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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
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Posts
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portfolio
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publications
ProtozoaDB: dynamic visualization and exploration of protozoan genomes.
Published in Nucleic acids research, 2008
Use Google Scholar for full citation
Recommended citation: Alberto Dávila, Pablo Mendes, Glauber Wagner, Diogo Tschoeke, Rafael Cuadrat, Felipe Liberman, Luciana Matos, Thiago Satake, Kary Ocaña, Omar Triana, Sérgio Cruz, Henrique Jucá, Juliano Cury, Fabricio Silva, Guilherme Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano Silva, Christian Probst, Edmundo Grisard, Marco Krieger, Samuel Goldenberg, Maria Cavalcanti, Milton Moraes, Maria Campos, Marta Mattoso, "ProtozoaDB: dynamic visualization and exploration of protozoan genomes.." Nucleic acids research, 2008.
Detecting distant homologies on protozoans metabolic pathways using scientific workflows.
Published in International journal of data mining and bioinformatics, 2010
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Recommended citation: da SM, Batista V, Silva E, Tosta F, Vilela C, Cuadrat R, Tschoeke D, Dávila AM, Campos ML, Mattoso M, "Detecting distant homologies on protozoans metabolic pathways using scientific workflows.." International journal of data mining and bioinformatics, 2010.
An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.
Published in Omics : a journal of integrative biology, 2014
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Recommended citation: Rafael Cuadrat, Sérgio Serra, Diogo Tschoeke, Edno Silva, Frederico Tosta, Henrique Jucá, Rodrigo Jardim, Maria Campos, Marta Mattoso, Alberto Dávila, "An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.." Omics : a journal of integrative biology, 2014.
Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS.
Published in International journal of molecular sciences, 2015
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Recommended citation: Cuadrat RR, Cury JC, Dávila AM, "Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS.." International journal of molecular sciences, 2015.
Distribution and Classification of Serine ?-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases.
Published in Frontiers in microbiology, 2016
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Recommended citation: Adriana Fróes, Fábio Mota, Rafael Cuadrat, Alberto Dávila, "Distribution and Classification of Serine ?-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases.." Frontiers in microbiology, 2016.
Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo–Brazil).
Published in Omics : a journal of integrative biology, 2016
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Recommended citation: Rafael Cuadrat, Isabel Ferrera, Hans-Peter Grossart, Alberto Dávila, "Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil).." Omics : a journal of integrative biology, 2016.
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa.
Published in Evolutionary bioinformatics online, 2018
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Recommended citation: Darueck Campos, Elisa Pereira, Rodrigo Jardim, Rafael Cuadrat, Juliana Bernardes, Alberto Dávila, "Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa.." Evolutionary bioinformatics online, 2018.
Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.
Published in Frontiers in microbiology, 2018
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Recommended citation: Rafael Cuadrat, Danny Ionescu, Alberto Dávila, Hans-Peter Grossart, "Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.." Frontiers in microbiology, 2018.
Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples
Published in GigaScience, 2020
Recommended citation: Rafael Cuadrat, Maria Sorokina, Bruno Andrade, Tobias Goris, Alberto Dávila, "Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples." GigaScience, 2020. http://doi.org/10.1093/gigascience/giaa046
Replication of 15 loci involved in human plasma protein N-glycosylation in 4802 samples from four cohorts
Published in Glycobiology, 2020
Recommended citation: Sodbo Zh Sharapov, Alexandra S Shadrina, Yakov A Tsepilov, Elizaveta E Elgaeva, Evgeny S Tiys, Sofya G Feoktistova, Olga O Zaytseva, Frano Vuckovic, Rafael Cuadrat et al, "Replication of 15 loci involved in human plasma protein N-glycosylation in 4802 samples from four cohorts." Glycobiology, 2020. http://doi.org/10.1093/glycob/cwaa053
The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen.
Published in Journal of animal science and biotechnology, 2020
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Recommended citation: Bruno Andrade, Flavia Bressani, Rafael Cuadrat, Polyana Tizioto, Priscila Oliveira, Gerson Mourão, Luiz Coutinho, James Reecy, James Koltes, Paul Walsh, Alexandre Berndt, Julio Palhares, Luciana Regitano, "The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen.." Journal of animal science and biotechnology, 2020.
Desaturase Activity and the Risk of Type 2 Diabetes and Coronary Artery Disease: A Mendelian Randomization Study
Published in Nutrients, 2020
Recommended citation: Jäger, S.; Cuadrat, R.; Hoffmann, P.; Wittenbecher, C.; Schulze, M.B. Desaturase Activity and the Risk of Type 2 Diabetes and Coronary Artery Disease: A Mendelian Randomization Study. Nutrients 2020, 12, 2261.
Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine as Causal Trait for Type 2 Diabetes
Published in Nutrients, 2020
Recommended citation: Jäger, S.; Cuadrat, R.; Wittenbecher, C.; Floegel, A.; Hoffmann, P.; Prehn, C.; Adamski, J.; Pischon, T.; Schulze, M.B. Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine as Causal Trait for Type 2 Diabetes. Nutrients 2020, 12, 3890. https://doi.org/10.3390/nu12123890
Obesity Partially Mediates the Diabetogenic Effect of Lowering LDL Cholesterol
Published in Diabetes Care, 2021
Recommended citation: Obesity Partially Mediates the Diabetogenic Effect of Lowering LDL Cholesterol. Peitao Wu, Jee-Young Moon, Iyas Daghlas, Giulianini Franco, Bianca C. Porneala, Fariba Ahmadizar, Tom G. Richardson, Jonas L. Isaksen, Georgy Hindy, Jie Yao, Colleen M. Sitlani, Laura M. Raffield, Lisa R. Yanek, Mary F. Feitosa, Rafael R.C. Cuadrat, Qibin Qi, M. Arfan Ikram, Christina Ellervik, Ulrika Ericson, Mark O. Goodarzi, Jennifer A. Brody, Leslie Lange, Josep M. Mercader, Dhananjay Vaidya, Ping An, Matthias B. Schulze, Lluis Masana, Mohsen Ghanbari, Morten S. Olesen, Jianwen Cai, Xiuqing Guo, James S. Floyd, Susanne Jäger, Michael A. Province, Rita R. Kalyani, Bruce M. Psaty, Marju Orho-Melander, Paul M. Ridker, Jørgen K. Kanters, Andre Uitterlinden, George Davey Smith, Dipender Gill, Robert C. Kaplan, Maryam Kavousi, Sridharan Raghavan, Daniel I. Chasman, Jerome I. Rotter, James B. Meigs, Jose C. Florez, Josée Dupuis, Ching-Ti Liu, Jordi Merino Diabetes Care Nov 2021, dc211284; DOI: 10.2337/dc21-1284
Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19
Published in Frontiers in Microbiology, 2021
Recommended citation: Maria Paz Ventero*; Rafael R C Cuadrat*; Inmaculada Vidal; Bruno G N Andrade; Carmen Molina-Pardines; Jose M Haro-Moreno; Felipe H Coutinho; Esperanza Merino; Luciana C A Regitano; Cynthia B Silveira; Haithem Afli; Mario López-Pérez; Juan Carlos Rodríguez. Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19. Frontiers in Microbiology 2021.
Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells
Published in Pathogens, 2021
Recommended citation: Islam, M.D.A.; Albarracin,L.; Melnikov, V.;,Andrade,B.G.N.; Cuadrat, R.; Kitazawa, H.; Eichelmann, F.; Villena, J. Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells. Pathogens. 2021.
Advanced glycation end-products, measured as skin autofluorescence, associate with vascular stiffness in diabetic, pre-diabetic and normoglycemic individuals: a cross-sectional study
Published in Cardiovascular Diabetology, 2021
Recommended citation: Birukov, A.; Cuadrat, R.; Polemiti, E.; Eichelmann, F.; Schulze, M.B. Advanced glycation end-products, measured as skin autofluorescence, associate with vascular stiffness in diabetic, pre-diabetic and normoglycemic individuals: a cross-sectional study. Cardiovascular Diabetology 2021.
Putative mobilized colistin resistance genes in the human gut microbiome
Published in BMC Microbiology, 2021
Recommended citation: Andrade BGN, Goris T, Afli H, Coutinho FH, Dávila AMR, Cuadrat RRC. Putative mobilized colistin resistance genes in the human gut microbiome. BMC Microbiology. 2021;21:220.
Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study
Published in Nutrients, 2021
Recommended citation: Goris, T.; Cuadrat, R.R.C.; Braune, A. Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study. Nutrients 2021, 13, 2688.
Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis
Published in Nutrients, 2021
Recommended citation: Pinart, M.; Nimptsch, K.; Forslund, S.K.; Schlicht, K.; Gueimonde, M.; Brigidi, P.; Turroni, S.; Ahrens, W.; Hebestreit, A.; Wolters, M.; Dötsch, A.; Nöthlings, U.; Oluwagbemigun, K.; Cuadrat, R.R.C.; Schulze, M.B.; Standl, M.; Schloter, M.; De Angelis, M.; Iozzo, P.; Guzzardi, M.A.; Vlaemynck, G.; Penders, J.; Jonkers, D.M.A.E.; Stemmer, M.; Chiesa, G.; Cavalieri, D.; De Filippo, C.; Ercolini, D.; De Filippis, F.; Ribet, D.; Achamrah, N.; Tavolacci, M.-P.; Déchelotte, P.; Bouwman, J.; Laudes, M.; Pischon, T. Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis. Nutrients 2021, 13, 3292. https://doi.org/10.3390/nu13093292
Immunobiotic Lactobacilli Improve Resistance of Respiratory Epithelial Cells to SARS-CoV-2 Infection
Published in Pathogens, 2021
Recommended citation: Islam, M.A.; Albarracin, L.; Tomokiyo, M.; Valdez, J.C.; Sacur, J.; Vizoso-Pinto, M.G.; Andrade, B.G.N.; Cuadrat, R.R.C.; Kitazawa, H.; Villena, J. Immunobiotic Lactobacilli Improve Resistance of Respiratory Epithelial Cells to SARS-CoV-2 Infection. Pathogens 2021, 10, 1197. https://doi.org/10.3390/pathogens10091197
Dihydroceramide-and ceramide-profiling provides insights into human cardiometabolic disease etiology
Published in Nature Communications, 2022
Recommended citation: Wittenbecher, C., Cuadrat, R., Johnston, L. et al. Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology. Nat Commun 13, 936 (2022). https://doi.org/10.1038/s41467-022-28496-1
The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19
Published in Bioscience of Microbiota, Food and Health, 2022
Recommended citation: Bruno G. N. ANDRADE, Rafael R. C. CUADRAT, Fernanda Raya TONETTI, Haruki KITAZAWA, Julio VILLENA, The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19, Bioscience of Microbiota, Food and Health, Article ID 2022-009
Stool and ruminal microbiome components associated with methane emission and feed efficiency in Nelore beef cattle
Published in Frontiers in Genetics, 2022
Recommended citation:
Deep Lipidomics in Human Plasma - Cardiometabolic Disease Risk and Effect of Dietary Fat Modulation.
Published in Circulation, 2022
Recommended citation: Eichelmann F, Sellem L, Wittenbecher C, Jäger S, Kuxhaus O, Prada M, Cuadrat R, Jackson KG, Lovegrove JA, Schulze MB. Deep Lipidomics in Human Plasma - Cardiometabolic Disease Risk and Effect of Dietary Fat Modulation. Circulation. 2022 Apr 15. doi: 10.1161/CIRCULATIONAHA.121.056805. Epub ahead of print. PMID: 35422138.
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Winter School - Computational Biology
Workshop, Oswaldo Cruz Institute, 2010
Two lectures: Structural Bioinformatics and Sequence functional annotation
Advanced Approaches in Molecular Biology
Masters, Oswaldo Cruz Institute, 2014
Cellular and Molecular Biology (BCM) grad school (Masters)
Introduction to Python
Workshop, Max Plank Institute for Biology of Ageing, 2018
Introduction to Python Workshop in the MPI-AGE Bioinformatics Core Facility
Data wrangling in Python
Workshop, Max Plank Institute for Biology of Ageing, 2018
Data wrangling in Python Workshop in the MPI-AGE Bioinformatics Core Facility
Biodiversity and Evolution
Masters in Bioinformatcis course, Free University Berlin, 2019
Contributing Lecturer for Biodiversity and Evolution Core module in the Bioinformatics Master program