Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 40 /hr

★★★★★

☆☆☆☆☆

Hire Nejc S.

Slovenia

USD 40 /hr

Microbiome researcher | Genomics | Bioinformatics | Data analytics & visualization

Profile Summary

Coming soon

Subject Matter Expertise

• ★ Microbiome Research
• ★ Data Analysis
• ★ Bioinformatics
• ☆ Natural Product Chemistry
• ☆ Molecular Biology
• ☆ Omics
• ☆ Metabolomics
• ☆ Genomics
• ☆ Next Generation Sequencing (NGS)
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Microbial Ecology
• ☆ Agroecology
• ☆ Python
• ☆ R

Services

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Technical Writing, Newswriting

Research Market Research, User Research, Fact Checking, Gap Analysis, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Big Data Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Product Development Formulation, Product Validation

Work Experience

Senior Scientist

National Laboratory of Health, Environment and Food

March 2022 - Present

Postdoctoral Scholar

NIOO-KNAW

January 2021 - Present

Postdoctoral Scholar

Michigan State University

April 2017 - December 2020

Postdoc

University of Washington

November 2014 - March 2017

Research assistent

University of Ljubljana

2009 - 2010

Education

Ph.D. (Institute of plant biology)

University of Zurich

2010 - 2014

Diploma thesis (Biotechnical faculty)

University of Ljubljana

2004 - 2009

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Nejc Stopnisek, Eliana Guedes Stehling, João Pedro Rueda Furlan, Ralf Lopes, John Chodkowski, Eduardo Angelino Savazzi, Ashley Shade (2024). The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil . Environmental Pollution.

Nejc Stopnisek, Stalin Sarango Flores, Viviane Cordovez, Ben Oyserman, Jos M. Raaijmakers, Pieter van ‘t Hof (2024). The Tomato's Tale: Exploring Taxonomy, Biogeography, Domestication, and Microbiome for Enhanced Resilience . Phytobiomes Journal.

Nejc Stopnisek, Ritam Sinha, Rhiannon M. LeVeque, Sean M. Callahan, shramana chatterjee, Matti Kuipel, Jeremiah G. Johnson, Victor DiRita (2024). Gut metabolite L-lactate supports Campylobacter jejuni population expansion during acute infection . Proceedings of the National Academy of Sciences.

Nejc Stopnisek, Adina Howe, Shane K. Dooley, Fan Yang, Keara L. Grady, Ashley Shade (2023). Seasonal activities of the phyllosphere microbiome of perennial crops . Nature Communications.

Nejc Stopnisek, Ben Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte J. U. Pronk, Wouter Lokhorst, Azkia Nurfikari, Joseph N Paulson, et al. (2022). Disentangling the genetic basis of rhizosphere microbiome assembly in tomato . Nature Communications.

A. F. Bintarti, A. Sulesky-Grieb, N. Stopnisek, A. Shade(2022). Endophytic Microbiome Variation Among Single Plant Seeds . Phytobiomes Journal. Scientific Societies

Nejc Stopnisek, Ashley Shade (2021). Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype . The ISME Journal.

Ari Fina Bintarti and Abby Sulesky-Grieb and Nejc Stopni{\v{s}}ek and Ashley Shade(2021). Endophytic microbiome variation among single plant seeds . Phytobiomes Journal. Scientific Societies

Nejc Stopnisek, Serdar Turkarslan, Anne W Thompson, Christina E Arens, Jacob J Valenzuela, James Wilson, Kristopher A Hunt, Jessica Hardwicke, Adrián López García de Lomana, Sujung Lim, et al. (2021). Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions . The ISME Journal.

Kristopher A. Hunt and Jonathan Forbes and Fred Taub and Nicholas Elliott and Jessica Hardwicke and Robert Petersen and Nejc Stopnisek and David A.C. Beck and David A. Stahl(2021). An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates . Journal of Microbiological Methods. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 106294. Elsevier {BV}

Nejc Stopnisek, Muhammad Syamsu Rizaludin, Jos M. Raaijmakers, Paolina Garbeva(2021). The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots . Metabolites. 11. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 357. {MDPI} {AG}

(2019). Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops . Nature Communications.

Nejc Stopnisek, Keara L. Grady, Jackson W. Sorensen, John Guittar, Ashley Shade (2019). Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops . Nature Communications.

(2019). Abundance-occupancy distributions to prioritize plant core microbiome membership . Current Opinion in Microbiology.

(2019). Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities .

Bell, T.H., Hockett, K.L., Alcalá-Briseño, R.I., Barbercheck, M., Beattie, G.A., Bruns, M.A., Carlson, J.E., Chung, T., Collins, A., Emmett, B., et al.(2019). Manipulating wild and tamed phytobiomes: Challenges and opportunities . Phytobiomes Journal. 3. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3-21.

Grady, K.L., Sorensen, J.W., Stopnisek, N., Guittar, J., Shade, A.(2019). Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops . Nature Communications. 10. (1).

Shade, A., Stopnisek, N.(2019). Abundance-occupancy distributions to prioritize plant core microbiome membership . Current Opinion in Microbiology. 49. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 50-58.

Nejc Stopnisek, Kelley A. Meinhardt, Manmeet W. Pannu, Stuart E. Strand, Steven C. Fransen, Karen L. Casciotti, David A. Stahl(2018). Ammonia-oxidizing bacteria are the primary N2O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil . Environmental Microbiology. Wiley

Meinhardt, K.A., Stopnisek, N., Pannu, M.W., Strand, S.E., Fransen, S.C., Casciotti, K.L., Stahl, D.A.(2018). Ammonia-oxidizing bacteria are the primary N<inf>2</inf>O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil . Environmental Microbiology. 20. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2195-2206.

Stopnisek, N., Zuhlke, D., Carlier, A., Barberan, A., Fierer, N., Becher, D., Riedel, K., Eberl, L., Weisskopf, L.(2016). Molecular mechanisms underlying the close association between soil Burkholderia and fungi . ISME Journal. 10. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 253-264.

Nejc Stopnisek, Daniela Z&#252;hlke, Aur&#233;lien Carlier, Albert Barber&#225;n, Noah Fierer, D&#246;rte Becher, Katharina Riedel, Leo Eberl, Laure Weisskopf(2015). Molecular mechanisms underlying the close association between soil Burkholderia and fungi . ISME J. 10. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 253--264. Nature Publishing Group

Stopnisek, N., Bodenhausen, N., Frey, B., Fierer, N., Eberl, L., Weisskopf, L.(2014). Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations . Environmental microbiology. 16. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1503-1512.

Nejc Stopnisek, Thomas Kost, Kirsty Agnoli, Leo Eberl, Laure Weisskopf(2014). Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans . Front. Microbiol. 4. Frontiers Media {SA}

Nejc Stopnisek, Natacha Bodenhausen, Beat Frey, Noah Fierer, Leo Eberl, Laure Weisskopf(2013). Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations . Environ Microbiol. 16. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1503--1512. Wiley-Blackwell

Kost, T., Stopnisek, N., Agnoli, K., Eberl, L., Weisskopf, L.(2013). Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans . Frontiers in Microbiology. 4. (JAN).

N. Stopnisek, C. Gubry-Rangin, S. Hofferle, G. W. Nicol, I. Mandic-Mulec, J. I. Prosser(2010). Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment . Applied and Environmental Microbiology. 76. (22). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 7626--7634. American Society for Microbiology

Stopnišek, N., Gubry-Rangin, C., H&#246;fferle, S., Nicol, G.W., Mandič-Mulec, I., Prosser, J.I.(2010). Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment . Applied and Environmental Microbiology. 76. (22). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 7626-7634.

PREPRINT

Nejc Stopnisek, Ben O Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Anne Kupczok, et al. (2021). Disentangling the genetic basis of rhizosphere microbiome assembly in tomato .

Nejc Stopnisek, Adina C. Howe, Shane K. Dooley, Fan Yang, Keara L. Grady, Ashley Shade (2021). Life on the leaf: Seasonal activities of the phyllosphere microbiome of perennial crops .