Raphy Zarecki
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View article: The MISOPRED score: Development and validation of a clinical scoring system to predict the effectiveness of Misoprostol treatment for early pregnancy loss
The MISOPRED score: Development and validation of a clinical scoring system to predict the effectiveness of Misoprostol treatment for early pregnancy loss Open
Background Misoprostol treatment for early pregnancy loss has varied success demonstrated in previous studies. Incorporating predictors in a single clinical scoring system would be highly beneficial in clinical practice. Objective To devel…
View article: PR052/#439 Distinct vaginal microbiome ovarian cancer patients – a possible screening and prognostic biomarker?
PR052/#439 Distinct vaginal microbiome ovarian cancer patients – a possible screening and prognostic biomarker? Open
Introduction Microbiome plays an important role in development of cancer and response to chemotherapy. We aim to examine the significance of vaginal microbiome in epithelial ovarian cancer. Methods A prospective cohort study was conducted …
View article: ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction Open
Since the release of ModelSEED in 2010, the systems biology research community has used the ModelSEED genome-scale metabolic model reconstruction pipeline to build over 200,000 draft metabolic reconstructions that support hundreds of publi…
View article: #249 Distinct vaginal microbiome ovarian cancer patients – a possible screening and prognostic biomarker?
#249 Distinct vaginal microbiome ovarian cancer patients – a possible screening and prognostic biomarker? Open
Introduction/Background Microbiome plays an important role in development of cancer and response to chemotherapy. Vaginal microbiome constitutes a new study field. We aim to examine the significance of vaginal microbiome in epithelial ovar…
View article: Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil
Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil Open
Providing the food requirements of a growing population comes at the cost of intensive use of agrochemicals, including pesticides. Native microbial soil communities are considered key players in the degradation of such exogenous substances.
View article: Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling Open
Phenyl urea herbicides are being extensively used for weed control in both agricultural and non-agricultural applications. Linuron is one of the key herbicides in this family and is in wide use. Like other phenyl urea herbicides, it is kno…
View article: Prebiotic-Induced Anti-tumor Immunity Attenuates Tumor Growth
Prebiotic-Induced Anti-tumor Immunity Attenuates Tumor Growth Open
Growing evidence supports the importance of gut microbiota in the control of tumor growth and response to therapy. Here, we select prebiotics that can enrich bacterial taxa that promote anti-tumor immunity. Addition of the prebiotics inuli…
View article: Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5−/− mice
Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5−/− mice Open
Accumulating evidence points to an important role for the gut microbiome in anti-tumor immunity. Here, we show that altered intestinal microbiota contributes to anti-tumor immunity, limiting tumor expansion. Mice lacking the ubiquitin liga…
View article: Genome-Scale reconstruction of<i>Paenarthrobacter aurescens</i>TC1 metabolic model towards the study of atrazine bioremediation
Genome-Scale reconstruction of<i>Paenarthrobacter aurescens</i>TC1 metabolic model towards the study of atrazine bioremediation Open
Atrazine is an herbicide and pollutant of great environmental concern that is naturally biodegraded by microbial communities. The efficiency of biodegradation can be improved through the stimulating addition of fertilizers, electron accept…
View article: Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions Open
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine th…
View article: Diet‐induced changes of redox potential underlie compositional shifts in the rumen archaeal community
Diet‐induced changes of redox potential underlie compositional shifts in the rumen archaeal community Open
Summary Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem – a …
View article: Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli Open
Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that use…
View article: Building the KOMODO media database
Building the KOMODO media database Open
This protocol describes the process used to convert >1300 microbial media recipes, listed on the website of the Leibniz Institute DSMZ \(see: https://www.dsmz.de/?id=441), into a machine readable format, and then to read them into a SQL da…
View article: Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm Open
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable…