Menu:

Homepage of Neetika Nath

Name

Research Interest

  • Variant identification I like to develop pipeline (workflow) for studing human genetic variation and their signatures associated with a specific disease type.
  • Classification via Machine Learning I like to develop a pipeline (workflow) that includes supervised classification techniques to identify biomarkers from other high dimension clinical datasets like Study of Health in Pomerania Data (SHIP).
  • Microbial communities I am interested in understanding the associations between microbial community with thyroid dysfunction.

Ongoing Research Projects

Discovering association patterns of individual serum Thyrotropin concentrations using machine learning: An example from the Study of Health in Pomerania (SHIP)
Our aim in this project is to predict thyroid dysfunction using machine learning algorithms -- an example from the Study of Health in Pomerania.

Collaboration partners: Prof. Dr. Henry Völzke, Dr. Till Ittermann, Ann-Kristin Becker

Association between microbiome and thyroid dysfunction using SHIP dataset
Our aim in this project is to develop NN predictive model to find important association between thyroid dysfunction and gut microbiomes.

Collaboration partners: Dr. Fabian Frost, Dr. Till Ittermann, Prof. Dr. Stefan Simm, Jan Oldenburg

Radiation-induced DNA-alterations in the genome of human gingiva fibroblasts
Ionizing radiation (IR) such as X-rays is frequently used in medical diagnostics where typically low doses of IR are preferred. While chemotherapy expose patients at a high dose at different fractions of doses. Such exposer of cells could lead to damaging DNA double-strand, if left unrepaired, may compromise cellular functions or survival. Currently, there is still only limited knowledge on the molecular impact of IR exposure on a genome-wide level.

Collaboration partners: Prof. Dr. Harry Scherthan, Dr. Lisa Hagenau, Dr. Stefan Weiss, Ana Tzvetkova, Dr. Lars R Jensen, PD Dr. Matthias Port, Prof. Dr. Andreas W Kuss

INDIRA: INtegrative Data analytIcs for Respiratory syncytial virus risk Assessment
The Respiratory Syncytial Virus (RSV) is the most frequent cause of lower respiratory tract infections among infants. The course and outcome of primary RSV infection are highly variable and the factors controlling severe disease poorly defined. The aim of INDIRA is to investigate the causes that are responsible for different RSV disease progressions among young children.

Collaboration partners: Prof. Dr. Thomas Pietschmann et al.

Microbiome study in wildlings
Aim of this study is to investigate the association between the microbiome markers with wildling mouse.

Collaboration partners: Prof. Dr.Stefan Simm, Christian Nitzsche

microRNA
Investigating the genetic difference between SHAM and TAC Hearth surgery, manuscript preparation

Collaboration partners: Alexander Benkner

Single Cell data
Aim of this project is to investigating single cell data for differentially expression analysis

Collaboration partners: Dr. Cassandra Falckenhayn

Bioinformatics Services

In addition to my research interest, I also perform different bioinformatics services that lies in the following categories.

Using machine learning algorithms to analysis medical data.


Analysing NGS data for different biological question



Formal research/Collaboration Projects

  • Heart Rate Variability and Annotation/Segmentation of the ECG:
    • Collaboration partners: Dr. Marcus Vollmer, Philipp Sodmann
    • AF Classification from a short single lead ECG recording: the PhysioNet/Computing in Cardiology Challenge 2017 (see challenge);
  • Sreening for Leiomyosarcoma | DKSM
    • Collaboration partners: Prof. Dr. Günter Köhler, Dr. Marcus Vollmer
    • development of risk score app to screen for leiomyosarcoma.
  • Differentially expression analysis using transcriptome dataset
    • Collaboration partners: Prof. Dr. Wolfgang Poller
    • Immune system-mediated atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in ApoE-/- mice, Manuscript Accepted 2018.
  • Differentially expression analysis using transcriptome dataset
    • Collaboration partners: Dr. Julia Rüdebusch
    • Investigating the genetic difference between SHAM and TAC Hearth surgery, Manuscript accepted 2020.
  • Differentially expression analysis using transcriptome dataset
    • Collaboration partners: Prof. Dr. Nicole Endlich
    • Investigating the genetic difference between SHAM and TAC Hearth surgery,manuscript accepted 2018.

  • Publications

    • Julia Rüdebusch, Alexander Benkner, Neetika Nath, Lina Fleuch, Lars Kaderali, Karina Grube, Karin Klingel, Gertrud Eckstein, Thomas Meitinger, Jens Fielitz, Stephan B Felix
    Stimulation of soluble guanylate cyclase by riociguat attenuates heart failure and pathological cardiac remodelling British Journal of Pharmacology; 2020; doi: 10.1111/bph.15333. Epub ahead of print. PMID: 33247945.

    Neetika Nath, Lisa Hagenau, Stefan Weiss, Ana Tzvetkova, Lars R Jensen, Lars Kaderali, Matthias Port, Harry Scherthan, Andreas W Kuss
    Ionizing Radiation Alters the Transition/Transversion Ratio in the Exome of Human Gingiva Fibroblasts Health Physics; 2020; doi: 10.1097/HP.0000000000001251

    Neetika Nath, Lisa Hagenau, Stefan Weiss, Ana Tzvetkova, Lars R Jensen, Lars Kaderali, Matthias Port, Harry Scherthan, Andreas W Kuss
    Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts International Journal of Molecular Sciences; 2020; https://doi.org/10.3390/ijms21165778

    Günter Köhler, Marcus Vollmer, Neetika Nath, Philipp-Andreas Hessler, Katarina Dennis, Angela Lehr, Martina Köller, Christine Riechmann, Helena Bralo, Dominika Trojnarska, Hanka Lehnhoff, Johann Krichbaum, Manfred Krichbaum, Katja Evert, Matthias Evert, Marek Zygmunt, Lars Kaderali
    Benign uterine mass discrimination from leiomyosarcoma by a preoperative risk score: a multicenter cohort study Archives of Gynecology and Obstetrics; 2019; https://doi.org/10.1007/s00404-019-05344-0

    Julia Rüdebusch, Alexander Benkner, Neetika Nath, L Kaderali, K Klingel, G Eckstein, T Meitinger, J Fielitz, K Grube, SB Felix
    P1614 Soluble guanylate cyclase as a therapeutic target in heart failure: myocardial gene expression in response to sGC stimulation in pressure overload European Heart Journal; 2019; Vol 40; https://doi.org/10.1093/eurheartj/ehz748.0373

    Marcus Vollmer, Philipp Sodmann, Leonard Caanitz, Neetika Nath, Lars Kaderali
    A Convolutional Neural Network for ECG Annotation as the Basis for the Classification of Cardiac Rhythms Ulmer Informatik-Berichte, 2019

    Martina Gast, Bernhard H Rauch, Shinichi Nakagawa, Arash Haghikia, Andrzej Jasina, Jan Haas, Neetika Nath, Lars Jensen, Andrea Stroux, Andreas Böhm, Julian Friebel, Ursula Rauch, Carsten Skurk, Stefan Blankenberg, Tanja Zeller, Kannanganattu V Prasanth, Benjamin Meder, Andreas Kuss, Ulf Landmesser, Wolfgang Poller
    Immune system-mediated atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in ApoE-/- mice. Cardiovascular Research; 115(2):302-314. doi: 10.1093/cvr/cvy202. PMID: 30101304.

    Neetika Nath, Jennifer Esche, Jessica Müller, Lars R. Jensen, Matthias Port, Mario Stanke, Lars Kaderali, Harry Scherthan, Andreas W. Kuss
    Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva Fibroblasts. Health physics; 2018; Vol 115 doi: 10.1097/HP.0000000000000880

    Nicole Endlich, Tim Lange, Jana Kuhn, Paul Klemm, Ahmed M. Kotb, Florian Siegerist, Frances Kindt, Maja T. Lindenmeyer, Clemens D. Cohen, Andreas W. Kuss, Neetika Nath, Rainer Rettig, Uwe Lendeckel, Uwe Zimmermann, Kerstin Amann, Sylvia Stracke, Karlhans Endlich BDNF: mRNA expression in urine cells of patients with chronic kidney disease and its role in kidney function
    Journal of Cellular and Molecular Medicine; 2018 Nov;22(11):5265-5277. doi: 10.1111/jcmm.13762. Epub 2018 Aug 21.

    Marcus Vollmer, Philipp Sodmann, Leonard Caanitz, Neetika Nath, Lars Kaderali
    Can Supervised Learning Be Used to Classify Cardiac Rhythms?
    Computing in Cardiology (CinC), 2017; Vol 44; DOI:10.22489/CinC.2017.347-176

    Matthias Rath, Stefanie Spiegler, Neetika Nath, Konrad Schwefel, Nataliya Di Donato, Johannes Gerber, G Christoph Korenke, Yorck Hellenbroich, Ute Hehr, Stephanie Gross, Ulrich Sure, Barbara Zoll, Eberhard Gilberg, Lars Kaderali, Ute Felbor
    Constitutional de novo and postzygotic mutations in isolated cases of cerebral cavernous malformations
    Molecular Genetics and Genomic Medicine, 2016; 5(1):21-27. doi: 10.1002/mgg3.256. PMID: 28116327; PMCID: PMC5241208..

    Thomas Wolf, Vladimir Shelest, Neetika Nath, Ekaterina Shelest
    CASSIS and SMIPS: Promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes
    Bioinformatics, 2016, 15;32(8):1138-43. doi: 10.1093/bioinformatics/btv713. Epub 2015 Dec 9. PMID: 26656005; PMCID: PMC4824125.713

    Neetika Nath, John B. O. Mitchell, Gustavo Caetano-Anolles
    The Natural History of Biocatalytic Mechanisms
    PLoS Computational Biology; 2014;10(5):e1003642; https://doi.org/10.1371/journal.pcbi.1003642

    James L McDonagh, Neetika Nath, Luna De Ferrari, Tanja van Mourik, John BO Mitchell
    Uniting Cheminformatics and Chemical Theory To Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules
    Journal of chemical information and modeling; 2014, 54 (3), pp 844-856;DOI: 10.1021/ci4005805

    Lazaros Mavridis, Neetika Nath, John BO Mitchell
    PFClust: a novel parameter free clustering algorithm
    BMC Bioinformatics; 2013; 14:213;DOI:10.1186/1471-2105-14-213

    Rosanna G Alderson, Luna De Ferrari, Lazaros Mavridis, James L McDonagh, John BO Mitchell, Neetika Nath
    Enzyme Informatics.
    Current topics in medicinal chemistry. 2012;12(17):1911-1923.

    Neetika Nath, John BO Mitchel
    Is EC class predictable from reaction mechanism?
    BMC bioinformatics; 2012; 13:60;DOI:10.1186/1471-2105-13-60

    Other things I like to do

    Teaching Experience

    Student Projects

    Talks

    Detection of Radiation-Induced Alterations in the Transcriptome and Exome of Human Gingiva Fibroblasts

    10 April 2018, Barcelona, Spain Next Generation Sequencing Conference 2018 (NGS 2018)

    Chicken Soup of Indian Women!

    04 November 2014, Business and Professional Women Germany - Club Erfurt e. V., Germany

    Understanding enzyme biocatalytic mechanisms and its evolution: bioinformatics point of view

    02 July 2014, Hans-Knoll-Institute (HKI), Jena, Germany

    Classification of Enzymes via Machine Learning Approaches

    10 November 2011, Department of Crop Sciences, University of Illinois, USA

    Poster Presentation

    Lipoinformatics – machine learning approach to study lipid profiless Nath N, Klose C, Gerl M et al. [version 1; not peer reviewed]. F1000Research 2016, 5:2144 (poster) (doi: 10.7490/f1000research.1112979.1)

    The natural history of biocatalytic mechanisms

    International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB) 2013

    Quantitative Global Analysis of Enzyme Reaction Mechanisms

    The Seventh International Workshop on Machine Learning in Systems Biology (MLSB13) in Berlin, Germany 2013

    Uniting Cheminformatics and Chemical Theory to Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

    Advancing Computational Chemistry in Scotland, University of St Andrews, UK 2013

    Global Analysis of Enzyme Reaction Mechanisms

    Sixth International Workshop on Machine Learning in Systems Biology held in Basel, Switzerland 2012

    Classification of Enzymes via Machine Learning Approaches

    UseR! University of Warwick, Coventry, UK 2011