TSSi – An R package for transcription start


Aichinger, E., Kornet, N., Friedrich, T., and Laux, T. (2012). Plant Stem Cell Niches. Annu Rev Plant Biol. 2012 Feb 9
Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin KB Sy, Verena Becker, Ursula Klingmuller and Jens Timmer (2012). In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. BMC Systems Biology 2012, 6:13
Kreutz, C., J.S. Gehring, D. Lang, R. Reski, J. Timmer, S.A. Rensing (2012): TSSi – An R package for transcription start site identification from 5’ mRNA tag data. Bioinformatics, DOI: 10.1093/bioinformatics/bts189.
A. Depperschmidt, A. Greven and P. Pfaffelhuber (2012) Tree-valued Fleming-Viot dynamics with mutation and selection. Ann. Appl. Probab. [in press]
P. Pfaffelhuber, P. R. Staab and A. Wakolbinger (2012). Muller's ratchet with compensatory mutations. Ann. Appl. Probab. [in press]
A. Greven, P. Pfaffelhuber and A. Winter (2012) Tree-valued resampling dynamics. Martingale problems and applications. Prob. Theo. Rel. Fields [in press]
S. Will, T. Joshi, I. L. Hofacker, P. F. Stadler, and R. Backofen. (2012) LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA published online March 26, 2012 (doi:10.1261/rna.029041.111)
Baumdicker F, Hess WR, Pfaffelhuber P. (2012). The infinitely many genes model for the distributed genome of bacteria. Genome Biol Evol. 2012 Jan;4(4):443-56.
Anika Erxleben, Arthur Gessler, Marco Vervliet-Scheebaum, Ralf Reski (2011). Metabolite profiling of the moss Physcomitrella patens reveals evolutionary conservation of osmoprotective substances. Plant Cell Rep, Published online, Plant Cell Rep (2012) 31:427–436
Lieber D, Lora J, Schrempp S, Lenhard M, Laux T. (2011). Arabidopsis WIH1 and WIH2 genes act in the transition from somatic to reproductive cell fate. Curr Biol. 2011 Jun 21;21(12):1009-17. Epub 2011 Jun 9.
Almut Dufner, Wolfgang W. A. Schamel (2011). B cell antigen receptor-induced activation of an IRAK4-dependent signaling pathway revealed by a MALT1-IRAK4 double knockout mouse model. Cell Commun Signal. 2011; 9: 6.
Fiala, G., Schamel, W., Blumenthal, B. (2011) Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates. J. Vis. Exp. (48), e2164, DOI: 10.3791/2164 (2011).
Deswal S, Schulze AK, Höfer T, Schamel WW. (2011). Quantitative analysis of protein phosphorylations and interactions by multi-colour IP-FCM as an input for kinetic modelling of signalling networks. PLoS One. 2011;6(7):e22928. Epub 2011 Jul 29.
P. Pfaffelhuber and H. Weisshaupt (2012). Sensitivity analysis of one parameter semigroups exemplified by the Wright-Fisher diffusion, Intern. J. Funct. Anal., Oper. Th. Appl., 3(2), 109–128, 2011
Rüdinger M., Szövényi P., Rensing S.A., Knoop V. (2011). Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica. The Plant Journal (2011) 67, 370–380
A. Depperschmidt, A. Greven and P. Pfaffelhuber (2011). Marked metric measure spaces. Elec. Comm. Probab. 16: 174–188, 2011
Hess W.R, (2011). Cyanobacterial genomics for ecology and biotechnology. Curr Opin Microbiol. 2011 Oct;14(5):608-14.
Belting HG, Wendik B, Lunde K, Leichsenring M, Mössner R, Driever W, Onichtchouk D. (2011). Pou5f1 contributes to dorsoventral patterning by positive regulation of vox and modulation of fgf8a expression. Dev Biol. 2011 Aug 15;356(2):323-36.
Krol E, Becker A. (2011) ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome. Mol Microbiol 81(5):1233-54
Georg J, Hess WR. (2011). Cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev. 2011 Jun;75(2):286-300.
Mitschke J, Vioque A, Haas F, Hess WR, Muro-Pastor AM. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc Natl Acad Sci U S A. 2011 Nov 30. [Epub ahead of print]
Kim Y, Joachimiak G, Ye Z, Binkowski TA, Zhang R, Gornicki P, Callahan SM, Hess WR, Haselkorn R, Joachimiak A. (2011). Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10109-14. Epub 2011 May 31.
Rausenberger, Julia, Anke Tscheuschler, Wiebke Nordmeier, Florian Wüst, Jens Timmer, Eberhard Schäfer Christian Fleck, and Andreas Hiltbrunner. 2011. “Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light..” Cell 146 (5) (September 2): 813–825.
Jo Ann Banks, Stefan Rensing, Andreas Zimmer, Igor V. Grigoriev et. al The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants Science Published Online 5 May 2011
Max Warncke, Maike Buchner, Gudrun Thaller, Anna Dodero, Alla Bulashevska, Dietmar Pfeifer, Jens Timmer, Hendrik Veelken: Control of the specificity of T cell-mediated anti-idiotype immunity by natural regulatory T cells. Cancer Immunol Immunother (2011) 60:49–60
Zhike Zi: SBML-PET-MPI: A parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. Bioinformatics (2011)
Raue A., C. Kreutz, T. Maiwald, U. Klingmüller, J. Timmer. Addressing Parameter Identifiability by Model-Based Experimentation, IET Systems Biology
Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, and Jan Gorodkin.
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics, 27 no. 2 pp. 211-219, 2011.
Engelhart M, Lebiedz D, Sager S.: Optimal control for selected cancer chemotherapy ODE models: A view on the potential of optimal schedules and choice of objective function. Math Biosci. 2011 Jan;229(1):123-34
Iwafuchi-Doi M, Yoshida Y, Onichtchouk D, Leichsenring M, Driever W, Takemoto T, Uchikawa M, Kamachi Y, Kondoh H.: The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates. Dev Biol. 2010 Dec 23. [Epub ahead of print]
Jan Mitschke, Jens Georg, Ingeborg Scholz, Cynthia M. Sharma, Dennis Dienst, Jens Bantscheff, Björn Voß, Claudia Steglich, Annegret Wilde, Jörg Vogel, Wolfgang R. Hess: An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2124-2129. Epub 2011 Jan 18.
Lang, E.G.E., S.J. Mueller, S.N.W. Hoernstein, J. Porankiewicz-Asplund, M. Vervliet-Scheebaum, R. Reski (2010): Simultaneous isolation of pure and intact chloroplasts and mitochondria from moss as basis for sub-cellular proteomics. Plant Cell Rep. 2011 Feb;30(2):205-15.
Omar Saleh, Noa Issman, Gotelinde I. Seumel, Ran Stav, Alon Samach, Ralf Reski, Wolfgang Frank, Tzahi Arazi: MicroRNA534a control of BLADE-ON-PETIOLE 1 and 2 mediates juvenile-to-adult gametophyte transition in Physcomitrella patens. The Plant Journal (2011) 65, 661–674
Jianying Yang, Michael Reth (2010). The dissociation activation model of B cell antigen receptor triggering. FEBS Letters Volume 584, Issue 24, 15 December 2010, Pages 4872–4877
Molnár E, Deswal S, Schamel WW. (2010). Pre-clustered TCR complexes. FEBS Lett. 2010 Dec 15;584(24):4832-7. Epub 2010 Sep 7.
Georg J, Honsel A, Voss B, Rennenberg H, Hess WR. (2010). A long antisense RNA in plant chloroplasts. New Phytol. 2010 May;186(3):615-22.
Santos, F., Teale, W., Fleck, C., Volpers, M., Ruperti, B., and Palme, K.: Modelling polar auxin transport in developmental patterning. Plant Biol (Stuttg). 2010 Sep;12 Suppl 1:3-14.
Bernhard Haubold, Floyd A. Reed and Peter Pfaffelhuber: Alignment-free estimation of nucleotide diversity. Bioinformatics. Advance Access published December 14, 2010
Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich.
Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics, 26 no. 1 pp. 1-5, 2010.
Raheleh Salari, Rolf Backofen, and S. Cenk Sahinalp: Fast prediction of RNA-RNA interaction. Algorithms Mol Biol, 5 pp. 5, 2010.
Raheleh Salari, Mathias Möhl, Sebastian Will, S. Sahinalp, and Rolf Backofen.
Time and space efficient RNA-RNA interaction prediction via sparse folding. In Bonnie Berger, editor, Proc. of RECOMB 2010, volume 6044 of Lecture Notes in Computer Science, pages 473-490. Springer Berlin / Heidelberg, 2010.
Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, and Rolf Backofen.
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Research, 38 Suppl pp. W373-7, 2010.
Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, and Rolf Backofen.
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms Mol Biol, 5 pp. 22, 2010.
D. Schilling, S. Findeiss, A. S. Richter, J. A. Taylor, and U. Gerischer.
The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Arch Microbiol, 192 no. 9 pp. 691-702, 2010.
Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, and Matthias Platzer:
TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics, 11 pp. 216, 2010.
A. Raue, V. Becker, U. Klingmüller, J. Timmer: Identifiability and observability analysis for experimental design in nonlinear dynamical models. CHAOS 20, 045105 2010
Susana Minguet, Elaine-Pashupati Dopfer, Wolfgang W. A. Schamel: Low-valency, but not monovalent, antigens trigger the B-cell antigen receptor (BCR). Int. Immunol. (2010) 22 (3): 205-212.
Jianying Yang, Michael Reth: Oligomeric organization of the B-cell antigen receptor on resting cells. Nature Volume: 467, Pages: 465–469
Rausenberger J, Hussong A, Kircher S, Kirchenbauer D, Timmer J, Nagy F, Schäfer E, Fleck C.: An integrative model for phytochrome B mediated photomorphogenesis: from protein dynamics to physiology. PLoS One. 2010 May 19;5(5):e10721.
Krol E, Blom J, Winnebald J, Berhörster A, Barnett MJ, Goesmann A, Baumbach J, Becker A.: RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. J Biotechnol. 2010 Nov 16.
Engelhart, M., Lebiedz, D., Sager, S. Optimal control for selected cancer chemotherapy ODE models: A view on the potential of optimal schedules and choice of objective function, Math. Biosci. (2010)
Skanda, D., Lebiedz, D. An optimal experimental design approach to model discrimination in dynamic biochemical systems. Bioinformatics 26, 939 (2010)
A. Raue, C. Kreutz, T. Maiwald, U. Klingmüller , J. Timmer. Addressing Parameter Identifiability by Model-Based Experimentation, IET Systems Biology, [in press]
Depperschmidt, A., P. Pfaffelhuber. Asymptotics of a Brownian ratchet for Protein Translocation, Stoch. Proc. Appl., 120, 901-925, 2010
Best, K. and P. Pfaffelhuber. The Aldous-Shields Model revisited with application to cellular ageing, Elec. Comm. Probab., 15, 475–488, 2010
Pfaffelhuber, P. A. Wakolbinger, H. Weisshaupt. The tree length of an evolving coalescent, Prob. Theo. Rel. Fields, 2010
Ewing, G., J. Hermisson, P. Pfaffelhuber and J. Rudolf. Selective sweeps for recessive alleles and for other modes of dominance, J. Math. Biol., 2010
Haubold B., P. Pfaffelhuber and M. Lynch. mlRho – A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes, Molecular Ecology, 19 (Supp 1), 274-284, 2010
Onichtchouk D, Geier F, Polok B, Messerschmidt DM, Mössner R, Wendik B, Song S, Taylor V, Timmer J, Driever W. (2010): Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Mol Syst Biol. 2010;6:354.
Péter Szövényia, Stefan A. Rensing, Daniel Lang, Gregory A. Wraya, A. Jonathan Shawa (2010): Generation-biased gene expression in a bryophyte model system, Mol Biol Evol (2010)
Büttner-Mainik, A., J. Parsons, H. Jérome, A. Hartmann, S. Lamer, A. Schaaf, A. Schlosser, P.F. Zipfel, R. Reski, E.L. Decker (2010): Production of biologically active recombinant human factor H in Physcomitrella. Plant Biotechnology Journal (2011) 9, pp. 373–383
Daniel Lang, Benjamin Weiche, Gerrit Timmerhaus, Sandra Richardt, Diego M. Riaño-Pachón, Luiz G. G. Corrêa, Ralf Reski, Bernd Mueller-Roeber and Stefan A. Rensing: Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity, Genome Biology and Evolution, Genome Biol Evol (2010) 2 488-503
Tobias Hermle, Deniz Saltukoglu, Julian Grünewald, Gerd Walz, Matias Simon: Regulation of Frizzled-Dependent Planar Polarity Signaling by a V-ATPase Subunit. Current Biology, Volume 20, Issue 14, 1269-1276, 24 June 2010
Andrew D Millard, Gregor Gierga, Martha R J Clokie, David J Evans, Wolfgang R Hess and David J Scanlan (2010) An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease. The ISME Journal (2010), 1–15
Wolf L., Rizzini L., Stracke R., Ulm R., Rensing S.A. (2010) The molecular and physiological response of Physcomitrella patens to UV-B. Plant Physiology Published on April 28, 2010
Sinha, R., A.D. Zimmer, K. Bolte, D. Lang, R. Reski, M. Platzer, S.A. Rensing, R. Backofen (2010): Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biology 10, 76.
Ionescu D., Voss B., Oren A., Hess W.R., Muro Pastor A. (2010): Heterocyst-specific transcription of a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria. J. Mol. Biol., 398, 177–188.
Baumdicker F., Hess W.R., Pfaffelhuber P. (2010): The diversity of a distributed genome in bacterial populations. The Annals of Applied Probability 2010, Vol. 20, No. 5, 1567–1606
McDaniel, S.F., M. von Stackelberg, S. Richardt, R.S. Quatrano, R. Reski, S.A. Rensing.The Speciation History of the Physcomitrium-Pyscomitrella species complex. Volume 64, Issue 1, pages 217–231, January 2010.
Rolf Backofen and Wolfgang R. Hess (2010): Computational prediction of sRNAs and their targets in bacteria. RNA Biol. 2010 Jan 13;7(1) [Review]
Khraiwesh, B., M.A. Arif, G.I. Seumel, S. Ossowski, D. Weigel, R. Reski, W. Frank (2010): Transcriptional control of gene expression by microRNAs. Cell 140, 111-122. Cover Image
Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten and Bernd Mueller-Roeber (2009) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 2010 January; 38 (Database issue): D822–D827. Published online 2010 January
van der Graaff E, Laux T, Rensing SA. (2009). The WUS homeobox-containing (WOX) protein family. Genome Biol. 2009;10(12):248. Epub 2009 Dec 29.
Scanlan D.J., Ostrowski M., Mazard S., Dufresne A., Garczarek L., Hess W.R., Post A.F., Hagemann M., Paulsen I., Partensky F. (2009). Ecological Genomics of Marine Picocyanobacteria. Microbiol Mol Biol Rev. 2009 Jun;73(2):249-99.
Voss B., Hölscher M., Baumgarth B., Kalbfleisch A., Kaya C., Hess W.R., Becker A., Evguenieva-Hackenberg, E. (2009a) Expression of small RNAs in Rhizobiales and protection of a small RNA and its degradation products by Hfq in Sinorhizobium meliloti. Biochem. Biophys. Res. Comm. 390, 331-336.
Gierga G, Voss B, Hess WR.: The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. RNA Biol. 2009 Jul;6(3):222-7. Epub 2009 Jul 1.
Hamidreza Chitsaz, Rolf Backofen, and S. Cenk Sahinalp: biRNA: Fast RNA-RNA binding sites prediction. In Steven Salzberg and Tandy Warnow, editors, Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), volume 5724 of Lecture Notes in Computer Science, pages 25-36. Springer Berlin / Heidelberg, 2009.
Sandra Richardt, Gerrit Timmerhaus, Daniel Lang, Enas Qudeimat, Luiz G. G. Corrêa, Ralf Reski, Stefan A. Rensing and Wolfgang Frank: Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling. Plant Molecular Biology Volume 72, Numbers 1-2, 27-45
Yogesh Kulathu, Gesina Grothe, Michael Reth: Autoinhibition and adapter function of Syk Immunological Reviews Volume 232, Issue 1, Article first published online: 23 OCT 200
van der Graaff E., Laux T., Rensing S.A. (2009) The WUS homeobox-containing (WOX) protein family. Genome Biology 10:248
McIntosh M, Meyer S, Becker A (2009) Novel Sinorhizobium meliloti quorum sensing positive and negative regulatory feedback mechanisms respond to phosphate availability. Mol Microbiol 2009 Nov 2
Allison C. Mallory, Annika Hinze, Matthew R. Tucker, Nicolas Bouché, Virginie Gasciolli, Taline Elmayan, Dominique Lauressergues, Hervé Vaucheret and Thomas Laux. Redundant and Specific Roles of the ARGONAUTE Proteins AGO1 and ZLL in Development and Small RNA-Directed Gene Silencing. PLoS Genet. 2009 Sep;5(9):e1000646.
Jens Georg, Bjorn Voß, Ingeborg Scholz, Jan Mitschke, Annegret Wilde and Wolfgang R Hess. Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Molecular Systems Biology 5: 305
Raheleh Salari, Rolf Backofen, and S. Cenk Sahinalp. . In Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), 2009.
Raheleh Salari, Rolf Backofen, and S. Cenk Sahinalp.
Fast prediction of RNA-RNA interaction. In Steven Salzberg and Tandy Warnow, editors, Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), volume 5724 of Lecture Notes in Computer Science, pages 261-272. Springer Berlin / Heidelberg, 2009.
Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, and Rolf Backofen. A partition function algorithm for interacting nucleic acid strands. Bioinformatics, 25 no. 12 pp. i365-73, 2009.
Rolf Backofen, Dekel Tsur, Shay Zakov, and Michal Ziv-Ukelson. Sparse RNA folding: Time and space efficient algorithms. In Proc. 20th Symp. Combinatorial Pattern Matching, pages 249-262, 2009.
Mosquna, A., A. Katz, E.L. Decker, S.A. Rensing, R. Reski, N. Ohad (2009): Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution. Development 136, 2433-2444. [Cover]
Batholomé K., Kreutz C., Timmer J. Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets, Journal of computational Biology, Volume 16, Number 7, 2009, p. 1–9
Rausenberger, J., Fleck, C., Timmer, J., and Kollmann, M. (2009) Signatures of Gene Expression Noise in Cellular Systems. Prog Biophys Mol Biol.
Raue, A., Kreutz, C., Maiwald, T., Bachmann, J., Schilling, M., Klingmuller, U., and Timmer, J. (2009) Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics.
Gerstung, M., Timmer, J., and Fleck, C. (2009) Noisy signaling through promoter logic gates. Phys Rev E Stat Nonlin Soft Matter Phys 79, 011923.
Slaby, O., Lebiedz, D. Oscillatory NAD(P)H waves and calcium oscillations in neutrophils ? A modeling study of feasibility. Biophys. J. 96, 417 (2009)
Haubold, B., P. Pfaffelhuber, M. Domazet-Loso and T. Wiehe. Estimating Mutation Distances from Unaligned Genomes, Journal of Computational Biology, 16(10): 1487-1500, 2009
Sämann J, Hegermann J, von Gromoff E, Eimer S, Baumeister R, Schmidt E. Caenorhabditits elegans LRK-1 and PINK-1 Act Antagonistically in Stress Response and Neurite Outgrowth. J. Biol. Chem., Vol. 284, Issue 24, 16482-16491, June 12, 2009
Paponov, I.A., W. Teale, D. Lang, M. Paponov, R. Reski, S.A. Rensing, K. Palme. The evolution of nuclear auxin signalling. BMC Evolutionary Biology 2009. 9, 126.
Mitschke, J., J. Fuss, T. Blum, A. Höglund, R. Reski, O. Kohlbacher, S.A. Rensing. Prediction of dual targeting to plant organelles. New Phytologist (2009) 183: 224–236
Björn Voß, Jens Georg, Verena Schön, Susanne Ude and Wolfgang R Hess. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 2009, 10:123
Kreutz, C., and Timmer, J. Experimental design in systems biology: FEBS Journal 276 (2009) 923–942
Silke Lassmann, Clemens Kreutz, Anja Schoepflin, Ulrich Hopt, Jens Timmer, Martin Werner (2008) A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. Journal of Molecular Medicine Volume 87, Number 2 / Februar 2009
Staedler, T., Haubold, B., Merino, C., Stephan, W., and Pfaffelhuber, P. (2008) The impact of sampling schemes on the site frequency spectrum in non-equilibrium subdivided populations : Genetics. February 23, 2009
Qudeimat, E., W. Frank. Ca2+ signatures: The role of Ca2+ ATPases. Plant Signaling & Behavior volume 4, issue 4 April 2009, Pages 350 - 352
Steffen Heyne, Sebastian Will, Michael Beckstette and Rolf Backofen. Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches. Bioinformatics, 25 no. 16 pp. 2095-2102, 2009.
Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V. RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genomics. Volume 281 (2009), Number 5, 473-481
Tucker MR, Hinze A, Tucker EJ, Takada S, Jürgens G, Laux T. (2008) Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo. Development. 2008 Sep;135(17):2839-43. Epub 2008 Jul 24.
Dufresne A., Ostrowski M., Scanlan D.J., Garczarek L., Mazard S., Palenik B.P., Paulsen I.T., Tandeau de Marsac N., Wincker P., Dossat C., Ferriera S., Johnson J., Post A.F., Hess W.R., Partensky F. (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 2008; 9(5): R90.
McIntosh M, Krol E, Becker A. Competitive and cooperative effects in quorum-sensing-regulated galactoglucan biosynthesis in Sinorhizobium meliloti. J Bacteriol 190(15):5308-17
Lebiedz, D., Skanda, D., Fein, M. Automatic complexity analysis and model reduction of nonlinear biochemical systems [Bookchapter]. In M. Heiner and A.M. Uhrmacher eds. "Computational Methods in Systems Bioloy", Lecture Notes in Bioinformatics, pp. 123-140, Volume 5307, Springer (2008)
Hermisson, J. and P. Pfaffelhuber. The pattern of genetic hitchhiking under recurrent
mutation, Electronic Journal of Probability
, 13(68), 2069–2106, 2008.
Anke Busch, Andreas S. Richter, and Rolf Backofen. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 2008, 24(24), 2849-56.
Steffen Heyne, Sebastian Will, Michael Beckstette, and Rolf Backofen. Lightweight comparison of RNAs based on exact sequence-structure matches. In Proceedings of German Conference on Bioinformatics (GCB'2008), volume P-136 of LNI, pages 189-198. GI, (ISBN-10: 3885792303) 2008
Qudeimat E, Faltusz AM, Wheeler G, Lang D, Brownlee C, Reski R, Frank W (2008) A PIIB-type Ca2+-ATPase is essential for stress adaptation in Physcomitrella patens. Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19555-60. Epub 2008 Dec 2. (press release EN / D )
Bahlawane, C., McIntosh, M., Krol, E., and Becker, A. (2008) Sinorhizobium meliloti regulator MucR couples exopolysaccharide synthesis and motility. Mol Plant-Microbe Interact: November 2008, Volume 21, Number 11, Pages 1498-1509
Pfaffelhuber, P., Lehnert, A., and Stephan, W. (2008) Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics 179, 527-37.
Launhardt, H., Stemmer, C., Jost, W., Gorr, G., Reski, R., and Rensing, S. (2008) in Galactosyltransferase [Patent] http://depatisnet.dpma.de WO2008037490 pp 1, Germany.
Kulathu, Y., Hobeika, E., Turchinovich, G., and Reth, M. (2008) The kinase Syk as an adaptor controlling sustained calcium signalling and B-cell development. Embo J 27, 1333-44
Khraiwesh, B., Ossowski, S., Weigel, D., Reski, R., and Frank, W. (2008) Specific gene silencing by artificial microRNAs in Physcomitrella patens: An alternative to targeted gene knockouts Plant Physiology 148:684-693 (2008)
Bahlawane, C., Baumgarth, B., Serrania, J., Ruberg, S., and Becker, A. (2008) Fine-tuning of galactoglucan biosynthesis in Sinorhizobium meliloti by differential WggR (ExpG)-, PhoB-, and MucR-dependent regulation of two promoters. J Bacteriol 190, 3456-66.
Digiuni, S., Schellmann, S., Geier, F., Greese, B., Pesch, M., Wester, K., Dartan, B., Mach, V., Srinivas, B. P., Timmer, J., Fleck, C., and Hulskamp, M (2008) A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves Molecular Systems Biology 4 Article number: 217, 2; September 2008
Steglich, C., Futschik, M. E., Lindell, D., Voss, B., Chisholm, S. W., and Hess, W. R. (2008) The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus PLoS Genet 4(8): e1000173; 29 August 2008
Maier, U. G., Bozarth, A., Funk, H. T., Zauner, S., Rensing, S. A., Schmitz-Linneweber, C., Borner, T., and Tillich, M. (2008) Complex Chloroplast RNA Metabolism: Just Debugging the Genetic Programme? BMC Biology 6:36; 28 August 2008
Lang, D., Zimmer, A. D., Rensing, S. A., and Reski, R. (2008) Exploring plant biodiversity: the Physcomitrella genome and beyond Trends in Plant Science Vol.13 No.10, Pages 542-549
Kamisugi, Y., von Stackelberg, M., Lang, D., Care, M., Reski, R., Rensing, S. A., and Cuming, A. C (2008) A sequence-anchored genetic linkage map for the moss Physcomitrella patens The Plant Journal Volume 56, Issue 5, Pages 855-866
Bouyer, D., Geier, F., Kragler, F., Schnittger, A., Pesch, M., Wester, K., Balkunde, R., Timmer, J., Fleck, C., and Hulskamp, M.(2008) Two-dimensional patterning by a trapping/depletion mechanism: the role of TTG1 and GL3 in Arabidopsis trichome formation PLoS Biol. 2008 June; 6(6): e141
Holtzendorff, J., Partensky, F., Mella, D., Lennon, J. F., Hess, W. R., and Garczarek, L.(2008)Genome Streamlining Results in Loss of Robustness of the Circadian Clock in the Marine Cyanobacterium Prochlorococcus marinus PCC 9511 J Biol Rhythms 2008; 23; 187
McIntosh, M., Krol, E., and Becker, A. (2008) Competitive and co-operative effects in quorum sensing regulated galactoglucan biosynthesis in Sinorhizobium meliloti Journal of Bacteriology, August 2008, p. 5308-5317, Vol. 190, No. 15
Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., Tandeau de Marsac, N., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., and Partensky, F. (2008) Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria Genome Biology 2008, 9:R90; 28 May 2008
Bahlawane, C., Baumgarth, B., Serrania, J., Ruberg, S., and Becker, A. (2008) Fine-tuning of galactoglucan biosynthesis in Sinorhizobium meliloti by differential WggR (ExpG)-, PhoB-, and MucR-dependent regulation of two promoters J Bacteriol 190(10): 3456-3466 May 2008
Tullet, J. M., Hertweck, M., An, J. H., Baker, J., Hwang, J. Y., Liu, S., Oliveira, R. P., Baumeister, R., and Blackwell, T. K (2008) Direct Inhibition of the Longevity-Promoting Factor SKN-1 by Insulin-like Signaling in C. elegans Cell, Vol 132, 1025-1038; 21 March 2008
Balsa-Canto, E., Peifer, M., Banga, J. R., Timmer, J., and Fleck, C (2008) Hybrid optimization method with general switching strategy for parameter estimation BMC Syst Biol. 2008; 2: 26.; 24 March 2008
Neumann-Haefelin, E., Qi, W., Finkbeiner, E., Walz, G., Baumeister R. and Hertweck, M. (2008) SHC-1/p52Shc targets the insulin/IGF-1 and JNK signaling pathways to modulate life span and stress response in C. elegans. Genes Dev. 22(19):2721-35.
Dirnberger, D., Messerschmid, M., and Baumeister R. (2008) An optimized split-ubiquitin cDNA-library screening system to identify novel interactors of the human Frizzled1 receptor.May 23, 2008 The Journal of Biological Chemistry, 283, 14257-14268.