Good day, Subramaniyam Ravichandran. I'm Arjun. I've had a look through your background and your professional record. I'm interested in hearing more about your work and how you see yourself fitting in here with our faculty. Ready to start?

Yes.

Please start by introducing your professional journey in academia.

Yeah, so I finished my 10th and 12th standard from Chennai from Balalok Matriculation Higher Secondary School and after that I joined my BSc in Plant Biology and Biotechnology from Ramakrishna Vivekananda College, Madras University.

I finished my BSc in 2008 and actually when I was doing my BSc I also joined the three-year diploma course in Software Engineering from NAIT called JNIT in Software Engineering.

And I joined it when I was in my second year and I during my final year during the project, I actually got a campus placement in a, in a, in an educational sector company called Element K, which was at that time the second largest e-learning provider in the world. And my job was to actually. Develop courses, Develop curriculum in the domain of databases, operating systems in networking.

So during my I worked there until 2010 and during my tenure there I developed courses.

For Linux, specifically Red Hat Linux.

Uh, in systems administration, uh, and uh, also in databases, I have developed courses, uh, on sequel on Oracle database track related courses such as Oracle data application clusters, level 1 DB track, et cetera. So after my, this was, I mean, I kind of deviated from science, from biology a little bit because I had to complete this one year of internship to compulsorly.

Qualify for my J and IT certificate. And after that, uh, uh, I ended up getting, uh, a lot of awards at the company and they basically asked to stay, stay, asked me to stay on for another year. So in 2010, I finally decided to switch, pivot back to biology because that was my, uh, that has been my interest always.

And I was also interested interested in.

In applying computational computer science to biology as well to facilitate discovery, I did my I joined for my Masters in Applied Microbiology at VIP Vellore between 2010 to 2012 and during this tenure I during my final year project I I did I did my final year project from BARC Mobile. On the topic of cyanobacteria.

Tenants and their role in bioremediation of nickel and uranium.

I was the second rank holder in my masters course and I also came first in my DC course as well. So I have been a very high achiever throughout. So after my masters complete, it was completed in 2012, I went on to do my PhD abroad in South Korea in Song Kinquan University, which is the oldest university in South Korea.

And I joined the School of Medicine I my mentor was Professor Kim Kyung Kyu.

And I worked on. Primarily DNA, RNA, nucleic acid, non canonical nucleic acid structures.

And my main research was how these nucleic acid secondary structures like non B DNA structures such as G quarter, plexus crossi forms, et cetera, how these how these are?

How these are kind of affecting?

Cancer biology and cancer progression, etcetera. And I also worked on their role in neurodegeneration and my primary thesis title was De quadruplexis in gene promoters.

And their roles in parkaging associated with neurogenesis, neurodegeneration. So during my during my PhD time I actually.

Apart from my main focus which was on nucleic acid and non BDN structures and how they have structural and functional roles align well with these progression and diagnosis, I also worked on a lot of other topics. Now during my MSA bit they had first introduced the SET program SET conference which is basically it was like a small project. And I actually published all my set projects which I started at the IT. My first publication was from VIT under Professor Gibla.

Uh, which is also one of my most highly cited review articles. And uh, two of my papers were with Professor Bhaskar Rao, uh, on nanoparticle, uh.

Biological extracts. Specifically, I used the extract from Calista melancholatus to to make silver oxide nanoparticles, which was a novel saline itself, and I ended up publishing all of these when I after I joined my PhD in in South Korea.

On green synthesis of nanoparticles using using.

Uh, I continued this interest in nanotech as well, uh, when I was in South Korea and one of my papers was on, uh, the development of protein chill nanoparticles on which I was co-fus author. And uh, we were able to use it as a catalyst for the development of, for the smooth synthesis of acetaminophen.

After this, during my PhD, I also participated in a lot of projects pertaining to the development of antivirals. The study of.

These the study of deep water plexus specifically as therapeutic targets in cancer and neurodegeneration and one of my blockbuster publications was when I discovered a novel non canonical DNA structure called the hairpinchi quarterback, which is like a jaksupposition of.

Ajit quarterplex and a headband structure in one of the loops.

So this was published in Nucleic Acid Research and it was highlighted in many places, including the the Korean Korean science society called BRIX.

And I'd also given an interview. It was also highlighted in my university and I also appeared in on TV.

For my research and I also ended up after my PhD was over, I I got a grant from the National Research Foundation of South Korea.

I did. I essentially did. Got a fully funded fellowship from the National Research Foundation of Korea for my PhD and after that I got another grant from DNRF to pursue my research on.

The role of the quadruplexes in the Parkin gene, which contributes to idiopathic juvenile parkinsonism and many other mitochondrial related disorders through the pink and parking pathway.

So.

After this, during this tenure, I with my grant, I was able to train one PhD student.

Who was just finished a PhD and after my I did three years as a postdoc in university in the in two different departments. 1 is Structural biology lab as well as the second one is Institute of Antimicrobial Research in Therapy.

So after this tenure I moved to Stanford University to study RNA biology. Now I have been studying the role of G quadruplexes from individual gene level to the transcriptome level kind of. And I've been interested in looking at things from a holistic perspective. So I believe that omics based technologies and high throughput sequencing NGS. Can give you an overall big picture view.

Their how their processes are intertwined and how the downstream processes are going to be affected. So based to continue or advance this interest of mine, I joined the lab of Professor Mary Hines at Stanford University in Stanford University in in the in the Department of Biology.

Perspective of how genes interact, how proteins interact, how?

And my main goal was to study RNA biology how how three prime UTS or isolated 3 prime UTRS can affect gene regulation and contribute to contribute to like metasses and cell proliferation in in cancer. My name specific focus has been on breast cancer and.

We have found that all the sequencing technologies, they just.

The the structure of the transcript and the read is actually not considered. So we took long reads and we found that actually there are certain reads where the entire transcript is not present. Only the three prime UTR is being sequenced. So we were curious as to why these these reads are still present. How? How is it that?

They just take the recounts of transcripts.

The entire transcript is not present either. So because when a gene is transcribed, it usually, uh, transcripts the entire gene or uh, uh, semi transcribed, uh, uh, genes are usually D mrnas are usually degraded afterwards. But why are these present? So it eventually there was a publication from our lab, uh, previously which talked about the role of these isolated 3 primary UTS in regulation.

In in the case of neurons and we extrapolated that study.

We had a couple of novel pipelines to it and we were essentially able to quantify a split the mRNA into coding region and the three-point UTR and quantify them separately. And we were able to essentially find novel biomarkers from this because when we look at transcripts.

Uh, and, and sometimes let's say a gene only has maybe 3 copies of a whole transcript, so you will end up omitting it. And what we found out was that that same gene could have 3000 copies of just the 300 year. So which means that that gene, that there is some role, biological role, which requires the gene to produce just the UTR. And, and we found that especially in the case of epithelial to me and camel transition, there is a coordinated distinct switch from high 3.

You end up looking at the entire transcript and not.

Ctr. to high CDs. So this was the topic of my study and we found that a particular gene called C, not 9 has has a significant role.

Uh, in, uh, breast cancer progression and we were able to test it across different cell lines, uh, to evaluate the effect of the three prime UTR in, on, on meta sizes, on proliferation, on and on therapeutic effectiveness, et cetera. So we are currently testing this in in vivo and.

Yeah, let's study which is going on right now.

Yes.

So the the reason I'm sorry. So I have been in constant touch with VIT. I have been associated with VIT throughout my academic career, right for my MSC to my PhD, my postdoc, et cetera. I have been on the panel on the to evaluate the final thesis of.

Thanks for sharing that,

Two or three three Finally a PD students and also.

Uh, I recently gave, uh, in November last year, I gave a talk in VIT under the research development series. Uh, so, uh, uh, yeah. So I have been always interested in being in academia and now I have enough experience, right from curriculum development to developing courses to computers to, uh, molecular biology to therapeutics. And I believe that I can bring this entire wealth of exper.

And also the collaborations, international collaborations which come into the picture like with the USA, with with institutes in South Korea, I can bring all this expertise. And when I gave that lecture in November, I really enjoyed myself and seeing the students interact with me, seeing the students also getting interested, it cemented. My perspective that I should be in academia and especially in vit because that has been my alma mater and.

It has given me so much and it is my time to give back to the community there. Also, I my hometown is in Chennai, so it's not too far off from my home. So that's one of the primary reasons I would like to join VIT.

Yes.

Thank you for sharing such a detailed and inspiring journey through your academic and professional career, Professor. Your multifaceted experiences and dedication to the field are commendable. I appreciate the depth of your contributions across various domains and how they align with your passion for education and research.

Thank you. Thank you for asking the question. I really enjoyed explaining my career until now. Although it's a very brief outline, I really enjoyed it.

Professor Ravichandran, let's dive into verifying expertise for this role step by step. First, let's focus on your research and practical experience in **Cancer Bioinformatics**. Can you elaborate on how your work, for example, on untranslated regions or G-quadruplex structures, integrates bioinformatic analysis and contributes to cancer research?

2 So G quantum plexus actually based on certain patterns in the genome. They are formed in GC rich G rich regions and they follow certain patterns like you need 4G runs consecutive GS which are separated by tracts of any ethyl type combinations which are called loops. So what did I develop pipelines to?

Yes, so I'll start with my PhD work and my first post op work which was on the quadruplexels so.

Identify these sequences from various genomes, human virus, etcetera.

Uh, this was all done using, uh, using, uh, Python based, uh, uh, tools which were dependent on uh, pattern matching. So I created separate rejects for uh, registries for.

Different pattern matching tools for each and every kind of the quarterplex which I was looking for.

And these patterns are referred to as rejects. So I input these patterns and I searched the entire whole genome search.

And based on this, I narrowed down to basically the regulatory agents like promoters, announcers.

The untranslated regions etcetera. So from this study, what I found was that there was a significant enrichment of G rich sequences in the promoter region and.

The other thing was there was an enrichment of GG quarterplex for me reasons especially close to the TSS. Now I did some data mining in here and I found that DT quarterplexes which are closest to the transcription start site, they seem to have more effect and in terms of attenuating transcription. So the G there was a, there was an association between. There was significant correlation rather between the.

The position of the G quadruplex with with respect to its transcription chart site and the transcription, the attenuation of of improvement of transcription. And so I did a couple of I published a couple of papers using these studies. In addition, my last project of which my student has taken over.

Was on these on was on analyzing on rather comparing the effects of two different.

The quadruplex associated small molecules, small molecules on cancer cells, breast cancer. I did this study because until now there has been no G quarter Plex binding drug which has reached the reached the which have been approved by FDA and has reached the market because there are a variety of reasons. So I felt that by comparing two different drugs, we should be able to identify.

Whether there are any non specific interactions or any normal genes which are.

Being specifically targeted by a particular drug. And I believe this approach is very important because by creating a database of all of these, all of these, like all of these studies, we can identify unique genes which are, which are targeted by specific small molecules, specific ligands. And in my study I found I kind of overlaid. Many different layers of of data.

Of essays like DNA is hypersensitivity, like chromatin occupancy, ataxi, Chipseek and also G4 DNA seek. And by layering all of these I have found a particular gene whose promoter is specifically targeted by pyridocytin, which is a very well known G quarterplex binding ligand.

And I correlated this data set with the Harmonism database CCLE.

To to find out the specific gene called CYLD which is which plays a very important role in cancer migration and metastasis. And I have found that G quadruplex G quadruplex targeting can be a very viable method to attenuate breast cancer progression.

Um, NDT and explanation cancer gene expression Atlas along with along with datasets from TCGA.

Uh, during my postdoc, I have extensively worked on single cell RNA sync data and long range RNA sequencing datasets. Basically to, uh, uh, you basically to process them, uh, you think like star RSM, RSM and to split the reads, split the transcripts into CDs and the UTI separately. And then instead of using FPKMS to quantify them, we have used.

2:00 PM because TPM is easier to compare between multiple samples and.

I've also created like I've also found many clusters in the the I I took, I took a previously published study where they had around 4000 patients, cancer patients and we found that there were many genes when we did the heat map of CDs UTR ratios.

We found that there were a lot of genes which were high CDs in one cluster whereas in the other cluster they were high UTR. So this clearly indicates that there is a coordinated switch between different cancer states. And with other markers such as such as Wilmington, E-catherine, we were able to annotate these specific clusters as cancer stem cell like as epithelial as medium time and we were able to find that. This CDs UTR switch is a plays a very key role in epithelial to mesenchymal transition.

Yeah.

significant depth in cancer bioinformatics, particularly in relating genomic patterns, regulatory impacts, and drug-target interactions. You've clearly developed robust computational methods, such as customized pattern-matching pipelines and multi-layered data integration, to derive actionable insights in cancer mechanisms. Additionally, your exploration of CDS-UTR ratios in cancer progression adds a novel layer of understanding to tumor biology. Next, I'd like to understand your approach to **teaching theory and laboratory courses**. How would you ensure that students with varying levels of expertise can grasp complex bioinformatics concepts effectively?

So I believe that bioinformatics is best taught by practice.

Initially we should we need to have thinking at it, some very algorithmic point of view.

Any project starts with a problem and the problem needs to be understood at the Basel level. Whenever we are teaching, we really need to explain the nuances of the problem and then come up with an algorithm which clearly explains to the student.

Algorithm by a flow chart method. The steps which are which which are involved in coming up with the solution to that problem. Now at each step, the student will contribute his or her own perspective in order to come up with novel ideas or different parts on how to solve this particular step. I believe in learning by practice and.

At least step of.

Having them practice and then learn while they are practicing is a very important is a very important aspect of teaching students. From my point of view, I have actually seen this in practice with my students as well. When I had a lot of trainees when I was doing my PhD and in my post-doc, I had an A specific student who was assigned to me for. For the CDs UTF projects so.

Uh, I was able to teach them very effectively, uh, on primer design, uh, on, uh, on transcript transcriptomic analysis, genomic analysis, uh, and I was able to explain how they can, uh, incorporate different omics techniques into their research as well. So I believe that this is a very effective way for students to learn bioinformatics, learn cancer concepts as well. So both cancer concepts as well as informatic concepts must be taught simultaneously.

So as students understand, both of them together.

Yeah.

Your emphasis on problem-based learning and integrating theoretical concepts with hands-on practice is commendable. By encouraging algorithmic thinking and involving students in each step of problem-solving, you create an interactive learning environment that not only builds technical skills but also fosters independent thought. Your experience in mentoring trainees adds further credibility to your approach. Let’s now explore your capabilities in handling **student evaluations and exam duties**. How do you ensure fairness and consistency while evaluating students' performance in theory and practical assessments?

Our scheduled time for the interview is now up. Before we conclude, do you have any questions related to the role or the company?

Yeah, so.

The the cancer biology part is needs to be looked at separately and the bioinformatics part needs to be looked at separately because the bioinformatics part requires theory as well as practical application. Now from what I have seen there are multiple ways of solving a single problem. So in terms of bioinformatics if there is a the the shortest way or the most efficient way is most effective.

I mean, I would like to answer the question actually because I believe that in terms of fairness.

So I think that bioinformatics grading should be according to this metric. And whereas theory, theory always requires a lot of understanding in terms of basic concepts. So if anybody can understand the basic concept and they can explain it in a very disciplined and a simple manner, I think that is the way that we grade, we can grade them fairly. So that's my outlook on on grading and ensuring fairness.

While teaching.

Yes, I have no further questions.

Thank you, Professor Ravichandran, for your detailed responses and insights throughout this session. It was valuable to hear about your research and teaching methodologies. I wish you the best for the next steps in the selection process. Would you like me to formally conclude the interview now?

Yes, if you're done, thank you very much.