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Almut Heinken - Publications

Affiliations: 
2011-2015 Center for Systems Biology University of Iceland, Reykjavík, Iceland 
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V. A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of . Msystems. e0073624. PMID 39158303 DOI: 10.1128/msystems.00736-24  0.705
2024 Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, et al. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Scientific Reports. 14: 6095. PMID 38480804 DOI: 10.1038/s41598-024-55960-3  0.566
2023 Heinken A, El Kouche S, Rodriguez-Guéant RM, Guéant JL. Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications. Metabolism: Clinical and Experimental. 155738. PMID 37981189 DOI: 10.1016/j.metabol.2023.155738  0.395
2023 Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O'Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, et al. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. Biorxiv : the Preprint Server For Biology. PMID 37873072 DOI: 10.1101/2023.10.02.560573  0.713
2023 Hertel J, Heinken A, Fässler D, Thiele I. Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses. Cell Reports Methods. 3: 100615. PMID 37848031 DOI: 10.1016/j.crmeth.2023.100615  0.668
2023 Martinelli F, Heinken A, Henning AK, Wörheide MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston M, Johnson S, Kastenmüller G, et al. Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Research Square. PMID 37720019 DOI: 10.21203/rs.3.rs-3306891/v1  0.535
2023 Ternes D, Tsenkova M, Pozdeev VI, Meyers M, Koncina E, Atatri S, Schmitz M, Karta J, Schmoetten M, Heinken A, Rodriguez F, Delbrouck C, Gaigneaux A, Ginolhac A, Nguyen TTD, et al. Author Correction: The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. PMID 37709964 DOI: 10.1038/s42255-023-00898-5  0.533
2023 Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. Plos Computational Biology. 19: e1011363. PMID 37578975 DOI: 10.1371/journal.pcbi.1011363  0.322
2023 van der Spek A, Stewart ID, Kühnel B, Pietzner M, Alshehri T, Gauß F, Hysi PG, MahmoudianDehkordi S, Heinken A, Luik AI, Ladwig KH, Kastenmüller G, Menni C, Hertel J, Ikram MA, et al. Circulating metabolites modulated by diet are associated with depression. Molecular Psychiatry. PMID 37495887 DOI: 10.1038/s41380-023-02180-2  0.546
2023 Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I. Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. Gut Microbes. 15: 2226921. PMID 37438876 DOI: 10.1080/19490976.2023.2226921  0.666
2023 Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. Plos Biology. 21: e3002125. PMID 37205710 DOI: 10.1371/journal.pbio.3002125  0.717
2023 Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nature Biotechnology. PMID 36658342 DOI: 10.1038/s41587-022-01628-0  0.826
2023 Kindschuh WF, Baldini F, Liu MC, Liao J, Meydan Y, Lee HH, Heinken A, Thiele I, Thaiss CA, Levy M, Korem T. Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome. Nature Microbiology. PMID 36635575 DOI: 10.1038/s41564-022-01293-8  0.708
2022 Hertel J, Fässler D, Heinken A, Weiß FU, Rühlemann M, Bang C, Franke A, Budde K, Henning AK, Petersmann A, Völker U, Völzke H, Thiele I, Grabe HJ, Lerch MM, et al. NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health. Metabolites. 12. PMID 35448495 DOI: 10.3390/metabo12040308  0.636
2022 Ternes D, Tsenkova M, Pozdeev VI, Meyers M, Koncina E, Atatri S, Schmitz M, Karta J, Schmoetten M, Heinken A, Rodriguez F, Delbrouck C, Gaigneaux A, Ginolhac A, Nguyen TTD, et al. The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. 4: 458-475. PMID 35437333 DOI: 10.1038/s42255-022-00558-0  0.561
2022 Heinken A, Thiele I. Microbiome Modelling Toolbox 2.0: Efficient, tractable modelling of microbiome communities. Bioinformatics (Oxford, England). PMID 35157025 DOI: 10.1093/bioinformatics/btac082  0.594
2021 Heinken A, Magnúsdóttir S, Fleming RMT, Thiele I. DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. Bioinformatics (Oxford, England). PMID 34473240 DOI: 10.1093/bioinformatics/btab622  0.772
2021 Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine. Annual Review of Microbiology. PMID 34314593 DOI: 10.1146/annurev-micro-060221-012134  0.681
2021 Hertel J, Heinken A, Martinelli F, Thiele I. Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of spp. on community butyrate production. Gut Microbes. 13: 1-23. PMID 34057024 DOI: 10.1080/19490976.2021.1915673  0.682
2021 Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. Npj Systems Biology and Applications. 7: 19. PMID 33958598 DOI: 10.1038/s41540-021-00178-6  0.653
2020 Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ, Arnold M, Kastenmüller G, Griffiths WJ, Thiele I, et al. Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. Cell Reports. Medicine. 1: 100138. PMID 33294859 DOI: 10.1016/j.xcrm.2020.100138  0.596
2020 Thiele I, Sahoo S, Heinken A, Hertel J, Heirendt L, Aurich MK, Fleming RM. Personalized whole-body models integrate metabolism, physiology, and the gut microbiome. Molecular Systems Biology. 16: e8982. PMID 32463598 DOI: 10.15252/Msb.20198982  0.829
2019 Hertel J, Harms AC, Heinken A, Baldini F, Thinnes CC, Glaab E, Vasco DA, Pietzner M, Stewart ID, Wareham NJ, Langenberg C, Trenkwalder C, Krüger R, Hankemeier T, Fleming RMT, et al. Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease. Cell Reports. 29: 1767-1777.e8. PMID 31722195 DOI: 10.1016/J.Celrep.2019.10.035  0.736
2019 Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. 7: 75. PMID 31092280 DOI: 10.1186/S40168-019-0689-3  0.795
2019 Greenhalgh K, Ramiro-Garcia J, Heinken A, Ullmann P, Bintener T, Pacheco MP, Baginska J, Shah P, Frachet A, Halder R, Fritz JV, Sauter T, Thiele I, Haan S, Letellier E, et al. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Reports. 27: 1621-1632.e9. PMID 31042485 DOI: 10.1016/J.Celrep.2019.04.001  0.624
2019 Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2  0.721
2018 Baldini F, Heinken A, Heirendt L, Magnusdottir S, Fleming RMT, Thiele I. The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinformatics (Oxford, England). PMID 30462168 DOI: 10.1093/Bioinformatics/Bty941  0.781
2018 Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, et al. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. PMID 30371894 DOI: 10.1093/Nar/Gky992  0.79
2018 Magnúsdóttir S, Heinken A, Fleming RMT, Thiele I. Reply to "Challenges in modeling the human gut microbiome". Nature Biotechnology. 36: 686-691. PMID 30080835 DOI: 10.1038/Nbt.4212  0.795
2018 Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072  0.787
2017 Thiele I, Clancy CM, Heinken A, Fleming RMT. Quantitative systems pharmacology and the personalized drug-microbiota-diet axis. Current Opinion in Systems Biology. 4: 43-52. PMID 32984662 DOI: 10.1016/J.Coisb.2017.06.001  0.565
2017 Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. PMID 28393285 DOI: 10.1007/S00394-017-1445-8  0.678
2017 Heinken A. Systems biology: Prediction of health-relevant human-microbial co-metabolism through a computational framework Toxicology Letters. 280: S12. DOI: 10.1016/j.toxlet.2017.07.017  0.367
2017 Thiele I, Clancy CM, Heinken A, Fleming RM. Quantitative systems pharmacology and the personalized drug–microbiota–diet axis Current Opinion in Systems Biology. 4: 43-52. DOI: 10.1016/J.COISB.2017.06.001  0.448
2016 Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. PMID 27893703 DOI: 10.1038/Nbt.3703  0.786
2015 Heinken A, Thiele I. Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 7: 195-219. PMID 25929487 DOI: 10.1002/Wsbm.1301  0.673
2015 Heinken A, Thiele I. Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes. 6: 120-30. PMID 25901891 DOI: 10.1080/19490976.2015.1023494  0.719
2015 Heinken A, Thiele I. Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico. Applied and Environmental Microbiology. 81: 4049-61. PMID 25841013 DOI: 10.1128/Aem.00101-15  0.599
2014 Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I. Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. Journal of Bacteriology. 196: 3289-302. PMID 25002542 DOI: 10.1128/Jb.01780-14  0.719
2013 Thiele I, Heinken A, Fleming RM. A systems biology approach to studying the role of microbes in human health. Current Opinion in Biotechnology. 24: 4-12. PMID 23102866 DOI: 10.1016/J.Copbio.2012.10.001  0.695
2013 Heinken A, Sahoo S, Fleming RM, Thiele I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes. 4: 28-40. PMID 23022739 DOI: 10.4161/Gmic.22370  0.807
2012 Sigurdsson G, Fleming RM, Heinken A, Thiele I. A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. Plos One. 7: e34337. PMID 22523548 DOI: 10.1371/Journal.Pone.0034337  0.566
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