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Published: 26 March 2021 on Nature Communications
Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
https://www.nature.com/articles/s41467-021-22135-x
Carlo Vittorio Cannistraci
Zhou Yahui Chair Professor
Chief Scientist, Tsinghua Laboratory of Brain and Intelligence (THBI)
Director, Center for Complex Network Intelligence (CCNI) at THBI
Adjunct Professor, Department of Computer Science
Adjunct Professor, Department of Biomedical Engineering
Tsinghua University, Beijing, China
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Affiliated Faculty, Center for Systems Biology Dresden (CSBD)
An initiative of Max-Planck Society and Technische Universität Dresden, Germany
"... I am a bioengineer expert in biocybernetics ...
... I search for applications of complex systems theory, information theory and machine learning in ...
... biology and medicine ..."
(I am dysle'ss'ic, you frequently might encounter mistakes as 'his' written 'is', 'where' written 'were', and so on ... sorry)
SICILY
Carlo Vittorio Cannistraci is a bioengineer and often employs his knowledge for Analysis and Reverse Engineering of Biosystems. He was born in Milazzo (ME), in the East of Sicily, an active volcanic land in front of the Eolian Islands. He obtained High School Diploma in Science and won the competition for admission to the prestigious Italian Naval Academy, but he declined because in the same period he developed an overwhelming interest for natural and artificial intelligent systems and started to defy the regular educational model proposed in Italian universities.
He embraced a period of independent research as autodidact following the Ancient Greek Educational approach called KALOKAGATHIA (from καλός καi αγαθός, "Kalos kai agathos") in philosophy, mathematics, poetry, arts and physical (body and soul) culture. He trained for strength, freediving and finswimming.
In 2005, Carlo graduated from the Polytechnic of Milano with a Master Degree in Biomedical Engineering after an internship at the Department of Biological and Technological Research (DIBIT) of the San Raffaele Scientific Institute that regarded an advanced proteomic analysis of brain synapses, under the supervision of Antonio Malgaroli and Massimo Alessio. In the same year he won the Italian Championship of Finswimming in 4x100 relay and entered in the elite group of the strongest freedivers in the world with more than 150 mt in dynamic freediving (youtube: http://www.youtube.com/watch?v=kUn1SMeIS9I). Then he received a six month research grant from ISIB-CNR (Biomedical Engineering Institute of the National Research Council), after which he joined the Proteome Biochemistry Laboratory at the San Raffaele Scientific Institute.
Since January 2007, he was Ph.D. student of the Scuola Interpolitecnica di Dottorato (SIPD, http://sipd.polito.it/), a special project involving the three Italian Technical Universities (Polytechnics of Torino, Bari and Milano) that selects the most talented candidates to run joint international relations and cooperation programs in high level research projects.
In 2009, he spent one year in San Diego, California (USA), as visiting scholar in the Ideker Lab (http://chianti.ucsd.edu/idekerlab/), working on application of information theory, machine learning and optimization theory in integrative systems biology. There he met Timothy Ravasi who became his supervisor along with Trey Ideker. And they started a fruitful collaboration that is continuing.
In February 2010, he obtained his PhD in Bioengineering under the supervision of Franco Maria Montevecchi and Massimo Alessio, who were 'Deus ex machina' of his scientific growth. Master Franco has been guiding him since 1999 and is still his mentor.
From August 2010 to January 2014 he was Post-Doc and later Research Scientist in the the Integrative Systems Biology Lab lead by Timothy Ravasi.
Currently, he is head of the Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Technische Universität Dresden (TUD), Germany .
He works on development and application of complex network theory, systems theory, information theory and machine learning in biology and medicine.
Keywords:
Cybernetics - Intelligent Systems and Machine Learning - Adaptive Complex Systems and Networks - Signal/Image Processing and Information Theory - Computational and Systems Biology - Computational Neuroscience - Network and Personalised Medicine
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