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
Monograph published by Aarthi Ravikrishnan / Karthik Raman
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.

Seminar by Dr. Adam Rubin
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.

Please be advised that the entire application process is strictly online.

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)
Indian Institute of Technology Madras

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

Recent work from IBSE was featured in The Hindu Business Line. This article refers to the recent paper published by Karthik Raman and Sayan Ranu, in Bioinformatics.

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

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
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