Transient colonizing microbes promote gut dysbiosis and functional impairment

Authors: Sunjae Lee, Victoria Meslier, Gholamreza Bidkhori, Fernando Garcia-Guevara, Lucie Etienne-Mesmin, Frederick Clasen, Junseok Park, Florian Plaza Oñate, Haizhuang Cai, Emmanuelle Le Chatelier, Nicolas Pons, Marcela Pereira, Maike Seifert, Fredrik Boulund, Lars Engstrand, Doheon Lee, Gordon Proctor, Adil Mardinoglu, Stéphanie Blanquet-Diot, David Moyes, Mathieu Almeida, S. Dusko Ehrlich, Mathias Uhlen, Saeed Shoaie

Source: npj Biofilms and Microbiomes, Vol 10, Iss 1, Pp 1-11 (2024)

Subject Terms: Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2055-5008

Access URL: https://doaj.org/article/a887eb4803374d36b77690db31148648

Identification of SPP1+ macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics

Authors: Han Jin, Woonghee Kim, Meng Yuan, Xiangyu Li, Hong Yang, Mengzhen Li, Mengnan Shi, Hasan Turkez, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: hepatocellular carcinoma, co-expression network, tumor-associated macrophage, macrophage heterogeneity, single-cell sequencing, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1446453/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/e8476c5fe8284c0a96763992a412a4af

Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment

Authors: Bouchra Ezzamouri, Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee, Mathias Uhlen, Saeed Shoaie

Source: npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-8 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2056-7189

Access URL: https://doaj.org/article/89849651f01544f3b2f52806c5993f83

Integrative functional analysis uncovers metabolic differences between Candida species

Authors: Neelu Begum, Sunjae Lee, Theo John Portlock, Aize Pellon, Shervin Dokht Sadeghi Nasab, Jens Nielsen, Mathias Uhlen, David L. Moyes, Saeed Shoaie

Source: Communications Biology, Vol 5, Iss 1, Pp 1-12 (2022)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/ed773267446344fa9204e94dfdd48fed

Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Authors: Fei Wang, Peiwen Ding, Xue Liang, Xiangning Ding, Camilla Blunk Brandt, Evelina Sjöstedt, Jiacheng Zhu, Saga Bolund, Lijing Zhang, Laura P. M. H. de Rooij, Lihua Luo, Yanan Wei, Wandong Zhao, Zhiyuan Lv, János Haskó, Runchu Li, Qiuyu Qin, Yi Jia, Wendi Wu, Yuting Yuan, Mingyi Pu, Haoyu Wang, Aiping Wu, Lin Xie, Ping Liu, Fang Chen, Jacqueline Herold, Joanna Kalucka, Max Karlsson, Xiuqing Zhang, Rikke Bek Helmig, Linn Fagerberg, Cecilia Lindskog, Fredrik Pontén, Mathias Uhlen, Lars Bolund, Niels Jessen, Hui Jiang, Xun Xu, Huanming Yang, Peter Carmeliet, Jan Mulder, Dongsheng Chen, Lin Lin, Yonglun Luo

Source: Nature Communications, Vol 13, Iss 1, Pp 1-18 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c21d50994fe24c6aa783a0e4f2146142

Genome-wide annotation of protein-coding genes in pig

Authors: Max Karlsson, Evelina Sjöstedt, Per Oksvold, Åsa Sivertsson, Jinrong Huang, María Bueno Álvez, Muhammad Arif, Xiangyu Li, Lin Lin, Jiaying Yu, Tao Ma, Fengping Xu, Peng Han, Hui Jiang, Adil Mardinoglu, Cheng Zhang, Kalle von Feilitzen, Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, Wen Zhong, Linn Fagerberg, Cecilia Lindskog, Fredrik Pontén, Jan Mulder, Yonglun Luo, Mathias Uhlen

Source: BMC Biology, Vol 20, Iss 1, Pp 1-18 (2022)

Subject Terms: Annotation, Protein-coding genes, Genome-wide, Transcriptome, Gene expression, Tissue expression profile, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/1a4c2eb074664d69abac78894b05f1bc

Host-mycobiome metabolic interactions in health and disease

Authors: Neelu Begum, Azadeh Harzandi, Sunjae Lee, Mathias Uhlen, David L. Moyes, Saeed Shoaie

Source: Gut Microbes, Vol 14, Iss 1 (2022)

Subject Terms: Mycobiome, microbiome, metabolism, host-mycobiome interaction, systems biology, secondary metabolism, Diseases of the digestive system. Gastroenterology, RC799-869

File Description: electronic resource

Relation: https://doaj.org/toc/1949-0976; https://doaj.org/toc/1949-0984

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Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

Authors: Cheng Zhang, Mengnan Shi, Woonghee Kim, Muhammad Arif, Martina Klevstig, Xiangyu Li, Hong Yang, Cemil Bayram, Ismail Bolat, Özlem Özdemir Tozlu, Ahmet Hacımuftuoglu, Serkan Yıldırım, Jihad Sebhaoui, Shazia Iqbal, Yongjun Wei, Xiaojing Shi, Jens Nielsen, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu

Source: EBioMedicine, Vol 83, Iss , Pp 104214- (2022)

Subject Terms: Systems biology, Drug repositioning, NAFLD, PKLR, Circadian rhythms, Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396422003966; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/36818a6a57cf492cbc5540d8d174de87

Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders

Authors: Ceri Proffitt, Gholamreza Bidkhori, Sunjae Lee, Abdellah Tebani, Adil Mardinoglu, Mathias Uhlen, David L. Moyes, Saeed Shoaie

Source: iScience, Vol 25, Iss 7, Pp 104513- (2022)

Subject Terms: Microbiome, Systems biology, Metabolomics, Omics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004222007842; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/1218c72e51e849f2b695c26beafefd83

Integration of molecular profiles in a longitudinal wellness profiling cohort

Authors: Abdellah Tebani, Anders Gummesson, Wen Zhong, Ina Schuppe Koistinen, Tadepally Lakshmikanth, Lisa M. Olsson, Fredrik Boulund, Maja Neiman, Hans Stenlund, Cecilia Hellström, Max J. Karlsson, Muhammad Arif, Tea Dodig-Crnković, Adil Mardinoglu, Sunjae Lee, Cheng Zhang, Yang Chen, Axel Olin, Jaromir Mikes, Hanna Danielsson, Kalle von Feilitzen, Per-Anders Jansson, Oskar Angerås, Mikael Huss, Sanela Kjellqvist, Jacob Odeberg, Fredrik Edfors, Valentina Tremaroli, Björn Forsström, Jochen M. Schwenk, Peter Nilsson, Thomas Moritz, Fredrik Bäckhed, Lars Engstrand, Petter Brodin, Göran Bergström, Mathias Uhlen, Linn Fagerberg

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/4e06e15116714dfc930064890d3c4d1a

Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach

Authors: Xiangyu Li, Koeun Shong, Woonghee Kim, Meng Yuan, Hong Yang, Yusuke Sato, Haruki Kume, Seishi Ogawa, Hasan Turkez, Saeed Shoaie, Jan Boren, Jens Nielsen, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu

Source: EBioMedicine, Vol 78, Iss , Pp 103963- (2022)

Subject Terms: Systems biology, Co-expression network, Target chemotherapy, Drug repositioning, ccRCC, Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396422001475; https://doaj.org/toc/2352-3964

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Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase

Authors: Umberto Maria Battisti, Leticia Monjas, Fady Akladios, Josipa Matic, Eric Andresen, Carolin H. Nagel, Malin Hagkvist, Liliana Håversen, Woonghee Kim, Mathias Uhlen, Jan Borén, Adil Mardinoğlu, Morten Grøtli

Source: Pharmaceuticals, Vol 16, Iss 5, p 668 (2023)

Subject Terms: NAFLD, liver pyruvate kinase, allosteric inhibitors, urolithin C, SAR studies, Medicine, Pharmacy and materia medica, RS1-441

File Description: electronic resource

Relation: https://www.mdpi.com/1424-8247/16/5/668; https://doaj.org/toc/1424-8247

Access URL: https://doaj.org/article/030b7f82a2c046bcb5af2aeb60b25820

Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Authors: Fei Wang, Peiwen Ding, Xue Liang, Xiangning Ding, Camilla Blunk Brandt, Evelina Sjöstedt, Jiacheng Zhu, Saga Bolund, Lijing Zhang, Laura P. M. H. de Rooij, Lihua Luo, Yanan Wei, Wandong Zhao, Zhiyuan Lv, János Haskó, Runchu Li, Qiuyu Qin, Yi Jia, Wendi Wu, Yuting Yuan, Mingyi Pu, Haoyu Wang, Aiping Wu, Lin Xie, Ping Liu, Fang Chen, Jacqueline Herold, Joanna Kalucka, Max Karlsson, Xiuqing Zhang, Rikke Bek Helmig, Linn Fagerberg, Cecilia Lindskog, Fredrik Pontén, Mathias Uhlen, Lars Bolund, Niels Jessen, Hui Jiang, Xun Xu, Huanming Yang, Peter Carmeliet, Jan Mulder, Dongsheng Chen, Lin Lin, Yonglun Luo

Source: Nature Communications, Vol 13, Iss 1, Pp 1-2 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d4cf4c7a7e6b438db4f2246d1eed4075

Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms

Authors: Wen Zhong, Ozlem Altay, Muhammad Arif, Fredrik Edfors, Levent Doganay, Adil Mardinoglu, Mathias Uhlen, Linn Fagerberg

Source: EBioMedicine, Vol 74, Iss , Pp 103723- (2021)

Subject Terms: COVID-19, Protein profiling, Plasma proteome, Immune response, Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S235239642100517X; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/7164b72146b44fdc9e77d6fdcc3f62b6

Systems biology perspective for studying the gut microbiota in human physiology and liver diseases

Authors: Ozlem Altay, Jens Nielsen, Mathias Uhlen, Jan Boren, Adil Mardinoglu

Source: EBioMedicine, Vol 49, Iss , Pp 364-373 (2019)

Subject Terms: Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396419306486; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/617acadb0bc14ea894b3420f8af1adc6

Discovery of therapeutic agents for prostate cancer using genome-scale metabolic modeling and drug repositioningResearch in context

Authors: Beste Turanli, Cheng Zhang, Woonghee Kim, Rui Benfeitas, Mathias Uhlen, Kazim Yalcin Arga, Adil Mardinoglu

Source: EBioMedicine, Vol 42, Iss , Pp 386-396 (2019)

Subject Terms: Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396419301495; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/9cf566f76b6448b196142f1d5b3f9f34

Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning

Authors: Xiangyu Li, Woonghee Kim, Kajetan Juszczak, Muhammad Arif, Yusuke Sato, Haruki Kume, Seishi Ogawa, Hasan Turkez, Jan Boren, Jens Nielsen, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu

Source: iScience, Vol 24, Iss 7, Pp 102722- (2021)

Subject Terms: bioinformatics, systems biology, cancer systems biology, omics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004221006908; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/52a93b00478d4a87a1b9119115bb9801

Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans

Authors: J. R. Bosley, Elias Björnson, Cheng Zhang, Hasan Turkez, Jens Nielsen, Mathias Uhlen, Jan Borén, Adil Mardinoglu

Source: Frontiers in Pharmacology, Vol 12 (2021)

Subject Terms: Pharmacokinectics, L-Serine (ser), systems biology, NAFLD (non alcoholic fatty liver disease), oral supplementation, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fphar.2021.643179/full; https://doaj.org/toc/1663-9812

Access URL: https://doaj.org/article/050788f1b9954409a6125468655b936f

Current Status of COVID-19 Therapies and Drug Repositioning Applications

Authors: Ozlem Altay, Elyas Mohammadi, Simon Lam, Hasan Turkez, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu

Source: iScience, Vol 23, Iss 7, Pp 101303- (2020)

Subject Terms: Health Sciences, Medicine, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004220304909; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/35343d1548aa4bf1b16857380aeb4f8d

Systems Biology Approaches to Understand the Host–Microbiome Interactions in Neurodegenerative Diseases

Authors: Dorines Rosario, Jan Boren, Mathias Uhlen, Gordon Proctor, Dag Aarsland, Adil Mardinoglu, Saeed Shoaie

Source: Frontiers in Neuroscience, Vol 14 (2020)

Subject Terms: systems biology, microbiota-gut-brain axis, neurodegenerative diseases, Parkinson’s disease, Alzheimer’s disease, biologic network, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fnins.2020.00716/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/b95de6fe83be4acd83149ab1a6a33308