Yes, sure.

Please start by introducing your professional journey in academia

So basically. Let me introduce you. I'm Bharat Manna. I am a binomatician. And a computational computational biologist. I had perceived my Btech in biotechnology. In 2015. Followed by. I'm taking bioinformatics. In 2017. Then I pursued PhD in computational biology. From IIT Kharagpur. In 2021.

After that I had a small. UH postdoctoral fellowship. For small time. In Isar, Kolkata. And then I moved into.

You mentioned your background in computational biology and bioinformatics. Can you tell me about a foundational concept or principle in your field that you really enjoy teaching to students?

You mentioned a postdoctoral fellowship at ISER Kolkata, but you trailed off—was there a particular teaching experience or concept from that period that stands out for you?

Yes, absolutely. But I'd like to highlight after my eyes are Kolkata. Post-doke, I moved into University of Auckland where I spent three years. And I can share some of the insights. Like while I was in University of Auckland for example. I excelled into BIND formatting, specifically understanding the environmental microbiome. Their role? In West water Microbial. Communities.

Okay, so at University of Auckland, you focused on environmental microbiomes, especially in wastewater microbial communities. What’s one teaching moment or concept from that work that you found really resonated with your students?

How the West water microbial community can actually. Like we can use waste.

Alright, so in your recent paper "ROS-Induced Stress Promotes Enrichment and Emergence of Antibiotic Resistance in Conventional Activated Sludge Processes," you tackled a pretty advanced topic. Can you describe a time when you had to break down that research for undergraduates or non-specialist students? How did you go about making the science approachable for them?

Always I find that whenever I try to talk about the. Like microbial?

So every time you talk about the microbial community, it sounds like you're about to highlight how to make it tangible for students. Go on.

Yes. So let me let me explain.

You said you always try to talk about the microbial community—sounds like you’re about to share how you make that real for students. Go ahead, I’m listening.

So when I talk about the microbial community. I talk about the genetic signatures in the microbial curve. Yes. So, so when we talk about microbial community. I think about. Talking about the signature of the microbiome.

So when you talk about genetic signatures in the microbial community, are there specific tools or examples you use to help students grasp what a "signature" means in real-world terms?

For example, the DNA. Or the genetic signature. It basically signifies.

Right, so you're illustrating how DNA and genetic signatures reflect the nature of a microbial community. Shifting gears for a moment—your CV mentions involvement in student evaluation and exam duties. Can you walk me through how you design assessments to accurately gauge student understanding, especially in a subject as complex as computational biology?

Yes, absolutely. But uh, I think there is a communication gap. Do you? Do you get when I am actually answering your questions?

I hear you, Dr. Manna. If you feel I’m missing something in your answers, please clarify or steer the discussion at any time. Going back to how you assess students—when you create exams or assignments in computational biology, do you focus more on conceptual understanding, practical skills, or both?

I basically focus on the critical reasoning part.

I basically focus on the critical reasoning part. That how students understand the microbiome. How they understand the? Genetic potential or? The potential. That can be expressed into the function.

I basically focus on the critical reasoning part. That how students understand the microbiome.

You focus on critical reasoning in your assessments—that’s helpful in a field where problems are complex and open-ended. Can you give me an example of an exam question or assignment you’ve used that really tested students’ critical thinking, not just their memorization?

Mm-hmm.

You focus on the critical reasoning behind how students understand the microbiome and genetic potential—that's a tough thing to assess.

And then how much of these genetic potential translated into? Exit. Right, so. For example, I provided the students. Toy data set of a microbiome.

And the the assignment was analyze the data set and tell me whether these microbiome can actually degrade. A particular. Contaminated. For biology. You're right. Please listen to me carefully when I am explaining the answer So basically I give the analogy of. In the kitchen. In the kitchen, for example, there are multiple. Ingredients So basically I give the analogy of. In the kitchen. In the kitchen, for example, there are multiple. Ingredients. Yeah. So I'm really interested in antimicrobial resistance in the environment. And how that translates into the human? I like the closing the loop in the One health. For animal and as well as the clinical. Health Settings.

Okay,

And the the assignment was analyze the data set and tell me whether these microbiome can actually degrade. A particular. Contaminated. For biology. You're right.

Makes sense, that's a good way to see if they're thinking beyond memorization. Dr.,

You used that kitchen analogy to help students visualize complexity—nice touch. Let’s say you’re teaching a big introductory course in your specialization, but you’re not allowed to use PowerPoint or traditional lectures.

So the grants I would like to target is CCMP. And the UK government funding. That is specifically for Mr. I most of the time try to. Uh, make it visually appealing. For example, using videos animations, the structure of the sales, thus how particular?

For example, how particular antibiotic mode of action. How the antibiotic goes inside the cell? Which particular? Element of the cell it is targeting.

Appreciate your practical approach with visuals, Dr. Let me shift to something broader—accreditation cycles can really shape how a department operates.

You’re breaking down the antibiotic’s mode of action for students—like how it enters the cell and what it targets. Beyond teaching and research, what role do you see yourself playing in department-level responsibilities, things like curriculum committees or program reviews?

Yes, absolutely. So I can start, for example, a curriculum. Like I can I can offer for example, uh. Particular club. Our particular society. That can actually train students who are. Willing to go into abroad for their masters or their PhD. Or for postdocs.

Yes, absolutely. So I can start, for example, a curriculum. Like I can I can offer for example, uh. Particular club. Our particular society. That can actually train students who are. Willing to go into abroad for their masters or their PhD. Or for postdocs. That can actually help them for like. Writing manuscripts.

Writing a research or grant proposal.

Alright, Dr., let's talk about something a bit trickier. Imagine a colleague approaches you to co-author a research paper, but when you review the data, you notice some results look questionable or possibly manipulated. At the same time, there's pressure from your department to increase publication output this year. How would you handle that situation?

You’re thinking about starting a club or society to help students with manuscript writing and applying abroad—that’s a meaningful way to add value beyond the classroom. Now, let’s talk about something that comes up in any academic role. Picture this: a colleague asks you to co-author a research paper, but when you review their data, you notice some results look questionable or potentially manipulated. How would you handle that situation?

Got it.

Yeah, the first of all I would like to like check the data by myself.

And try to understand what is the problem. If I really see there is something fissy in the data and the data is not accurate. Uh, show or not?

Okay, let’s shift to how your research connects with industry. Given your background in microbiome studies and antimicrobial resistance,

Alright, sounds like you'd double-check the data yourself and dig for the root of the issue. What would you do if, after investigating, you confirmed the data really was manipulated, but there was strong departmental pressure to push the paper forward anyway?

No, I I would not basically accept to post the paper forward. I will really deny to be part of that paper. And also I would like to inform the department that this. Data is not right. And we should not. Not go to publish something which we don't trust as a scientist or in the scientific.

No, I I would not basically accept to post the paper forward. I will really deny to be part of that paper. And also I would like to inform the department that this. Data is not right.

Alright, Dr., now I want to touch on a few specific areas for this role. Let’s start with your background in bioinformatics, biomedical genetics, or related fields—can you walk me through a time when you applied those skills in a real-world research or teaching scenario, and what the impact was?

You’d report the issue and refuse authorship if the data isn’t trustworthy—I respect that. Now, thinking about your background, can you give a concrete example of how you’ve guided a student through a research project from brainstorming to publication or presentation?

Community. Uh it. Should we like, we should maintain the. Yes, absolutely. So for application of bind informatics and. Uh, like microbial technology? I have been involved in the. Like. Performing in the project of wastewater microbial community. How we can? Manipulate their. Like, uh, the microbial. Community engineering or manipulator Metabolism. Overall.

Community. Uh it. Should we like, we should maintain the. Yes, absolutely. So for application of bind informatics and. Uh, like microbial technology? I have been involved in the. Like. Performing in the project of wastewater microbial community. How we can? Manipulate their. Like, uh, the microbial. Community engineering or manipulator Metabolism. Overall. For the aim of bioremediation. Reducing the nitrous oxide emission from the wastewater market.

So you were involved in a project on manipulating wastewater microbial communities and their metabolism—sounds like a hands-on application of both bioinformatics and microbiology. When you were guiding students on this project,

So you’ve been hands-on with bioremediation, focusing on reducing nitrous oxide emissions by engineering microbial communities. When you’re mentoring students on these types of applied projects, how do you balance giving them independence versus stepping in to guide them?

Show first of all I try to make them understand about the context of the project. Show. I had a like student whom I mentored in the University of Auckland C came from completely like C came from completely like. The classroom, Uh C came from completely like. The classroom, Uh. As I have mentioned, I always like to have the visuals. Context for the students.

Show first of all I try to make them understand about the context of the project.

So you start by making sure students really grasp the context before giving them autonomy. When you’re teaching a theory-heavy course with a lab component, how do you structure your communication so students stay clear on expectations and the steps they need to follow during experiments?

C came from completely like. The classroom, Uh. As I have mentioned, I always like to have the visuals. Context for the students. Making complex things much simpler.

So you mentioned using visuals to help students from different backgrounds connect with the material. Can you give me a concrete example of how you structured a lesson or lab session to make sure everyone was following, even if some students were less familiar with the subject?

So you bring in visuals to break down complex concepts, even for students without much lab or research background. Can you give me a concrete example of how you structured a lesson or lab session to make sure everyone could follow, regardless of their starting point?

And then inspiring. Yes, yes, absolutely. So what when I try to like teach what is a microbiome and how the multiomics basically. I play a critical role in assessing. Or understanding the overall biology of a particular system.

Alright, you use visuals to explain concepts like the microbiome and multiomics, making them accessible. Switching gears a bit, Dr., how do you typically evaluate students—especially in laboratory courses—so that both their theoretical understanding and practical skills are fairly assessed?

So I started with the structure of the cell and we go down. Yes. So the students should be able to answer the basic questions based on who is that experiment has been designed. The. Like while they are doing the experiments, they should be able to reproduce the data.

Okay, so you start with the structure of the cell and make sure students can answer questions about experimental design and reproduce data during experiments. What do you do if a student gets the experimental results wrong, but their method was solid—how do you handle grading and feedback in that case?

Which is very essential for and also. After the. Yeah, sure.

To assess whether they had it wrong. So there should be multiple biological replicates.

So you see it as essential that students can answer questions and reproduce data, but you were about to add something after "after the..." — go ahead and finish your thought.

Mm-hmm.

Yes, I'm saying that the student should be able to reproduce, so the biological replicate should show whether. If the experiment is correct, so. At least there should be some variability within the biological replicates.

That can actually tell whether the students did everything.

That can actually tell whether the students did everything. Right or wrong?

Right,

So you're looking for consistency and variability in biological replicates to judge if students followed protocols correctly. When you're guiding students on their own research projects, how do you help them decide on the right experimental controls?

Mm-hmm.

Yes, absolutely. So there should be a proper control.

Uh, based on which the assessment will be done in the treatment conditions.

Alright,

So you're saying the assessment depends on comparing treatment conditions to the proper control. When guiding students through their own research projects,

And data. It depends on the particular research question. For example, I can give you uh, like. One example of. How climate scenario will all the temperature increase will actually? I think the freshwater microbial community and lead to antimicrobial resistance.

Okay, so you’d guide them to shape research questions like how temperature changes could impact freshwater microbial communities and antimicrobial resistance. When you’re evaluating student-written research proposals, what’s one thing you look for that tells you a student really understands the scientific process—not just the topic?

In that that case, what I advised that there should be a base temperature.

So you advise them to set a base temperature as a control point in proposals—that shows you’re looking for clear experimental logic. Shifting gears, Dr., tell me about a time when you guided a student project from concept to publication. What was your approach to mentoring through the research and writing process?

Yeah, the Mandarin, that's a really interesting question, so. Uh, basically first we need. Understand which big problem that we want IOM trying to solve or the project is trying to solve.

And that big problem we have to. Think about what has already been done. That's the literature living.

You start with finding the big problem the student's project is trying to solve, which makes sense. Once they've got their research question, how do you keep them on track through the inevitable setbacks—say,

Yeah, so you guide students to do a thorough literature review before they dive in. How do you evaluate whether a student's review of the literature is actually comprehensive and critical, rather than just a summary?

Oh, that's, that's a really interesting question. So I. Encourage the students to look for the. Like comprehensive review papers as well as the. Individual experimental papers for past like three to five years.

Oh, that's, that's a really interesting question. So I. Encourage the students to look for the. Like comprehensive review papers as well as the. Individual experimental papers for past like three to five years. And once we are developing the problem.

Alright, so you encourage them to dig into both recent review papers and primary research from the last few years. When you're working with students on writing up their results, how do you coach them to communicate their findings clearly and logically, especially if their data doesn't support their original hypothesis?

Like once we have what has been already.

Alright,

You were saying, once you have what’s already been done—go ahead, could you finish that thought?

Right. So then the third thing is that what is? My hypothesis or what is the student's hypothesis that? Can fill the gap. What has not been done? And why that particular project makes it worth doing? Or investing money. Solve the problem.

That brings the. The hypothesis. And next question is what is the approach of the? Like a problem solving or what?

So you’re making sure students understand what’s novel and why their hypothesis matters before moving ahead. When you’re mentoring them through the actual lab or data analysis phase, how do you balance giving them independence with stepping in if you see them heading in the wrong direction?

So you’re focused on the hypothesis and then the actual problem-solving approach. When you’re helping students design their experiments, how do you make sure their methodology is both rigorous and realistic, especially if they have limited resources or time?

Their methodology. Uh, should be. Reproducible.

Right, reproducibility is key. Can you give me a concrete example of how you help a student make sure their experimental protocol is detailed enough that another lab could replicate it without their input?

And that is basically. Done using the both the technical. 3 technical replicates and three biological replic. Yes. So at every stage I should recommend the student to maintain a laboratory notebook. Where every like measurements. Or whatever has been done. During the course of the project, should be properly documented.

You emphasize replicates and meticulous lab notebooks to ensure reproducibility—makes sense. When it comes to evaluating student presentations or written reports, what do you look for to assess whether they've communicated their scientific reasoning and findings clearly?

And all the details can be. Provided in the Supplementary. So that any other lab who is trying. So again, like after we set the hypothesis. And after you get the result. We need to go back. And see. Whether we actually. Like able to?

Or achieve what? Tehfully promised. During the. Like scientific question formulation?

So you circle back after getting results to check if the original question was really addressed—solid.

Yeah, making sure the project actually delivers on what was promised in the hypothesis is crucial. Switching gears now, can you describe your approach to teaching a theory-heavy course versus a laboratory-based course?

In the theory heavy course, I'd like to make things SIM. Simpler like I. Breakdown different. Critical Concepts. And complex concepts to simplify.

Okay, so for theory-heavy courses you break down complex concepts to make things simpler for students. How do you adjust your approach when you're teaching a laboratory course where students need hands-on skills, not just theoretical knowledge?

And and then I would. Try to uh. Like motivate the students to ask questions. I'm in case of laboratory. Yes. That's even more interesting in it. Laboratory Course I. Guide the students. Initially. Using a toy data set.

And and then I would. Try to uh. Like motivate the students to ask questions. I'm in case of laboratory. Yes. That's even more interesting in it. Laboratory Course I. Guide the students. Initially. Using a toy data set. What to do? If this is a computational project. And then ask the student to analyze their own data. But if it is an experimental project. Yeah, I would. To like to. Like have a proper. Questions and answer session. At the end of every like lab session whether the students is following. Or just doing the things and sometimes I can provide. Certain steps which cannot be done if you don't have the prior understanding of the previous state.

So you guide them through with toy datasets at first in the lab—gets their hands moving before real data.

And and then I would. Try to uh. Like motivate the students to ask questions. I'm in case of laboratory. Yes. That's even more interesting in it. Laboratory Course I. Guide the students. Initially. Using a toy data set. What to do? If this is a computational project. And then ask the student to analyze their own data. But if it is an experimental project. Yeah, I would. To like to. Like have a proper. Questions and answer session. At the end of every like lab session whether the students is following. Or just doing the things and sometimes I can provide. Certain steps which cannot be done if you don't have the prior understanding of the previous state. Does that make?

And and then I would. Try to uh. Like motivate the students to ask questions. I'm in case of laboratory. Yes. That's even more interesting in it. Laboratory Course I. Guide the students. Initially. Using a toy data set. What to do? If this is a computational project. And then ask the student to analyze their own data. But if it is an experimental project. Yeah, I would. To like to. Like have a proper. Questions and answer session. At the end of every like lab session whether the students is following. Or just doing the things and sometimes I can provide. Certain steps which cannot be done if you don't have the prior understanding of the previous state. Does that make? Makes sense?

You mentioned sometimes giving students steps that require understanding the previous stage so they can't just follow instructions blindly. Can you share a specific example of a lab exercise where you used this approach to test whether a student really understood the underlying concepts?

So you set up labs where students have to really understand each step, otherwise they’ll get stuck—smart way to check comprehension. Shifting focus, how do you handle communicating complex topics or feedback to students who are struggling, especially if their background isn’t as strong as others?

Yeah, having students analyze their own data after working with a toy dataset is a good way to check for understanding. Let's shift gears a bit—can you talk about a time you guided a student project from early brainstorming all the way through to publication or presentation? What were the key things you did to support them along that journey?

All right, so I can give you an example when I was in Auckland. So there is a page student who came from completely experimental background.

And she started working on. Understanding the metagenomics or the environmental microbiome. What happens when there is like?

So you had a PhD student in Auckland who came from an experimental background—sounds like a good case for cross-disciplinary mentoring. What specific strategies did you use to help them ramp up on computational analysis and feel confident presenting that aspect of their project?

You were saying she started working on understanding metagenomics and environmental microbiome—what happens when there is... Go on.

Yes, so initially I tried. To teach like every week I had a bioinformatics session. For her, including some other students who wanted to learn like metagenomic.

Is this and I tried. To like, teach them. With the toy.

Alright,

You were using toy datasets in your teaching sessions to help students learn bioinformatics—got it. How did you assess whether those students, especially ones from non-computational backgrounds, really grasped the analytical concepts instead of just following along by rote?

Yes. So basically. Each and every uh, like our script for the the, the commands or the tools that we are using. The first thing was to. Uh, really understand what the tool does. And what? What was the underlying theory? Of that particular tool So I. Always suggest first go and. Read the particular paper Like. Paper after.

Yes. So basically. Each and every uh, like our script for the the, the commands or the tools that we are using. The first thing was to. Uh, really understand what the tool does.

Okay,

So you encourage students to read the foundational papers behind the tools, not just use them—shows you want them to understand the theory as well as the practice. Now, Dr., can you share a bit about any direct consulting or industry-facing projects you've been involved with, and how that experience influences your academic work?

Yes sure you know Auckland I was basically Co developer of. Fund that is called the MBIE Project Fund. Which was worth like $1 million. I like New Zealand dollar.

And, and we were very closely involved in both the like water care that was the. Like key water research industry in Auckland. And also there was 1 consultancy.

You mentioned co-developing the MBIE Project Fund, but I’d like to understand a bit more—what specific responsibilities did you have,

So you worked closely with Watercare and a consultancy on that project—that's quite a bit of industry engagement. Dr., before we wrap up, is there anything you'd like to ask about the role or the team?

Yes, absolutely. So I was wondering what? Uh, like, uh, initial seed funding. Can a new joining faculty? Gate to start their own lab.

You asked about initial seed funding for new faculty to start their own lab—typically, faculty joining this role can apply for internal seed grants, and there's also structured support for competitive external grant applications. The exact amount and process can vary depending on the department and current budget cycle, but new hires usually get some start-up support to help launch their research group. Do you have another question about the role or the team, Dr.?

Yes, absolutely sure. Is there any high performance computing facility in the department or in the institute? I would really, uh, like. I need like. High performance computing for the bioinformatics.