Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Tập 7 Số 1 - 2011
Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo López, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie Thompson, Desmond G. Higgins
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection Tập 2 Số 1 - 2006
Tomoya Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Kirill A. Datsenko, Masaru Tomita, Barry L. Wanner, Hirotada Mori
Potential of fecal microbiota for early‐stage detection of colorectal cancer Tập 10 Số 11 - 2014
Georg Zeller, Julien Tap, Anita Y. Voigt, Shinichi Sunagawa, Jens Roat Kultima, Paul Igor Costea, Aurélien Amiot, Jürgen Böhm, Francesco Brunetti, Nina Habermann, Rajna Hercog, Moritz Koch, Alain Luciani, Daniel R. Mende, Martin Schneider, Petra Schrotz‐King, Christophe Tournigand, Jeanne Tran Van Nhieu, Takuji Yamada, Jürgen Zimmermann, Vladimı́r Beneš, Matthias Kloor, Cornelia M. Ulrich, Magnus von Knebel Doeberitz, Iradj Sobhani, Peer Bork
AbstractSeveral bacterial species have been implicated in the development of colorectal carcinoma (CRC), butCRC‐associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguishedCRCpatients from tumor‐free controls in a study population of 156 participants. Accuracy of metagenomicCRCdetection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to theFOBT, while maintaining its specificity. Accuracy of metagenomicCRCdetection did not differ significantly between early‐ and late‐stage cancer and could be validated in independent patient and control populations (N = 335) from different countries.CRC‐associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor‐related host–microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids inCRCpatients, accompanied by an increase of lipopolysaccharide metabolism.
Revisiting biomarker discovery by plasma proteomics Tập 13 Số 9 - 2017
Philipp E. Geyer, Lesca M. Holdt, Daniel Teupser, Matthias Mann
AbstractClinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)‐based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous “triangular strategies” aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a “rectangular” plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision‐making, and we discuss some first steps in this direction.
