News from the group:
CAMDA'18 Conference
ISMB Track
7-8 July 2018,
Chicago, U.S.A.
(read more)
Outstanding Presentation Prize
for MM Kańduła
at CAMDA'17
Outstanding Presentation Prize
for PP Łabaj
at CAMDA'15 (photo)
OeAW APART fellowship
for PP Łabaj
(photo)

Sequencing Quality Control (SEQC) project,
MAQC Consortium 2011–2014 (read more)
Host–parasite interactions in biocontrol, WWTF grant 2010–2013 (read more)

Power and limitations of RNA-Seq,
FDA SEQC, Nature Biotechnology (read more)
Characterization and improvement of RNA-Seq precision,
Bioinformatics (read more)
Impact of heavy tails in microarray analysis, Bioinformatics (read more)
Novel conserved repeats in sorting signals,
FEBS Journal (read more)
Sound sensation gene,
Nature communications
(read more)
RNA interference in ageing research,
Gerontology (read more)

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.

Legend:
  1 joint first authorship  
  * joint senior/corresponding authorship, where marked explicitly  

2017

Shridhar, S; Klanert, G; Auer, N; Hernandez-Lopez, I; Kańduła, MM; Hackl, M; Grillari, J; Stralis-Pavese, N; Borth, N; Kreil, DP. Design and validation of a high-performance microarray for the comprehensive genome-scale expression profiling of Chinese Hamster Ovary (CHO) cells. J Biotechnology, 2017; accepted

Dame, K; Cincotta, S; Lang, A; Sanghrajka, R; Zhang, L; Kwok, L; Wilson, T; Choi, J; Kańduła, MM; Monti, S; Hollenberg, A; Mehta, P; Kotton, D; Ikonomou, L. Thyroid progenitors are robustly derived from embryonic stem cells through transient, developmental stage-specific overexpression of Nkx2-1. Stem Cell Reports, 2017; 8(2):216-225

2016

Łabaj, PP and Kreil, DP. Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls. Biology Direct, 2016; 11:66

MetaSUB Consortium [Łabaj, PP]. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome, 2016; 4:24

Koehbach, J; Gruber, CW; Becker, C; Kreil, DP; Jilek, A. MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins. J Proteome Res., 2016; 15(5):1487-96

2015

Spjuth, O; Bongcam-Rudloff, E; Carrasco Hernández, G; Forer, F; Giovacchini, M; Guimera, RV; Kallio, A; Korpelainen, E; Kańduła, MM; Krachunov, M; Kreil, DP; Kulev, O; Łabaj, PP; Lampa, S; Pireddu, L; Schönherr, S; Siretskiy, A; Vassilev; D. Experiences with workflows for automating data-intensive bioinformatics. Biology Direct, 2015; 10:43

Harreither, E; Hackl, M; Pichler, J; Shridhar, S; Auer, N; Łabaj, PP; Scheideler, M; Karbiener, M; Grillari, J; Kreil, DP;* Borth, N.* Gene expression patterns of host cell subclones with increased productivity capacity. Biotechnology Journal, 2015; 10(10):1625-38

Sayegh, RG; Zotter, S; Roberts, PK; Kańduła, MM; Sacu, S; Kreil, DP; Baumann, B; Pircher, M; Hitzenberger, CK; Schmidt-Erfurth, U. Polarization-Sensitive Optical Coherence Tomography and Conventional Retinal Imaging Strategies in Assessing Foveal Integrity in Geographic Atrophy. Invest Ophthalmol Vis Sci., 2015; 56(9):5246-55

Griesser, M; Lawo, NC; Crespo-Martinez, S; Schoedl-Hummel, K; Wieczorek, K; Gorecka, M; Liebner, F; Zweckmair, T; Stralis Pavese, N; Kreil, D; Forneck, A. Phylloxera (Daktulosphaira vitifoliae Fitch) alters the carbohydrate metabolism in root galls to allowing the compatible interaction with grapevine (Vitis ssp.) roots. Plant Sci., 2015; 234:38-49

2014

Su, Z;1 Łabaj, PP;1 Li, S;1 Thierry-Mieg, J; Thierry-Mieg, D; Shi, W; Wang, C; Schroth, GP; Setterquist, RA; Thompson, JF; Jones, WD; Xiao, W; Xu, W; Jensen, RV; Kelly, R; Xu, J; Conesa, A; Furlanello, C; Gao, H; Hong, H; Jafari, N; Letovsky, S; Liao, Y; Lu, F; Oakeley, EJ; Peng, Z; Praul, CA; Santoyo-Lopez, J; Scherer, A; Shi, T; Smyth, GK; Staedtler, F; Sykacek, P; Tan, X-X; Thompson, A; Vandesompele, J; Wang, MD; Eli, JW; Wolfinger, RD; Zavadil, J; Auerbach, SS; Bao, W; Binder, H; Blomquist, T; Brilliant, MH; Bushel, PR; Cai, W; Catalano, JG; Chang, C-W; Chen, T; Chen, G; Chen, R; Chierici, M; Chu, T-M; Clevert, D-A; Deng, Y; Derti, A; Devanara, V; Dong, Z; Dopazo, J; Du, T; Fang, H; Fang, Y; Fasold, M; Fernandez, A; Fischer, M; Furió-Tarí, P; Fuscoe, JC; Gaj, S; Gandara, J; Gao, H; Ge, W; Gondo, Y; Gong, B; Gong, M; Gong, Z; Green, B; Guo, C; Guo, L; Guo, L-W; Hadfield, J; Hellemans, J; Hochreiter, S; Jia, M; Jian, M; Johnson, CD; Kay, S; Kleinjans, J; Lababidi, S; Levy, S; Li, Q-Z; Li, L; Li, P; Li, Y; Li, H; Li, J; Li, S; Lin, SM; López, FJ; Lu, X; Luo, H; Ma, X; Meehan, J; Megherbi, DB; Mei, N; Mu, B; Ning, B; Pandey, A; Pérez-Florido, J; Perkins, RG; Peters, R; Phan, JH; Pirooznia, M; Qian, F; Qing, T; Rainbow, L; Rocca-Serra, P; Sambourg, L; Sansone, S-A; Schwartz, S; Shah, R; Shen, J; Smith, TM; Stegle, O; Stralis-Paves, N; Stupka, E; Suzuki, Y; Szkotnicki, LT; Tinning, M; Tu, B; van, J; Vela, A; Venturini, E; Walker, SJ; Wan, L; Wang, W; Wang, J; Wang, J; Wieben, ED; Willey, JC; Wu, P-Y; Xuan, J; Yang, Y; Ye, Z; Yin, Y; Yu, Y; Yuan, Y-C; Zhang, J; Zhang, KK; Zhang, W; Zhang, W; Zhang, Y; Zhao, C; Zheng, Y; Zhou, Y; Zumbo, P; Tong, W; Kreil, DP;* Mason, CE;* Shi, L.* A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology, 2014; 32:903-914

Li, S1; Łabaj, PP1; Zumbo, P1; Sykacek, P; Shi, W; Shi, L; Phan, J; Wu, PY; Wang, M; Wang, C; Thierry-Mieg, D; Thierry-Mieg, J; Kreil, DP;* Mason, CE.* Detecting and correcting systematic variation in large-scale RNA sequencing data. Nature Biotechnology, 2014; 32, 888-895

Munro, SA; Lund, SP; Pine, PS; Binder, H; Clevert, D-A; Conesa, A; Dopazo, J; Fasold, M; Hochreiter, S; Hong, H; Jafari, N; Kreil, DP; Łabaj, PP; Li, S; Liao, Y; Lin, SM; Meehan, J; Mason, CE; Santoyo, J; Setterquist, RA; Shi, L; Shi, W; Smyth, GK; Stralis-Pavese, N; Su, Z; Tong, W; Wang, C; Wang, J; Xu, J; Ye, Z; Yang, Y; Yu, Y; Salit, M. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures Nature Communications, 2014; 5:5125

Wang, C; Gong, B; Bushel, PR; Thierry-Mieg, J; Thierry-Mieg, D; Xu, J; Fang, H; Hong, H; Shen, J; Su, Z; Meehan, J; Li, X; Yang, L; Li, H; Łabaj, PP; Kreil, DP; Megherbi, D; Gaj, S; Caiment, F; van Delft, J; Kleinjans, J; Scherer, A; Devanarayan, V; Wang, J; Yang, Y; Qian, HR; Lancashire, LJ; Bessarabova, M; Nikolsky, Y; Furlanello, C; Chierici, M; Albanese, D; Jurman, G; Riccadonna, S; Filosi, M; Visintainer, R; Zhang, KK; Li, J; Hsieh, JH; Svoboda, DL; Fuscoe, JC; Deng, Y; Shi, L; Paules, RS; Auerbach, SS; Tong, W. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology, 2014; 32:926-932

Hu, J; Su, Z; Hong, H; Thierry-Mieg, J; Thierry-Mieg, D; Kreil, DP; Mason, CE; Tong, W; Shi, L. Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq. Scientific Data, 2014; 1; 140020

Ali, MA; Wieczorek, K; Kreil, DP; Bohlmann, H. The Beet Cyst Nematode Heterodera schachtii Modulates the Expression of WRKY Transcription Factors in Syncytia to Favour Its Development in Arabidopsis Roots. PLoS One. 2014;

Simader, C; Sayegh, RG; Montuoro, A; Azhary,M; Koth, AL; Baratsits, M; Sacu, S; Prünte, C; Kreil, DP; Schmidt-Erfurth, U. A Longitudinal Comparison of Spectral-Domain Optical Coherence Tomography and Fundus Autofluorescence in Geographic Atrophy. Am J Ophthalmol. 2014;

Sayegh, RG; Kiss, CG; Simader, C; Kroisamer, J; Montuoro, A; Mittermüller, TJ; Azhary, M; Bolz, M; Kreil, DP; Schmidt-Erfurth, U. A systematic correlation of morphology and function using spectral domain optical coherence tomography and microperimetry in patients with geographic atrophy. Br J Ophthalmol. 2014;

Abell, GC; Stralis-Pavese, N; Pan, Y; Bodrossy, L. Analysis of methanotroph community structure using a pmoA-based microarray . Methods Mol Biol. 2014; 1096:111-22

Ferrando-Martínez, S; Ruiz-Mateos, E; Dudakov, JA; Velardi, E; Grillari, J; Kreil, DP; Muñoz-Fernandez, MA; van den Brink,MR and Leal, M. WNT Signaling Suppression in the Senescent Human Thymus . J Gerontol A Biol Sci Med Sci, 2014; in press

Rao, S; Tortola, L; Perlot, T; Wirnsberger,G; Novatchkova,M; Nitsch, R; Sykacek, P; Frank, L; Schramek, D; Komnenovic, V; Sigl, V; Aumayr, L; Schmauss, G; Fellner, N; Handschuh, D; Glösmann, M; Pasierbek, P; Schlederer, M; Resch, G.P; Ma, Y; Yang; H; Popper, H; Kenner, L; Kroemer, G; and Penninger A dual role for autophagy in a murine model of lung cancer. Nature Communications, 2014; 5; 3056

Juste, C; Kreil, DP; Beauvallet, C; C; Guillot, A; Vaca, S; Carapito, C; Mondot, S; Sykacek, P; Sokol, H; Blon, F; Lepercq, P; Levenez, F; Valot, B; Carré, W; Loux, V; Pons, N; David ,O; Schaeffer, B; Lepage, P; Martin, P; Monnet, V; Seksik, P; Beaugerie, L; Ehrlich, S.D; Gibrat, J. F; Van Dorsselaer, A; and Doré, J. Bacterial protein signals are associated with Crohn's disease. Gut, 2014; in press

2013

Jadhav, V; Hackl, M; Druz, A; Shridhar, S; Chung, CY; Heffner, KM; Kreil, DP; Betenbaugh, M; Shiloach, J; Barron, N; Grillari, J; Borth, N. CHO microRNA engineering is growing up: Recent successes and future challenges. Biotechnology Advances, 2013; 31(8); 1501-1513

Elashry A, Okumoto S, Siddique S, Koch W, Kreil DP, Bohlmann, H. The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis. Plant Physiology and Biochemistry, 2013; 70:379-386

Emeakaroha, VC; Maurer, M; Stern, P; Łabaj, PP; Brandic, I; Kreil, DP. Managing and Optimizing Bioinformatics Workflows for Data Analysis in Clouds. Journal of Grid Computing, 2013; 11(3); 407-428

Schweiger, W; Steiner, B; Ametz, C; Siegwart, G; Wiesenberger, G; Berthiller, F; Lemmens, M; Jia, H; Adam, G; Muehlbauer, GJ; Kreil, DP;* Buerstmayr, H.* Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa-5A, identifies novel candidate genes. Molecular Plant Biology, 2013; 14(8):772-85

Ali, MA; Abbas, A; Kreil, DP; Bohlmann, H. Overexpression of the transcription factor RAP2.6 leads to enhanced callose deposition in syncytia and enhanced resistance against the beet cyst nematode Heterodera schachtii in Arabidopsis roots. BMC PLant Biology, 2013; 13(1):47

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, 2013; 41(5):2779-2796

2012

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; 49(10); 1100-1107

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; 118(9); 1844-1851

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;1 Kreil, DP;1 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 2010; 56; 496-506

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

Reprints / preprints

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