28 Jun 2024
Protein function prediction and classification using deep learning models and knowledge graph mining
IBSE is pleased to invite you to the 16th IBSE Colloquium. In this instance Professor Dr. Kannan will talk about “Protein function prediction and classification using deep learning models and knowledge graph mining”. Abstract: Proteins are essential biological macromolecules that perform a wide range of cellular functions. Accurately predicting these functions is a significant challenge in bioinformatics and biotechnology. In this talk, I will share our recent advancements in predicting protein functions by combining deep learning, knowledge graph mining, and experimental techniques.
05 Apr 2024
IBSE is very pleased to introduce you all to our guest speaker Dr. Bharath Prithiviraj. The title of his presentation will be: “Exposome Relevance to the Human Resistome: A One Health Conundrum” Dr. Prithiviraj has spent a decade in the field of microbiome research and metagenomics. More specifically his focus is on environmental surveillance thereby informing impact on public health directives. He has experience working with startups, contract research organizations and academic research laboratories.
28 Mar 2024
Abstract: He will speak about some of the principles of drug discovery that he has learnt over the years as a researcher. He will then use examples of his research work to illustrate bench-to-bedside cases. Speaker: Dr. Pravin Iyer started his science journey started with a Pharmacy degree in Bombay, followed by a move to Pittsburgh, USA where he completed a doctorate and post-doctoral training in organic chemistry. He learned the ropes of drug discovery under the tutelage of some intrepid, world-class scientists at Roche Palo Alto, in sunny California.
22 Mar 2024
Abstract: The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 60, 700 Studies, 204, 171 Biosamples, 506, 126 Organisms, 551, 483 Sequencing Projects and 408, 866 Analysis Projects with a total of 650 metadata fields, of which 95 are based on controlled vocabulary (CV) terms.
11 Mar 2024
Speaker: Dr. Mamatha Bhat, Hepatologist & Co-Lead of Transplant AI initiative (TAI), Ajmera Transplant Centre Bhat Lab - Precision Medicine to Enhance Life after Liver Transplantation Transplant AI Initiative Abstract: Artificial Intelligence (AI) tools have been increasingly applied to clinical questions in transplant medicine in recent years. As we continue to push the limits of transplantation, with the older age and complex comorbidities of candidates, there are many challenges throughout transplant medicine that must be better addressed.
22 Feb 2024
Speaker: Associate Professor. Sriram Chandrasekaran, Who is an Associate Professor of Biomedical Engineering at the University of Michigan-Ann Arbor, and he leads the Systems Biology & Drug Discovery lab. He received his PhD in Biophysics from the University of Illinois at Urbana-Champaign and worked at Harvard University and MIT as a Harvard Junior Fellow. He has developed over 10 different systems biology algorithms for drug discovery and bioengineering. A key focus of his lab is the development of mechanistic AI methods that use both engineering models and machine learning.
21 Feb 2024
Prof Victor De Lorenzo (FEMS Expert: Prof Victor de Lorenzo - FEMS (fems-microbiology.org) ) is a lead researcher within the Systems Biology Program at the Centro Nacional de Biotecnología (CSIC) in Madrid. His current research focus involves deep engineering of soil bacteria both as cell factories for industrial biotransformations and as agents for environmental bioremediation and valorisation of toxic waste. Other areas of research include environmental microbiology, metabolic engineering, Pseudomonas putida biology and biotechnology, gene expression regulation, synthetic (micro)biology, and global warming.
05 Feb 2024
Speaker: Prof. Mustafa Khammash, (ETH Zürich) Abstract: Adaptation is a recurring theme in biology, offering vital survival mechanisms in dynamic environments through precise regulation of physiological variables. This talk dives into the intriguing concept of robust perfect adaptation (RPA), a phenomenon where a system maintains a specific variable at a setpoint despite persistent perturbations. The objective of this talk is to explore the fundamental problem of achieving maximal RPA, focusing on a designated output variable and its robustness to perturbations across almost all network parameters.
04 Dec 2023
IBSE is pleased to invite to a talk by Dr. Arvind Ramanathan on Plasma metabolomics and lipidomics of healthy skeletal muscle aging in an older Indian Cohort. Please do join us at 2:00 pm to 3:30 pm at RBCDSAI Seminar Hall, Dept. of Biotechnology Block 2, 5th floor, IIT Madras.
19 Oct 2023
IBSE is pleased to invite you to the 12th IBSE Colloquium. In this instance Prof. Juho Rousu will about Machine Learning for Small Molecules. Small molecules have a pivotal role in many applications in life sciences, including biomedicine and drug discovery, enviromental sciences and biotechnology. At the same time, the emergence of large open datasets is fuelling the development of new machine learning technologies. Prof. Juho Rousu will discuss a generic machine learning task of predicting the a compatibility score F(x,y) of a pair of objects x and y, or in general a set of multiple interacting objects.
16 Oct 2023
IBSE is delighted to invite you to our next seminar by Prof. Ganesh Bagler, IIIT D, jointly with Centre For Innovation (CFI), IIT Madras. Abstract Cooking is an art. Humans are unique in ingeniously combining and processing ingredients to create delicious dishes. Besides being the basis of nutrition and health, these culinary idiosyncrasies are at the core of our cultural identity. The increasing availability of data and the advent of computational methods for their scrutiny are dramatically changing the artistic outlook toward gastronomy.
03 Oct 2023
IBSE is proud to invite you to an internal symposium, jointly with Cancer Science Institute, NUS, Singapore. This symposium will feature research talks by faculty from both institutes. This event is open for all IITM students and researchers. Symposium Website
21 Sep 2023
IBSE is pleased to invite to by Dr. Krishnan. J, Dept. of Chemical Engineering, Imperial College, London. Please do join us at 2:30 pm at RBCDSAI Seminar Hall.
27 Sep 2023
IBSE is pleased to invite you to the 11th IBSE Colloquium. In this instance Associate Professor Dr.Karthik Anantharaman will (Re)defining the roles of viruses in microbiomes. please do join us.
13 Jul 2023
IBSE is delighted to organize a Hands-on Workshop on single-cell transcriptomics by Prof. Vijay Tiwari, Professor and Chair, Wellcome-Wolfson Institute for Experimental Medicine, QUB, UK & Institute of Molecular Medicine, SDU, Denmark.
05 Apr 2023
RBCDSAI and IBSE are delighted to host Prof. Vijay Tiwari, Professor and Chair, Wellcome-Wolfson Institute for Experimental Medicine, QUB, UK & Institute of Molecular Medicine, SDU, Denmark for an ARP Talk.
05 Apr 2023
IBSE is delighted to organize a tutorial on NGS by Prof. Vijay Tiwari, Professor and Chair, Wellcome-Wolfson Institute for Experimental Medicine, QUB, UK & Institute of Molecular Medicine, SDU, Denmark.
03 Mar 2023
IBSE is very pleased to introduce you all to our guest speaker Dr. Suresh Sudarsan. The title of his talk is understanding fermenterphiles by integrating big data with bioprocess development.
22 Feb 2023
We are pleased to announce “Data Science-driven solutions to improve maternal and child health”, a one-day event on 22nd February 2023, organized by IIT Madras and GARBH-Ini (Interdisciplinary Group for Advanced Research on BirtH outcomes - DBT INdia Initiative), at The Terrace, IIT Madras, Chennai.
02 Mar 2023
IBSE is pleased to invite you to a hands-on workshop on Synthetic Biology. Synthetic Biology is about looking at biological systems through the lens and formalisms of engineering. This results in a phenomenal tool to gain fundamental insights into the functions and molecular basis of biological phenomena as well as in a suite of technologies for programming biological objects at user’s will, from cells to new materials. The course will address such a double-sided ability of SynBio (for understanding and for doing) along with its potential not only to transform the health & agricultural sectors but also moving the current oil-based industry into a sustainable bio-based economy.
28 Nov 2022
The workshop is aimed at providing exposure to one of the biggest healthcare challenge of antimicrobial resistance the world is facing today with specific focus on how to address the same. The workshop structure includes utilizing pan-genomics and AI/ML driven approaches to identify potential drug targets for most critical pathogens. It is also important to note that microbes undergo rapid evolution when exposed to antibiotics and therefore the challenge is to understand a dynamically evolving system and identify its strengths and weaknesses to devise novel strategies like identification of previously unknown target space based on new mechanisms of bacterial survival under antibiotic exposure and use this knowledge to scan unexplored chemical space.
31 Oct 2022
During the 3-day meeting, we will discuss microbial omics approaches associated with human, gut, and environment where computational advancements have been made to analyze biological “big data”. Microbial omics and its translational aspects will be correlated with new biotechnological discovery. In addition, renowned scientists will be presenting how the microbial omics technologies are enabling for the safe exploration of future space missions with respect to astrobiology and planetary protection. The study of microbial communities or microbiomes has widespread applications, from human health, agriculture and animal husbandry to waste treatment, bioremediation and environmental health.
21 Jun 2022
Prof. Vijay Tiwari, Group Head and Reader, The Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast will deliver the Tenth IBSE colloquium on June 21, 2022. The title of his talk is “Deciphering Disease Mechanisms through Functional Genomics”. This colloquium will be a hybrid event happening both online and offline. Attendees can either attend the talk in-person at CRC 302, IIT Madras (or) attend via Zoom. Register here Brief biosketsch Prof.
01 Feb 2022
We seek to bring biomedical scientists, computational biologists, and data scientists to present and discuss the latest developments in various omics technologies transforming clinical and translational research through this symposium. A key focus will be novel techniques, methods and algorithms to dissect omics data at multiple levels, enabling a deeper understanding of complex human diseases. The symposium seeks to bring together about 25 leading scientists from India and abroad and provide an opportunity for at least 100 early career researchers to participate.
04 Jan 2022
We seek to bring scientists working in HPC, and also those from disciplines that apply HPC, particularly to AI & biology, to present and discuss the latest developments in HPC that are transforming research across disciplines. A key focus will be a pedagogical touch, to cater to a number of students and early career researchers, to pique their interest. The symposium seeks to bring together about 20 leading scientists from India and abroad, and provide an opportunity for at least 100 early career researchers to participate.
09 Dec 2021
Prof. James Glazier, Professor of Physics, Adjunct Professor of Informatics and Biology and Director of the Biocomplexity Institute at Indiana University, USA will deliver the Ninth IBSE colloquium on December 9, 2021. The title of his talk is “From Network Models to Multiscale Virtual-Tissue Computer Simulations of Development, Homeostasis and Disease”. Watch the livestream of the colloquium on YouTube.
15 Sep 2021
Abstract Are DNA variants bugs or features? The recent increase in accessibility of sequencing has facilitated a rise in precision medicine efforts focused on the interpretation of the effects of individual-specific genome variation. Evaluation of variants in terms of their functional contributions to molecular mechanisms holds promise for both a better understanding of the said mechanisms, as well as of drivers of disease and drug discovery/optimization. Many computational tools have been developed to evaluate the functional effects of non-synonymous variants, but most are not informative of the type of effect they annotate.
10 Mar 2021
IBSE is very pleased to introduce you all to our guest speaker Dr. Sabarinathan Radhakrishnan. The title of his presentation will be: “Understanding cancer evolution through genomics data science” Dr. Sabarinathan Radhakrishnan is a faculty at the National Centre for Biological Sciences (NCBS), Bangalore; and his lab is interested in the application of computational and functional genomics approaches to study the genetic and molecular basis of cancer. He obtained his PhD in Bioinformatics from the University of Copenhagen, Denmark and then did his post-doctoral training in the area of computational cancer genomics at the Institute for Research in Biomedicine (IRB), Barcelona.
09 Feb 2021
The Seventh Colloquium of the IBSE will be held on 9th February 2021. Dr. Manimozhiyan Arumugam, Group Leader and Associate Professor at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen has kindly agreed to be our guest speaker. Register here. Biography of the speaker : Dr. Manimozhiyan Arumugam leads the “Microbiome Systems Biology” research group that investigates how health and diseases are influenced by our gut microbiome; how the gut microbiome interacts with the host and environmental factors; and how we can therapeutically modulate the gut microbiome to improve health.
31 Jan 2021
IIT Madras Researchers are poring over millions of data points to see why babies are delivered prematurely in India. Work from IBSE was featured in The Hindu BusinessLine.
12 Jan 2021
To be held on 12 January 2021 from 2.30 pm. REGISTRATION
Venue: Online
| 1430 - 1455 | Microbial community analyses for metabolite production | Maziya Ibrahim, Post Doctoral Fellow |
| 1455 - 1520 | Understanding the patterns of co-occurrence of somatic mutations in cancer | Samyugdha V M, MS Scholar |
| 1520 - 1545 | Multi-objective optimization for co-production of metabolites | Lavanya Raajaraam, PhD Scholar |
| 1545 - 1610 | A method for identification of feature contribution to classes using multiple equally discriminatory subsets of features | Malvika Sudhakar, PhD Scholar |
| 1610 - 1635 | Estimation of gestational age in the second and third trimesters for participants in the Garbhini cohort | Nikhita Damaraju, Dual Degree student |
05 Jan 2021
IBSE-Queen’s MiniSymposium will be held on 5 January 2021 by online from 3.30 pm - 5.50 pm.
Venue: Online
| 1530 - 1535 | Introduction to IBSE | Karthik Raman, IBSE |
| 1535 - 1555 | Towards an AI for radical uncertainty | Dr Jose Sousa, Queen’s University |
| 1555 - 1615 | Deep learning applied to mobile malware detection by analysing executable code | Dr Niall McLaughlin, Queen’s University |
| 1615 - 1635 | Unlocking genomics for predicting therapy response in breast cancer | Mr Ryan Lusby, Queen’s University |
| 1635 - 1655 | Cross-omic Deep Learning Networks for Identifying Disease Biomarkers and Pathways | Aditya Jeevannavar, IBSE |
| 1655 - 1715 | Reinforcement Learning to design clinical trials | Senthamizhan V, IBSE |
| 1715 - 1735 | Sequence neighbourhoods enable reliable prediction of pathogenic mutations in cancer genomes | Shayantan Banerjee, IBSE |
| 1735 - 1750 | Discussion |
15 Dec 2020
IBSE is very pleased to introduce you all to our guest speaker Dr. Sushmita Paul who gave the 14th IBSE Seminar on Tuesday, 15th December 2020 at 3.30 pm Online. Dr. Sushmita Paul is an Assistant Professor at the Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur. The title of her talk was A Feature Weighting-Assisted Approach for Cancer Subtypes Identification from Paired Expression profiles.
28 Nov 2020
To be held on 28 November 2020 from 10.00 am. REGISTRATION (Only for IIT Madras students and staff.)
Venue: Online
| 1000 - 1100 | Python for Beginners | Pavan Ravishankar, MS Scholar |
| 1100 - 1200 | Git Fundamentals | Senthamizhan V, Post Baccalaureate Fellow |
20 Nov 2020
To be held on 20 November 2020 from 2.30 pm. REGISTRATION
Venue: Online
| 1430 - 1455 | picCASO: Cellular Automaton for Spatial Organization | Sankalpa Venkatraghavan and Sathvik Anantakrishnan, Dual Degree students |
| 1455 - 1520 | Systems biology of Diabetes-Helminths interaction study | Nilesh Anantha Subramanian, Post Baccalaureate Fellow |
| 1520 - 1545 | Computational analysis of ocular microbiome in bacterial keratitis infected eye | K B Dinesh Kumar, MS student |
| 1545 - 1610 | Localgini: A novel Thresholding Algorithm for Developing Context-specific Models from Omics Data | Pavan Kumar S, MTech student |
| 1610 - 1635 | Metabolic network analysis provides insight into microbial interactions of Klebsiella pneumoniae accompanying distinctive microbial modules on the ISS | Rachita K. Kumar, Post Baccalaureate Fellow |
20 Aug 2020
The Sixth Colloquium of the IBSE will be held on 20th August 2020. Prof. Partha Majumder, Distinguished Professor, National Institute of Biomedical Genomics (NIBMG), Kolkata, India has kindly agreed to be our guest speaker. Register here. Biography of the speaker : Partha Majumder is the founder of the National Institute of Biomedical Genomics, and concurrently a Professor of the Indian Statistical Institute, Kolkata, India. His scientific contributions to human and population genetics span a vast range; from structure and evolution of human populations to genomics of diseases and development of statistical methods for genomic analyses.
06 Aug 2020
IIT Madras Researchers have designed novel algorithm to enhance plant productivity. Recent work from IBSE was featured in India Science Wire .
12 Aug 2020
IITM-NUS workshop to be held on 12 August 2020 from 2.00 pm.
Venue: Online
| 1400 - 1405 | Introduction | Dr. Himanshu Sinha, Department of Biotechnology, IIT Madras |
| 1405 - 1425 | Voice-based Cancer Genomics with Melvin | Dr Jason J. Pitt, Principal Investigator, Cancer Science Institute of Singapore |
| 1425 - 1440 | Effect of neighbourhood flanking sequences on the pathogenicity of cancer-causing mutations | Shayantan Banerjee, MS Scholar, Department of Biotechnology, IIT Madras |
| 1440 - 1455 | The Role of High RAD51 Expression on Genomic Instability | Stefanus Lie, PhD Student, Cancer Science Institute of Singapore |
| 1455 - 1510 | Analysing Alzheimer’s brain coexpression network using cellular deconvolution | Kailash BP, Dual Degree Student, Department of Biotechnology, IIT Madras |
| 1510 - 1530 | Prognostic relevance of MYC BCL2 and BCL6 in diffuse large B-cell lymphoma; revealed by multiplex IHC and transcriptomic analyses | Dr Anand Jeyasekharan, Principal Investigator, Cancer Science Institute of Singapore |
| 1530 - 1545 | Ratio-metric features for identification of novel tumour suppressor genes and oncogenes | Malvika Sudhakar, PhD Student, Department of Biotechnology, IIT Madras |
| 1545 - 1600 | Copy-number Based Analysis in Breast Cancer | Hannan Wong, PhD Student, Cancer Science Institute of Singapore |
| 1600 - 1615 | Impact of Helminth on Type 2 diabetes; A disease-disease interaction study | Dr Philge Philip, Senior Project Officer, IBSE & RBCDSAI, IIT Madras |
| 1615 - 1630 | Enabling Economical Genome Analyses through Optimization and Scalable Workflows | Akila Perera, Software Engineer, Cancer Science Institute of Singapore |
| 1635 - 1645 | Mir-34b in cervical cancer | Ashley Xavier, Undergraduate Student, Department of Biotechnology, IIT Madras |
| 1645 - 1650 | Closing remarks | Dr. Karthik Raman, Department of Biotechnology, IIT Madras |
07 Jul 2020
Scientists identify 21 microbes that help build a healthy gut. Recent work from IBSE was featured in The Hindu Businessline.
13 Jun 2020
IIT Madras study reveals metabolism of key gut microbiota. Recent work from IBSE was featured in The Hindu .
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] (https://www.indiatoday.in/education-today/news/story/iits-jnu-to-collaborate-with-german-university-for-bio-big-data-science-project-1499301-2019-04-11), 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/] (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 (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.
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 |