Patiño-Navarrete, Rafael Rosinski-Chupin, Isabelle Cabanel, Nicolas Gauthier, Lauraine Takissian, Julie Madec, Jean-Yves Hamze, Monzer Bonnin, Remy A. Naas, Thierry Glaser, Philippe
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Published in
Genome Medicine
BackgroundCarbapenem-resistant Enterobacteriaceae are considered by WHO as “critical” priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largel...
Hillary, Robert F. Trejo-Banos, Daniel Kousathanas, Athanasios McCartney, Daniel L. Harris, Sarah E. Stevenson, Anna J. Patxot, Marion Ojavee, Sven Erik Zhang, Qian Liewald, David C.
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Published in
Genome Medicine
BackgroundThe molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.MethodsIn thi...
Creswell, Richard Tan, Jie Leff, Jonathan W. Brooks, Brandon Mahowald, Michael A. Thieroff-Ekerdt, Ruth Gerber, Georg K.
Published in
Genome Medicine
BackgroundDietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds ...
Xiao, Minfeng Liu, Xiaoqing Ji, Jingkai Li, Min Li, Jiandong Yang, Lin Sun, Wanying Ren, Peidi Yang, Guifang Zhao, Jincun
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Published in
Genome Medicine
BackgroundCOVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-...
Benech, Nicolas Sokol, Harry
Published in
Genome Medicine
Fecal microbiota transplantation (FMT) has demonstrated efficacy in treating inflammatory bowel diseases and irritable bowel syndrome in an increasing number of randomized controlled trials. Recently published data gives striking insights into the factors associated with FMT success paving the road for the use of precision medicine in gastrointesti...
Teschendorff, Andrew E.
Published in
Genome Medicine
BackgroundDNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic “mitotic” clocks that can measure the lifetime number of stem cell divisions is of par...
Erger, Florian Nörling, Deborah Borchert, Domenica Leenen, Esther Habbig, Sandra Wiesener, Michael S. Bartram, Malte P. Wenzel, Andrea Becker, Christian Toliat, Mohammad R.
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Published in
Genome Medicine
Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion b...
Trzupek, Dominik Dunstan, Melanie Cutler, Antony J. Lee, Mercede Godfrey, Leila Jarvis, Lorna Rainbow, Daniel B. Aschenbrenner, Dominik Jones, Joanne L. Uhlig, Holm H.
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Published in
Genome Medicine
BackgroundTraditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing (scRNA-seq) and antibody-based cytometry. Here, we present a multi-omics approach allowing the simultaneous targeted quantification of mRNA ...
Zhong, Wen Gummesson, Anders Tebani, Abdellah Karlsson, Max J. Hong, Mun-Gwan Schwenk, Jochen M. Edfors, Fredrik Bergström, Göran Fagerberg, Linn Uhlén, Mathias
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Published in
Genome Medicine
BackgroundThe human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors to determine the specific protein levels in individuals and to gain a deeper insight of the importance of genetic architecture rela...
Oak, Ninad Cherniack, Andrew D. Mashl, R. Jay Carrot-Zhang, Jian Chambwe, Nyasha Damrauer, Jeffrey S. Knijnenburg, Theo A. Robertson, A. Gordon Yau, Christina Zhou, Wanding
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Published in
Genome Medicine
BackgroundDistinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of germline genomes are required to inform cancer genetic risk and prognosis of diverse populations.MethodsWe conducted analyses using germline and somatic sequencing data generated by ...
