Search Results - "Brazma, A."

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis by Durinck, Steffen, Moreau, Yves, Kasprzyk, Arek, Davis, Sean, De Moor, Bart, Brazma, Alvis, Huber, Wolfgang

“…biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene…”
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ArrayExpress--a public database of microarray experiments and gene expression profiles by Parkinson, H, Kapushesky, M, Shojatalab, M, Abeygunawardena, N, Coulson, R, Farne, A, Holloway, E, Kolesnykov, N, Lilja, P, Lukk, M, Mani, R, Rayner, T, Sharma, A, William, E, Sarkans, U, Brazma, A

“…ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts--the ArrayExpress Repository, which is a…”
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ArrayExpress--a public database of microarray experiments and gene expression profiles by Parkinson, H, Kapushesky, M, Shojatalab, M, Abeygunawardena, N, Coulson, R, Farne, A, Holloway, E, Kolesnykov, N, Lilja, P, Lukk, M, Mani, R, Rayner, T, Sharma, A, William, E, Sarkans, U, Brazma, A

“…ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts--the ArrayExpress Repository, which is a…”
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ArrayExpress—a public repository for microarray gene expression data at the EBI by Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, Holloway, Ele, Kapushesky, Misha, Kemmeren, Patrick, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Rocca-Serra, Philippe, Sansone, Susanna-Assunta

“…ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all…”
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ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments by Parkinson, Helen, Sarkans, Ugis, Kolesnikov, Nikolay, Abeygunawardena, Niran, Burdett, Tony, Dylag, Miroslaw, Emam, Ibrahim, Farne, Anna, Hastings, Emma, Holloway, Ele, Kurbatova, Natalja, Lukk, Margus, Malone, James, Mani, Roby, Pilicheva, Ekaterina, Rustici, Gabriella, Sharma, Anjan, Williams, Eleanor, Adamusiak, Tomasz, Brandizi, Marco, Sklyar, Nataliya, Brazma, Alvis

“…The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting…”
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ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression by Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, Berube, Hugo, Dylag, Miroslaw, Emam, Ibrahim, Farne, Anna, Holloway, Ele, Lukk, Margus, Malone, James, Mani, Roby, Pilicheva, Ekaterina, Rayner, Tim F, Rezwan, Faisal, Sharma, Anjan, Williams, Eleanor, Bradley, Xiangqun Zheng, Adamusiak, Tomasz, Brandizi, Marco, Burdett, Tony, Coulson, Richard, Krestyaninova, Maria, Kurnosov, Pavel, Maguire, Eamonn, Neogi, Sudeshna Guha, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sklyar, Nataliya, Zhao, Mengyao, Sarkans, Ugis, Brazma, Alvis

“…ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository--a public archive of functional genomics experiments…”
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ArrayExpress—a public repository for microarray gene expression data at the EBI by Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawardena, N., Contrino, S., Coulson, R., Farne, A., Garcia Lara, G., Holloway, E., Kapushesky, M., Lilja, P., Mukherjee, G., Oezcimen, A., Rayner, T., Rocca-Serra, P., Sharma, A., Sansone, S., Brazma, A.

“…ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores…”
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The BioSample Database (BioSD) at the European Bioinformatics Institute by Gostev, Mikhail, Faulconbridge, Adam, Brandizi, Marco, Fernandez-Banet, Julio, Sarkans, Ugis, Brazma, Alvis, Parkinson, Helen

“…The BioSample Database (http://www.ebi.ac.uk/biosamples) is a new database at EBI that stores information about biological samples used in molecular…”
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Expression Profiler: next generation—an online platform for analysis of microarray data by Kapushesky, Misha, Kemmeren, Patrick, Culhane, Aedín C., Durinck, Steffen, Ihmels, Jan, Körner, Christine, Kull, Meelis, Torrente, Aurora, Sarkans, Ugis, Vilo, Jaak, Brazma, Alvis

“…Expression Profiler (EP, http://www.ebi.ac.uk/expressionprofiler) is a web-based platform for microarray gene expression and other functional genomics-related…”
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P59 Transcriptome analysis in a mouse model of FKRP-deficient muscular dystrophy by Lin, Y-Y, Fonseca, N, Maruyama, S.R, Fernandez-Fuente, M, Brazma, A, Marioni, J, Muntoni, F, Brown, S.C

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One-stop shop for microarray data by Brazma, Alvis, Robinson, Alan, Cameron, Graham, Ashburner, Michael

“…Advances such as the publication of the human chromosome 22 sequence can create the false impression that everything about life at the molecular level will…”
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A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings by Torrente, Aurora, Kapushesky, Misha, Brazma, Alvis

“…Motivation: Clustering is one of the most widely used methods in unsupervised gene expression data analysis. The use of different clustering algorithms or…”
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Building and analysing genome-wide gene disruption networks by Rung, J., Schlitt, T., Brazma, A., Freivalds, K., Vilo, J.

“…Motivation: Microarray experiments comparing expression levels of all genes in yeast for hundreds of mutants allow us to examine properties of gene regulatory…”
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The ArrayExpress gene expression database: a software engineering and implementation perspective by Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, Contrino, Sergio, Holloway, Ele, Rocca-Serra, Philippe, Mukherjee, Gaurab, Shojatalab, Mohammadreza, Kapushesky, Misha, Sansone, Susanna-Assunta, Farne, Anna, Rayner, Tim, Brazma, Alvis

“…Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While…”
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Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments by Kapushesky, M., Adamusiak, T., Burdett, T., Culhane, A., Farne, A., Filippov, A., Holloway, E., Klebanov, A., Kryvych, N., Kurbatova, N., Kurnosov, P., Malone, J., Melnichuk, O., Petryszak, R., Pultsin, N., Rustici, G., Tikhonov, A., Travillian, R. S., Williams, E., Zorin, A., Parkinson, H., Brazma, A.

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Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop by Brazma, A, Freeman, T, Gardiner, K, Weissman, S, Werner, T, Korn, B

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Gene expression data analysis by Brazma, Alvis, Vilo, Jaak

“…Microarrays are one of the latest breakthroughs in experimental molecular biology, which allow monitoring of gene expression for tens of thousands of genes in…”
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Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma by Vasudev, Naveen S, Scelo, Ghislaine, Glennon, Kate I, Wilson, Michelle, Letourneau, Louis, Eveleigh, Robert, Nourbehesht, Nazanin, Arseneault, Madeleine, Paccard, Antoine, Egevad, Lars, Viksna, Juris, Celms, Edgars, Jackson, Sharon M, Abedi-Ardekani, Behnoush, Warren, Anne Y, Selby, Peter J, Trainor, Sebastian, Kimuli, Michael, Cartledge, Jon, Soomro, Naeem, Adeyoju, Adebanji, Patel, Poulam M, Wozniak, Magdalena B, Holcatova, Ivana, Brisuda, Antonin, Janout, Vladimir, Chanudet, Estelle, Zaridze, David, Moukeria, Anush, Shangina, Oxana, Foretova, Lenka, Navratilova, Marie, Mates, Dana, Jinga, Viorel, Bogdanovic, Ljiljana, Kovacevic, Bozidar, Cambon-Thomsen, Anne, Bourque, Guillaume, Brazma, Alvis, Tost, Jörg, Brennan, Paul, Lathrop, Mark, Riazalhosseini, Yasser, Banks, Rosamonde E

“…Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk…”
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Urinary metabolic phenotyping for Alzheimer’s disease by Kurbatova, Natalja, Garg, Manik, Whiley, Luke, Chekmeneva, Elena, Jiménez, Beatriz, Gómez-Romero, María, Pearce, Jake, Kimhofer, Torben, D’Hondt, Ellie, Soininen, Hilkka, Kłoszewska, Iwona, Mecocci, Patrizia, Tsolaki, Magda, Vellas, Bruno, Aarsland, Dag, Nevado-Holgado, Alejo, Liu, Benjamine, Snowden, Stuart, Proitsi, Petroula, Ashton, Nicholas J., Hye, Abdul, Legido-Quigley, Cristina, Lewis, Matthew R., Nicholson, Jeremy K., Holmes, Elaine, Brazma, Alvis, Lovestone, Simon

“…Finding early disease markers using non-invasive and widely available methods is essential to develop a successful therapy for Alzheimer’s Disease. Few studies…”
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User-friendly, scalable tools and workflows for single-cell RNAseq analysis by Moreno, P., Huang, N., Manning, J.R., Mohammed, S., Solovyev, A., Polanski, K., Bacon, W., Chazarra, R., Talavera-López, C., Doyle, M.A., Marnier, G., Grüning, B., Rasche, H., George, N., Fexova, S., Alibi, M., Miao, Z., Perez-Riverol, Y., Haeussler, M., Brazma, A., Teichmann, S., Meyer, K.B., Papatheodorou, I.

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