Systems Biology

Modelling of zero-inflation improves inference of metagenomic gene count data

Jonsson V, Österlund T, Nerman O, Kristiansson E

Stat Methods Med Res - (-) 096228021881135 [2018-11-25; online 2018-11-25]

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ

PLoS Comput. Biol. 14 (10) e1006541 [2018-10-18; online 2018-10-18]

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G

pmc GEO GEO

Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Systems Biology [Collaborative]

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Systems Biology [Collaborative]

Year 2017

Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases

Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K

Journal of Experimental Biology - (-) - [2017-12-01; online 2017-11-27]

Bioinformatics Long-term Support WABI [Collaborative] Systems Biology [Collaborative]

Genome scale metabolic modeling of cancer

Nilsson A, Nielsen J

Metabolic Engineering 43 (-) 103-112 [2017-09-00; online 2017-09-00]

Systems Biology of Metabolism

Nielsen J

Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-06-20]

Year 2016

Integrative analysis of human omics data using biomolecular networks.

Robinson JL, Nielsen J

Mol Biosyst 12 (10) 2953-2964 [2016-10-20; online 2016-08-12]

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

Gatto F, Schulze A, Nielsen J

Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J

pmc

Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J

Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]

Transcriptomics resources of human tissues and organs.

Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J

pmc

Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]

NGI Stockholm (Genomics Production) [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]

Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.

Gatto F, Nielsen J

pmc

J Hematol Oncol 9 (-) 15 [2016-03-02; online 2016-03-02]

Year 2015

In search for symmetries in the metabolism of cancer.

Gatto F, Nielsen J

Wiley Interdiscip Rev Syst Biol Med 8 (1) 23-35 [2015-11-05; online 2015-11-05]