before graduating (with almost 2 full years of lab experience at the time of graduation!), I also made lifelong friends and some amazing memories. Because my undergrad was such a positive experience, I couldn’t imagine going anywhere else to earn my graduate degree. And again, the co-op as part of the bioinformatics program is invaluable. I think I chose well! Northeastern has proven to be another amazing decision.
What other organizations or activities are you involved with outside of your degree program?
While I’m not involved with activities on campus, I do work full time at the Broad Institute. I’ve also started a hiking club for Armenians in the greater Boston area. So far we’ve gone on 3 hikes with some great turnouts!
What is your favorite part about Northeastern?
Academics wise, my favorite part about Northeastern is the co-op program. It has helped immensely to supplement the learning in the classroom with real experiences in the field. Non-academics wise, my favorite part about Northeastern is the sense of community that has been ever present since I first stepped on campus back in 2012.
What is your favorite part of Boston?
The food! There is no shortage of restaurants and all different types of cuisines to try. I always love trying out new spots in Boston, Cambridge, Somerville and Medford.
What is the best perk of being a Northeastern student?
The global community! Northeastern has such far reaches around the world and it’s an amazing perk to take advantage of. Talk to your advisors about co-op connections abroad if you’re at all interested!
What advice would you give to an incoming graduate student?
Forget about the lesson structure from undergrad – graduate classes are a whole new ball game. Be prepared to do almost all of the learning on your own, since most professors change their ‘lecture’ time into a ‘recitation’ time where you can go at your own will and ask questions, rather than sitting through powerpoint slides.
What are your plans after degree completion?
I’m hoping to make a smooth transition from my current wet lab position into a more computational or analytics role. I’m hoping that I can either stay in the lab that I’m presently in, or find another opportunity within the Broad. I’ve loved working there the past year and a half and it’s one of the best places to be for bioinformatics!
Tell us a fun fact about yourself.
I’m hiking all the 4000 foot mountains in New England. There are 67 total in New Hampshire, Maine and Vermont. I’ve done 17 so far!
Co-op Coordinator discusses diversity during MassBioEd’s Life Sciences Workforce conference
Co-op Coordinator Vanecia Harrison-Sanders sat on a panel titled “Increasing Opportunities: What Life Sciences Industry Can Do to Increase Diversity Within” during MassBioEd’s Life Sciences Workforce 2018: 3rd Annual Massachusetts Conference.
The conference, hosted at Northeastern University, centered on advancing discussion on workforce development issues related to the life sciences industry and seeks to increase engagement and collaboration between higher education and industry.
Harrison-Sanders’ panel talked about recent research highlighting the lack of minorities represented in the industry and discussed various diversity initiatives underway. Serving with her was Jeffrey Herrera, Senior Associate, Global Diversity & Inclusion, Biogen; Melodie Knowlton, Head, Vertex Learning Lab; and Joan Reede, Dean of Diversity, Director of Minority Faculty Development, Harvard Medical School. It was moderated by Travis McCready, President & CEO, MLSC.
The goal of the panel was to discuss potential ways in which industry, government, and educational systems can partner to alleviate underrepresentation in the life sciences industry.