#Bioinformatics

[felixcloud6288]

Seriously, genetics is weird.

I was reading one paper on long noncoding RNAs and there's this one part that just really stood out to me.

So to catch everyone up, genetic data is stored as DNA. Then parts of it go through a process called transcription to build a strand of RNA. Certain RNAs get translated into proteins, but there are noncoding RNAs that don't make proteins but instead do a secret second thing (and I mean secret cause there are tons of ncRNAs that no one knows what they do). long noncoding RNAs are just noticeably longer than average.

Anyway, one lncRNA mentioned in the paper is called WINCR1. When the researchers managed to block it from being used, they noted that cells lost the ability to divide and there was one particular gene GADD45B, which is responsible for triggering apoptosis, was more common in the cells.

So my guess is one of WINCR1's jobs is to just confirm to the self-destruct system that the DNA isn't broken. Like, it being transcribed essentially tells the cell that that part of the DNA is still working and it can then go and turn off the kill switch.

So I guess cells are just designed to kill themselves as their default setting and WINCR1 is the drinking bird pressing the Y key to tell the system to not just blow up.

[cbirt]

Bile acids, simple molecules that live in our intestines, have long been relegated to the role of digestive workhorses, faithfully emulsifying fats for absorption. However, recent scientific revelations are rewriting the story, revealing a complex hidden world within these seemingly simple compounds. This new recognition stems from the discovery that bile acids make a remarkable difference in the hands of our gut microbes—a symphony of changes that infuses them with a surprising array of potential health benefits.

This blog dives into groundbreaking research that escapes in light of this underappreciated diversity of bile acids. With the help of this research, we can explore how our gut microbes orchestrate this complex chemical choreography and present a powerful tool scientists have developed to unlock the secrets of these modified bile acids.

Bile acids, synthesized in the liver from cholesterol, are essential for a healthy digestive system. They emulsify fats and help their breakdown and absorption. However, their impact extends far beyond the gut. These act as signaling molecules that interact with receptors throughout the body and influence functions such as metabolism, immune response, and even brain health.

Continue Reading

[tired-coffee-addict]

I love autumn! 🍁

I'm getting interested in bioinformatics these days, but I'm not sure if i want to pursue it academically by master's degree or with a seminar. I started learning R coding this week by myself and it's going great, though it's too soon to determine if I enjoy it or not.

If anyone in bioinformatics stumbles on this post, comment what you like in your career and if you recommend it for someone interested in research!

[everythingaboutbiotech]

Summary of the 7 Habits of Highly Effective People by Stephen Covey. This book has had a profound impact on my life, and I hope it can help you too.

The 7 Habits are:🧵

Habit 1: Be Proactive

Don't be reactive to circumstances. Take responsibility for your life and the choices you make.

Focus on the things you can control, and let go of the things you can't.

Be proactive in your relationships and interactions with others.

Habit 2: Begin with the End in Mind

Have a clear vision for your life and what you want to achieve.

Break down your vision into smaller goals and steps.

Live each day in alignment with your vision.

Habit 3: Put First Things First

Distinguish between what is urgent and what is important.

Focus your time and energy on the things that are most important.

Learn to say no to things that are not a priority.

Habit 4: Think Win-Win

Look for ways to create mutually beneficial outcomes in your relationships and interactions.

Be willing to compromise and give and take.

Focus on the interests of others, not just your own.

Habit 5: Seek First to Understand, Then to Be Understood

Listen with the intent to understand, not just to reply.

Put yourself in the other person's shoes.

Be open to learning from others.

Habit 6: Synergize

Work together with others to create something greater than what you could achieve alone.

Appreciate the unique contributions of others.

Be open to new ideas and perspectives.

Habit 7: Sharpen the Saw

Take care of yourself physically, mentally, and emotionally.

Invest in your personal growth and development.

Be a lifelong learner.

I hope you found it helpful and inspiring.

Follow @everythingaboutbiotech for more inspiring stuff.

Remember, the 7 Habits are not a magic bullet. They take time and effort to implement, but they can be incredibly powerful tools for personal and professional growth.

[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

[studentbyday]

30 days of intentionality

starting this challenge with the goal of taking it one day at a time. i have a hard time doing that these days. i spend more time ruminating on the past or worrying about the future than staying in the present, even if that's when i'm most content. not sure how i'll format my posts and most likely, i'll only do weekly updates bc daily ones are too overwhelming. i'll just go with the flow, trying to trust that everything will end up as it's meant to be and maybe i'll be more productive as focusing primarily on the present moment becomes a habit.

---

1. suo gân (arr. john williams for the ambrosian junior choir): i believe that if everyone lived by the idea of global citizenship and so saw the humanity in every individual from every background, there would be no war. reading the news fills me with fear, sorrow, and anxiety, but i also feel the responsibility to stay informed. did some studying today, more than yesterday, but it was kind of uncomfortable with the state of global politics lurking in the back of my mind. i'm still a little behind on school.

2. souvenir de paganini (chopin): today is not so bad. i'm making progress academically, but i do need to make time for social activities soon or i will get lonely and lose what little motivation i have very quickly.

3. once upon a december (arr. emile pandolfi): sometimes in the face of events and issues much bigger than myself that i have no control over, i feel like my dreams are pointless bc i think there's no way achieving them or trying to achieve them could possibly empower me to make real and important change that can truly benefit many. who knows if the future would even allow me to get that far. there are many things that could change the course of our lives that we don't have control over. but if others in worse situations than me and others much better informed than me can still have hope, then so can i. i didn't do much other than pharmacology and a little bit of philosophy today. i made more progress in pharmacology than expected, but that's only bc i didn't do any psych work. i also earned a few more mastery points on khan academy's integrated math 1 (not a priority, i know, but i wanted an easy win) and started lab tasks. i'm far from done with that, i need to do a little every day... i don't want to let them down! 🥺 (note to self: lying in bed is maybe NOT a good study break activity bc that just makes me not wanna do anything else after that and it's very very very hard to get out of that procrastination rut once i let myself fall into it.) 4. let's stay together (al green): everything should be going well, except i'm easily overwhelmed, and this time, it wasn't in an openly frazzled way, it was in a tired and slightly defeated "what's the point?" way, so i didn't realize it as quickly as i usually do. after some bed rest, cuddles 🧸, listening to steve jobs' commencement speech, and a little yoga, i felt better. "You can't connect the dots looking forward; you can only connect them looking backwards. So you have to trust that the dots will somehow connect in your future." was something i didn't know i needed to hear today. i modified my to-do list and found that the list of things i "must do" was nearly as long as the list of things i "want to do" 😅

5. kreutzer sonata, movt. 1 (beethoven): pretty sure i've mentioned some of these songs before but...they really fit the mood! sometimes i feel things so strongly that i develop a tightening in my chest that can only be relieved in a scream... since i can't actually scream and i don't actually really like the physical feeling of it, i scream through exercise and music 😅 beethoven is very nice for when i'm feeling very annoyed or angry, especially if it's an anxious kind of angry or if it's anger at injustice/inequality. i can't find a piano solo version that does the fiery spirit of the violin justice. so in the vague future when i actually play this, either i try (and perhaps fail) to replicate that on the piano, or i find a violinist friend who would want to play with me 😅 right now though, imagining how i would physically create that sound on the piano will have to be enough. the prevailing thought/feeling of the day: sometimes i just really wanna believe in the good in people and believe that i can trust (some of) them. i long for that feeling of safety in a broader irl community that i actually belong in. i'm surprised by how often i long for it. but then my negativity is reinforced by news and people's opinions on it.

6. violin sonata no. 1 in g minor, bwv 1001 (j.s. bach): stuff was done. i felt calm/chill throughout the day, but even tho i feel good whenever that happens, it usually means i don't get an extraordinary amount of things done that day (lol since when do i ever). i'm not sure if it's enough, as there is still lots to do and i'm pretty sure that it's just wishful thinking that i'll achieve all my goals for this week by its end. i need to cut down my goals list to the realistic rather than idealistic version as always (school, lab, and basic self-maintenance tasks) 😅 gaawwwdd i hope i can do this...good night.

7. waltz in a minor, b. 150 (chopin): today and yesterday i have been able to keep my phone time under an hour. the days are blissful (if not at least calmer) and focused. 📚

8. only mine (laufey): cuddles in bed while listening to laufey is so soothing 🧸 takes me back to my childhood listening to lullabies in the dark 🥺 motivation to study is hard to find today. i just want to relax 🥺 i'll just do one tiny thing and see where i wanna go from there...

[sparklingstudycare]

100 days of productivity challenge

Day 2

This image is not mine.

Academics:

Bioinformatics- 2 and a half hour

Structural biology- 1 and a half hour

Downloaded required material for course on immunology

General:

Bit of journalling

Meditate

Laundry

Made some good coffee

Went for a walk

@discountscholar @itsviiistudying @clipolscitrekkie

[febos]

Happy to share, ARTEMIS is now published at NAR!

https://doi.org/10.1093/nar/gkae758

ARTEMIS is a new tool for RNA/DNA 3D structure superposition and structure-based sequence alignment. Our benchmarks show that it outperforms the existing tools for both sequentially-ordered and topology-independent alignment.

ARTEMIS allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches (see the figure) and to describe the minor-groove/minor-groove helical packing motif. ARTEMIS is the first tool able to report several alternative superpositions, which makes it suitable for structural motif identification tasks.

ARTEMIS is available at GitHub: https://github.com/david-bogdan-r/ARTEMIS

Thanks to Davyd Bohdan, Janusz Bujnicki, & International Institute of Molecular and Cell Biology in Warsaw!

[shxbh]

what would i do without ritalin and friends that are up for body doubling reliably <3

[dailycupofcreativitea]

This is a shameless pitch for my field of work but if you like biology and you like coding...consider bioinformatics as a career  👀  Especially if you live in the US, as it's well-known for its bionformatics scene.

[inheritance-beyond-genes]

Guys who work in bioinformatics and come from biology studies: how do you handle lack of inspiration problems? I like to code i find it very creative and genomics is an area that can help today's scientists answer many questions but i miss drawing anatomic parts and learning about fun molecules and pathways that was a big part of my joy during my undergraduate studies. Do you have any suggestions on this? Im currently reading Austin's Kleon book steal like an artist and he proposes having two desks one analog and one digital and work mostly on analog and edit final work on digital. But i struggle find a way to apply this in everyday tasks like NCBI data upload or run jobs in a cluster. Any thoughts?

[felixcloud6288]

messenger RNAs are used to code proteins.

microRNAs(miRNA) block messenger RNAs from doing that.

Both are produced in the cell.

Every time I'm reading about miRNAs, I imagine a cartoon factory putting together a series of widgets along a complex conveyor belt that ends with it throwing the widget in an incinerator.

[cbirt]

In a major scientific breakthrough, researchers at the University of Chicago have succeeded in creating a comprehensive model of the nuclear pore complex with the HIV-1 virus capsid. This sheds new light on the complex processes viruses like HIV use to enter host cell nuclei and replicate.

HIV-1 transports genetic material into the nucleus through nuclear import and viral capsid uncoating, two essential stages in the life cycle. The process is facilitated by the nuclear pore complex (NPC), where complete capsid transit is frequently accommodated in the central channel. The specific mechanisms behind this process are still unknown. 

This study published in PNAS looks at the molecular mechanisms that control capsid translocation via the central channel by interacting with the HIV-1 capsid and the NPC. The transfer of the capsid to the central channel from the cytoplasmic side of a human NPC is the main subject of the investigation. The compatibility of capsid form and channel dimension, along with the correct orientation of the capsid, drive the translocation dynamics. Additionally, the study finds that docked intact capsids exhibit associated striated patterns of lattice disorder, which are probably connected to intrinsic capsid elasticity. According to the study, the capsid’s inherent “elasticity” may aid in stress adaptation and structural integrity during translocation.

Continue Reading

[kikothedragoncat]

I swear a solid 90% of bioinformatics is spent troubleshooting the bioinformatic tools

[everythingaboutbiotech]

Common uses of bioinformatics

💡Sequence analysis Analyzing DNA and protein sequences to identify genes, regulatory regions & mutations.

💡Gene expression Analyzing RNA expression data from experiments like microarrays or RNA-seq to understand gene regulation.

💡Phylogenetics Constructing evolutionary relationships between organisms based on genetic data and genomic comparisons.

💡Molecular modeling Predicting protein structure and docking drugs to proteins using computational modeling and simulation.

💡Databases & Data mining Developing databases like GenBank to store biological data and mining it to find patterns.

💡Genomics Studying entire genomes, including sequencing and assembling genomes as well as identifying genes and genomic variations.

Follow @everythingaboutbiotech for useful posts.

[megumi-fm]

Hey Meg! I was just catching up on your posts and wow, congrats on publishing the paper! I'm so excited for you and how far you'll go (it's so cool that you're working with alpha fold!!)! 🥳 How did you learn bioinformatics? Are there any resources you'd recommend for a complete beginner? (I'm trying to learn how to do proteomics analyses rn, but I can't seem to find many resources I can easily understand 🙈)

hii!! thank you so much for the wishes! the paper was a part of my final project with my team + guide so it was really a group effort <3 my teammates and I are all first authors, they were just kind enough to put my name first xD and yes! my current alphafold work is a lot of fun ^=^ I'm really enjoying my internship hehe

okay so I learnt bioinformatics as a part of my uni curriculum, and we mainly relied on these two textbooks

Essential Bioinformatics by Jin Xiong

Bioinformatics: Sequence and Genome Analysis

In addition to this, I also recently found this textbook titled Bioinformatics: An Introductory Textbook by Thomas Dandekar, Meik Kunz which focuses both on basic bioinformatics concepts and how to use the available tools. I especially like this book because I found it super easy to understand

EMBL also offers courses! even for synchronous online/in person courses that have ended, they tend to upload course materials. There's one for proteomics analyses as well- I've checked out the mass spectrometry videos under this course and they start with the very basics

In addition to these, here are some playlists on youtube that've helped:

Foundations of Systems and Computational Biology, MIT OpenCourseWare // classroom videos, I'd suggest to check specific videos for a topic of your choice rather than actually going through all of them

Computational Systems Biology, IITM // videos on the basics of systems biology, networks and modelling

Bioinformatics 101 // videos on how to use a lot of tools, however this primarily focuses on gene expression and RNA seq data

lastly, I don't know if this would be particularly helpful given what you're looking for, but this textbook on Computational Genomics with R is a blessing for Omics related Data Analysis. So if you ever need to use R in a biological context, this would be a great place to start

yeah! so these are the majority of the resources that I've used, I hope they help! Just a heads up that the links to the textbooks I mentioned in the beginning are direct download links and won't take you to any website.

If there's anything else I can help with, feel free to reach out ^=^ best of luck!