Review: Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.

Thiele M, Villesen IF, Niu L, Johansen S, Sulek K, Nishijima S, Van Espen L, Keller M, Israelsen M, Suvitaival T, de Zawadzki A, Juel HB, Brol MJ, Stinson SE, Huang Y, Alvarez Silva MC, Kuhn M, Anastasiadou E, Leeming DJ, Karsdal M, Matthijnssens J, Arumugam M, Dalgaard LT, Legido-Quigley C, Mann M, Trebicka J, Bork P, Jensen LJ, Hansen T, Krag A, MicrobLiver and GALAXY consortia, GALAXY consortium, MicrobLiver consortium

Journal of hepatology, 2024

doi:10.1016/j.jhep.2024.03.035.

Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P

Molecular systems biology, 2023

doi:10.15252/msb.202311525.

Sphingolipids are depleted in alcohol-related liver fibrosis.

Thiele M, Suvitaival T, Trošt K, Kim M, de Zawadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Moitinho-Silva L, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, MicrobLiver, GALAXY Consortia

Gastroenterology, 2023

doi:10.1053/j.gastro.2023.02.023.

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort.

Nishijima S, Nagata N, Kiguchi Y, Kojima Y, Miyoshi-Akiyama T, Kimura M, Ohsugi M, Ueki K, Oka S, Mizokami M, Itoi T, Kawai T, Uemura N, Hattori M

Nature communications, 2022

doi:10.1038/s41467-022-32832-w.

Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome.

Nagata N, Nishijima S, Miyoshi-Akiyama T, Kojima Y, Kimura M, Aoki R, Ohsugi M, Ueki K, Miki K, Iwata E, Hayakawa K, Ohmagari N, Oka S, Mizokami M, Itoi T, Kawai T, Uemura N, Hattori M

Gastroenterology, 2022

doi:10.1053/j.gastro.2022.06.070.

Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study.

Nagata N, Nishijima S, Kojima Y, Hisada Y, Imbe K, Miyoshi-Akiyama T, Suda W, Kimura M, Aoki R, Sekine K, Ohsugi M, Miki K, Osawa T, Ueki K, Oka S, Mizokami M, Kartal E, Schmidt TSB, Molina-Montes E, Estudillo L, Malats N, Trebicka J, Kersting S, Langheinrich M, Bork P, Uemura N, Itoi T, Kawai T

Gastroenterology, 2022

doi:10.1053/j.gastro.2022.03.054.

Erratum to: Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.

Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W

DNA research : an international journal for rapid publication of reports on genes and genomes, 2021

doi:10.1093/dnares/dsab025.

Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA preprocessing chimeric reads.

Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W

DNA research : an international journal for rapid publication of reports on genes and genomes, 2021

doi:10.1093/dnares/dsab019.

Association of the liver and plasma lipidomes with the histological stage of alcohol-related liver disease.

Thiele M, Suvitaival T, Trošt K, Kim M, de Zewadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Silva LM, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, on behalf of the MicrobLiver and GALAXY Consortia

medRxiv, 2021

doi:10.1101/2021.07.13.21260429.

Emergence of the novel aminoglycoside acetyltransferase variant aac(6')-Ib-D179Y and acquisition of colistin heteroresistance in carbapenem-resistant Klebsiella pneumoniae due to a disrupting mutation in the DNA repair enzyme MutS.

Sato T, Wada T, Nishijima S, Fukushima Y, Nakajima C, Suzuki Y, Takahashi S, Yokota SI

mBio, 2020

doi:10.1128/mBio.01954-20.