India|EMBO Symposium - Engineering meets evolution: Designing biological systems
12 Nov 2019

Richard Feynman once famously remarked, “What I cannot create, I do not understand”. As engineers strive to create complex systems, biologists have strived to understand the evolved complexities of biological systems. This Symposium will bring together biologists, engineers, and theoreticians to discuss exciting advancements and exchange ideas and challenges in the field of synthetic biology. The invited speakers are leaders in the fields of synthetic biology, metabolic engineering, and microbial communities. We will also have a panel discussion on the future of biology as an engineering discipline. Set in the beautiful campus of India’s top-ranked Institute, this Symposium will bring together minds to further biological advances drawing on engineering principles.

IBSE Seminar by Dr. Akash Gulyani
05 Nov 2019

IBSE is very pleased to introduce you all to our guest speaker Dr. Akash Gulyani who will give IBSE Seminar on Friday, 8th November 2019 in BT Seminar Hall (Biotechnology Dept. Block 1, Ground Floor), at 12:00 pm. The title of his presentation will be: “Natural and engineered biological sensors: visualizing cellular dynamics and discoveries in natural light sensing”. Dr. Akash Gulyani received his Ph.D. in Chemical Sciences from the Indian Institute of Science, Bangalore and post-doctoral training at The Scripps Research Institute, San Diego and the Department of Pharmacology, University of North Carolina, Chapel Hill, US. Akash’swork is highly interdisciplinary, and he has established a unique program on natural and engineered biosensors, spanning multiple facets of life sciences, chemistry, imaging, and bioengineering. The Gulyani lab has pioneered several new biosensors for cellular dynamics. His group has also made major new discoveries in the area of natural light sensing, establishing completely new lines of inquiries using simple flatworm model organisms (work covered by major international publications like NY Times, The Atlantic and New Scientist). A recent work won the 2018 CellPress-TNQ award for the best paper in life sciences in India. He has also been awarded the American Heart Fellowship and an award for excellence in mentorship by the University of North Carolina, US. He has received multiple national and international grants. From 2012 onwards he is an Assistant Investigator at the Institute of Stem Cell Biology and Regenerative Medicine (inStem), Bangalore. (https://instem.res.in/faculty/akash)

Abstract: I will present our multi-disciplinary approach of devising new measurements, sensing dynamics across scales and exploring new natural biosensors for basic biology and health. Often, cellular outputs are controlled not by protein levels but local protein activity. For this, we have pioneered fluorescent biosensors that directly recognize ‘active’ states of signaling proteins in live cells and tissues (Mukherjee-Gulyani et al manuscript in review; BioRxiv https://doi.org/10.1101/726133; Gulyani et al Nature Chemical Biology 2011). Our approach is general and compatible with microscopy readouts like FRET and fluorescence lifetime imaging (FLIM) and multi-color ratio imaging. A new biosensor for a specific Src family kinase (Fyn) reveals how signaling activity can be spatially compartmentalized, show oscillations over time and subject to localized signal integration between integrins and growth factor receptors.
For mapping cell states, we have also developed new mitochondrial sensors. Currently, live imaging of mitochondrial activity relies on measuring mitochondrial potential, but this has significant drawbacks. To address this gap, we have developed new bright, highly stable chemical probes that sense changes in the local micro-environment, activity and the state of the mitochondria, with high spatial and temporal resolution (US and India Patent pending, Raja-Gulyani et al 2017, Gulyani lab manuscripts 2019). These probes offer a platform to study mitochondrial dysfunction in cellular models of human disease.
Our search for new sensing systems has led us back to nature. I will showcase our recent ground-breaking discoveries on how organisms can sense and process light itself. We have established a new sensory paradigm wherein ‘colorblind’ worms are able to ‘sense’ small changes in light wavelengths (‘colors’) and completely switch their behavior (Shettigar-Gulyani et al Science Advances 2017). This is a fascinating example of organisms with very simple eyes and ‘early brains’ showing acute gradient sensing coupled to binary processing. Since flatworms regenerate, natural light sensing itself can now be used to assay for molecular mechanisms underpinning functional eye-brain regeneration. We can essentially watch how an ability to ‘compute’ recovers in a simple sensory network. Further, we have ALSO uncovered extraordinary new mechanisms through which simple organisms can sense light independent of their eyes. This has led to the discovery of new light sensing proteins (molecular switches), unique photoreceptor cells and delocalized but functional neural networks. This has radical implications in the evolution of light sensing in nature, human health, biomimetic devices, and novel optogenetics.

IBSE 6th Workshop
02 Nov 2019

IBSE In-house workshop to be held on 7 November 2019 from 2.30 pm.

## Venue: BT Seminar Hall

 1430 - 1500 Analysis of complex reaction networks: Theory to Practice Nirav Bhatt, IBSE Faculty 1500 - 1515 Analysis of differential gene expression of Ribosomal Protein genes in different cancers Sakshi Agrawal, IBSE 1515 - 1530 MinReact: An efficient method to identify minimal metabolic networks Gayathri S, IBSE 1530 - 1600 Coffee break 1600 - 1615 Tuning Functional Modes via DNA-Driven Population Re-Distribution in both Disordered and Ordered Proteins Soundhara Rajan G, IBSE 1615 - 1630 Two-species community design of Lactobacilli for production of D-Lactate Maziya Ibrahim, IBSE 1630 - 1645 Centrality in multilayer networks Tarun Kumar, IBSE 1645 - 1700 Inferring spatial correlation of Alzheimer’s disease from multi-tissue gene expression data B P Kailash, IBSE
IITM-EBI modelling workshop
16 Oct 2019

The four days workshop will train researchers from life science and mathematics to communicate and work together to learn to build and analyse computer models using user-friendly open-source software.
Date: Monday 2 - Thursday 5 December 2019
Venue: Indian Institute of Technology Madras - IIT P.O.Chennai, Tamil Nadu, 600 036, India
Application opens: Wednesday 25 September 2019
Application deadline: Thursday 31 October 2019
Participation: Open application with selection
Registration fee: Student/Postdoc ₹2,500 / Faculty ₹5,000 / Industry ₹10,000

IBSE Seminar by Dr. Ulf Schmitz
27 Aug 2019

IBSE is very pleased to introduce you all to our guest speaker Dr. Ulf Schmitz who will give IBSE Seminar on Thursday, 12th September 2019 in BT Seminar Hall (Biotechnology Dept. Block 1, Ground Floor), at 4:00 pm. The title of his presentation will be: “Unpeeling the layers of post-transcriptional gene regulation”. Dr. Ulf Schmitz is head of the Computational BioMedicine Lab at the Centenary Institute (University of Sydney). He is also Conjoint Senior Lecturer at the Faculty of Medicine and Health (University of Sydney). (http://sydney.edu.au/medicine/people/academics/profiles/usch6281.php).

Abstract: In this presentation, I will discuss two forms of post-transcriptional gene regulation as well as the interdisciplinary analysis pipelines that we developed to decipher their roles in normal physiology and in diseases such as cancer. While microRNA-mediated target repression is a well-known and extensively studied form of post-transcriptional gene regulation, intron retention (IR) is still underexplored but has gained more attention recently after we have shown that IR is a widespread and conserved mechanism of gene expression control. We found that IR controls the expression of functionally-related genes during hematopoietic cell differentiation and that IR induces gene regulatory complexity and exhibits well-conserved characteristics in over 430 million years of evolution. We have explored epigenetic modifications as mediators of IR and discovered significantly reduced DNA methylation levels as well as an increased presence of specific histone marks near and within the DNA encoding retained introns. IR is common across liquid and solid tumours and differentially regulated in comparison to normal tissue. We study the role of IR in chronic myeloid leukemia and breast cancer and found distinct patterns of IR in both cancers. Finally, I will discuss a potential cross-talk between microRNA and IR-mediated gene regulation.

IBSE Seminar by Dr. Anjali Krishnan
07 Aug 2019

IBSE is very pleased to introduce you all to our guest speaker Dr. Anjali Krishnan who will give IBSE Seminar on Wednesday, 7th August 2019 in BT Seminar Hall (Biotechnology Dept. Block 1, Ground Floor), at 12:00 pm. The title of her presentation will be: “Multivariate approaches to examine cognitive brain function”. Dr. Anjali Krishnan is an Assistant Professor of Quantitative Methods in the Psychology Department at Brooklyn College of the City University of New York (http://www.brooklyn.cuny.edu/web/academics/faculty/faculty_profile.jsp?faculty=1262).

Abstract: If we were to compile a list of complex biological systems, the brain would, undoubtedly, find a worthy mention. Not only is brain function complex, modern imaging technologies that measure this function from tens of thousands of studies across hundreds of thousands of brain coordinates generate millions of data points. The rise of such massive functional brain imaging datasets has resulted in the development of specialized analytic tools through collaborations with other disciplines (e.g., psychology, biology, computer science, statistics). Here, I highlight how functional brain imaging experiments are designed, what type of data are collected, how these data are pre-processed and analyzed, and then further meta-analyzed to consolidate major neuroscientific findings. I will specifically focus on how we can represent complex information in an intuitive way, and provide a framework for insightful data analytic practices informed by cognitive neuroscience.

IBSE Seminar by Dr. Shyam K. Masakapalli
12 Jun 2019

IBSE is very pleased to introduce you all to our guest speaker Dr. Shyam K. Masakapalli who will give IBSE Seminar on Monday 17th June in RBC-DSAI Seminar Hall (Biotechnology Dept. Block 2, 5th Floor), at 11:30 am. The title of his presentation will be: “Introducing 13C Fluxomics and Smart Agriculture in Indian context”. Dr. Shyam K. Masakapalli is an Assistant Professor at BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi (http://faculty.iitmandi.ac.in/~shyam/).

Abstract: This talk will focus on two research aspects of much relevance to Indian Science - 13C Fluxomics towards defining cellular metabolic phenotypes and FarmerZone™, A DBT initiative towards smart Agriculture in India. Understanding the phenotypes of cellular systems using omics platforms is of core interest to Biologists. 13C Metabolic Flux Analysis (MFA) defines flux maps that provide detailed quantitative insights into cell metabolism. The underlying workflow including the 13C tracer feeding, analytical techniques for isotopomer analysis and metabolic modelling we are adopting to understand metabolism of microbes and plant systems with relevance to agriculture and industry will be discussed. The case studies of selected systems will highlight the potential of integrating 13C fluxomics with other complementary omics approaches for novel discoveries. In the second half of the talk, I will briefly introduce the current status of FarmerZone™ project, a Dept. of Biotechnology’s (Govt. of India) vision of an integrated information delivery service for smallholder farmers for improved yields and enhance livelihood. The cloud platforms we are developing provides advisories related to crop and soil health, desired growing conditions, preferred seed varieties, availability of seed, and may also include market linkages in future. This first sentinel lead by IIT Mandi and other partners is targeted towards data driven advisories for potato and the talk will provide insights into the strategies we are adopting.

IBSE Job Opening
04 Jun 2019

### IBSE Post-doctoral Fellowships

IBSE Seminar by Dr. T.S. Suryanarayanan
09 May 2019

IBSE is very pleased to introduce you all to our guest speaker Dr. T.S. Suryanarayanan. The title of his presentation will be: “Fungal endophytes: concerted effort needed for realizing their technological potential”. Dr. T.S. Suryanarayanan is the Director of from VINSTROM, RKM Vidyapith, Chennai (https://rkmvc.ac.in/vinstrom/).

Abstract: Fungal endophytes are a constant constituent of plant microbiome. They may have played an essential role in the colonization of land by early plants nearly 425 M year ago. My lab has been studying the diversity, adaptations and economically important traits of endophytes for the past 30 years. It houses about 1700 endophyte strains isolated from different ecosystems of the country. It is well known that endophytes produce novel secondary metabolites of unprecedented molecular architecture vested with interesting pharmaceutical and other desirable bioactivities. Some endophytes even produce plant-derived metabolites. Of more recent discovery is that they also produce industrially important enzymes and enhance the abiotic and biotic stress tolerance of their host plants. Despite exhibiting such economically valuable traits, the technological use of endophytes have stopped with demonstrations. This lecture will highlight the gaps in our knowledge and bottlenecks that hinder progress in this line. It will underscore the immediate need for collaborations from scientists of different specializations for better exploiting the technological potential of this ecological group of fungi.

IBSE 5th Workshop
17 Apr 2019

IBSE In-house workshop to be held on 25 April 2018 from 2.30 pm to 5.30 pm .

## Venue: BT Seminar Hall

 1430 - 1445 Context-Specific independence in understanding Huntington progression from postmortem data Sriram R, IBSE 1445 - 1500 Reduction of genome-scale metabolic networks Gayathri S, IBSE 1500 - 1530 Specialised ribosomes – buffers of phenotypic variation? Dr. Himanshu Sinha, IBSE 1530 - 1545 Developing the India-specific model for estimating gestational age in the first trimester in GARBH-Ini cohort Nikhita Damaraju & Ramya Vijayram, IBSE 1545 - 1615 Coffee break 1615 - 1630 Can simulating mutations in driver genes help us understand them better? Malvika Sudhakar, IBSE 1630 - 1645 Network Analysis for Identification of Hub RNAs in Triple Negative Breast Cancer Associated Metastasis Satarupa Banerjee, Dept. of BT 1645 - 1700 Inferring Causal Relationships from Noisy Observational Data Amol Dumrewal, IBSE 1700 - 1715 Multi-objective optimization for co-production of metabolites Lavanya Raajaraam, IBSE 1715 - 1730 Identifying the context of mutations in a cancer genome Shayantan Banerjee, IBSE 1730 - 1745 Software Demo Anjana A S, IBSE
IITs, JNU to collaborate with German University for Bio Big Data Science project
13 Apr 2019

Given the rich expertise in data science at IBSE & RBC-DSAI, IIT Madras, this initiative will be catalytic in developing strong collaborations with University of Heidelberg in frontier areas of biological data analysis, and to train future leaders in these emerging areas. The Indian Express, India Today, NDTV

R/tidyverse workshop with Genomic dataset
01 Mar 2019

Interested in learning #RStats #tidyverse w/ a genomic dataset? Dr. Janani Ravi, Senior Research Associate, Pathobiology and Diagnostic Investigation, Michigan State University (https://jananiravi.github.io/) will be organizing a half day R/tidyverse workshop. Co-hosting w/ Dr. Arjun Krishnan, Group Leader , Dept. Computational Mathematics, Science and Engineering, Dept. Biochemistry and Molecular Biology, Michigan State University (https://www.thekrishnanlab.org/), and RLadiesChennai (https://twitter.com/RLadiesChennai). Join our workshop on March 05 ‘19, 2–5pm at RBC-DSAI Seminar hall, Biotech Dept. Block II, 5th Flr.

IBSE 4th Colloquium
01 Mar 2019

The Fourth Colloquium of the IBSE will be held on 7th March 2019. Dr. John S. Tsang, Chief, Systems Genomics and Bioinformatics Unit, Laboratory of Immune System Biology and Co-Director, NIH Center for Human Immunology (CHI) has kindly agreed to be our guest speaker. His lab works on developing and applying systems biology approaches— combining computation, modeling, and experiments—to study the immune system at both the organismal and cellular levels. He will discuss work on developing predictive models and uncovering correlates of immune responsiveness in humans and on evaluating human immune states across health and diseases.

IIT Madras, THSTI to work on predicting pregnancy outcomes and childhood mortality
23 Feb 2019

IBSE, IIT Madras is going to collaborate on applying advanced analytical approaches for predicting pregnancy outcomes with Translational Health Science and Technology Institute (THSTI) in Faridabad, Haryana. A Research Collaboration Agreement between the two Institutes was signed on February 22, 2019 during the IITM-THSTI Conclave on ‘Transforming Maternal and Child Healthcare Using Data Science.’

The broad objectives of this Collaboration include:

Ø Bringing physician-scientists, biologists, engineers and data scientists together to solve public health problems related to maternal and child health,

Ø Applying advanced analytical approaches for prediction of adverse pregnancy outcomes, childhood morbidity and mortality,

Ø Evaluating maternal and childhood consequences of exposure to environmental pollutants,

Ø Studying the role of maternal and childhood nutrition on pregnancy outcomes, immune response to vaccines and childhood morbidity and mortality, and

Ø Undertaking capacity building exercises for students and young researchers of either Party in the fields of public health research and data science by enabling student exchange programs and training courses.
Biospectrum
The Indian Express
NDTV

IBSE 3rd Colloquium
13 Feb 2019

The Third Colloquium of the IBSE will be held on 14th February 2019. Prof. Michael Knop, Group leader at the Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and German Cancer Research Institute (DKFZ) Heidelberg, Germany has kindly agreed to be our guest speaker. His laboratory develops software and advanced microscopy methods in biology, and methods for genome engineering in model organisms. He also investigates processes that regulate cellular morphogenesis, cell signalling and protein homeostasis. His research work uses methods from quantitative biology in combination with genetics, deterministic and stochastic simulations, and new instrumentation.

Seminar by Dr. Kavita Jain
12 Dec 2018 by Priyanka Maripuri

IBSE is very pleased to introduce you all to our guest speaker Dr. Kavita Jain.

Abstract of her talk: In an influential essay, evolutionary biologist Theo Dobzhansky stated that “nothing in biology makes sense except in the light of evolution”. Indeed, evolution shapes diversity at all levels of biological organization, ranging from cells to species. Population genetics and quantitative genetics have been used for over a century to describe biological evolution at genetic and phenotypic level, respectively. But there has been little effort to connect these two levels. In this talk, I will describe a bottom-up approach to describe rapid adaptation dynamics of a phenotype with an explicit reference to the underlying genetics.

IBSE 4th Workshop
09 Nov 2018 by Priyanka Maripuri

IBSE In-house workshop to be held on 15 November 2018 from 2.30 pm to 5.45 pm .

## Venue: BT Seminar Hall

 1430 - 1500 A network perspective on chemical spaces for drug discovery and toxicology Dr. Areejit Samal, The Institute of Mathematical Sciences, Chennai 1500 - 1515 Co-expression of genes in different tissues: tissue-tissue communication or developmental lineage effects? Arjun Sarathi, IBSE 1515 - 1530 Deciphering metabolism of Bifidobacteria using constraint-based genome scale models Dr. N.T.Devika, IBSE 1530 - 1545 Clustering in hypergraphs: A modularity maximization approach Tarun Kumar, RBCDSAI 1545 - 1615 Coffee break 1615 - 1630 How does functional redundancy evolve in metabolic networks? Gayathri S, IBSE 1630 - 1645 A priori Parameter Identifiability for Biochemical Reaction Networks with Mass Action Kinetics Ragini Sreenath, IBSE 1645 - 1700 Neighbourhood bases of driver and passenger mutations differ significantly across cancers Shayantan Banerjee, IBSE 1700 - 1715 A Comprehensive toolkit for RNA-Seq data analysis Priyanka Maripuri, IBSE 1715 - 1730 A graph-theoretic approach to understand metabolic interactions in microbial communities Aarthi Ravikrishnan, IBSE 1730 - 1745 Model Selection Using Approximate Bayesian Computing Abhijeet Mavi, IBSE
24 Sep 2018 by Karthik Raman

by Aarthi Ravikrishnan and Karthik Raman

Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.

Check the book out on Amazon

Seminar by Srikiran Chandrasekaran
05 Sep 2018 by

IBSE is very pleased to introduce you all to our guest speaker Mr. Srikiran Chandrasekaran. The title of his presentation will be: “Bayesian optimization for fitting dynamical systems in environmental engineering”. Srikiran Chandrasekaran graduated from IIT Madras with a B. Tech in Biotechnology in 2015. Currently, He is a PhD candidate in the Mathematical, Computational and Systems Biology programme at the University of California, Irvine in the lab of Prof. Sunny Jiang.

In light of limited water resources, wastewater is being used for agricultural and recreational purposes. Complete purification of wastewater is not economical and the microbial risk posed by reuse must be understood to manage resources optimally. The overarching goal of his research is to develop mathematical models that enable better prediction and understanding of microbial risk from wastewater reuse.

New IBSE Space!
18 Aug 2018 by Priyanka Maripuri

Our new IBSE space

A brand new lab space for IBSE was opened on August 17th, 2018 in Block II of Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras alongside the Robert Bosch Center for Data Science and Artificial Intelligence (RBCDSAI). The lab accommodates several researchers and visiting faculty. Each workstation in the lab is provided with high end personal computers that have fast connectivity to clusters and internet. There is great intermingling of researchers from diverse fields as we share the floor with RBCDSAI leading to interesting discussions over coffee.

26 Jul 2018 by

IBSE is very pleased to introduce you all to our guest speaker Dr. Adam Rubin. He is currently transitioning between Stanford and MIT. He is a data analysis expert in ATAC-seq, HiChiP. He has recently submitted a paper on Perturb-ATAC to Cell. You can look into his publications at his Google Scholar page.

Grand Challenges India, PMU-BIRAC Outreach Event at IITM
17 Jul 2018 by

Grand Challenges India and the Program Management Unit at BIRAC (PMU-BIRAC) are pleased to announce the launch of a call on ‘ki Data Challenge for Maternal and Child Health’, a program directed at addressing key knowledge gaps in our understanding of how nutrition, prenatal and antenatal care, maternal support, and environmental and social factors contribute to an elevated risk of poor maternal and childhood health outcomes.

Grand Challenges India is a partnership of Department of Biotechnology, Government of India, BIRAC and the Bill & Melinda Gates Foundation.

The call aims at encouraging the development of innovative data analytics solutions by analyzing existing data arising from multiple sources in India and formulating public health recommendations that are data-driven and cost-effective, results from which shall be used to inform policy decisions related to maternal and child health.

Interested researchers are required to submit a proposal online by 17th August, 2018, 2:00 P.M. IST. If selected, proposals may be supported for up to 18 months, funded at up to \$100,000 USD per project. These awards are meant to provide an opportunity to develop, refine, and rigorously test novel approaches to the outlined challenge as well as develop data science capacity in India.

For a complete understanding of the scope, please visit microsite BIRAC.

Seminar by Dr. Nathan Bachmann
13 Jul 2018 by

IBSE is very pleased to introduce you all to our guest speaker Dr Nathan Bachmann from University of Sydney. He is currently working with Dr. Sivaraman at National Institute for Research in Tuberculosis (NIRT). Dr. Nathan and Dr. Sivaraman are working on whole-genome sequencing of Mycobacterium Tuberculosis samples. IBSE is very excited to explore potential collaborations with Dr. Nathan’s group at University of Sydney and NIRT on topics ranging from evolution of drug resistance to how social networks drive spread of Tuberculosis infection.

2nd IBSE Colloquium
20 Jun 2018 by

The second seminar of the IBSE Seminar Series will be held on 29th June, 2018. Dr. Anurag Agrawal has kindly agreed to be your guest speaker of this seminar series. Dr. Anurag Agrawal is interested in experimental and computational approaches for understanding biological and clinical aspects of respiratory diseases, especially asthma.

IBSE 3rd Workshop
09 Apr 2018 by

IBSE In-house workshop to be held on 21 April 2018.

## Venue: BT Seminar Hall

 0930 - 1030 Natural variation in gene expression as a route towards multimodal systems biology Dr. Manikandan Narayanan 1030 - 1100 Coffee break 1100 - 1115 Novel ratio-metric features enable the identification of new driver genes across cancer types Malvika Sudhakar 1115 - 1130 MKT1 mediated post-transcriptional regulation of stress resistance in yeast Koppisetty Viswa Chaithanya 1130 - 1145 Identifying driver genes from a Pan-cancer study Shayantan Banerjee 1145 - 1200 Determining the role of ribosomal protein genes in phenotypic diversity and adaptation Purnima K V K 1200 - 1215 Mining evolutionary gene expression patterns in mammalian tissues Gaurav Bilolikar 1215 - 1230 Understanding microbial interactions in communities through an integrated computational and experimental framework Aarthi Ravikrishnan 1230 - 1245 Systematic comparison of NGS pipelines using five gold standard datasets Likith Reddy P 1245 - 1300 Designing Modular Gene Circuits Saransh Umale

If you wish to attend this workshop, please register here by 18 April 2018.

Seminar by Dr. Rahuman Sheriff
08 Mar 2018 by

IBSE is very pleased to introduce you all to our guest speaker Dr. Rahuman Sheriff. The title of his presentation will be: “Dynamics of cellular signalling networks: lessons from quantitative imaging”

Dr. Rahuman Sheriff is a Project Leader at European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI). His interest pertains to Systems Biology, Mathematical modelling of Biological processes, BioModels tools and resource development, curation, Translational quantitative systems toxicology data analysis and data management platform development. In his joint postdoctoral position between, EMBL-EBI and MRC-LMS, Imperial College London, UK, he developed image processing tools and theoretical approaches to reconstruct the signalling networks from single cell imaging data of human embryonic stem cells differentiation. During his PhD at Max Planck Institute of Molecular Physiology (MPI), Germany, he established a multi-colour live cell imaging system and developed novel statistical approaches and advanced software to analyze multidimensional imaging data to capture complex regulations observed in the dynamics of cell-matrix adhesion sites. He had worked in collaboration with MPI and Department of Statistics, University of Dortmund, to develop a novel Bayesian approach for resolving a mixture of signalling networks. Furthermore, he had also worked on an interdisciplinary research collaboration between TIFR Centre for Applied Mathematics and National Centre for Biological Sciences (NCBS). Through IASc fellowship he had also visited Centre for Cellular and Molecular Biology (CCMB). With hands-on experience in both wet and dry lab work, he custom developed novel computational tools to facilitate quantitative analysis of experimental data and collaboration between theoretical and experimental groups and institutions.

Welcoming Dr. Manikandan Narayanan to IBSE
18 Jan 2018 by Priyanka Maripuri

IBSE welcomes Dr. Manikandan Narayanan, who has joined IIT, Madras as an Associate Professor. He received his MS and PhD (2007) from UC Berkeley and his B.E. from CEG, Anna Univ. Until December 2017, he was with NIH, Bethesda, MD, USA.

His research interests are in: Bioinformatics, Computational network biology, Systems biology/genomics in health and disease, Data science. See more about Dr. Mani’s work here.

An MoU was signed today!
11 Jan 2018 by Priyanka Maripuri

IBSE is very happy to inform you that an MoU was signed today, with a generous endowment from Dr. Prakash Arunachalam.

Can you guess who's gonna join IBSE soon?
26 Dec 2017 by Priyanka Maripuri

IBSE is pleased to announce “The Wellcome Trust/DBT India Alliance Research Fellowship in Biomedical Research schemes” to Dr. Manikandan Narayanan. We are extremely proud to inform you all that Dr. Manikandan will be joining IBSE soon.

First International IBSE Symposium
20 Nov 2017 by Karthik Raman

The first IBSE International Symposium was organised from 22-24th January 2018, at the IC&SR Auditorium, IIT Madras. Preceding the symposium, student participants were trained and challenged to perform next-generation sequence analyses as part of a day long workshop conducted by Rohit Gupta (MedGenome Labs). The symposium was inaugurated by Prof. Bhaskar Ramamurthi (Director, IITM) who pointed out the importance of this symposium to not only usher in a transition from genotype to phenotype but eventually also to actionable prototypes, and Prof. R. Nagarajan (Dean, International & Alumni Relations, IITM), who talked about the importance and convergence of interdisciplinary activities in the campus. On Day 1, we had five talks by including from Amit Dutt (ACTREC), Michael Gromiha (BT), Rune Linding (Univ. Copenhagen), and Shamith Samarajiwa (MRC, Cambridge). Two poster flash talks and an energetic poster session were the other highlights of the day. Following the scientific sessions, the delegates paid a visit to the IITM Research Park, where they had an opportunity to see the synergy between established companies and IITM as well as entrepreneurial ventures. Following this, we hosted a banquet dinner at Holiday Inn. On Day 2, we had an exciting session with talks by Edda Klipp (HU Berlin), Simon Anders (ZMBH Heidelberg), Shekhar Mande (NCCS) and Niranjan Nagarajan (GIS Singapore). Following another set of poster talks and a poster session, we had talks by Manikandan Narayanan (CS), Erik van Nimwegen (Biozentrum, Basel) and B. Ravindran (CS). Following the talks, we had an entertaining Carnatic music concert by “Kalaimamani” Smt. Gayathri Girish. Day 3 began with a stimulating talk by Giriraj Chandak (CCMB) highlighting the key drivers of “diabesity” in the Indian populace. Other talks were by Rudiyanto Gunawan (ETH Zürich), Vinod Scaria (IGIB), Amit Chaudhuri (VP R&D MedGenome), Haja Kadarmideen (Director, DTU Bioinformatics) and the final talk was by Lars Steinmetz (EMBL Heidelberg & Stanford Univ.), on cutting edge technologies that will impact experimental systems biology over the next few years, thereby actually suggesting a path for going from genotype to phenotype to prototype. Two poster prizes were awarded, and the meeting concluded with thanks to all involved, notably the student volunteers who made the whole event possible. The event was attended by students from all over the country, and a faculty each from IITG and IITKGP. These and our own IBSE students’ involvement and energy at the symposium was applauded by Rune Linding in the final feedback session.

Acknowledgements: IBSE is grateful to Dr. Prakash Arunachalam, Lead Data Scientist, BNY Mellon, USA, for his generous contribution supporting the IBSE and funding this Symposium through the Office of International and Alumni Relations, IIT Madras. We also gratefully acknowledge support from the Office of International and Alumni Relations, the Centre for Continuing Education (CCE) and the Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras. The organisers also acknowledge the support and mentorship of Prof. Ashok Venkitaraman, Mehta Distinguished Chair (IIT Madras) and Director of the Medical Research Council (MRC) Cancer Unit (University of Cambridge, UK). We also gratefully acknowledge the support of our Director, Prof. Bhaskar Ramamurthi, Prof. R. Nagarajan, Dean, International & Alumni Relations, and Prof. D. Karunagaran, Head, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences. Finally, we acknowledge the hard work of all student volunteers from our laboratories.

– Himanshu Sinha & Karthik Raman (Co-Ordinators)

For further details, visit the Symposium Website and the Gallery

DBT-funded JRF and PhD positions
19 Oct 2017 by Karthik Raman

## Open Positions

Applications are invited for two Junior Research Fellow (JRF) positions in a project funded by the Department of Biotechnology at the Computational Systems Biology Lab, IIT Madras.

## PhD applications are also welcome

Apply at https://research.iitm.ac.in/ to one of the following departments:
(a) Interdisciplinary Stream on “Data Science and Artificial Intelligence”
(b) Biotechnology
(c) Chemical Engineering
(d) Computer Science

## Project

The burgeoning amounts of cancer genome data have opened several avenues for computational analysis of these sequences to gain insights into disease associations of genes, as well as the molecular bases of diseases. While many recent studies have proposed approaches to identify driver and passenger mutations in cancer genes, the studies have not examined the context of these mutations in detail, which might have significant influence on the effect of the mutations and the subsequent progression of cancer. In this study, we seek to apply a combination of statistical and machine learning techniques to analyse novel genomic data generated from Cambridge, as well as sequence data available in the public domain, to build a computational pipeline for the identification of the context of cancer mutations in genome sequences.

## Qualifications

BE/BTech/MTech in any branch of engineering, with a GPA of 7.5 and above. Programming experience in at least one high-level programming language (e.g. Python) is mandatory. Some exposure to biological data analysis will be helpful; familiarity with NGS data analysis pipelines / RNASeq will be a major plus.

Interested candidates can send their CV by e-mail with subject line [DBT JRF] to:

Dr. Karthik Raman (kraman@iitm·ac·in)
BT 104, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences
Co-ordinator, Initiative for Biological Systems Engineering
Member, Robert Bosch Centre for Data Sciences and Artificial Intelligence (RBC-DSAI)

IBSE Seminar Series: What transcriptional noise tells us about the cell inside
18 Oct 2017 by Karthik Raman

## What transcriptional noise tells us about the cell inside

Speaker: Victor de Lorenzo

Venue: Central Lecture Theatre (CLT), at 3:30 pm on Friday, 3rd November 2017

Systems Biology Program. Centro Nacional de Biotecnologia, CSIC, C/ Darwin, 3 (Campus de Cantoblanco), Madrid 28049, Spain.

### Abstract

Transcriptional noise is a necessary consequence of the molecular events that drive gene expression in prokaryotes. However, the m-xylene degrading soil bacterium Pseudomonas putida mt-2 seem to have co-opted evolutionarily such a noise for deploying a metabolic diversification strategy that allows a cautious exploration of new chemical landscapes. In reality, noise is not only the mere consequence of stochasticity, but also a signal that reflects the upstream physical dynamics of the cognate molecular machinery. Noise of catabolic promoters can thus be exploited to deploy beneficial phenotypes such as metabolic bet-hedging and/or division of biochemical labour. Although the role of upstream promoter-regulator interplay in the origin of this noise is little understood, its specifications are probably ciphered in flow cytometry data patterns. We studied the activity of the Pm promoter of Pseudomonas putida mt-2 and its cognate regulator XylS by following expression of Pm-gfp fusions in single cells. Using mathematical modelling and computational simulations, we determined the kinetic properties of the system and used them as a baseline code to interpret promoter activity in terms of upstream regulator variability. Transcriptional noise was predicted to depend on the intracellular physical distance between regulator source (where XylS is produced) and the target promoter. Experiments with engineered bacteria in which this distance is minimised or enlarged confirmed the predicted effects of source/target proximity on noise patterns. This approach allowed deconvolution of cytometry data into mechanistic information on gene expression flow. It also provided a basis for selecting programmable noise levels in synthetic regulatory circuits.

Goñi-Moreno Á, Benedetti I, Kim J, de Lorenzo V. (2017) Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor-Promoter Interplay. ACS Synth Biol. 6: 1359-1369

Guantes R, Benedetti I, Silva-Rocha R, de Lorenzo V. (2016) Transcription factor levels enable metabolic diversification of single cells of environmental bacteria. ISME J. 10: 1122-1133

Silva-Rocha, R. and de Lorenzo, V. (2012) Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene. Mol. Microbiol. 86: 199- 211

IBSE in the news
13 Oct 2017 by Karthik Raman

IBSE 2nd workshop
01 Sep 2017 by Karthik Raman

IBSE in-house workshop to be held on 9-September-2017.

## Venue: BT Seminar Hall

 0930 - 1015 Role of gut microbiota in autism Swagatika Sahoo 1015 - 1030 Coffee break 1030 - 1045 Mining evolutionary gene expression patterns in mammalian tissues Gaurav Bilolikar 1045 - 1100 Quantifying Microscopic Pathway Heterogeneity in Protein Folding Soundhara Rajan G 1100 - 1115 Understanding the evolutionary design principles underlying metabolism Gayathri S 1115 - 1130 Rational development of microbial consortia for metabolic engineering Aarthi Ravikrishnan 1130 - 1145 Mapping microRNA gene regulatory network to understand its role in cervical cancer Ashley Xavier 1145 - 1200 Disease Module Identification in Biological Networks Beethika Tripathi 1200 - 1215 Understanding redundancies in metabolic networks through synthetic lethals Omkar Mohite 1215 - 1230 Novel sequence-based and network-based approaches to predict essential genes across diverse organisms Karthik Azhagesan 1230 - 1245 Binning of genes using optimisation Malvika Sudhakar
IBSE Seminar Series Inaugural Lecture
29 Aug 2017 by Karthik Raman

The first seminar of the IBSE Seminar Series will be held on 3rd November, 2017. Prof. Victor de Lorenzo has kindly agreed to be the first speaker of this seminar series. Prof. de Lorenzo is an eminent scientist in the area of synthetic biology / environmental engineering, and his group has pioneered research using Pseudomonas putida for several biotechnological applications.

Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI) established
04 Aug 2017 by Karthik Raman

Robert Bosch Engineering and Business Solutions (RBEI) and IIT Madras today signed an MoU for establishing the Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI). RBC-DSAI will undertake foundational research in various areas of AI and Data Science.

IBSE / systems biology research has been a strong vertical at the erstwhile Interdisciplinary Laboratory for Data Sciences (ILDS); we hope this will give further fillip to IBSE activities!

DBT Grant: Computational Tools for Studying Mutations in Cancer
01 Aug 2017 by Karthik Raman

The DBT award comprises two projects:

• Karthik Raman, B Ravindran and Raghunathan Rengaswamy: A computational pipeline for Identifying the Context of Key Mutations in Cancer Genomes
• Michael Gromiha and Suresh Rayala: Development of computational tools for analysis and prediction of disease-causing mutations
IBSE posters @ ILDS Workshop
30 Oct 2016 by Karthik Raman

## IBSE Posters

• Predicting the Role of Diet and Gut Microbiota in Autism
• Identification of Disease Modules using Integrated Biological Networks
• A Graph-Theoretic Algorithm to Design Microbial Communities for Metabolic Engineering
• Understanding Cancer Expression Profiles using I-COMIC Pipeline
IBSE 1st workshop
26 Feb 2016 by Karthik Raman

The 1st IBSE workshop will happen as part of the ILDS Workshop on Data Analytics on 5-Mar-2016. The IBSE session is from 11 am onwards, till 1 pm.

## Venue: CS 25

 0915 - 0930 Introduction to ILDS-IBSE activities Dr. B Ravindran (CSE) 0930 - 1000 Bridge Correlational Neural Networks for Multilingual Multimodal Representation Learning Janarthanan R (CSE) 1000 - 1030 Phase and Topology Identification in Smart Distribution Networks Jayadev Satya P (EE) 1030 - 1100 Coffee Break 1100 - 1200 Integration and analysis of multi-omics data within metabolic network context Dr. Swagatika Sahoo (ChE/IBSE) 1200 - 1230 Understanding cancer mutations in the context of their neighbourhoods Abhishek Sivaram (ChE), Pallavi Gudipati (CSE) 1230 - 1300 Classification of genes as tumour suppressors and oncogenes Maharishi R B (ED) 1300 - 1430 Lunch Break