Publications

Grigory Genikhovich, Patrick Fried, M. Mandela Prünster, Johannes B. Schinko, Anna F. Gilles, David Fredman, Karin Meier, Dagmar Iber, and Ulrich Technau. Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints. Cell Reports, 2015.

Yehu Moran*, David Fredman*, Daniela Praher, Xin Z Li, Liang Meng Wee, Fabian Rentzsch, Phillip D Zamore, Ulrich Technau, and Hervé Seitz. Cnidarian microRNAs frequently regulate targets by cleavage. Genome Research, 24(4):651--663, April 2014.

Michaela Schwaiger, Anna Schönauer, André F Rendeiro, Carina Pribitzer, Alexandra Schauer, Anna F Gilles, Johannes B Schinko, Eduard Renfer, David Fredman, and Ulrich Technau. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Research, 24(4):639--650, April 2014.

David Fredman , Michaela Schwaiger, Fabian Rentzsch, and Ulrich Technau. The developmental and adult sex-specific transcriptomes of the sea anemone Nematostella vectensis. Figshare, doi:10.6084/m9.figshare.807696, 2013.

Antje Fisher, Sarah Thulin, David Fredman, and Joel Smith. Employing bac-reporter constructs in the sea anemone nematostella vectensis. Integrative and Comparative Biology, 2013.

Yehu Moran, Daniela Praher, David Fredman, and Ulrich Technau. The evolution of microRNA pathway protein components in Cnidaria. Molecular Biology and Evolution (accepted), 2013.

Lydia M Zopf, Axel Schmid, David Fredman, and Bo Joakim Eriksson. Spectral Sensitivity of the ctenid spider Cupiennius salei Keys. The Journal of Experimental Biology, 2013.

Bo Joakim Eriksson, David Fredman, Gerhard Steiner, and Axel Schmid. Characterisation and localisation of the opsin protein repertoire in the brain and retinas of a spider and an onychophoran. BMC Evolutionary Biology, 2013.

Yehu Moran, David Fredman, Pawel Szczesny, Marcin Grynberg, and Ulrich Technau. Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Molecular Biology and Evolution, 29(9):2223--2230, September 2012.

David Fredman, Xianjun Dong, and Boris Lenhard. Making enhancers from spare parts of the genome. Genome Biology, 12(12):138, 2011.

Xianjun Dong, Pavla Navratilova, David Fredman, Oyvind Drivenes, Thomas S Becker, and Boris Lenhard. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Research, 38(4):1071--1085, March 2010.

Pavla Navratilova, David Fredman, Boris Lenhard, and Thomas S Becker. Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Molecular genetics and genomics : MGG, 283(2):171--184, February 2010.

Anja Ragvin, Enrico Moro, David Fredman, et al. Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proceedings Of The National Academy Of Sciences Of The United States Of America, 107(2):775--780, January 2010.

David Fredman, Pär G Engström, and Boris Lenhard. Web-based tools and approaches to study long-range gene regulation in Metazoa. Briefings in Functional Genomics and Proteomics, 8(4):231--242, July 2009.

Anthony J Brookes et al. The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation. Human mutation, 30(6):968--977, June 2009.

FANTOM Consortium. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41(5):553--562, May 2009.

Pavla Navratilova, David Fredman, Thomas A Hawkins, Katherine Turner, Boris Lenhard, and Thomas S Becker. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Developmental Biology, 327(2):526--540, March 2009.

Xianjun Dong, David Fredman, and Boris Lenhard. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biology, 10(8):R86, 2009.

Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O Daub, Yoshihide Hayashizaki, and Boris Lenhard. Transcriptional features of genomic regulatory blocks. Genome Biology, 10(4):R38, 2009.

Minjie Luo, Xiangfeng Cui, David Fredman, Anthony J Brookes, Marco A Azaro, Danielle M Greenawalt, Guohong Hu, Hui-Yun Wang, Irina V Tereshchenko, Yong Lin, Yue Shentu, Richeng Gao, Li Shen, and Honghua Li. Genetic structures of copy number variants revealed by genotyping single sperm. PLoS ONE, 4(4):e5236, 2009.

Pär G Engström, David Fredman, and Boris Lenhard. Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biology, 9(2):R34, 2008.

Hiroshi Kikuta et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Research, 17(5):545--555, May 2007.

Hiroshi Kikuta, David Fredman, Silke Rinkwitz, Boris Lenhard, and Thomas S Becker. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biology, 8 Suppl 1:S4, 2007.

Martin C Frith, Jasmina Ponjavic, David Fredman, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Yoshihide Hayshizaki, and Albin Sandelin. Evolutionary turnover of mammalian transcription start sites. Genome Research, 16(6):713--722, June 2006.

David Fredman*, Sarah L Sawyer*, Linda Strömqvist, Salim Mottagui-Tabar, Kenneth K Kidd, Claes Wahlestedt, Stephen J Chanock, and Anthony J Brookes. Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection. Human mutation, 27(2):173--186, February 2006.

David Fredman, Stefan J White, Susanna Potter, Evan E Eichler, Johan T den Dunnen, and Anthony J Brookes. Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics, 36(8):861--866, August 2004.

David Fredman, M Jobs, L Strömqvist, and A J Brookes. DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications. Human mutation, 24(1):1--8, July 2004.

David Fredman, Gillian Munns, Daniel Rios, Fredrik Sjöholm, Marianne Siegfried, Boris Lenhard, Heikki Lehväslaiho, and Anhony J Brookes. HGVbase: a curated resource describing human DNA variation and phenotype relationships. Nucleic Acids Research, 32(Database issue):D516--9, January 2004.

David Fredman, Marianne Siegfried, Yan P Yuan, Peer Bork, Heikki Lehväslaiho, and Anthony J Brookes. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Research, 30(1):387--391, January 2002.

Tesfai Emahazion et al. SNP association studies in Alzheimer's disease highlight problems for complex disease analysis. Trends in genetics : TIG, 17(7):407--413, July 2001.