\ Rajiv Gandhi Centre for Biotechnology

Profile

Research

Publications

Team

Alumni

Shijulal Nelson Sathi, PhD

DST-INSPIRE faculty, Computational Biology & Bioinformatics, BIC Campus, Kinfra

+91-471-2781-236

shijulalns@rgcb.res.in

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Shijulal Nelson Sathi, PhD

DST-INSPIRE faculty, Computational Biology & Bioinformatics, BIC Campus, Kinfra

+91-471-2781-236

shijulalns@rgcb.res.in

  • Profile

    • 2009-2013: PhD (Dr. rer. nat.) Heinrich-Heine-University Düsseldorf, Germany
    • 2004-2006: MSc in Bioinformatics, Mahatma Gandhi University, India
    • 2001-2004: BSc in Computer Science, Kerala University, India
    • 2015-2016: Postdoc position at the Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany (Supervisor Prof. Dr. William F. Martin)
    • 2014 (Jan-Dec): Postdoc position at Christian-Albrechts-University of Kiel, Germany (Supervisor Prof. Dr. Tal Dagan)
    • 2009-2013: PhD stipend at the Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany (Supervisor Prof. Dr. William F. Martin)
    • 2007-2008: Research Assistant, Institute of Biomedical Sciences (IBMS), Academia Sinica, Taipei, Taiwan (Supervisor: Dr. Ming-Jing Hwang)
    • 2006-2007: Project Trainee & Research assistant, Center for Cellular and Molecular Biology (CCMB), Hyderabad, India (Supervisor: Prof. Somdatta Sinha)
    • Young researcher startup grant [SFF - F 2015/946-7] - Strategic Research Fund (SFF), Heinrich-Heine University, Germany - 83,998 Euro for 2 years.
    • Karl-Arnold Pries, Outstanding Young Researcher Award, North Rhine-Westphalia Academy of Sciences Humanities and the Arts, May 11, 2016, Düsseldorf, Germany (10,000 EUR)
    • Swiss Institute of Bioinformatics (SIB) International Young Bioinformatician Award 2015, Laureate announced during 12th [BC]2 – the Basel Computational Biology Conference, June 08-10, 2015, Basel, Switzerland  (10,000 CHF)
    • Travel grant ,“Kick-off Conference: Life? – A New Funding Initiative Introduces Itself”, Dec 17-18, 2015, Hannover, Germany (200 Euro)
    • Young Investigator Travel Award, SMBE 2015, Annual Meeting of Society for Molecular Biology and Evolution, July 12-17, Vienna, Austria (1500 Euro)
    • International Travel Award, Symbioses becoming permanent: the origins and evolutionary trajectories of organelles. Sackler Symposium of the National Academy of Sciences of the USA. October 16-17, 2014, Irvine, CA (300 Dollar)
    • First prize, poster presentation - SMBE satellite meeting on reticulated microbial evolution April 27 - 30, 2014, Kiel, Germany
    • International summer school fellowship (FIND project 2007) at the European Molecular Biology Laboratory (EMBL-EBI), Cambridge, UK
    • Summer traineeship (2006) at Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
    • 2010-till date Society for Molecular Biology and Evolution (SMBE)
    • Genome Biology and Evolution
    • Microbial Genomics
    • Bioinformatics
    • International Journal of Biotechnology and Bioengineering (2015-)
  • Research

    Evolutionary Biology unravels important findings that strike the attention of scientists from all disciplines, as well as, the public in general. By focusing on microbial evolution, the emphasis of my research will be on the evolutionary history of existing pathogenic and non-pathogenic microbes whose genomes are completely sequenced. Currently, microbiologists accept the fact that genome evolution is heavily influenced by lateral gene transfer (LGT or HGT), an important evolutionary process that allows the spread of innovations between closely and distantly related organisms. With a major focus on LGTs, my research focus is on better understanding of the overall process of microbial genome evolution and origin, adaptation, transmission and evolution of pathogenicity and antibiotic resistance among microbes in a wide variety of environments.

    By using enormous amount of publically available sequence data and combination of phylogenomic and network approaches, I would like to address the following questions:

    • What is the relative contribution of (LGT) and vertical inheritance during microbial genome evolution?
    • LGTs are largely responsible for antibiotic-resistant infections worldwide, what is the impact of LGTs in evolution of antibiotic resistance in pathogenic bacteria? 
    • Where do these bacterial virulent genes come from?  What are the common mechanisms of LGTs in pathogenic bacteria?
    • What novel approaches to preventing or treating antibiotic resistance can be derived from knowledge of ecology and evolutionary biology?

    The groundbreaking nature of the research is that I will present and employ a fundamentally new and far more suitable mathematical and graphical vehicle for the study of microbial genome evolution that captures the dynamics of gene distributions across genomes.

    • 2016-2020: DST INSPIRE young faculty award [DST/INSPIRE/04/2015/002935] – Department of Science and Technology, India - 700,000 INR per year.
  • Publications

    Peer Reviewed

    1. Martin WF, Roettger M, Ku C, Garg S, Nelson-Sathi S, Landan G (2016) Late mitochondrial origin is an artefact. Genome Biology and Evolution. (In press)
    2. Weiss M, Sousa F, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF (2016) The physiology and habitat of LUCA. Nature Microbiology 1: 16116.
    3. Sousa F, Nelson-Sathi S, Martin W (2016) The ancient anaerobic core: Gene content and the nature of the earliest prokaryotes. BBA Bioenergetics 1857:1027-38.
    4. Nelson-Sathi S, Martin WF (2015) The origin of a killer revealed by Bronze Age Yersinia genomes.  Cell Host Microbe 18:513-514.
    5. Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF (2015) Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524:427-432.
    6. Nelson-Sathi S*, Ku C*, Roettger M, Garg S, Hazkani-Covo E, Martin WF (2015) Endosymbiotic gene transfer from prokaryotic pangenomes: inherited chimaerism in eukaryotes. Proc Natl Acad Sci USA 112:10139-10146.
      *Equal contribution
    7. Nelson-Sathi S, Sousa F, Röttger M, Lozada-Chávez N, Tiergart T, Janssen  A, Bryant D, Landan  G, Schönheit P, Siebers B, McInerney JO, Martin WF (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77-80.
      Featured in Research Highlights at Nature Rev Microbiol 12, 793 (2014)
    8. Ku C, Roettger M, Zimorski V, Nelson-Sathi S, Sousa FL, Martin WF (2014) Plastid origin: Who, when, and why? Acta Soc Bot Poln 83:281–289.
    9. List J-M, Nelson-Sathi S, Geisler H, Martin W (2014) Networks of lexical borrowing and lateral gene transfer in language and genome evolution. BioEssays 36:141-150. 
    10. List J-M, Nelson-Sathi S, Martin WF, Geissler H (2014) Using phylogenetic networks to model Chinese dialect history. Language Dynamics and Change 4:222–252.
    11. Nelson-Sathi S, Popa O, List J-M, Geisler H, Martin WF, Dagan T (2013) Reconstructing the lateral component of language history and genome evolution using network approaches.In: Classification and Evolution in Biology, Linguistics and the History of Science. Concepts – Methods – Visualization, eds Fangerau H, Geisler H, Halling T, Martin W (Steiner, Stuttgart) pp. 163–180.
    12. Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IAC, Allen, JF,  Lane N,  Martin WF (2013) Early bioenergetic evolution. Phil Trans Roy Soc Lond B  368:20130088.
    13. Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF (2012) Acquisition of 1,000 eubacterial genes physiologically  transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci USA 109:20537-20542.
    14. Nelson-Sathi S, List JM, Geisler H, Fangerau H, Gray RD, Martin W, Dagan T (2010) Networks reveal abundant hidden borrowing in the evolution of Indo-European languages. Proc Roy Soc Lond B 278:1794-1803.
      Featured in Research Highlights at Nature 468:735 (2010)
    1. National Institute of Plant Genome Research (NIPGR), New Delhi, 09 Dec 2015
    2. School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 08 Dec, 2015 
    3. BMFZ Meeting in Düsseldorf, Current Concepts in Microbiome Research, 12-13 Nov, 2015
    4. Archaea: Ecology, Metabolism & Molecular Biology, Gordon Research Conference, July 26 – 31, 2015, Sunday River in Newry, ME, USA
    5. Evolution 2015, Joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB) and the American Society of Naturalists (ASN), June 26-30, 2015, Guarujá, Brazil (1,500 participants)
    6.  [BC2] Basel Computational Biology Conference, 7-10 June 2015, Basel, Switzerland
    7. Horizontal DNA transfer spurring evolution, German Genetics Society spring academy meeting, May 15-17, 2015, Wittenberg, Germany
    8. E-Norm lecture series- Networks, Heinrich-Heine University, July 03 2014, Düsseldorf, Germany
    9. Bridging Disciplines: Evolution and Classification in Biology, Linguistics and the History of Sciences, June 24-26, 2011, Ulm University, Germany
    10. An Interdisciplinary Workshop, Schloss Mickeln, June 11-12, 2009, Düsseldorf, Germany 
  • Team


    Jiffy John, Ph.D. Research Scholar

    Microbes acquired a significant proportion of their genetic material through a process called Lateral or Horizontal Gene Transfer (HGT/LGT). Emergence of antibiotic resistance and novel infectious diseases often results from bacterial virulence mechanisms that can be newly acquired, for example in the form of pathogenicity islands, via LGT. By using enormous amount of publically available sequence data and combination of phylogenomic and network approaches, I am studying the impact of LGTs in evolution of antibiotic resistance in pathogenic bacteria.

    Syed Khaja Mohieddin
    Syed Khaja Mohieddin

    Jiffy John, Ph.D. Research Scholar

    Microbes acquired a significant proportion of their genetic material through a process called Lateral or Horizontal Gene Transfer (HGT/LGT). Emergence of antibiotic resistance and novel infectious diseases often results from bacterial virulence mechanisms that can be newly acquired, for example in the form of pathogenicity islands, via LGT. By using enormous amount of publically available sequence data and combination of phylogenomic and network approaches, I am studying the impact of LGTs in evolution of antibiotic resistance in pathogenic bacteria.

  • Alumni