Literature list

Papers related to the example study, metabolomics from Nightingale and transcriptomics from Illumina Bead chip

Replacing Saturated Fat with Polyunsaturated Fat Modulates Peripheral Blood Mononuclear Cell Gene Expression and Pathways Related to Cardiovascular Disease Risk Using a Whole Transcriptome Approach.
Sunniva V Larsen, Kirsten B Holven, Jacob J Christensen, Arnar Flatberg, Amanda Rundblad, Lena Leder, Rune Blomhoff, Vibeke Telle-Hansen, Marjukka Kolehmainen, Carsten Carlberg, Mari C Myhrstad, Magne Thoresen, Stine M Ulven
Mol Nutr Food Res 65(24):e210063 (2021)

Using metabolic profiling and gene expression analyses to explore molecular effects of replacing saturated fat with polyunsaturated fat-a randomized controlled dietary intervention study.
Stine M Ulven, Jacob J Christensen, Ottar Nygård, Asbjørn Svardal, Lena Leder, Inger Ottestad, Vegard Lysne, Johnny Laupsa-Borge, Per Magne Ueland, Øivind Midttun, Klaus Meyer, Adrian McCann, Lene F Andersen, Kirsten B Holven
Am J Clin Nutr 1;109(5):1239-1250 (2019)

Paper example study transcriptomics from Illumina HiSeq 4000

High-protein diet more effectively reduces hepatic fat than low-protein diet despite lower autophagy and FGF21 levels.
Chenchen Xu, Mariya Markova, Nicole Seebeck, Anne Loft, Silke Hornemann, Thomas Gantert, Stefan Kabisch, Kathleen Herz, Jennifer Loske, Mario Ost, Verena Coleman, Frederick Klauschen, Anke Rosenthal, Volker Lange, Jürgen Machann, Susanne Klaus, Tilman Grune, Stephan Herzig, Olga Pivovarova-Ramich, Andreas F H Pfeiffer.
Liver Int;40(12):2982-299 (2020)

Papers related to the tools

WikiPathways: connecting communities.
Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M.
Nucleic Acids Res. 49(D1):D613-D621 (2021).)