Publications
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan,
Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart,
Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, and Nicola Segata.
eLife, 10: e65088, 2021.
[ pdf ]
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Large scale genome reconstructions illuminate Wolbachia evolution.
Matthias Scholz,
Davide Albanese, Kieran Tuohy, Claudio Donati, Nicola Segata, and Omar Rota-Stabelli.
Nature Communications, 11(1): 5235, 2020.
[
pdf |
download genomes ]
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Gut microbiota associations with diet in irritable bowel syndrome and the effect of low FODMAP diet and probiotics.
Heidi M. Staudacher, Matthias Scholz,
Miranda CE. Lomer, Frances S. Ralph, Peter M. Irving, James O. Lindsay,
Francesca Fava, Kieran Tuohy, and Kevin Whelan.
Clinical Nutrition, 2020.
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Effects of diet-modulated autologous fecal microbiota transplantation on weight regain.
Ehud Rinott, Ilan Youngster, Anat Yaskolka Meir, Gal Tsaban, Hila Zelicha,
Alon Kaplan, Dan Knights, Kieran Tuohy, Francesca Fava, Matthias Scholz,
Oren Ziv, Elad Reuven, Amir Tirosh, Assaf Rudich, Matthias Blüher, Michael Stumvoll,
Uta Ceglarek, Karine Clement, Omry Koren, Dong D. Wang, Frank B. Hu,
Meir J. Stampfer, and Iris Shai.
Gastroenterology, 2020.
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Manipulation of dietary amino acids prevents and reverses obesity in mice through multiple mechanisms that modulate energy homeostasis.
Chiara Ruocco, Maurizio Ragni, Fabio Rossi, Pierluigi Carullo, Veronica Ghini, Fabiana Piscitelli,
Adele Cutignano, Emiliano Manzo, Rafael Maciel Ioris, Franck Bontems, Laura Tedesco,
Carolina M. Greco, Annachiara Pino, Ilenia Severi, Dianxin Liu, Ryan P. Ceddia,
Luisa Ponzoni, Leonardo Tenori, Lisa Rizzetto, Matthias Scholz,
Kieran Tuohy, Francesco Bifari, Vincenzo Di Marzo, Claudio Luchinat, Michele O. Carruba,
Saverio Cinti, Ilaria Decimo, Gianluigi Condorelli, Roberto Coppari, Sheila Collins,
Alessandra Valerio, and Enzo Nisoli.
Diabetes, 69(11): 2324-2339, 2020.
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Two apples a day modulate human:microbiome co-metabolic processing of polyphenols, tyrosine and tryptophan
Maria M. Ulaszewska, Athanasios Koutsos, Kajetan Trošt, Jan Stanstrup, Mar Garcia-Aloy,
Matthias Scholz, Francesca Fava, Fausta Natella,
Cristina Scaccini, Urska Vrhovsek, Kieran Tuohy, Julie Lovegrove, and Fulvio Mattivi
European Journal of Nutrition, 59: 3691-3714, 2020.
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White wine light-strike fault: A comparison between flint and green glass bottles under the typical supermarket conditions.
Panagiotis Arapitsas, Stefano Dalledonne, Matthias Scholz, Antonio Catapano,
Silvia Carlin, and Fulvio Mattivi.
Food Packaging and Shelf Life, 24: 100492, 2020.
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Effects of woody biochar on dry thermophilic anaerobic digestion of organic fraction of municipal solid waste.
Daniela Bona, Giovanni Beggio, Tobias Weil, Matthias Scholz, Sara Bertolini,
Luca Grandi, Marco Baratieri, Andrea Schievano, Silvia Silvestri, and Alberto Pivato.
Journal of Environmental Management, 267, 110633, 2020.
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Diet Low in FODMAPs Reduces Symptoms in Patients with Irritable Bowel Syndrome and Probiotic Restores Bifidobacterium Species: a Randomized Controlled Trial.
Heidi M. Staudacher, Miranda C.E. Lomer, Freda M. Farquharson, Petra Louis, Francesca Fava, Elena Franciosi,
Matthias Scholz,
Kieran Tuohy, James O. Lindsay, Peter M. Irving, and Kevin Whelan.
Gastroenterology, 153(4): 936-947, 2017.
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Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling.
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini,
Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, and Nicola Segata
mSystems, 2(1), e00164-16, 2017.
[
pdf ]
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Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
Matthias Scholz*, Doyle V. Ward*, Edoardo Pasolli*, Thomas Tolio, Moreno Zolfo,
Francesco Asnicar, Duy Tin Truong, Adrian Tett, Ardythe L. Morrow, and Nicola Segata.
Nature Methods, 13, 435–438, 2016. (* Equal contribution)
[
pdf |
PanPhlAn software tool |
Strain-level article by Vivien Marx |
genomeweb.com ]
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Metagenomic sequencing with strain level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and death in preterm infants.
Doyle V. Ward*, Matthias Scholz*, Moreno Zolfo, Diana H. Taft, Kurt R. Schibler,
Adrian Tett, Nicola Segata*, and Ardythe L. Morrow*.
Cell Reports, 14, 2912-2924, 2016. (* co-first author / co-senior author)
[
pdf ]
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Duy Tin Truong, Eric A. Franzosa, Timothy L. Tickle, Matthias Scholz, George Weingart,
Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata.
Nature Methods, 12, 902-903, 2015.
[
pdf |
MetaPhlAn2 software tool ]
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Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut.
Christian Milani, Gabriele Andrea Lugli, Sabrina Duranti, Francesca Turroni,
Leonardo Mancabelli, Chiara Ferrario, Marta Mangifesta, Arancha Hevia,
Alice Viappiani, Matthias Scholz, Stefania Arioli,
Borja Sanchez, Jonathan Lane, Doyle V. Ward, Rita Hickey, Diego Mora,
Nicola Segata, Abelardo Margolles, Douwe van Sinderen, and Marco Ventura
Scientific reports, Nature Publishing Group, 5: 15782, 2015.
[
pdf]
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Computational Tools for Taxonomic Microbiome Profiling of Shotgun Metagenomes.
Matthias Scholz, Adrian Tett, and Nicola Segata.
In Metagenomics for Microbiology,
edited by Jacques Izard and Maria Rivera,
1st edition, pages 67-80, Academic Press, 2014.
[
Book website |
Academic Press / Elsevier ]
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MetaDB a data processing workflow in untargeted MS-based metabolomics experiments.
Pietro Franceschi, Roman Mylonas, Nir Shahaf, Matthias Scholz,
Panagiotis Arapitsas, Domenico Masuero, Georg Weingart, Silvia Carlin,
Urska Vrhovsek, Fulvio Mattivi, and Ron Wehrens.
Frontiers in bioengineering and biotechnology 2:72, 2014.
[
pdf ]
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Stable isotope ratios and aroma profile changes induced due to innovative wine dealcoholisation approaches.
Bruno Fedrizzi, Enrico Nicolis, Federica Camin, Enrico Bocca, Cristina Carbognin,
Matthias Scholz, Paolo Barbieri, Fabio Finato, Roberto Ferrarini.
Food and Bioprocess Technology 7(1):62-70, 2014.
[
pdf ]
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Metabonomic investigation of rat tissues following intravenous administration of cyanidin 3-glucoside at a physiologically
relevant dose.
Andreja Vanzo, Matthias Scholz, Mattia Gasperotti, Federica Tramer, Sabina Passamonti, Urska Vrhovsek and Fulvio Mattivi.
Metabolomics 9(1):88-100, 2013.
[
pdf ]
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Validation of nonlinear PCA.
Matthias Scholz
Neural Processing Letters, Volume 36, Number 1, Pages 21-30, 2012.
[
pdf (pre-print) |
pdf (Neural Process Lett) |
poster RECOMB 2012 |
Matlab code]
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A Metabolomic Approach to the Study of Wine Micro-Oxygenation.
Panagiotis Arapitsas, Matthias Scholz, Urska Vrhovsek, Stefano Di Blasi,
Alessandra Biondi Bartolini, Domenico Masuero, Daniele Perenzoni, Adelio Rigo, and Fulvio Mattivi.
PLoS ONE, 2012.
[
pdf ]
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Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids.
Rhonda C. Meyer, Hanna Witucka-Wall, Martina Becher, Anna Blacha, Anastassia Boudichevskaia, Peter Dörmann, Oliver Fiehn,
Svetlana Friedel, Maria von Korff, Jan Lisec, Michael Melzer, Dirk Repsilber, Renate Schmidt,
Matthias Scholz, Joachim Selbig, Lothar Willmitzer, and Thomas Altmann.
The Plant Journal, 2012.
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LC-MS based global metabolite profiling of grapes: solvent extraction protocol optimisation.
Georgios Theodoridis, Helen Gika, Pietro Franceschi, Lorenzo Caputi, Panagiotis Arapitsas,
Matthias Scholz, Domenico Masuero, Ron Wehrens, Urska Vrhovsek and Fulvio Mattivi.
Metabolomics 8:175-185, 2012.
[
pdf ]
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Node similarity as a basic principle behind connectivity in complex networks.
Matthias Scholz.
arXiv:1010.0803 [physics.soc-ph] 2010.
Journal of Data Mining & Digital Humanities, jdmdh:77, 2015.
[
pdf
| matlab code ]
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A computational model of gene expression reveals early transcriptional events at the subtelomeric
regions of the malaria parasite, Plasmodium falciparum.
Matthias Scholz and Martin J. Fraunholz.
Genome Biology 9:R88, 2008.
[
pdf |
Animation of gene regulation ]
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Integration of metabolomic and proteomic phenotypes - Analysis of data-covariance dissects starch and
RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana.
Stefanie Wienkoop, Katja Morgenthal, Florian Wolschin,
Matthias Scholz, Joachim Selbig, and Wolfram Weckwerth.
Molecular & Cellular Proteomics, 2008.
[
pdf ]
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Nonlinear principal component analysis: neural network models and applications.
Matthias Scholz, Martin Fraunholz,
and Joachim Selbig.
In Principal Manifolds for Data Visualization and
Dimension Reduction,
edited by Alexander N. Gorban, Balázs Kégl,
Donald C. Wunsch, and Andrei Zinovyev.
Volume 58 of LNCSE, pages 44-67.
Springer Berlin Heidelberg, 2007.
[
pdf (all book chapters) |
pdf (Springer) |
entire book (Springer) |
nonlinear PCA toolbox for MATLAB ]
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Analysing periodic phenomena by circular PCA.
Matthias Scholz.
In S. Hochreiter and R. Wagner, editors,
Proceedings of the Conference on Bioinformatics
Research and Development BIRD'07,
LNCS/LNBI Vol. 4414, pages 38-47.
Springer-Verlag Berlin Heidelberg, 2007.
[
pdf (final version at Springer) |
pdf (author's pre-version) |
bibtex |
nonlinear PCA toolbox for MATLAB ]
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pcaMethods — a bioconductor package providing PCA methods for incomplete data.
Wolfram Stacklies, Henning Redestig,
Matthias Scholz,
Dirk Walther, and Joachim Selbig.
Bioinformatics, 23(9):1164-1167. 2007.
[
pdf |
nonlinear PCA ported to R by Henning Redestig ]
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Integrated data analysis for genome-wide research.
Matthias Steinfath, Dirk Repsilber, Matthias Scholz,
Dirk Walther and Joachim Selbig.
In Plant Systems Biology, pages 309-329
edited by Sacha Baginski and Alisdair R. Fernie,
Birkhäuser-Verlag, Basel, Boston, Berlin, 2007.
(distributed by Springer)
[
pdf |
entire book ]
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Visualization and analysis of molecular data.
Matthias Scholz and Joachim Selbig.
In Wolfram Weckwerth, editor,
Metabolomics: methods and protocols.
Methods in Molecular Biology Series 358:87-104.
Humana Press, New York, 2006.
[
pdf ]
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Approaches to analyse and interpret biological profile data.
Matthias Scholz.
University of Potsdam, Germany. Ph.D. thesis. 2006.
URN: urn:nbn:de: kobv:517-opus-7839
URL: http://opus.kobv.de/ubp /volltexte/2006/783/
[
pdf (library) |
pdf (copy) |
bibtex |
figures ]
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Profile data analysis, dimension reduction, clustering and classification.
Matthias Steinfath, Matthias Scholz,
and Joachim Selbig.
In European Training and Networking Activity.
Plant Genomics and Bioinformatics:
Expression Micro Arrays and Beyond - a course book.
Ljubljana Slovenia, 2005.
[
pdf |
www.eu-summer-school.org ]
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Non-linear PCA: a missing data approach.
Matthias Scholz,
Fatma Kaplan, Charles L. Guy,
Joachim Kopka, and Joachim Selbig.
Bioinformatics 21(20):3887-3895. 2005.
[
pdf (final version) |
pdf (pre-version in colour) |
bibtex ]
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Correlative GC-TOF-MS-based metabolite profiling and
LC-MS-based protein profiling reveal time-related systemic regulation of
metabolite-protein networks and improve pattern recognition
for multiple biomarker selection.
Katja Morgenthal, Stefanie Wienkoop,
Matthias Scholz,
Joachim Selbig, and Wolfram Weckwerth.
Metabolomics 1(2):109-121. 2005.
[
pdf
]
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Independent Component Analysis of Starch Deficient PGM Mutants.
Matthias Scholz, Yves Gibon,
Mark Stitt, and Joachim Selbig.
In R. Giegerich and J. Stoye, editors,
Proceedings of the German Conference on
Bioinformatics, pages 95-104. 2004.
[
pdf
]
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Metabolite fingerprinting: detecting biological features by
independent component analysis.
Matthias Scholz, Stephan Gatzek,
Alistair Sterling, Oliver Fiehn, and Joachim Selbig.
Bioinformatics 20(15):2447-2454. 2004.
[
pdf
| poster ISMB04
| more about ICA
| matlab code
| web tool
]
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Nonlinear PCA based on neural networks.
Matthias Scholz.
Dep. of Computer Science, Humboldt-University
Berlin. Diploma Thesis. 2002. In German.
DOI: 10.18452/14087
[
pdf (library) |
pdf (pre-print version)
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Nonlinear PCA: a new hierarchical approach.
Matthias Scholz and
Ricardo Vigário.
In M. Verleysen, editor,
Proceedings ESANN. 2002.
[
pdf (pre-print version) |
pdf (ESANN)
]
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Kernel PCA and de-noising in feature spaces.
Sebastian Mika, Bernhard Schölkopf,
Alexander J. Smola,
Klaus-Robert Müller, Matthias Scholz, and
Gunnar Rätsch.
In M.S. Kearns, S.A. Solla, and D.A. Cohn, editors,
Advances in Neural Information Processing Systems (NIPS) 11,
pages 536-542. MIT Press, 1999.
[
pdf |
NIPS:pdf |
NIPS:djvu
]
ORCID iD: 0000-0003-1414-5924
Scopus Author ID: 24467097000
Publons - Web of Science - ResearcherID: B-3508-2018
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