Browse by Research Team

2015

A protocol for chemical mutagenesis in Strongyloides ratti.
Guo, L., Chang, Z., Dieterich, C. and Streit, A.
Experimental Parasitology 158 : 2-7. November 2015

Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae).
Lamanna, F., Kirschbaum, F., Waurick, I., Dieterich, C. and Tiedemann, R.
BMC Genomics 16 (1): 668. 3 September 2015

2014

Changes in metabolite profiles caused by genetically determined obesity in mice.
Schaefer, N., Yu, Z., Wagener, A., Millrose, M.K., Reissmann, M., Bortfeldt, R., Dieterich, C., Adamski, J., Wang-Sattler, R., Illig, T. and Brockmann, G.A.
Metabolomics 10 (3): 461-472. June 2014

MOV10 is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs.
Gregersen, L.H., Schueler, M., Munschauer, M., Mastrobuoni, G., Chen, W., Kempa, S., Dieterich, C. and Landthaler, M.
Molecular Cell 54 (4): 573-585. 22 May 2014

Characterization of genetic diversity in the nematode pristionchus pacificus from population-scale resequencing data.
Roedelsperger, C., Neher, R.A., Weller, A.M., Eberhardt, G., Witte, H., Mayer, W.E., Dieterich, C. and Sommer, R.J.
Genetics 196 (4): 1153-1165. April 2014

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.
Munschauer, M., Schueler, M., Dieterich, C. and Landthaler, M.
Methods 65 (3): 302-309. February 2014

Differential protein occupancy profiling of the mRNA transcriptome.
Schueler, M., Munschauer, M., Gregersen, L.H., Finzel, A., Loewer, A., Chen, W., Landthaler, M. and Dieterich, C.
Genome Biology 15 (1): R15. 13 January 2014

2013

ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta, M. and Dieterich, C.
Bioinformatics 29 (14): 1809-1810. 15 July 2013

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
Li, N., You, X., Chen, T., Mackowiak, S.D., Friedlaender, M.R., Weigt, M., Du, H., Gogol-Doering, A., Chang, Z., Dieterich, C., Hu, Y. and Chen, W.
Nucleic Acids Research 41 (6): 3619-3634. 8 February 2013

Gas sorption isotherms in swelling glassy polymers: detailed atomistic simulations.
Hoelck, O., Boehning, M., Heuchel, M., Siegert, M.R. and Hofmann, D.
Journal of Membrane Science 428 : 523-532. 1 February 2013

Computational biology of RNA interactions.
Dieterich, C. and Stadler, P.F.
Wiley Interdisciplinary Reviews: RNA 4 (1): 107-120. January 2013

Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes.
Ahmed, R., Chang, Z., Younis, A.E., Langnick, C., Li, N., Chen, W., Brattig, N. and Dieterich, C.
Genome Biology and Evolution 5 (7): 1246-1260. 2013

2012

FLEXBAR: flexible barcode and adapter processing for next-generation sequencing platforms.
Dodt, M., Roehr, J.T., Ahmed, R. and Dieterich, C.
Biology 1 (3): 895-905. 14 December 2012

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans.
Sinha, A., Sommer, R.J. and Dieterich, C.
BMC Genomics 13 (1): 254. 19 June 2012

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.
Baltz, A.G., Munschauer, M., Schwanhaeusser, B., Vasile, A., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M., Wyler, E., Bonneau, R., Selbach, M., Dieterich, C. and Landthaler, M.
Molecular Cell 46 (5): 674-690. 8 June 2012

doRiNA: a database of RNA interactions in post-transcriptional regulation.
Anders, G., Mackowiak, S.D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

Prediction of transcription factor binding sites by integrating DNase digestion and histone modification.
Gusmao, E.G., Dieterich, C. and Costa, I.G.
Lecture Notes in Computer Science 7409 : 109-119. 2012

2011

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi, C., Wang, Y., Gruen, D., Mastrobuoni, G., You, X., Tolle, D., Dodt, M., Mackowiak, S.D., Gogol-Doering, A., Oenal, P., Rybak, A., Ross, E., Alvarado, A.S., Kempa, S., Dieterich, C., Rajewsky, N. and Chen, W.
Genome Research 21 (7): 1193-1200. July 2011

Pristionchus pacificus daf-16 is essential for dauer formation but dispensable for mouth form dimorphism.
Ogawa, A., Bento, G., Bartelmes, G., Dieterich, C. and Sommer, R.J.
Development 138 (7): 1281-1284. April 2011

Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.
Mayer, W.E., Schuster, L.N., Bartelmes, G., Dieterich, C. and Sommer, R.J.
BMC Evolutionary Biology 11 (1): 13. 13 January 2011

2010

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models.
Borchert, N., Dieterich, C., Krug, K., Schuetz, W., Jung, S., Nordheim, A., Sommer, R.J. and Macek, B.
Genome Research 20 (6): 837-486. June 2010

ACCUSA: accurate SNP calling on draft genomes.
Froehler, S. and Dieterich, C.
Bioinformatics 26 (10): 1364-1365. 15 May 2010

CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.
Roedelsperger, C. and Dieterich, C.
PLoS ONE 5 (1): e8861. 28 January 2010

2009

3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Froehler, S. and Dieterich, C.
BMC Genomics 10 (1): 635. 29 December 2009

mGene: Accurate SVM-based gene finding with an application to nematode genomes.
Schweikert, G., Zien, A., Zeller, G., Behr, J., Dieterich, C., Ong, C.S., Philips, P., De Bona, F., Hartmann, L., Bohlen, A., Krueger, N., Sonnenburg, S. and Raetsch, G.
Genome Research 19 (11): 2133-2143. November 2009

How to become a parasite - lessons from the genomes of nematodes.
Dieterich, C. and Sommer, R.J.
Trends in Genetics 25 (5): 203-209. May 2009

2008

Syntenator: multiple gene order alignments with a gene-specific scoring function.
Roedelsperger, C. and Dieterich, C.
Algorithms for Molecular Biology 3 6 November 2008

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.
Dieterich, C., Clifton, S.W., Schuster, L.N., Chinwalla, A., Delehaunty, K., Dinkelacker, I., Fulton, L., Fulton, R., Godfrey, J., Minx, P., Mitreva, M., Roeseler, W., Tian, H., Witte, H., Yang, S.P., Wilson, R.K. and Sommer, R.J.
Nature Genetics 40 (10): 1193-1198. October 2008

Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences.
Rae, R., Riebesell, M., Dinkelacker, I., Wang, Q., Herrmann, M., Weller, A.M., Dieterich, C. and Sommer, R.J.
Journal of Experimental Biology 211 (Pt 12): 1927-1936. June 2008

Evolution of a core gene network for skeletogenesis in chordates.
Hecht, J., Stricker, S., Wiecha, U., Stiege, A., Panopoulou, G., Podsiadlowski, L., Poustka, A.J., Dieterich, C., Ehrich, S., Suvorova, J., Mundlos, S. and Seitz, V.
PLoS Genetics 4 (3): e1000025. 21 March 2008

A Caenorhabditis motif compendium for studying transcriptional gene regulation.
Dieterich, C. and Sommer, R.J.
BMC Genomics 9 : 30. 23 January 2008

2007

Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model.
Hecht, J., Seitz, V., Urban, M., Wagner, F., Robinson, P.N., Stiege, A., Dieterich, C., Kornak, U., Wilkening, U., Brieske, N., Zwingman, C., Kidess, A., Stricker, S. and Mundlos, S.
Gene Expression Patterns 7 (1-2): 102-112. January 2007

Developments in CORG: a gene-centric comparative genomics resource.
Dieterich, C., Franz, M.W. and Vingron, M.
Nucleic Acids Research 35 (Database issue): D32-D35. January 2007

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.
Dieterich, C., Roeseler, W., Sobetzko, P. and Sommer, R.J.
Nucleic Acids Research 35 (Database issue): D498-D502. January 2007

2006

Comparative promoter analysis in vertebrate genomes with the CORG workbench.
Dieterich, C. and Vingron, M.
Methods in Molecular Biology 338 : 105-118. 2006

Pristionchus pacificus genomics: from genetics to genome sequence.
Dieterich, C., Roeseler, W. and Srinivasan, J.
WormBook : 1-14. 2006

2005

Ab initio identification of putative human transcription factor binding sites by comparative genomics.
Cora, D., Herrmann, C., Dieterich, C., Di Cunto, F., Provero, P. and Caselle, M.
BMC Bioinformatics 6 2005

Comparative promoter region analysis powered by CORG.
Dieterich, C., Grossmann, S., Tanzer, A., Roepcke, S., Arndt, P.F., Stadler, P.F. and Vingron, M.
BMC Genomics 6 (1): 24. 2005

Detecting functional modules of transcription factor binding sites in the human genome.
Manke, T., Dieterich, C. and Vingron, M.
Lecture Notes in Computer Science 3318 : 14-21. 2005

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors.
Michael, M., Dieterich, C. and Vingron, M.
Bioinformatics 21 (9): 2093-2094. 2005

2004

The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF.
Philippar, U., Schratt, G., Dieterich, C., Mueller, J.M., Galgoczy, P., Engel, F.B., Keating, M.T., Gertler, F., Schuele, R., Vingron, M. and Nordheim, A.
Molecular Cell 16 (6): 867-880. 22 December 2004

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
Dieterich, C., Rahmann, S. and Vingron, M.
Bioinformatics 20 (Suppl 1): i109-i115. 4 August 2004

Suboptimal local alignments across multiple scoring schemes.
Michael, M., Dieterich, C. and Stoye, J.
Lecture Notes in Computer Science 3240 : 99-110. 2004

2003

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.
Dieterich, C., Herwig, R. and Vingron, M.
Bioinformatics 19 (Suppl 2): ii50-ii56. October 2003

CORG: a database for COmparative Regulatory Genomics.
Dieterich, C., Wang, H., Rateitschak, K., Luz, H. and Vingron, M.
Nucleic Acids Research 31 (1): 55-57. 2003

2002

In vitro reconstructed human epithelia reveal contributions of Candida albicans EFG1 and CPH1 to adhesion and invasion.
Dieterich, C., Schandar, M., Noll, M., Johannes, F.J., Brunner, H., Graeve, T. and Rupp, S.
Microbiology 148 (Pt 2): 497-506. February 2002

Annotating regulatory DNA based on man-mouse genomic comparison.
Dieterich, C., Cusack, B., Wang, H., Rateitschak, K., Krause, A. and Vingron, M.
Bioinformatics 18 (Suppl 2): S84-S90. 2002