#Computational Biology

[feyosha]

Pssst. Hey. You.

Yea. You.

Want some of that good Stim?

Got headphones and 5 minutes?

“Order From Chaos” - Max Cooper (Emergence)

[cbirt]

In 2023, bioinformatics discoveries have catalyzed immense progress across the life sciences landscape. These ground-breaking discoveries have provided insight into the complex workings of biological systems, processes, and disease states. From discovering new diagnostic markers to mapping the complexity of the brain, these innovations promise to transform medicine, evolution, and beyond. The pace of bioinformatics discoveries fueled by the rise of artificial intelligence heralds a new era of opportunity. In this article, we take a closer look at 10 of the best bioinformatics innovations of the year and their profound impact on the field of biology. Get ready for an exciting journey to the greatest discoveries in bioinformatics!

#1 CRACKING THE CODE OF MYSTERIOUS “Y” CHROMOSOME

Scientists have struggled for decades to sequence the enigmatic Y chromosome essential to male biology. The Telomere-to-Telomere (T2T) consortium presented the complete sequence of the human Y chromosome, encompassing 62,460,029 base pairs from the HG002 genome (T2T-Y). Thanks to new computational techniques, they can finally peer into its genetic blueprint and understand male infertility and human evolution like never before.

Continue Reading

[megumi-fm]

Hi Meg, I was wondering if I could get your insight on something... I'm interested in bioinformatics as a career but am not sure whether I should pursue just a Master's or try for a PhD. How did you decide how far you want to go with your education? I noticed you mentioned you hope to do a PhD someday? Thank you so much!

hey anon! okay, so in this answer I'ma focus on two things:

my thought process behind finalizing on a PhD

my approach to furthering education

I. Why PhD?

1. I love my subjects. I love the interdisciplinary nature of computational biology and it's sister subjects and I can see myself in academia- constantly learning and researching and exploring. 2. Even on the off chance that if I don't pursue a career in academia, I think I need a PhD anyway? Most high level positions in the industry for life-sciences requires a level of expertise that only comes with a doctorate, and I think my career opportunities (+ growth) will be rather limited without it.

Considering these two points, a PhD would be most suitable for me.

———————

Now, choosing the right type of graduate program can always be challenging because there are so many ways to go about it, and I am a very indecisive person so this was especially difficult for me. Here is my approach

II. Factors I considered before taking my next steps

My Primary Short-Term Goal(s)

I opted for a B.Tech in Biotechnology after 12th grade, and it is through the course of this degree that I realized my interest in computational biology and bioinformatics. My undergrad focused on too many topics and often emphasized wet lab over dry lab, so although I'm graduating with a specialization in Medicinal and Computational Biology, I don't know nearly enough regarding the computational aspects Thus, my short-term goal is to expand my theoretical understanding of the important aspects of bioinformatics & computational biology.

2. Course Options that Work

Now, I know that I want to continue my education, I've got two options- Masters and PhD. When I considered my immediate goal against these two options, I realized four things: a. I'm not equipped with the required dry lab skills to dive headfirst into research. b. I don't know enough bioinformatics to commit to anything long term right now c. I'm looking for a course that feels like an extension of my undergrad d. I want to keep my options open and consider all career opportunities Given these three options (+ course-related expenses + my skill level), it made most sense for me to choose a MSc at the moment rather than a PhD.

3. How the Course Ties in to My Long Term Goals

As I mentioned, my long term goal is to do a PhD. However, my upcoming graduate course is actually an MSc by Coursework degree, which- unlike a Thesis program, focuses on skill development (especially industry related) rather than research. In fact, most Thesis Masters can be converted to a PhD, but my program does not have that option. At first glance, this course might seem like it's going against my long term goal but consider: - Industry related or not, I need to develop computational skills before I can pursue research - After this course I might prefer to gain work experience for a couple years before opting for a PhD. - My preferred uni(s) for PhD are different from my preferred uni for Masters. [^To give an example on the last point, for masters i considered countries/unis known for their quality of education + closer to my home country (this will be my first time living abroad alone) but for my PhD, I'm looking at countries/unis that are pioneers in research for my subjects of interest (even if they are a lot farther away from home)] So essentially, I'm relying on this course to give me the skills and knowledge I need for a PhD in the future, while also giving me a buffer to understand and align my future goals and plans. Jumping from this to a PhD would be a lot harder than from a Thesis Masters, but that's a risk I'm willing to take.

So yeah, this was the way I went about choosing both my short term and long term academic goals. I hope this provides a good starting point for you! Don't stress out too much about it though; the truth is that there is no right or wrong choice, whatever decision you make will warp around your intentions and work for you the way you want it to. Best of luck for your future endeavors!!! I'm sure it'll all work out <3

[tea-and-bio]

Rainy evening at the library 🩷

6/15/23

I rewrote my code to make it work with the full dataset, also to make it, uh, actually do what it's supposed to. Currently running it to test if it worked, which takes about an hour (look, I didn't realize I'd be coding when I bought my laptop, okay?). I was going to just take my laptop back to my apartment while it runs, but the rain prevented me from doing that, which means I have a lovely excuse to curl up in the library with a fun book. Fingers crossed the program finishes before the library closes.

[studentbyday]

Hii how are you doing!!!

You're taking Bioinformatics too right? What resources are you using to understand it HELP—

Hii I'm good, thanks! Hbu? That's so cool you're self-studying bioinformatics too! You're coming from the bio side as well, right?

I haven't really gotten into actual bioinformatics stuff yet bc last I tried, I was overwhelmed by all the info I was expected to know...biology, stats, and coding/computer science stuff. I feel I still need to know more on all of those fronts, but coming from a life science background, the part that's most foreign to me is the coding aspect, so I'm trying to work through an intro to computer science mooc by Harvard called cs50x and figure out where to go from there... Also, the codeblr community has been nothing but extremely encouraging and helpful. Many have compiled resources for learning to code like in this post.

Sorry if this wasn't very helpful, I'm at the very very very beginning in this 😅 Maybe once I'm further along, I'll know enough to make a masterpost of resources I used and found helpful!

If anyone has any other suggestions, please feel free to add in the reblogs!

[jcmarchi]

Student spotlight: Victory Yinka-Banjo

New Post has been published on https://thedigitalinsider.com/student-spotlight-victory-yinka-banjo/

Student spotlight: Victory Yinka-Banjo

This interview is part of a series from the MIT Department of Electrical Engineering and Computer Science featuring students answering questions about themselves and life at the Institute. Today’s interviewee, Victory Yinka-Banjo, is a junior majoring in MIT Course 6-7: Computer Science and Molecular Biology. Yinka-Banjo keeps a packed schedule: She is a member of the Office of Minority Education (OME) Laureates and Leaders program; a 2024 fellow in the public service-oriented BCAP program; has previously served as secretary of the African Students’ Association, and is now undergraduate president of the MIT Biotech Group; additionally, she is a SuperUROP Scholar; a member of the Ginkgo Bioworks’ Cultivate Fellowship (a program that supports students interested in synthetic biology/biotech); and an ambassador for Leadership Brainery, which equips juniors/leaders of color with the resources needed to prepare for graduate school. She recently found time to share a peek into her MIT experience.

Q: What’s your favorite building or room within MIT?

A: It has to be the Broad Institute of MIT and Harvard on Ames Street in Kendall Square, where I do my SuperUROP research in Caroline Uhler’s lab. Outside of classes, you’re 90 percent likely to find me on the newest mezzanine floor (between the 11th and 12th floor), in one of the UROP [Undergraduate Research Opportunities Program] rooms I share with two other undergrads in the lab. We have standing desks, an amazing coffee/hot chocolate machine, external personal monitors, comfortable sofas — everything, really! Not only is it my favorite building, it is also my favorite study spot on campus. In fact, I am there so often that when friends recently planned a birthday surprise for me, they told me they were considering having it at the Broad, since they could count on me being there. 

I think the most beautiful thing about this building, apart from the beautiful view of Cambridge we get from being on one of the highest floors, is that when I was applying to MIT from high school, I had fantasized working at the Broad because of the groundbreaking research. To think that it is now a reality makes me appreciate every minute I spend on my floor, whether I am doing actual research or some last-minute studying for a midterm. 

Q: Tell me about one interest or hobby you’ve discovered since you came to MIT.

A: I have become pretty involved in the performing arts since I got to MIT! I have acted in two plays run by the Black Theater Guild, which was revived during my freshman year by one of my friends. I played a supporting role in the first play called “Nkrumah’s Last Day,” which was about Ghana at a time of governance under Kwame Nkrumah, its first president. In the second play, a ghost story/comedy called “Shooting the Sheriff,” I played one of the lead roles. Both caused me to step way out of my comfort zone and I loved the experiences because of that. I also got to act with some of my close friends who were first-time stage actors as well, so that made it even more fun. 

Outside of acting, I also do spoken word/poetry. I have performed at events like the African Students Association Cultural Night, MIT Africa Innovate Conference, and Black Women’s Alliance Banquet. I try to use my pieces to share my experiences both within and beyond MIT, offering the perspective of an international Nigerian student. My favorite piece was called “Code Switch,” and I used concepts from [computer science] and biology (especially genetic code switching), to draw parallels with linguistic code-switching, and emphasize the beauty and originality of authenticity. This semester, I’m also a part of MIT Monologues and will be performing a piece called “Inheritance,” about the beauty of self-love found in affection transferred from a mother. 

Q: Are you a re-reader or a re-watcher — and if so, what are your comfort books, shows, or movies?

A: I don’t watch too many movies, although I used to be obsessed with all parts of “High School Musical;” and the only book I’ve ever reread is “Americanah.” I would actually say I am a re-podcaster! My go-to comfort-podcast is this episode, “A Breakthrough Unfolds”, by Google DeepMind. It makes me a little emotional every time I listen. It is such an exemplification of the power of science and its ability to break boundaries that humans formerly thought impossible. As a computer science and biology major, I am particularly interested in these two disciplines’ applications to relevant problems, like the protein-folding problem discussed in the episode, which DeepMind’s solution for has caused massive advances in the biotech industry. It makes me so hopeful for the future of biology, and the ways in which computation can advance human health and precision medicine.

Q: Who’s your favorite artist?

A: When I think of the word ‘artist,’ I think of music artists first. There are so many who I love; my favorites also evolve over time. I’m Christian, so I listen to a lot of gospel music. I’m also Nigerian so I listen to a lot of Afrobeats. Since last summer, I’ve been obsessed with Limoblaze, who fuses both gospel and Afrobeats music! KB, a super talented gospel rapper, is also somewhat tied in ranking with Limo for me right now. His songs are probably ~50 percent of my workout playlist.

Q: It’s time to get on the shuttle to the first Mars colony, and you can only bring one personal item. What are you going to bring?

A: Oooh, this is a tough one, but it has to be my Brass Rat. Ever since I got mine at the end of sophomore year, it’s been nearly impossible for me to take it off. If there’s ever a time I forget to wear it, my finger feels off for the entire day. 

Q: Tell me about one conversation that changed the trajectory of your life.

A: Two specific career-defining moments come to mind. They aren’t quite conversations, but they are talks/lectures that I was deeply inspired by. The first was towards the end of high school when I watched this TEDx Talk about storing data in DNA. At the time, I was getting ready to apply to colleges and I knew that biology and computer science were two things I really liked, but I didn’t really understand the possibilities that could be birthed from them coming together as an interdisciplinary field. The TEDx talk was my eureka moment for computational biology. 

The second moment was in my junior fall during an introductory lecture to “Lab Fundamentals for Bioengineering,” by Professor Jacquin Niles. I started the school year with a lot of confusion about my future post-grad, and the relevance of my planned career path to the communities that I care about. Basically, I was unsure about how computational biology fit into the context of Nigeria’s problems, especially because my interest in the field is oriented towards molecular biology/medicine, not necessarily public health. 

In the U.S., most research focuses on diseases like cancer and Alzheimer’s, which, while important, are not the most pressing health conditions in tropical regions like Nigeria. When Professor Niles told us about his lab’s dedication to malaria research from a molecular biology standpoint, it was yet another eureka moment. Like, Yes! Computation and molecular biology can indeed mitigate diseases that affect developing nations like Nigeria — diseases that are understudied, and whose research is underfunded. 

Since his talk, I found a renewed sense of purpose. Grad school isn’t the end goal. Using my skills to shine a light on the issues affecting my people that deserve far more attention is the goal. I’m so excited to see how I will use computational biology to possibly create the next cure to a commonly neglected tropical disease, or accelerate the diagnosis of one. Whatever it may be, I know that it will be close to home, eventually.

Q: What are you looking forward to about life after graduation? What do you think you’ll miss about MIT?

A: Thinking about graduating actually makes me sad. I’ve grown to love MIT. The biggest thing I’ll miss, though, is Independent Activities Period (IAP). It is such a unique part of the MIT experience. I’ve done a web development class/competition, research, a data science challenge, a molecular bio crash course, and a deep learning crash course over the past three IAPs. It is such an amazing time to try something low stakes, forget about grades, explore Boston, build a robot, travel abroad, do less, go slower, really rejuvenate before the spring, and embrace MIT’s motto of “mind and hand” by just being creative and explorative. It is such an exemplification of what it means to go here, and I can’t imagine it being the same anywhere else. 

That said, I look forward to graduating so I can do more research. My hours spent at the Broad thinking about my UROP are always the quickest hours of my week. I love the rabbit holes my research allows me to explore, and I hope that I find those over and over again as I apply and hopefully get into PhD programs. I look forward to exploring a new city after I graduate, too. I wouldn’t mind staying in Cambridge/Boston. I love it here. But I would welcome a chance to be somewhere new and embrace all the people and unique experiences it has to offer.

I also hope to work on more passion projects post-grad. I feel like I have this idea in my head that once I graduate from MIT, I’ll have so much more time on my hands (we’ll see how that goes). I hope that I can use that time to work on education projects in Nigeria, which is a space I care a lot about. Generally, I want to make service more integrated in my lifestyle. I hope that post-graduation, I can prioritize doing that even more: making it a norm to lift others as I continue to climb.

[bio-stem]

I can’t express how much pride this gave me????

[quotesfromall]

Machines could not be fashioned in the image of a man's mind, he said, but he betrayed every action that he preferred machines to men, statistics to individuals, the far away general view to the intimate personal touch requiring imagination and initiative.

Frank Herbert, Dune Messiah

[scientificinquirer-blog]

Computational tool developed to predict immunotherapy outcomes for patients with metastatic breast cancer

Using computational tools, researchers from the Johns Hopkins Kimmel Cancer Center and the Johns Hopkins University School of Medicine have developed a method to assess which patients with metastatic triple-negative breast cancer could benefit from immunotherapy. The work by computational scientists and clinicians was published Oct. 28 in the Proceedings of the National Academy of…

[lunar-goodness]

The cell-modeling approach underpinning the research was pioneered in the lab of Ilya Vakser, professor of computational biology and molecular biosciences and director of the Center for Computational Biology at KU. Vakser’s group is one of the foremost in the world in modeling macromolecular interactions.

"What we're doing is a virtual cell,” Vakser said. “It's a biological cell that exists in the computer. And it allows us to investigate all kinds of biological phenomena at atomic resolution, such as the effects of genetic mutations.

[cbirt]

Protein engineering is an emerging field in biological research – the improvement of existing proteins or the creation of new ones in order to improve efficiency or perform new functions has proved to be a field with much potential. Despite advancements in the field making protein engineering a sought-after field for industrial applications, it is still hampered by a lack of parameters by which different methods can be compared, a lack of large datasets that can be used as a basis for models, and a lack of accessibility for large numbers of researchers in the field. To rectify this, scientists from Align to Innovate, Cambridge, United States, and collaborators are introducing the Protein Engineering Tournament, a one-of-its-kind competition to characterize and design proteins in silico.

If cells can be considered living factories, proteins are the workers that allow life to persist by carrying out innumerable biochemical processes and functions. Composed of varying sequences of amino acids, these complex molecules do everything from ensuring structural stability to catalyzing chemical reactions. Their versatility and utility have made them the focus of much research in recent years. Protein engineering has emerged as a field with applications in nearly every area of biotechnology, from agricultural industries to therapeutics to environmental remediation. Engineered proteins can be used to recycle plastics, diagnose rare diseases, and reduce carbon emissions.

Advancements in technology have made the computational design of proteins an attractive prospect to many: theoretically, with the necessary inputs, a machine learning model should be able to train itself to recognize certain trends and mimic them when asked to make its own predictions. However, several things hamper its development: despite the creation of multiple machine learning models for this purpose, the scarcity of large, complex datasets, the lack of reproducibility, and the lack of available infrastructure to support the development and validation of such models make it difficult to take full advantage of the benefits that computational protein engineering has to offer.

Continue Reading

[techninja]

How Wetware Computers Are Being Used in Advanced Diagnostics

Wetware Computers: Pioneering the Next Era of Computing

As technology continues to evolve at a rapid pace, wetware computers stand out as a revolutionary innovation that blends biological elements with traditional computing. These cutting-edge systems promise to transform the landscape of computing, offering unparalleled efficiency and capabilities. This article delves deep into the realm of wetware computers, exploring their principles, current advancements, and future implications.

What Are Wetware Computers?

Wetware computers, also referred to as biocomputers or organic computers, incorporate biological materials with conventional hardware. Unlike traditional computers that depend on silicon-based semiconductors, wetware computers use living cells and tissues to execute computational tasks. This synergy of biology and technology unlocks new potential, leveraging the innate complexity and efficiency of biological systems.

Core Components of Wetware Computers

Wetware computers feature several distinct components that set them apart from conventional systems:

Living Cells: The foundation of wetware computers consists of living cells, such as neurons or engineered bacteria, which process information via biochemical reactions.

Biological Circuits: These circuits mimic the functions of electronic circuits, utilizing biological materials to transmit signals and perform logical operations.

Interface Technologies: Advanced interfaces are developed to facilitate communication between biological components and electronic hardware, ensuring smooth integration.

The Mechanisms of Wetware Computing

Biological Processing Units (BPUs)

At the core of wetware computing are biological processing units (BPUs), akin to central processing units (CPUs) in traditional computers. BPUs exploit the natural processing abilities of biological cells to perform complex computations. For instance, neurons can form intricate networks that process information simultaneously, offering significant advantages in speed and efficiency over traditional silicon-based processors.

Biochemical Logic Gates

Biochemical logic gates are crucial elements of wetware computers, operating similarly to electronic logic gates. These gates employ biochemical reactions to execute logical operations such as AND, OR, and NOT. By harnessing these reactions, wetware computers achieve highly efficient and parallel processing capabilities.

Synthetic Biology and Genetic Modification

Progress in synthetic biology and genetic modification has been instrumental in advancing wetware computers. Scientists can now engineer cells to exhibit specific behaviors and responses, tailoring them for particular computational tasks. This customization is essential for creating dependable and scalable wetware systems.

Potential Applications of Wetware Computers

Wetware computers have immense potential across a variety of fields, including:

Medical Research and Healthcare

In medical research, wetware computers can simulate complex biological processes, providing insights into disease mechanisms and potential treatments. In healthcare, these systems could lead to the development of advanced diagnostic tools and personalized medicine, where treatments are tailored to the individual’s unique biological profile.

Environmental Monitoring

Wetware computers can be deployed for environmental monitoring, using genetically engineered organisms to detect and respond to pollutants. These biocomputers can offer real-time data on environmental conditions, aiding in pollution management and mitigation.

Neuroscience and Brain-Computer Interfaces

The fusion of biological components with computing paves the way for significant advancements in neuroscience and brain-computer interfaces (BCIs). Wetware computers can help develop sophisticated BCIs, enabling direct communication between the human brain and external devices. This technology holds great promise for medical rehabilitation, enhancing the quality of life for individuals with neurological conditions.

Current Progress and Challenges

Advancements in Wetware Computing

Recent advancements in wetware computing have shown the feasibility of integrating biological components with electronic systems. Researchers have successfully created basic biocomputers capable of performing fundamental logical operations and processing information. These milestones highlight the potential of wetware computers to complement and eventually surpass traditional computing technologies.

Challenges and Obstacles

Despite promising progress, wetware computing faces several challenges:

Stability and Reliability: Biological systems are inherently complex and can be unstable. Ensuring the stability and reliability of biocomputers remains a significant challenge.

Scalability: Scaling wetware computing systems to handle more complex and large-scale computations is a critical hurdle.

Ethical Considerations: The use of living organisms in computing raises ethical questions regarding the manipulation of life forms for technological purposes.

The Future Prospects of Wetware Computers

The future of wetware computers is promising, with ongoing research and development aimed at overcoming current limitations and unlocking their full potential. As technology advances, we anticipate several key trends:

Hybrid Computing Models

Wetware computers are likely to complement traditional computing systems, creating hybrid models that leverage the strengths of both. This integration could lead to more efficient and powerful computing solutions, addressing complex problems that are currently beyond our reach.

Visit my blog here

Advancements in Synthetic Biology

Continued advancements in synthetic biology will enable the creation of more sophisticated biological components for wetware computers. Improved genetic engineering techniques will allow for greater precision and control, enhancing the performance and reliability of these systems.

Ethical and Regulatory Frameworks

As wetware computing technology advances, the development of robust ethical and regulatory frameworks will be essential. These frameworks will ensure that the use of biological components in computing is conducted responsibly and ethically, addressing concerns related to the manipulation of life forms.

Conclusion

Wetware computers represent a transformative leap in the field of computing, merging the biological and technological worlds in unprecedented ways. The potential applications of this technology are vast, from medical research and healthcare to environmental monitoring and neuroscience. While challenges remain, the continued progress in this area promises to revolutionize the way we approach computation, offering new possibilities and efficiencies.

[tea-and-bio]

July 16th - coffee shop day ft. ramen from my roommate's birthday

Visited a cute local coffee shop with my roommate! I got a latte with almond syrup, which was good, but not as good as hazelnut. I finally got a plot to show the overall results of my project, and it shows interesting stuff (that I can't explain in detail because it's confidential 😭), so that's super exciting! I also got a start on my final presentation slides. I'm glad I have an overall conclusion to make instead of just a bunch of random observations. Tomorrow is for working on the slides more, which I unfortunately no longer really have an excuse to put off.

[studentbyday]

day 20 // 100dop

day 2/3 of final exam review 🙈🙈

Goals today:

Finish module 2 review ✅

Finish module 3 review ✅

Finish module 4 review - i have 2 pages left to read but i think i need a fresh brain for me to remember it...

Continued filling cheatsheet ✅ (omg there's sm more i wanna put in here i hope i have the space 😬😬😬)

Day 13: What misconception about your subject annoys you?

That life sciences is the "easy science". IT ABSOLUTELY IS NOT!!!! 🤣 Asides from the great volume of info you have to remember, to really understand it, you have to know chemistry, which is based on quantum physics (which is... 90% math tho thankfully I don't have to know it) and they're making me cover allll this and more in my degree (don't even get me started on the complexity of biochemistry, which I can't understand until I've covered general chemistry) and... Idk who would call this easy if you're covering this stuff for the very first time??? Perhaps they were talking about high school biology because that was a breeze 🙄

Hehe...I just realized that this maybe sounds very discouraging to those who may be considering this degree or smth similar... 😅 Truth be told, no matter how much I complain, I would much rather be doing this than something else! It's so fascinating to learn about how all of the natural sciences intersect to create us and all other living beings and how what we know leads to so much more to know that it creates entirely new fields! Like, literally every word in the acronym STEM converges in the life sciences - how cool is that! And all of this can be used to help people! So for me, it's definitely a fulfilling field to be in. So...as long as you personally are interested in this field and are NOT thinking of getting into this program because "it's easy", I'd highly recommend it!