Resume

Name: Payam Emami Khoonsari

Email: payam.emami[at]scilifelab.se

Address: Science For Life Laboratory, Tomtebodavägen 23A, Solna

SUMMARY

Bioinformatician with over six years of hands-on experience with large scale data processing, mass spectrometry-based proteomics/metabolomics, machine learning, statistics, and cloud computing.


Payam received his Ph.D. in medical bioinformatics from the Uppsala University in 2017 where he worked on various bioinformatics projects mainly focusing on mass spectrometry (MS)-based proteomics, peptidomics, and metabolomics. The projects ranged from simple label-free proteomics to more sophisticated labeled/unlabelled experiments. In 2015, Payam joined the PhenoMeNal consortium where he worked on a variety of metabolomics projects including cloud-based metabolite identification and quantification tools/workflows.

In 2018, Payam started his Postdoc at Karolinska Institute where he primarily worked on the MS-based identification of intact (neuro)peptides. This includes designing and evaluating computational tools/workflows to facilitate automatic de novo and database-based characterization of intact peptides.


Payam mainly supports start to end pre-processing and statistical analyzing of various MS experiment. He also supports designing computational workflows for analyzing such data. His current research interests are proteomics, peptidomics, metabolomics, tool/workflow development, data integration, cloud-based data analysis, microservices-based architecture, Kubernetes-based infrastructures, Galaxy workflows, and reproducible data analysis.


CURRENT

Bioinformatician at National Bioinformatics Infrastructure Sweden. Primarily works on proteomics/metabolomics data analysis.


EXPERIENCE

  • Postdoctoral researcher at Department of Physiology and Pharmacology in Karolinska Institutet
    • Responsible for peptidomics and metabolomics bioinformatics

January, 2018 to November, 2018

February, 2017 to March, 2017


EDUCATION

PhD, Medical bioinformatics

June, 2013 to December, 2017

Thesis: Proteomics Studies of Subjects with Alzheimer’s Disease and Chronic Pain

M.Sc, Bioinformatics

September, 2011 to January, 2013

Thesis: Identification of genes involved in T-cell differentiation

B.Sc. Computer Software

September, 2008 to July, 2010

Thesis: Implementation and survey of ID3 algorithm

A.S. (Associate’s Degree) Computer

September, 2005 to February, 2008

Thesis: Implementation an application for voice and text chat in the LAN networks


PUBLICATIONS

  • Emami Khoonsari, P., Moreno, P., Bergmann, S., Burman, J., Capuccini, M., Carone, M., Cascante, M., Atauri, P., Dudova, Z., Foguet, C., Gonzalez-Beltran, A., Hankemeier, T., Haug, K., He, S., Herman, S., Johnson, D., Kale, N., Larsson, A., Salek, R., Neumann,S., Peters, K., Pireddu, L., Rocca-Serra, P., Roger, P., Rueedi, R., Ruttkies, C., Sadawi, N., Sansone, S., Schober, D., Selivanov, V., A. Thévenot, E., van Vliet, M., Zanetti, G., Steinbeck, C., Kultima, K., Spjuth, O., 2019. Interoperable and scalable data analysis with microservices: Applications in Metabolomics. Bioinformatics.
  • Herman, S., Niemelä, V., Emami Khoonsari, P., Sundblom, J., Burman, J., Landtblom, A.-M., Spjuth, O., Nyholm, D., Kultima, K., 2019. Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington’s disease subjects. Scientific Reports.
  • Karakitsou, E., Foguet, C., de Atauri, P., Kultima, K., Emami Khoonsari, P., Martins dos Santos, V.A.P., Saccenti, E., Rosato, A., Cascante, M., 2019. Metabolomics in Systems Medicine: an overview of methods and applications. Current Opinion in Systems Biology.
  • Emami Khoonsari, P.., Ossipova, E., Lengqvist, J., Svensson, C.I., Kosek, E., Kadetoff, D., Jakobsson, P.-J., Kultima, K., Lampa, J., 2019a. The human CSF pain proteome. J. Proteomics 190, 67–76.
  • Emami Khoonsari, P., Shevchenko, G., Herman, S., Remnestål, J., Giedraitis, V., Brundin, R., Degerman Gunnarsson, M., Kilander, L., Zetterberg, H., Nilsson, P., Lannfelt, L., Ingelsson, M., Kultima, K., 2019b. Improved Differential Diagnosis of Alzheimer’s Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers. J. Alzheimers. Dis. 67, 639–651.
  • Novella, J.A., Emami Khoonsari, P., Herman, S., Whitenack, D., Capuccini, M., Burman, J., Kultima, K., Spjuth, O., 2019. Container-based bioinformatics with Pachyderm. Bioinformatics 35, 839–846.
  • Peters, K., Bradbury, J., Bergmann, S., Capuccini, M., Cascante, M., de Atauri, P., Ebbels, T.M.D., Foguet, C., Glen, R., Gonzalez-Beltran, A., Günther, U.L., Handakas, E., Hankemeier, T., Haug, K., Herman, S., Holub, P., Izzo, M., Jacob, D., Johnson, D., Jourdan, F., Kale, N., Karaman, I., Khalili, B., Emami Khoonsari, P.., Kultima, K., Lampa, S., Larsson, A., Ludwig, C., Moreno, P., Neumann, S., Novella, J.A., O’Donovan, C., Pearce, J.T.M., Peluso, A., Piras, M.E., Pireddu, L., Reed, M.A.C., Rocca-Serra, P., Roger, P., Rosato, A., Rueedi, R., Ruttkies, C., Sadawi, N., Salek, R.M., Sansone, S.-A., Selivanov, V., Spjuth, O., Schober, D., Thévenot, E.A., Tomasoni, M., van Rijswijk, M., van Vliet, M., Viant, M.R., Weber, R.J.M., Zanetti, G., Steinbeck, C., 2019. PhenoMeNal: processing and analysis of metabolomics data in the cloud. Gigascience 8.
  • Herman, S., Emami Khoonsari, P., Tolf, A., Steinmetz, J., Zetterberg, H., Åkerfeldt, T., Jakobsson, P.-J., Larsson, A., Spjuth, O., Burman, J., Kultima, K., 2018. Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis. Theranostics 8, 4477–4490.
  • Ossipova, E., Emami Khoonsari, P., Lengqvist, J., Kosek, E., Kadetoff, D., -J. Jakobsson, P., Kultima, K., Lampa, J., 2018. AB1064 Exploring cerebrospinal fluid proteome in fibromyalgia. Ann. Rheum. Dis. 77, 1643–1644.
  • Sandor, K., Krishnan, S., Agalave, N.M., Krock, E., Salcido, J.V., Fernandez-Zafra, T., Emami Khoonsari, P.., Svensson, C.I., Kultima, K., 2018. Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice. Neuropeptides 69, 53–59.
  • Spjuth, O., Capuccini, M., Carone, M., Larsson, A., Schaal, W., Novella, J., Di Tommaso, P., Notredame, C., Moreno, P., Emami Khoonsari, P., Herman, S., Kultima, K., Lampa, S., 2018. Approaches for containerized scientific workflows in cloud environments with applications in life science ( No. e27141v1). PeerJ Preprints.
  • Almandoz-Gil, L., Welander, H., Ihse, E., Emami Khoonsari, P., Musunuri, S., Lendel, C., Sigvardson, J., Karlsson, M., Ingelsson, M., Kultima, K., Bergstrom, J., 2017. Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways. Free Radic. Biol. Med. 110, 421–431.
  • Herman, S., Emami Khoonsari, P., Aftab, O., Krishnan, S., Strömbom, E., Larsson, R., Hammerling, U., Spjuth, O., Kultima, K., Gustafsson, M., 2017. Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions. Metabolomics 13, 79.
  • Emami Khoonsari, P., Haggmark, A., Lonnberg, M., Mikus, M., Kilander, L., Lannfelt, L., Bergquist, J., Ingelsson, M., Nilsson, P., Kultima, K., Shevchenko, G., 2016. Analysis of the Cerebrospinal Fluid Proteome in Alzheimer’s Disease. PLoS One 11, e0150672.
  • Emami Khoonsari, P., Musunri, S., Herman, S., Svensson, C.I., Tanum, L., Gordh, T., Kultima, K., n.d. Systematic analysis of the cerebrospinal fluid proteome of fibromyalgia patients. J. Proteomics.
  • Nikitidou, E., Emami Khoonsari, P., Shevchenko, G., Ingelsson, M., Kultima, K., Erlandsson, A., 2017. Increased Release of Apolipoprotein E in Extracellular Vesicles Following Amyloid-β Protofibril Exposure of Neuroglial Co-Cultures. J. Alzheimers. Dis. 60, 305–321.
  • Musunuri., S., Emami Khoonsari, P., Mikus., M., Wetterhall., M., Häggmar., A., Lannfelt., L., Erlandsson., A., Bergquist., J., Ingelsson., M., Shevchenko., G., Nilsson., P., Kultima., K., 2016. Increased levels of extracellular microvesicle markers and decreased levels of endocytic/exocytic Increased levels of extracellular microvesicle markers and decreased levels of endocytic/exocytic” proteins in the Alzheimer’s disease brain”. Journal of Alzheimer’s Disease 54.
  • Lind, A.L., Emami Khoonsari, P., Sjodin, M., Katila, L., Wetterhall, M., Gordh, T., Kultima, K., 2016. Spinal Cord Stimulation Alters Protein Levels in the Cerebrospinal Fluid of Neuropathic Pain Patients: A Proteomic Mass Spectrometric Analysis. Neuromodulation 19, 549–562.
  • Emami Khoonsari, P and Motie, A., “A Comparison of Efficiency and Robustness of ID3 and C4.5 Algorithms Using Dynamic Test and Training Data Sets,” International Journal of Machine Learning and Computing vol. 2, no. 5, pp. 540-543, 2012.

CONFERENCES

2019

  • Kristian Peters, The PhenoMeNal consortium (Pablo Moreno, Payam Emami Khoonsari, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly Selivanov, Etienne A. Thévenot, Michael van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth), Karin Gorzolka, Helge Bruelheide, Steffen Neumann. A PhenoMeNal Workflow to Study the Metabolites Variation in Bryophytes across Seasons. The XXVII Plant & Animal Genome Conference (PAG), January 12-16, San Diego, CA, USA, 2019
  • Marco Capuccini, Anders Larsson, Matteo Carone, Jonathan Alvarsson, Arvid Berg, Staffan Arvidsson Mcshane, Stephanie Herman, Payam Emami Khoonsari, Kim Kultima, Ola Spjuth. Cloud computing and containerization in Big Data analytics with application in life science. The 1st R-CCS International Symposium, Kobe International Conference Center, February 18-19, Kobe, Japan, 2019
  • Martin Ingelsson, Payam Emami Khoonsari, Ganna Shevchenko, Stephanie Herman, Julia Remnestål, Vilmantas Giedraitis, RoseMarie Brundin, Malin Degerman Gunnarsson, Lena Kilander, Henrik Zetterberg, Peter Nilsson, Lars Lannfelt, Kim Kultima. Improved discrimination between healthy control subjects and patients with cognitive decline by integrating ELISA and mass spectrometry-based cerebrospinal fluid biomarkers. AD/PDTM 2019, the 14th​ International Conference on Alzheimer's and Parkinson's Diseases, March 26-31, Lisbon, Portugal, 2019

2018

  • Stephanie herman, Payam Emami Khoonsari, Valter Niemelä, Torbjörn Åkerfeldt, Joachim Burman, Kim Kultima. Clinical metabolomics: The stethoscope for the 21st century? Translational Research - Department of Medical Sciences, November 15, Uppsala, Sverige, 2018
  • Stephanie Herman, Payam Emami Khoonsari, Julia Steinmetz, Henrik Zetterberg, Andreas Tolf, Anders Larsson, Ola Spjuth, Torbjörn Åkerfeldt, Joachim Burman, Kim Kultima. Integration of clinical data, magnetic resonance imaging, and protein and metabolite measurements to enable early diagnosis of secondary progressive multiple sclerosis. Nordic Metabolomics Conference, August 26-28, Örebro, Sverige, 2018
  • Stephanie Herman, Payam Emami Khoonsari, Julia Steinmetz, Henrik Zetterberg, Andreas Tolf, Anders Larsson, Ola Spjuth, Torbjörn Åkerfeldt, Joachim Burman, Kim Kultima. Integrering av MRI data med protein- och metabolit mätningar i cerebrospinalvätska möjliggör tidig identifiering av sekundär progressiv multipel skleros. (Oral). Vårmöte Klinisk kemi, April 24-26, Uppsala, Sverige, 2018
  • Christopher Steinbeck, Payam Emami Khoonsari, Kim Kultima, Ola Spjuth on behalf of the PhenoMeNal consortium. Interoperable and scalable data analysis in metabolomics. (Oral). 1st International Conference on Chemical Structures, May 27-31, Noordwijkerhout, The Netherlands, 2018
  • Martin Ingelsson, Payam Emami Khoonsari, Ganna Shevchenko, Stephanie Herman, Julia Remnestål, Vilmantas Giedraitis, RoseMarie Brundin, Malin Degerman Gunnarsson, Lena Kilander, Henrik Zetterberg, Peter Nilsson, Lars Lannfelt, Kim Kultima. Improved discrimination between healthy control subjects and patients with cognitive decline by integrating ELISA and mass spectrometry-based cerebrospinal fluid biomarker. (Oral). 8th Kuopio Alzheimer Symposium, June 6-8, Kupio, Finland, 2018
  • Payam Emami Khoonsari, Pablo Moreno, Marco Capuccini, Namrata Kale, Anders Larsson, Steffen Neumann, Christoph Ruttkies, Christoph Steinbeck, Kim Kultima, Ola Spjuth, PhenoMeNal consortium. Metabolite profiling and annotation with interoperable and scalable microservices. The 14th International Conference of the Metabolomics Society, Seattle, June 24-28, Washington, USA, 2018
  • Payam Emami Khoonsari, Stephanie Herman, Marco Capuccini, Matteo Carone, Anders Larsson, Joachim Burman, Steffen Neumann, Christoph Steinbeck, Kim Kultima, Ola Spjuth and the PhenoMeNal project partners. Interoperable and scalable metabolomics data analysis with microservices. XXII International Mass Spectrometry Conference, August 26-31, Florence, Italy, 2018
  • Payam Emami Khoonsari, Stephanie Herman, Marco Capuccini, Matteo Carone, Anders Larsson, Joachim Burman, Steffen Neumann, Christoph Steinbeck, Kim Kultima, Ola Spjuth and the PhenoMeNal project partners. Interoperable and scalable metabolomics data analysis with microservices. 1st Metabolomics Conference, August 26-28, Örebro, Sweden, 2018
  • Stephanie Herman, Payam Emami Khoonsari, Julia Steinmetz, Andreas Tolf, Anders Larsson, Ola Spjuth, Joachim Burman, Kim Kultima. Integration of magnetic resonance imaging, and protein and metabolite measurements to enable early diagnosis of secondary progressive multiple sclerosis. 1st Metabolomics Conference, August 26-28, Örebro, Sweden, 2018
  • Stephanie Herman, Payam Emami Khoonsari, Andreas Tolf, Julia Steinmetz, Henrik Zetterberg, Torbjörn Åkerfeldt, Per-Johan Jakobsson, Anders Larsson, Ola Spjuth, Joachim Burman, Kim Kultima. Integration of Metabolite CSF Measurements, Magnetic Resonance Imaging and Protein Measurements to Enable Early Diagnosis of Secondary Progressive Multiple Sclerosis. (Oral). Benelux Metabolomics Days 2018, September 19-20, Rotterdam, The Netherlands, 2018

2017

  • Stephanie Herman, Payam Emami Khoonsari, Julia Steinmetz, Henrik Zetterberg, Andreas Tolf, Anders Larsson, Ola Spjuth, Torbjörn Åkerfeldt, Joachim Burman, Kim Kultima. Integration of clinical data, magnetic resonance imaging, and protein and metabolite measurements to enable early diagnosis of secondary progressive multiple sclerosis. Reearch Department Day (Oral), December 15, Uppsala, Sverige, 2017
  • Stephanie Herman, Payam Emami Khoonsari, Julia Steinmetz, Henrik Zetterberg, Andreas Tolf, Anders Larsson, Ola Spjuth, Torbjörn Åkerfeldt, Joachim Burman, Kim Kultima. Integration of clinical data, magnetic resonance imaging, and protein and metabolite measurements to enable early diagnosis of secondary progressive multiple sclerosis. Metabomeeting, December 11-13, Birmingham, UK, 2017
  • Stephanie Herman, Julia Steinmetz, Payam Emami Khoonsari, Andreas Tolf, Joachim burman, Kim Kultima. Metabolomic signature of Multiple sclerosis patients is associated to disease severity. 13th International Conference of the Metabolomics Society, June 25-29, Brisbane, 2017

2016

  • Payam Emami Khoonsari, Stephanie Herman, Obaid Aftab, Mats Gustafsson, Ola Spjuth, Lars Tanum, Torsten Gordh, Kim Kultima. Metabolomic analyses of the Cerebrospinal Fluid in Fibromyalgia. 12th Annual Conference of the metabolomics society, June 27-30, Dublin, Ireland, 2016
  • Stephanie Herman, Marco Capuccini, Payam Emami Khoonsari, Anders Larsson, Kim Kultima, Ola Spjuth. Scalable analysis setup enables high-throughput metabolomics. 12th Annual Conference of the metabolomics society, June 27-30, Dublin, Ireland, 2016

2015

  • Sravani Musunuri, Payam Emami Khoonsari, Martin Ingelsson, Lars Lannfelt, Jonas Bergquist, Kim Kultima, Ganna Shevchenko. Mass spectrometry-based proteomics in combination with quantitative stable isotope dimethyl labeling for the analysis of Alzheimer’s disease cerebrospinal fluid proteome. 29th Indian Society for Mass Spectrometry (ISMAS), February 2-6, Jodhpur, Rajasthan, India, 2015
  • AnneLi Lind, Payam Emami Khoonsari, Marcus Sjödin, Magnus Wetterhall, Torsten Gordh, Kim Kultima. New players in the mechanism of spinal cord stimulation for neuropathic pain. SASP annual meeting, April 12-14, Stockholm, 2015
  • Elisabeth Nikitidou, Payam Emami Khoonsari, Ganna Shevchenko, Lars Lannfelt, Kim Kultima, Anna Erlandsson. Identification of exosomal proteins specifically released following Aβ1-42 protofibril treatment in co-cultures of primary neurons and glia. Neuroscience, October 17-21, Chicago, USA, 2015

2014

  • AnneLi Lind, Payam Emami Khoonsari, Marcus Sjödin, Eva Freyhult, Linda Katila, Mats Gustafsson, Ulf Landegren, Magnus Wetterhall, Masood Kamali- Moghaddam, Kim Kultima, Torsten Gordh. Neuropeptides and Proteins with Potential Role in Analgesic Effect of Spinal Cord Stimulation on Neuropathic Pain”. IASP, The 15th World Congress On Pain, October 6 – 11, Buenos Aires, Argentina, 2014
  • Payam Emami Khoonsari, Ganna Shevchenko, Martin Ingelsson, Lars Lannfelt, Maria Lönnberg, Jonas Bergquist, Kim Kultima. Cerebrospinal Fluid Proteome of Patients Diagnosed with Alzheimer Disease: Focus on Data Analysis, IMSC 2014
  • Ganna Shevchenko, Payam Emami Khoonsari, Martin Ingelsson, Lars Lannfelt, Maria Lönnberg; Jonas Bergquist, Kim Kultima, “Cerebrospinal Fluid Proteome of Patients Diagnosed with Alzheimer Disease: Focus on Biomarkers”, US HUPO 2014
  • Gabriel Teku, Payam Emami Khoonsari, Francesco Mazzarotto, Mauno Vihinen, Csaba Ortutay, “Computational modeling of T and B cell development using gene co-regulatory and protein interaction networks”, Hungarian Molecular Life Sciences 2013.

TEACHING and WORKSHOPS

  • Teacher assistant: introduction to RNAseq, 13-15 May 2019, Uppsala
  • Organizer: Cloud Computing and Scientific Workflows, "National Bioinformatics Infrastructure Sweden", 2nd of April, 2019, Stockholm
  • Teacher assistant: introduction to bioinformatics using NGS data, 4-8 February 2019, Uppsala
  • Presenter at EMBnet COST.CHARME training school “Big Data for Life Sciences”, 18.-22.9.2017 Uppsala
  • Presenter at PhenoMeNal Workflow Workshop, Halle germany 04-04-2017
  • Member of organizing committee, PhenoMeNal e­-Infrastructures workshop in Uppsala, ​29-02-2016

FUNDINGS

  • Sederholm scholarship, for travel abroad (10000 Swedish krona), research retreat, 2016
  • Grant for research level students (5467 Swedish krona), Faculty of Medicine, Uppsala university, 2016
  • IF’s Foundation scholarship for pharmaceutical research (25000 Swedish krona), research retreat, 2016
  • Svenska Sällskapet för Medicinsk Forskning (24000 Swedish krona) travel grants for doctoral candidates in preclinical and clinical medical research, 2016
  • Geriatriska fonden (62000 Swedish krona) research grant to establish a workflow and computer cluster to process and model Alzheimer’s disease data, 2015
  • Grants for research level students (4470 Swedish krona), Faculty of Medicine, Uppsala university, 2015
  • Grants for research level students (4731 Swedish krona), Faculty of Medicine, Uppsala university, 2014
  • Berzelii PhD travel grants (10000 Swedish krona), 2014
  • Grants for research level students (4156 Swedish krona), Faculty of Medicine, Uppsala university, 2013

SKILLS

  • Experienced in mass spectrometry-based proteomics/metabolomics data processing and analysis including various related tools and algorithms
  • Experienced in multiple programming/scripting languages (C++, Java, R, Python)
  • Machine learning, data mining, and statistical analysis
  • Experienced in Kubernetes-based cloud computing and working knowledge of various related tools: e.g. ansible, terraform etc.
  • Workflow engines: Galaxy, Nextflow and Pachyderm