Publications by authors named "Stephen Rudd"

41Publications

Rapid analysis of metagenomic data using signature-based clustering.

BMC Bioinformatics 2018 Dec 21;19(Suppl 20):509. Epub 2018 Dec 21.

School of Electrical Engineering and Computer Science, Queensland University of Technology, 2 George Street, Brisbane, QLD 4001, Australia.

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http://dx.doi.org/10.1186/s12859-018-2540-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302383PMC
December 2018

Gene networks associated with non-syndromic intellectual disability.

J Neurogenet 2018 03 4;32(1):6-14. Epub 2017 Dec 4.

a Mater Research Institute, The University of Queensland , Woolloongabba , Australia.

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http://dx.doi.org/10.1080/01677063.2017.1404058DOI Listing
March 2018

Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

J Biotechnol 2017 Nov 8;261:37-45. Epub 2017 Jul 8.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2017.07.006DOI Listing
November 2017

Human mesenchymal stem cells alter the gene profile of monocytes from patients with Type 2 diabetes and end-stage renal disease.

Regen Med 2016 Mar 6;11(2):145-58. Epub 2015 Nov 6.

Department of Anatomy & Developmental Biology, Monash University, Clayton, Victoria, 3800, Australia.

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http://dx.doi.org/10.2217/rme.15.74DOI Listing
March 2016

Impact of Screening Implementing HCV Screening of Persons Born 1945-1965: A Primary Care Case Study.

J Prim Care Community Health 2016 Jan 8;7(1):30-2. Epub 2015 Sep 8.

Northwest Portland Area Indian Health Board, Portland, OR, USA.

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http://dx.doi.org/10.1177/2150131915602020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932669PMC
January 2016

Programmed ribosomal frameshift alters expression of west nile virus genes and facilitates virus replication in birds and mosquitoes.

PLoS Pathog 2014 Nov 6;10(11):e1004447. Epub 2014 Nov 6.

Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia.

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http://dx.doi.org/10.1371/journal.ppat.1004447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223154PMC
November 2014

Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen.

BMC Genomics 2013 Dec 10;14:870. Epub 2013 Dec 10.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland.

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http://dx.doi.org/10.1186/1471-2164-14-870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878897PMC
December 2013

Integrating clinical decision support to increase HIV and chlamydia screening.

Prev Med 2013 Dec 10;57(6):908-9. Epub 2013 Oct 10.

Indian Health Service (IHS), Portland, OR, USA.

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http://dx.doi.org/10.1016/j.ypmed.2013.09.017DOI Listing
December 2013

Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring.

Int J Syst Evol Microbiol 2013 Nov 14;63(Pt 11):4149-4157. Epub 2013 Jun 14.

Graduate Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK 73019, USA.

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http://dx.doi.org/10.1099/ijs.0.051425-0DOI Listing
November 2013

Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data.

BMC Genomics 2012 Oct 30;13:575. Epub 2012 Oct 30.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland.

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http://dx.doi.org/10.1186/1471-2164-13-575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534622PMC
October 2012

Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008.

Int J Syst Evol Microbiol 2013 Jan 9;63(Pt 1):254-259. Epub 2012 Mar 9.

Graduate Program in Ecology and Evolutionary Biology, University of Oklahoma, 660 Parrington Oval, Norman, OK 73019, USA.

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http://dx.doi.org/10.1099/ijs.0.037127-0DOI Listing
January 2013

Microarray analysis identifies candidate genes for key roles in coral development.

BMC Genomics 2008 Nov 14;9:540. Epub 2008 Nov 14.

Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1186/1471-2164-9-540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629781PMC
November 2008

Expression profiling of the lignin biosynthetic pathway in Norway spruce using EST sequencing and real-time RT-PCR.

Plant Mol Biol 2007 Oct 1;65(3):311-28. Epub 2007 Sep 1.

Department of Applied Biology, University of Helsinki, Latokartanonkaari 7, PO Box 27, Helsinki, 00014, Finland.

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http://link.springer.com/10.1007/s11103-007-9220-5
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http://dx.doi.org/10.1007/s11103-007-9220-5DOI Listing
October 2007

Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses.

Mol Genet Genomics 2007 Aug 12;278(2):197-209. Epub 2007 May 12.

Department of Plant Biology and Pathology and The Biotechnology Center for Agriculture & the Environment, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.

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http://link.springer.com/content/pdf/10.1007/s00438-007-0240
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http://link.springer.com/10.1007/s00438-007-0240-2
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http://dx.doi.org/10.1007/s00438-007-0240-2DOI Listing
August 2007

Separation of sequences from host-pathogen interface using triplet nucleotide frequencies.

Fungal Genet Biol 2007 Apr 10;44(4):231-41. Epub 2007 Jan 10.

Institut for Miljø og Bioteknologi, Aalborg Universitet, Sohngaardsholmsvej 49, 9000 Aalborg, Denmark.

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http://dx.doi.org/10.1016/j.fgb.2006.11.010DOI Listing
April 2007

Construction, database integration, and application of an Oenothera EST library.

Genomics 2006 Sep 10;88(3):372-80. Epub 2006 Jul 10.

Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, 80638 München, Germany.

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http://dx.doi.org/10.1016/j.ygeno.2006.05.010DOI Listing
September 2006

Genetic screen for signal peptides in Hydra reveals novel secreted proteins and evidence for non-classical protein secretion.

Eur J Cell Biol 2006 Sep 30;85(9-10):1107-17. Epub 2006 Jun 30.

Department Biologie II, Ludwig Maximilians University, Grosshadernerstr 2, D-82152, Planegg/Martinsried, Germany.

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http://dx.doi.org/10.1016/j.ejcb.2006.05.007DOI Listing
September 2006

A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.

BMC Genomics 2006 May 31;7:130. Epub 2006 May 31.

Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, USA.

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http://dx.doi.org/10.1186/1471-2164-7-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534037PMC
May 2006

Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana.

PLoS Comput Biol 2006 Mar 31;2(3):e21. Epub 2006 Mar 31.

GSF National Research Center for Environment and Health, MIPS, Institute for Bioinformatics, Neuherberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.0020021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1420657PMC
March 2006

Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians.

Trends Genet 2005 Dec 13;21(12):633-9. Epub 2005 Oct 13.

Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5008 Bergen, Norway.

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http://dx.doi.org/10.1016/j.tig.2005.09.007DOI Listing
December 2005

Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W724-7

Centre for Biotechnology, Tykistökatu 6 FIN-20521, Turku, Finland.

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http://dx.doi.org/10.1093/nar/gki434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160195PMC
July 2005

PlantMarkers--a database of predicted molecular markers from plants.

Nucleic Acids Res 2005 Jan;33(Database issue):D628-32

Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland.

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http://dx.doi.org/10.1093/nar/gki074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540028PMC
January 2005

openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections.

Authors:
Stephen Rudd

Nucleic Acids Res 2005 Jan;33(Database issue):D622-7

Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland.

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http://dx.doi.org/10.1093/nar/gki040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539994PMC
January 2005

Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.

Bioinformatics 2005 Apr 7;21(8):1383-8. Epub 2004 Dec 7.

Institut fuer Informatik, Ludwig-Maximilians-Universitaet Muenchen, Oettingenstrasse 67, 80538 Muenchen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bti200DOI Listing
April 2005

Identification of NdhL and Ssl1690 (NdhO) in NDH-1L and NDH-1M complexes of Synechocystis sp. PCC 6803.

J Biol Chem 2005 Jan 17;280(4):2587-95. Epub 2004 Nov 17.

Department of Biology, Plant Physiology and Molecular Biology, FIN-20014 University of Turku, Finland.

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http://dx.doi.org/10.1074/jbc.M410914200DOI Listing
January 2005

Characterization of the maize endosperm transcriptome and its comparison to the rice genome.

Genome Res 2004 Oct;14(10A):1932-7

Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.

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http://dx.doi.org/10.1101/gr.2780504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524417PMC
October 2004

Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.

Plant Physiol 2004 Jun;135(2):715-22

Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1104/pp.103.037861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514109PMC
June 2004

Expressed sequence tags: alternative or complement to whole genome sequences?

Authors:
Stephen Rudd

Trends Plant Sci 2003 Jul;8(7):321-9

Institut für Bioinformatik, GSF Forschungszentrum für Umwelt und Gesundheit, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.

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http://dx.doi.org/10.1016/S1360-1385(03)00131-6DOI Listing
July 2003

Sputnik: a database platform for comparative plant genomics.

Nucleic Acids Res 2003 Jan;31(1):128-32

Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165522PMC
http://dx.doi.org/10.1093/nar/gkg075DOI Listing
January 2003

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome.

Nucleic Acids Res 2002 Jan;30(1):91-3

Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99069PMC
http://dx.doi.org/10.1093/nar/30.1.91DOI Listing
January 2002