Search Results - "Jack A. M. Leunissen"

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain by Gavai, Anand K, Supandi, Farahaniza, Hettling, Hannes, Murrell, Paul, Leunissen, Jack A M, van Beek, Johannes H G M

“…Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic…”
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Primer3Plus, an enhanced web interface to Primer3 by Untergasser, Andreas, Nijveen, Harm, Rao, Xiangyu, Bisseling, Ton, Geurts, René, Leunissen, Jack A M

“…Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with…”
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QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species by Tang, Jifeng, Vosman, Ben, Voorrips, Roeland E, van der Linden, C Gerard, Leunissen, Jack A M

“…Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery…”
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Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates by Nie, H, Crooijmans, R.P.M.A, Lammers, A, Schothorst, E.M. van, Keijer, J, Neerincx, P, Leunissen, J.A.M, Megens, H.J.W.C, Groenen, M.A.M

“…The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for…”
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A text-mining analysis of the human phenome by VAN DRIEL, Marc A, BRUGGEMAN, Jorn, VRIEND, Gert, BRUNNER, Han G, LEUNISSEN, Jack A. M

“…A number of large-scale efforts are underway to define the relationships between genes and proteins in various species. But, few attempts have been made to…”
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The quest for orthologs: finding the corresponding gene across genomes by Kuzniar, Arnold, van Ham, Roeland C.H.J, Pongor, Sándor, Leunissen, Jack A.M

“…Orthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene…”
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HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands by Nijveen, Harm, Kester, Michel G. D, Hassan, Chopie, Viars, Aurélie, de Ru, Arnoud H, de Jager, Machiel, Falkenburg, J. H. Fred, Leunissen, Jack A. M, van Veelen, Peter A

“…T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology…”
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Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks by Kuzniar, Arnold, Dhir, Somdutta, Nijveen, Harm, Pongor, Sándor, Leunissen, Jack A.M.

“…Multi-netclust is a simple tool that allows users to extract connected clusters of data represented by different networks given in the form of matrices. The…”
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The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes by Hassan, Chopie, Kester, Michel G.D., de Ru, Arnoud H., Hombrink, Pleun, Drijfhout, Jan Wouter, Nijveen, Harm, Leunissen, Jack A.M., Heemskerk, Mirjam H.M., Falkenburg, J.H. Frederik, van Veelen, Peter A.

“…Peptides presented by human leukocyte antigen (HLA) molecules on the cell surface play a crucial role in adaptive immunology, mediating the communication…”
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Constraint-based probabilistic learning of metabolic pathways from tomato volatiles by Gavai, Anand K, Tikunov, Yury, Ursem, Remco, Bovy, Arnaud, van Eeuwijk, Fred, Nijveen, Harm, Lucas, Peter J. F, Leunissen, Jack A. M

“…Clustering and correlation analysis techniques have become popular tools for the analysis of data produced by metabolomics experiments. The results obtained…”
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The human genome encodes 10 α-crystallin–related small heat shock proteins: HspB1–10 by Kappé, Guido, Franck, Erik, Verschuure, Pauline, Boelens, Wilbert C., Leunissen, Jack A. M., de Jong, Wilfried W.

“…To obtain an inventory of all human genes that code for α-crystallin–related small heat shock proteins (sHsps), the databases available from the public…”
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Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks by Kuzniar, Arnold, Dhir, Somdutta, Nijveen, Harm, Pongor, Sándor, Leunissen, Jack A M

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Ten Simple Rules for Developing a Short Bioinformatics Training Course by Via, Allegra, De Las Rivas, Javier, Attwood, Teresa K, Landsman, David, Brazas, Michelle D, Leunissen, Jack A M, Tramontano, Anna, Schneider, Maria Victoria

“…  [...]as a consequence of the introduction of high-throughput technologies, there has already been an increase in demand for training relating to the use of…”
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pipeline for high throughput detection and mapping of SNPs from EST databases by Anithakumari, A. M, Tang, Jifeng, van Eck, Herman J, Visser, Richard G. F, Leunissen, Jack A. M, Vosman, Ben, van der Linden, C. Gerard

“…Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in…”
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HaploSNPer: a web-based allele and SNP detection tool by Tang, J, Leunissen, J.A.M, Voorrips, R.E, Linden, C.G. van der, Vosman, B

“…Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for…”
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Testing statistical significance scores of sequence comparison methods with structure similarity by Hulsen, Tim, de Vlieg, Jacob, Leunissen, Jack A M, Groenen, Peter M A

“…In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing…”
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ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins by Luo, Hong, Lin, Ke, David, Audrey, Nijveen, Harm, Leunissen, Jack A. M.

“…ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological…”
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SEQATOMS: a web tool for identifying missing regions in PDB in sequence context by Brandt, B.W, Heringa, J, Leunissen, J.A.M

“…With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files…”
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Role of the Synthase Domain of Ags1p in Cell Wall α-Glucan Biosynthesis in Fission Yeast by Vos, Alina, Dekker, Nick, Distel, Ben, Leunissen, Jack A.M., Hochstenbach, Frans

“…The cell wall is important for maintenance of the structural integrity and morphology of fungal cells. Besides β-glucan and chitin, α-glucan is a major…”
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Evolution of web services in bioinformatics by NEERINCX, Pieter B. T, LEUNISSEN, Jack A. M

“…Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to…”
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