Events

20 Apr 2020

IBSE-inSTEM MiniSymposium will be held on 20 April 2020 by online from 3.00 pm - 5.00 pm.

Venue: Online

1500 - 1505 Introduction to IBSE Karthik Raman, IBSE Faculty
1505 - 1520 Ratio-metric features for identification of novel tumour suppressor genes and oncogenes Malvika Sudhakar, IBSE
1520 - 1535 Effect of neighbourhood sequences on the pathogenicity of mutations in cancer genome Shayantan Banerjee, IBSE
1535 - 1550 Using RL to design dosage patterns for combination chemotherapy Senthamizhan V, IBSE
1550 - 1605 ICOMIC a comprehensive toolkit for genomic data analysis Anjana A S/ Keerthika M, IBSE
1605 - 1620 Understanding the patterns of somatic mutations through machine learning Samyugdha V M, IBSE
1620 - 1635 Tissue level differential correlation of Alzheimer’s disease Kailash B P, IBSE
1635 - 1650 Regulatory role of mir-34 family in cervical cancer and predicting new targets of mir-34b B P Kailash, IBSE
1650 - 1700 Thoughts on possible collaborations IBSE–inSTEM Dr. Anandi Karumbati & team, inSTEM

10 Apr 2020

IIT Madras Researchers develop Algorithms to detect Disease-causing Dysfunctional Proteins & Genes in Biological Networks. Recent work from IBSE was featured in The Times of India - Education Times, NDTV and The New Indian Express - EDEX.

11 Feb 2020

IBSE is very pleased to introduce you all to our guest speaker Dr. Anshu Bhardwaj who gave IBSE Seminar on Tuesday, 11th February 2020 in BT Seminar Hall (Biotechnology Dept. Block 1, Ground Floor), at 03:30 pm. The title of her presentation was: “Data-driven approaches to address Antimicrobial Resistance (AMR)”. Anshu Bhardwaj obtained her Ph.D. in understanding genotype-to-phenotype correlations in human mitochondrial diseases. She then joined CSIR as one of the founding PIs of the Open Source Drug Discovery Project in 2008.

30 Jan 2020

About the India-EMBO Symposium 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.

09 Dec 2019

We are happy to announce 5th IBSE Colloquium, by Prof. Radhakrishnan Mahadevan, Department of Chemical Engineering and Applied Chemistry, University of Toronto. The title of the talk is “Design Principles for Engineering Metabolism”. Radhakrishnan (Krishna) Mahadevan is a Professor in the Departments of Chemical Engineering & Applied Chemistry, and Institute of Biomaterials and Biomedical Engineering at the University of Toronto. He obtained his B. Tech from Indian Institute of Technology, Madras in Chemical Engineering in 1997 and then obtained his Ph.

20 Oct 2019

IIT Madras researchers develop method for enhanced Vitamin E production. Recent work from IBSE was featured in The Economic Times.

02 Dec 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

19 Nov 2019

Happy to announce that Dr. Nathan Bachmann from Center for Infectious Diseases and Microbiology (CIDM) will be presenting an overview of his work in Mycobacteria species and developing metagenomics. The title of his talk is “Key transitions in the evolution of rapid and slow growing Mycobacteria identified by comparative genomics”. Nathan has completed a Ph.D. in microbial genomics and bioinformatics at the University of Queensland. He then worked as a post-doc at the University of the Sunshine Coast on culture-independent genome sequencing of Chlamydia pecorum from swab samples collected from koalas.

18 Nov 2019

Happy to announce that Dr. Ranjeeta Menon from Univ. of Sydney will be presenting an overview of her work in pathogen genomics coming Monday. She will be presenting along with Nilesh Subramanian, IBSE Postbac working with Dr. Manikandan Narayanan who will talk about using bioinformatics and machine learning to guide Tuberculosis drug predictions. The title of her talk will be “Aspects of Whole Genome Sequencing application in translational research – Pathogen genomics”.

08 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.

07 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

12 Sep 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).

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.

17 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.

IBSE offers Post-baccalaureate Fellowships to exceptional graduates, who are desirous of pursuing a 1-2 year research internship at the interface of biology and engineering at IBSE, IIT Madras. IBSE also offers post-doctoral fellowships to exceptional doctorates, who are desirous of pursuing a 1-2 year research to initiate long-term research goals at the interface of biology and engineering at IBSE, IIT Madras.
IBSE Post-baccalaureate Fellowships | IBSE Post-doctoral Fellowships

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.

25 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

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

07 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.

05 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.

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,

14 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.

09 Feb 2019

IIT Madras Researchers have identified biochemical pathways that eye cancer (retinoblastoma) chooses preferentially for growth and survival. Recent work from IBSE was featured in The Hindu.

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.

15 Nov 2018

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

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.

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.

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.

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.

24 Jul 2018

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.

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.

29 Jun 2018

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.

21 Mar 2018

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

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.

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.

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

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.

22 Jan 2018

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.

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 © 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.

03 Nov 2017

The first talk of the IBSE seminar series will be delivered by Prof. Victor de Lorenzo. The title of the talk is “What transcriptional noise tells us about the cell inside”. Prof. Victor de Lorenzo currently works at 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.

09 Sep 2019

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

03 Nov 2017

The first lecture of the IBSE Colloquium 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 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!

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

Venue: ICSR Hall 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

05 Mar 2016

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