A
Almut Heinken
Researcher at National University of Ireland, Galway
Publications - 50
Citations - 5249
Almut Heinken is an academic researcher from National University of Ireland, Galway. The author has contributed to research in topics: Microbiome & Biology. The author has an hindex of 21, co-authored 41 publications receiving 3264 citations. Previous affiliations of Almut Heinken include National University of Ireland & University of Iceland.
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Journal ArticleDOI
Gut microbiota functions: metabolism of nutrients and other food components
Ian Rowland,Glenn R. Gibson,Almut Heinken,Karen P. Scott,Jonathan R. Swann,Ines Thiele,Kieran Tuohy +6 more
TL;DR: This review discusses the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates, proteins, plant polyphenols, bile acids, and vitamins, and the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism.
Journal ArticleDOI
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt,Sylvain Arreckx,Thomas Pfau,Sebastián N. Mendoza,Anne Richelle,Almut Heinken,Hulda S. Haraldsdóttir,Jacek Wachowiak,Sarah M. Keating,Vanja Vlasov,Stefania Magnusdottir,Chiam Yu Ng,German Preciat,Alise Žagare,Siu Hung Joshua Chan,Maike K. Aurich,Catherine M. Clancy,Jennifer Modamio,John T. Sauls,Alberto Noronha,Aarash Bordbar,Benjamin Cousins,Diana C. El Assal,Luis Vitores Valcárcel,Iñigo Apaolaza,Susan Ghaderi,Masoud Ahookhosh,Marouen Ben Guebila,Andrejs Kostromins,Nicolas Sompairac,Hoai M. Le,Ding Ma,Yuekai Sun,Lin Wang,James T. Yurkovich,Miguel A.P. Oliveira,Phan Tu Vuong,Lemmer P. El Assal,Inna Kuperstein,Andrei Zinovyev,H. Scott Hinton,William A. Bryant,Francisco J. Aragón Artacho,Francisco J. Planes,Egils Stalidzans,Alejandro Maass,Santosh Vempala,Michael Hucka,Michael A. Saunders,Costas D. Maranas,Nathan E. Lewis,Thomas Sauter,Bernhard O. Palsson,Bernhard O. Palsson,Ines Thiele,Ronan M. T. Fleming,Ronan M. T. Fleming +56 more
TL;DR: This protocol provides an overview of all new features of the COBRA Toolbox and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios.
Journal ArticleDOI
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Stefania Magnusdottir,Almut Heinken,Laura Kutt,Dmitry A. Ravcheev,Eugen Bauer,Alberto Noronha,Kacy Greenhalgh,Christian Jäger,Joanna Baginska,Paul Wilmes,Ronan M. T. Fleming,Ines Thiele +11 more
TL;DR: This work presents AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria, and identified a defined growth medium for Bacteroides caccae ATCC 34185.
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Recon3D enables a three-dimensional view of gene variation in human metabolism.
Elizabeth Brunk,Elizabeth Brunk,Swagatika Sahoo,Daniel C. Zielinski,Ali Altunkaya,Ali Altunkaya,Andreas Dräger,Nathan Mih,Francesco Gatto,Francesco Gatto,Avlant Nilsson,German Andres Preciat Gonzalez,Maike K. Aurich,Andreas Prlić,Anand V. Sastry,Anna Dröfn Daníelsdóttir,Almut Heinken,Alberto Noronha,Peter W. Rose,Stephen K. Burley,Stephen K. Burley,Ronan M. T. Fleming,Ronan M. T. Fleming,Jens Nielsen,Jens Nielsen,Ines Thiele,Bernhard O. Palsson,Bernhard O. Palsson +27 more
TL;DR: Recon3D is presented, a computational resource that includes three-dimensional metabolite and protein structure data and enables integrated analyses of metabolic functions in humans and is used to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs.
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The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Alberto Noronha,Jennifer Modamio,Yohan Jarosz,Elisabeth Guerard,Nicolas Sompairac,German Andres Preciat Gonzalez,Anna Dröfn Daníelsdóttir,Max Krecke,Diane Merten,Hulda S. Haraldsdóttir,Almut Heinken,Laurent Heirendt,Stefania Magnusdottir,Dmitry A. Ravcheev,Swagatika Sahoo,Piotr Gawron,Lucia Friscioni,Beatriz Garcia,Mabel Prendergast,Alberto Puente,Mariana Rodrigues,Akansha Roy,Mouss Rouquaya,Luca Wiltgen,Alise Žagare,Elisabeth John,Maren Krueger,Inna Kuperstein,Andrei Zinovyev,Reinhard Schneider,Ronan M. T. Fleming,Ronan M. T. Fleming,Ines Thiele +32 more
TL;DR: The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community and encapsulating current knowledge of human metabolism within five interlinked resources.