Publications

The PubMed bibliographic archive provides a publication list linking to most publications by members of the group. You can use RSS to view the PubMed group publications channel or take out a subscription.

There often is supplementary information available for publications by Peter Sykacek and papers by David Kreil.

2012

Harrison, A; Binder, H; Buhot, A; Burden, CJ; Carlon, E; Gibas, C; Gamble, LJ; Halperin, A; Hooyberghs, J; Kreil, DP; Levicky, R; Noble, PA; Ott, A; Pettitt, BM; Tautz, D; Pozhitkov, AE. Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research, 2012; [Epub ahead of print]

Sykacek, P. Bayesian assignment of gene ontology terms to gene expression experiments. Bioinformatics, 2012; 28(18):i603-i610

Gößler-Schöfberger, R; Hesser, G; Reif, MM; Friedmann, J; Duscher, B; Toca-Herrera, JL; Oostenbrink, C; Jilek; A. A stereochemical switch in the aDrs model system, a candidate for a functional amyloid. Arch Biochem Biophys, 2012; 522(2):100-106

Jilek, A; Mollay, C; Lohner, K; Kreil, G. Substrate specificity of a peptidyl-aminoacyl-l/d-isomerase from frog skin. Amino Acids, 2012; 42(5):1757-1764

Łabaj, PP; Linggi, BE; Wiley, HS; Kreil, DP. Improving RNA-Seq precision with MapAl. Frontiers in Genetics, 2012; 3:28

2011

Emeakaroha, VC; Łabaj, PP; Maurer, M; Brandic, I; Kreil, DP. Optimizing bioinformatics workflows for data analysis using cloud management techniques. In Proceedings of the 6th workshop on Workflows in support of large-scale science (WORKS '11). ACM, New York, NY, USA, 37-46.

Gehmayr, V; Mollay, C; Reith, L; Müller, N; Jilek, A. Tight binding of transition-state analogues to a peptidyl-aminoacyl-L/D-isomerase from frog skin. Chembiochem, 2011; 12(13):1996-2000

Siddique, S; Wieczorek, K, Szakasitsm D; Kreil, DP; Bohlmann, H. The promoter of a plant defensin gene directs specific expression in nematode-induced syncytia in Arabidopsis roots. Plant Physiology and Biochemistry, 2011; Epub ahead of print

Łabaj, PP; Leparc, GG; Linggi, BE; Markillie, LM; Wiley, HS; Kreil, DP. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics, 2011; Vol. 27; i383-i391

Łabaj, PP; Sykacek, P; Kreil, DP. An analysis of single amino acid repeats as use case for application specific background models. BMC Bioinformatics, 2011; Vol. 12; 173

Stralis-Pavese, N; Abel, GCJ ; Sessitsch, A; Bodrossy, L. Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray. Nature Protoc. 2011; Vol. 6; 609-624

Sayegh, RG; Simader, C; Scheschy, U; Montuoro, A; Kiss, C; Sacu, S; Kreil, DP; Prünte, C; Schmidt-Erfurth, U. A Systematic Comparison of Spectral-Domain Optical Coherence Tomography and Fundus Autofluorescence in Patients with Geographic Atrophy. Ophthalmology 2011; Epub ahead of print

Kumaresan, D; Hery, M; Bodrossy, L; Singer, AC; Stralis-Pavese, N; Thompson, IP; Murrell, JC. Earthworm activity in a simulated landfill cover soil shifts the community composition of active methanotrophs. Research in Microbiology 2011; 162:1027-1032

Böhmdorfer, G; Schleiffer, A; Brunmeir, R; Ferscha, S; Nizhynska, V; Kozák, J; Angelis, KJ; Kreil, DP; Schweizer, D. GMI1, a Structural-maintenance-of-chromosomes-hinge Domain-containing Protein, is Involved in Somatic Homologous Recombination in Arabidopsis. Plant J. 2011; Vol. 67; 420-433

Sykacek, P; Kreil, DP; Meadows, LA; Auburn, RP; Fischer, B; Russel, S; Micklem, G. The impact of quantitative optimization of hybridization conditions on gene expression analysis. BMC Bioinformatics 2011; Vol. 12; 73

Kumaresan, D; Stralis-Pavese, N; Abell, GCJ; Bodrossy, L; Murrell, JC. Physical disturbance to ecological niches created by soil structure alters community composition of methanotroph. Environmental Microbiology Reports 2011; 3(5):613-621

Posekany, A; Felsenstein, K; Sykacek, P. Biological Assessment of Robust Noise Models in Microarray Data Analysis. Bioinformatics 2011; Vol. 27; 807-814

Rahman, MT; Crombie, A; Chen, Y; Stralis-Pavese, N; Bodrossy, L; Meir, P; McNamara, NP; Murrell, JC. Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J. 2011; Vol. 5; 1061-1066

2010

Bechstedt, S; Albert, JT; Kreil, DP; Müller-Reichert, T; Göpfert, MC; Howard, J. A doublecortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia. Nat Commun. 2010; Vol. 1; 1-11

Łabaj, PP; Leparc, GG; Bardet, AF; Kreil, G; Kreil, DP. Single amino acid repeats in signal peptides. FEBS Journal. 2010; Vol. 277; 3147-3157

Minois, N; Sykacek, P; Godsey, B; Kreil, DP. RNA Interference in Ageing Research - A Mini-Review. In Gerontology

Kanno, T; Bucher, E; Daxinger, L; Huettel, B; Kreil, DP; Breinig, F; pnd, M; Schmitt, MJ; Simon, SA; Gurazada, SGR; Meyers, BC; Lorkovic, ZJ; Matzke, AJM; Matzke, M. RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO REP. 2010; 11(1): 65-71.

Mueckstein, U; Leparc, GG; Posekany, A; Hofacker, I; Kreil, DP. Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinformatics. 2010 January 19; 11:35

Dragosits, M; Stadlmann, J; Graf, A; Gasser, B; Maurer, M; Sauer, M; Kreil, DP; Altmann, F; Mattanovich, D. The response to unfolded protein is involved in osmotolerance of Pichia pastoris. BMC Genomics. 2010 Mar 26;11(1):207

2009

Furlong, R; Cheng, C-W; Sykacek, P; Morris, T; Licence, D; Affara, N; Charnock-Jones, DS. Comparison of Transcript Profiles from a Mouse Model of Deciduapsation and the Estrous Cycle Using a Bayesian Model of Shared Gene Function. In Reproductive Sciences, 2009, Vol. 16. No. 3 Suppl. S, pp 1014.

Leparc, GG; Tüchler, T; Striedner, G; Bayer, K; Sykacek, P; Hofacker, IL; Kreil, DP. Model-based probe set optimization for high-performance microarrays. In Nucleic Acids Research, 2009, Vol. 37, No. 3 e18

Bodelier, PLE; Kamst, M; Meima-Franke, M; Stralis-Pavese, N; Bodrossy, L. Whole-community genome amplification (WCGA) leads to compositional bias in methane-oxidizing communities as assessed by pmoA-based microarray analyses and QPCR. Environmental Microbiology Reports 2009; 5:434-441

Szakasits, D; Heinen, P; Wieczorek, K; Hofmann, J; Wagner, F; Kreil, DP; Sykacek, P; Grundler, FMW; Bohlmann, H. The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. In The Plant Journal, 2009; pp 771--784.

Leitner, J; Klauser, C; Pickl, WF; Stöckl, J; Majdic, O; Bardet, AF; Kreil, DP; Dong, C; Yamazaki, T; Zlabinger, G; Pfistershammer, K; Steinberger, P. B7-H3 is a potent inhibitor of human T-cell activation: No evidence for B7-H3 and TREML2 interaction. Eur J Immunol. 2009; 39(7):1754-1764

Abell, GCJ; Stralis-Pavese, N; Sessitsch, A; Bodrossy, L. Grazing affects methanotroph activity and diversity in an alpine meadow soil. Environmental Microbiology Reports 2009; 1:457-465

Siddique, S; Endres, S; Atkins, JM; Szakasits, D; Wieczorek, K; Hofmann, J; Blaukopf, C; Urwin, PE; Tenhaken, R; Grundler, FM; Kreil, DP; Bohlmann, H. Myo-inositol oxygenase genes are involved in the development of syncytia induced by Heterodera schachtii in Arabidopsis roots. New Phytol. 2009; 184(2):457-472

Kumaresan, D; Abell, GCJ; Bodrossy, L; Stralis-Pavese, N; Murrell, JC. Spatial and temporal diversity of methanotrophs in a landfill cover soil are differentially related to soil abiotic factors. Environmental Microbiology Reports 2009; 1:398-407

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