Centre for Brain Research, IISc

Faculty

Bratati Kahali's Lab

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The success of the Human Genome Project has ushered in a new era of biology in which we can use large-scale, high-throughput genomic data to investigate how DNA sequence variants contribute to complex human diseases. The research in my group engages sophisticated statistical methodology and the use of high performance computing resources for novel genetics analyses and methods development. The overarching goal of my laboratory is to develop and evaluate biological hypotheses for answering how human genetic variation can affect a wide range of practical issues – for example, why (a) humans have different genetic susceptibility to complex diseases, and (b) find genetic and structural variants that associate with the disease of interest, (c) unravel the physiological pathways relevant to disease being studied, delve deeper into intricate cross-phenotype associations and (d) how evolution have shaped these genomic characteristics; using integrative bioinformatics, statistical, and computational methods.

Bratati has been leading large scale genome wide association studies and trans-ethnic meta-analysis as part of collaboration within the GOLD (Genetics of Lipid Diseases) consortium and an active working group member of the Genetic Investigation of Anthropometric Traits (GIANT) consortium.

 

Lab News
  1. Dr. Kahali was awarded the Ramalingaswami Fellowship 2016-2017 by Department of Biotechnology, Government of India.

  2. Dr. Kahali was awarded the Science and Engineering Research Board Early Career Fellow 2019 by Department of Science and Technology, Government of India.

  3. Lab member Mr. Abhay Gupta (undergraduate at IISc) was awarded the Travel fellowship for presenting and participating in Alzheimer’s Association International Conference, July 14-18, 2019 at Los Angeles, USA.

Research

The technologies from genome wide association studies to whole genome sequencing using Next Generation Sequencing platforms are the ones we rely upon to identify rare and common genetic variants responsible for complex genetic diseases. My group’s research is aimed to better understand the shared genetic architecture between metabolic disorders and of psychiatric and neurodegenerative disorders, including genetic overlap between different disorders (i.e. pleiotropy) and genetic and phenotypic heterogeneity within disorders in Indian population.

The prevalence of obesity has increased steadily over the past 30 years, causing serious metabolic and neurological health problems and also imposing a substantial economic burden on societies. By identifying genetic variants that influence the risk of obesity and related neurological disorders, we aim to gain insight into the biological pathways through which these genes and their proteins control body weight and increase risk of neurodegenerative disease. In addition, we will examine whether a healthy lifestyle can reduce one’s genetic susceptibility. Because the general Indian population does not display obesity in proportions comparable to the western countries, measures of central obesity are also overlooked as being important indicators for related health concerns in India. The results from our research will be able to bridge this gap in information. Succeeding steps would ensure translating this information into better ways to diagnose, manage, and treat these conditions in the future.

After initial successes, a related goal is to integrate methylation, RNA expression and other -omics data in order to develop more powerful genomics-based predictors that incorporate variation due to disease-relevant environmental exposures.

People

Bratati KahaliBratati Kahali, PhD
Assistant Professor at the Centre for Brain Research
Bratati obtained her PhD at the Bose Institute (Kolkata, Jadavpur University, INDIA) in 2011 working at the Centre of Excellence in Bioinformatics. She was a postdoctoral fellow (2012-2016) at the University of Michigan Medical School (Ann Arbor, MI, USA), jointly affiliated with the Department of Internal Medicine (Gastroenterology division), and the Department of Computational Medicine and Bioinformatics. There, her research mainly focused on the identification of genetic loci for human obesity and non alcoholic fatty liver disease.
In September 2016, she joined as a faculty member in Centre for Brain Research at the Indian Institute of Science.

 
Present Lab Members

AbhishekAbhishek Panda
M.Tech CSE specialization in cloud computing,
School of Computing Science and Engineering,
Vellore Institute of Technology
Designation: Project Associate
Currently working on "Benchmarking computational frameworks on high throughput sequencing data"




KrithikaKrithika Subramanian
B.Tech, Bioinformatics
Department of Bioinformatics, Bharathidasan University, Tiruchirappalli
Designation: Project Assistant
Currently working on "Analyzing Human Whole Genome Sequencing(WGS) data"






ShreyaShreya Jha
B.E,Biotechnology
Department of Biotechnology, PES Institute of Technology, Bangalore
Designation: Project Assistant
Currently working on "Detecting signatures of selections in Human populations and how they shape disease traits"






AbhayAbhay Gupta
Bachelor of Science (Research) Program, 4th year Physics major student,
IISc, Bangalore
Currently working on "Optimizing Machine Learning Algorithms for Cognitive Impairment Classification"






DikshaDiksha Chaudhary
Designation: PhD Student








Former Lab Members

GreesmaGreeshma Thulasi
MSc. Computational Biology
Department of Computational Biology and Bioinformatics, University of Kerala , Karyavattom, Thiruvananthapuram
Integrative Computational Analysis of Complex Human Diseases





Rajesh Kumar MauryaRajesh Kumar Maurya
MSc. Computational Biology
Department of Computational Biology and Bioinformatics, University of Kerala , Karyavattom, Thiruvananthapuram, India
Inferring disease-specific signatures from human Exome sequencing data





ShraddhaShraddha Barke
B.E Electronics Engineering
BITS Pilani K.K.Birla Goa Campus
Computational Genomics of Human Complex Diseases






Sumanth Gowda







Publications

  1. The association between genetically elevated telomere length and risk of cancer and non- neoplastic diseases. Haycock P, Burgess S,...., Bratati Kahali*, ...,et al.
    JAMA Oncology, Feb, 2017.

  2. Rare and low-frequency coding variants alter human adult height. Marouli E, Graff M,..., Bratati Kahali*, ...,et al. paper from GIANT consortium.
    Nature, 542(7640):186-190, 2017.

  3. Genetic studies of body mass index yield new insights for obesity biology.
    Adam E Locke*, Bratati Kahali*, Sonja I Berndt*, Anne E Justice*, Tune H Pers*,……………….,Gonçalo R Abecasis, Lude Franke, Timothy M Frayling, Mark I McCarthy, Peter M Visscher, André Scherag, Cristen J Willer, Michael Boehnke, Karen L Mohlke, Cecilia M Lindgren, Jacques S Beckmann, Inês Barroso, Kari E North§, Erik Ingelsson§, Joel N Hirschhorn§, Ruth JF Loos§, Elizabeth K Speliotes§
    Nature 518(7538), 197-206, 2015.*  Equal contribution

  4. New genetic loci link adipose and insulin biology to body fat distribution.
    Dmitry Shungin, Thomas W Winkler, Damien C Croteau-Chonka, Teresa Ferreira, …, Bratati Kahali, ….., Cristen J Willer, Peter M Visscher, Jian Yang, Joel N Hirschhorn, M Carola Zillikens, Mark I McCarthy, Elizabeth K Speliotes, Kari E North, Caroline S Fox, Inês Barroso, Paul W Frank, Erik Ingelsson, Iris M Heid4, Ruth JF Loos, L Adrienne Cupples, Andrew P Morris, Cecilia M Lindgren, Karen L Mohlke.
    Nature 518(7538), 187-196, 2015.

  5. TM6SF2: Catch-22 in the Fight Against Nonalcoholic Fatty Liver Disease and Cardiovascular Disease?
    Bratati Kahali, Liu YL, Daly AK, Day CP, Anstee QM, Speliotes EK.
    Gastroenterology 148(4), 679-684, 2015.

  6. Population genetic differentiation of height and body mass index across Europe.
    Matthew R. Robinson, Gibran Hemani, ……, Bratati Kahali,……Elizabeth K. Speliotes, Michael E. Goddard, Jian Yang, Peter M. Visscher.
    Nature Genetics 47(11),1357-1362, 2015.

  7. Gene-based meta-analysis of genome-wide association studies implicates new gene regions involved in obesity.
    Sara Hägg, Andrea Ganna, Tonu Esko, Sander W van der Laan, Adam E Locke, Bratati Kahali, Sonja I Berndt, Anne E Justice,, Tune H Pers, Kari E North, Ruth JF Loos, Elizabeth K Speliotes, Timothy M Frayling, Peter M Visscher, David P Strachan, Joel N Hirschhorn, Yudi Pawitan, Erik Ingelsson.
    Human Molecular Genetics 24(23), 6849-6860, 2015.

  8. Characterization of European –ancestry NAFLD Associated Variants in Individuals of African and Hispanic Descent.
    Nicholette D Palmer, Solomon K Musani, Laura M Yerges, Mary F Feitosa, Lawrence F Bielak, Ruben Hernaez, Bratati Kahali, J Jeffrey Carr, Tamara B Harris, Min A Jhun, Sharon LR Kardia, Carl D Langefeld, Thomas H Mosley Jr, Jill M Norris, Albert V Smith, Herman A Taylor, Lynne E Wagenknecht, Jiankang Liu, Ingrid B Borecki, Patricia A Peyser, Elizabeth K Speliotes.
    Hepatology 58(3), 966-975, 2013.
  1. Mendelian randomization study of body mass index and colorectal cancer risk.
    Aaron P. Thrift, Jian Gong, Ulrike Peters, Jenny Chang-Claude, Anja Rudolph, Martha L. Slattery, Andrew T. Chan, Adam E. Locke, Bratati Kahali, …, Michael Hoffmeister, Hermann Brenner, Emily White, Li Hsu, Peter T. Campbell.
    Cancer Epidemiology, Biomarkers & Prevention 24(7), 1024-1031, 2015.

  2. Insights from genome wide association analyses of nonalcoholic fatty liver disease.
    Bratati Kahali, Brian Halligan, Elizabeth K Speliotes.
    Seminars in Liver Disease 35(4), 375-391, 2015.

  3. Disorderness in Escherichia coli proteome: perception of folding fidelity and protein-protein interactions.
    Bratati Kahali, Tapash Chandra Ghosh.
    J Biomol Struct Dyn 31(5), 472-476, 2013.

  4.  Selective constraints in yeast genes with differential expressivity:   Codon pair usage and mRNA stability perspectives.    
    Bratati Kahali *, Shandar Ahmad, Tapash Chandra Ghosh*.  Gene 481, 76-82, 2011.
    *Joint corresponding author

  5.  Protein complex forming ability is favored over the features of    interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks.
    Sandip Chakraborty, Bratati Kahali *, Tapash Chandra Ghosh*. 
    BMC Syst Biol 4:155, 2010.
    *Joint corresponding author

  6. On nucleotide solvent accessibility in RNA structure.
    Singh YH, Andrabi M, Bratati Kahali, Ghosh TC, Mizuguchi K, Kochetov AV, Ahmad S. Gene 463(1-2), 41-48, 2010.

  7. Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network.
    Bratati Kahali, Shandar Ahmad and Tapash Chandra Ghosh.
    Gene 429(1-2), 18-22, 2009.

  8. Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder.

    Baisali Manna, Tanusree Bhattacharya, Bratati Kahali, Tapash Chandra Ghosh. Gene 434(1-2), 50-55, 2009.

  9. Delving deeper into the unexpected correlation between gene expressivity   and codon usage bias of Escherichia coli genome. 
    Bratati Kahali, Surajit Basak and Tapash Chandra Ghosh.
    J Biomol Struct Dyn. 25, 6556-6561, 2008.

  10. Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis.
    Bratati Kahali, Surajit Basak and Tapash Chandra Ghosh.
    Biochemical and Biophysical Research Communications 354, 693-699, 2007.

Book Chapter(s):

  1. Genetic Pleiotropies of Obesity.
    Bratati Kahali and Elizabeth K. Speliotes.
    The Genetics of Obesity, Edited by Dr. Struan Grant.
    SpringerLink ISBN: 978-1-4614-8641-1

  2. Insights into Eukaryotic Interacting Protein Evolution.
    Sandip Chakraborty, Soumita Podder, Bratati Kahali, Tina Begum, Kamalika Sen, and Tapash Chandra Ghosh. (All authors contributed equally).
    Evolutionary Biology - Concepts, Biodiversity, Macroevolution and Genome Evolution.
    Springer-Verlag Berlin Heidelberg. Pontarotti, Pierre (Ed.) 1st Edition., 2011, XV, ISBN 978-3-642-20762-4.

 

Positions

I am looking for highly motivated research assistants, project students and post-doctoral fellows to work on computational genetics projects. Candidates having prior experience with computational work, statistical courses taken during undergraduate and postgraduate training, having programing experience are encouraged to apply.

Interested candidates are requested to contact the principal investigator Dr. Bratati Kahali (bratati@iisc.ac.in; bratatis@gmail.com).

Project Assistant and Post-doctoral position immediately available at Kahali Lab, CBR


Bioinformatics Positions Available
Candidates with programming experience encouraged to apply.
For details Contact PI : Dr. Bratati Kahali
bratati[at]iisc.ac.in ; bratatis[at]gmail.com

Contact

Centre for Brain Research
SID (Innovation centre) complex
Indian Institute of Science (IISc)
Malleswaram 18th Cross
Bangalore-560012
Karnataka, INDIA.

Email: bratati[at]iisc.ac.in; bratatis@gmail.com
Telephone: +91 80 2293 2798