Marie Bolger

Kontakt

+49 2461/61-85827

E-Mail

Adresse

Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße
52428 Jülich

Institut für Bio- und Geowissenschaften (IBG)

Bioinformatik (IBG-4)

Gebäude 14.6y / Raum 4041

Warum und woran ich forsche

The IBG-4 (Bioinformatics) division of the Institute of Bio- and Geosciences develops and applies methods and algorithms to achieve a fundamental understanding of high-dimensional data and processes in the bioeconomy/life sciences and to understand, predict and optimize the biological functions of molecules, genes and enzymes for breeding and for industrial and pharmaceutical applications, also on the basis of their structures. IBG-4 has a focus on omics/data-based bioinformatics on plant data storage, the evaluation of new genome analysis methods, and the integration, interpretation, and visualization of high-dimensional omics data from the field of bioeconomy and plant science. More information here

I am a bioinformatician focusing largely on plant genomes. My work involves using computational tools to unravel the complexities of plant genetics, facilitating advancements in genomics research. Additionally, I oversee and maintain the high-performance computing clusters within our group. I also administrate a number of websites and provide a web-based interface to a number of tools developed within our group for use by the wider scientific community

Publikationen

Holst, Felix, Anthony Bolger, Christopher Günther, Janina Maß, Sebastian Triesch, Felicitas Kindel, Niklas Kiel et al. "Helixer–de novo prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model." BioRxiv (2023): 2023-02.

Powell, Adrian F., Ari Feder, Jie Li, Maximilian H‐W. Schmidt, Lance Courtney, Saleh Alseekh, Emma M. Jobson et al. "A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity." The Plant Journal 110, no. 6 (2022): 1791-1810.

Hoopes, Genevieve, Xiaoxi Meng, John P. Hamilton, Sai Reddy Achakkagari, Fernanda de Alves Freitas Guesdes, Marie E. Bolger, Joseph J. Coombs et al. "Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity." Molecular plant 15, no. 3 (2022): 520-536.

Bolger, Marie, Rainer Schwacke, and Björn Usadel. "MapMan visualization of RNA-seq data using Mercator4 functional annotations." Solanum tuberosum: methods and protocols (2021): 195-212.

Schwacke, Rainer, Gabriel Y. Ponce-Soto, Kirsten Krause, Anthony M. Bolger, Borjana Arsova, Asis Hallab, Kristina Gruden, Mark Stitt, Marie E. Bolger, and Björn Usadel. "MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis." Molecular plant 12, no. 6 (2019): 879-892.

Bolger, Anthony M., Hendrik Poorter, Kathryn Dumschott, Marie E. Bolger, Daniel Arend, Sonia Osorio, Heidrun Gundlach et al. "Computational aspects underlying genome to phenome analysis in plants." The Plant Journal 97, no. 1 (2019): 182-198.

Vogel, Alexander, Rainer Schwacke, Alisandra K. Denton, Björn Usadel, Julien Hollmann, Karsten Fischer, Anthony Bolger et al. "Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris." Nature communications 9, no. 1 (2018): 2515.

Delventhal, Rhoda, Jeyaraman Rajaraman, Francesca L. Stefanato, Sajid Rehman, Reza Aghnoum, Graham RD McGrann, Marie Bolger et al. "A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley." BMC plant biology 17 (2017): 1-22.

Schmutzer, Thomas, Marie E. Bolger, Stephen Rudd, Jinbo Chen, Heidrun Gundlach, Daniel Arend, Markus Oppermann et al. "Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives." Journal of biotechnology 261 (2017): 37-45.

Bolger, Marie, Rainer Schwacke, Heidrun Gundlach, Thomas Schmutzer, Jinbo Chen, Daniel Arend, Markus Oppermann et al. "From plant genomes to phenotypes." Journal of Biotechnology 261 (2017): 46-52.

Bolger, Marie E., Borjana Arsova, and Björn Usadel. "Plant genome and transcriptome annotations: from misconceptions to simple solutions." Briefings in bioinformatics 19, no. 3 (2018): 437-449.

Schmidt, Maximilian H-W., Alexander Vogel, Alisandra K. Denton, Benjamin Istace, Alexandra Wormit, Henri van de Geest, Marie E. Bolger et al. "De novo assembly of a new Solanum pennellii accession using nanopore sequencing." The Plant Cell 29, no. 10 (2017): 2336-2348.

Bolger, Anthony, Alisandra Denton, Marie Bolger, and Björn Usadel. "LOGAN: A framework for LOssless Graph-based ANalysis of high throughput sequence data." BioRxiv (2017): 175976.

Fanourakis, Dimitrios, Habtamu Giday, Rubén Milla, Roland Pieruschka, Katrine H. Kjaer, Marie Bolger, Aleksandar Vasilevski, Adriano Nunes-Nesi, Fabio Fiorani, and Carl-Otto Ottosen. "Pore size regulates operating stomatal conductance, while stomatal densities drive the partitioning of conductance between leaf sides." Annals of botany 115, no. 4 (2015): 555-565.

Bolger, Anthony, Federico Scossa, Marie E. Bolger, Christa Lanz, Florian Maumus, Takayuki Tohge, Hadi Quesneville et al. "The genome of the stress-tolerant wild tomato species Solanum pennellii." Nature genetics 46, no. 9 (2014): 1034-1038.

Bolger, Marie E., Bernd Weisshaar, Uwe Scholz, Nils Stein, Björn Usadel, and Klaus FX Mayer. "Plant genome sequencing—applications for crop improvement." Current opinion in biotechnology 26 (2014): 31-37.

Riegler, Heike, Thomas Herter, Irina Grishkovskaya, Anja Lude, Malgorzata Ryngajllo, Marie E. Bolger, Bernd Essigmann, and Bjoern Usadel. "Crystal structure and functional characterization of a glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana." Biochemical Journal 443, no. 2 (2012): 427-437.

Steinhauser, Marie-Caroline, Dirk Steinhauser, Yves Gibon, Marie Bolger, Stéphanie Arrivault, Björn Usadel, Dani Zamir, Alisdair R. Fernie, and Mark Stitt. "Identification of enzyme activity quantitative trait loci in a Solanum lycopersicum× Solanum pennellii introgression line population." Plant Physiology 157, no. 3 (2011): 998-1014.

Letzte Änderung: 13.12.2024