Research Topics
| Martin J LercherSummaryAffiliation: Heinrich Heine University Country: Germany Publications
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Detail Information
Publications
Integration of horizontally transferred genes into regulatory interaction networks takes many million yearsMartin J Lercher
Department of Computer Science, Heinrich Heine University, Dusseldorf, Germany
Mol Biol Evol 25:559-67. 2008....- Minimal regulatory spaces in yeast genomesWei Hua Chen
Institute for Computer Science, Heinrich Heine University Dusseldorf, Germany
BMC Genomics 12:320. 2011..However, the size of this minimal regulatory space is not generally known. In particular, it is unclear if minimal promoter size differs between species and between uni- and bi-directionally acting regulatory regions... - Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactionsWei Hua Chen
Bioinformatics, Heinrich Heine University Duesseldorf, 40225, Germany
BMC Genomics 11:178. 2010..Currently, it is still unclear how much of this local co-expression is caused by direct transcriptional interactions, and how much is due to shared chromatin environments... - Does negative auto-regulation increase gene duplicability?Tobias Warnecke
Department of Biology and Biochemistry, University of Bath, UK
BMC Evol Biol 9:193. 2009..Using data from the transcriptional networks of E. coli and S. cerevisiae, we test the hypothesis that genes under negative auto-regulation show enhanced duplicability... - Human functional genetic studies are biased against the medically most relevant primate-specific genesLili Hao
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
BMC Evol Biol 10:316. 2010..Many functional, structural and evolutionary features of human genes have been observed to correlate with expression breadth and/or gene age. Here, we systematically explore these correlations... - Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotesGuang Zhong Wang
Bioinformatics Group, Heinrich Heine University, Dusseldorf, Germany
BMC Evol Biol 10:263. 2010..a causal relationship, or could the apparent trend be caused by phylogenetic relatedness among sampled organisms living at different temperatures? And do proteins from endothermic and exothermic vertebrates show similar differences?.. - ColorTree: a batch customization tool for phylogenic treesWei Hua Chen
Bioinformatics, Heinrich Heine University Duesseldorf, 40225, Germany
BMC Res Notes 2:155. 2009..CONCLUSION: ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files... - Coexpression of linked gene pairs persists long after their separationGuang Zhong Wang
Institute for Computer Science, Heinrich Heine University, 40225 Dusseldorf, Germany
Genome Biol Evol 3:565-70. 2011..Contrary to previous suggestions, selectively favorable coexpression appears not to be restricted to bidirectional promoters... - An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 speciesAndrea Bräutigam
Institute of Plant Biochemistry, Heinrich Heine University, 40225 Duesseldorf, Germany
Plant Physiol 155:142-56. 2011..We anticipate that comparative transcriptomics of closely related species will provide deep insight into the evolution of other complex traits... - A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactionsGuang Zhong Wang
Institute for Computer Science, Heinrich Heine University, Dusseldorf, Germany
PLoS ONE 6:e17650. 2011..Based on experimentally measured phenotypic capacity, it was suggested that knockout fitness was unimportant, but that phenotypic capacitors tend to be hubs in genetic and physical interaction networks... - The effects of network neighbours on protein evolutionGuang Zhong Wang
Institute for Computer Science, Heinrich Heine University, Dusseldorf, Germany
PLoS ONE 6:e18288. 2011.... - OGEE: an online gene essentiality databaseWei Hua Chen
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 40:D901-6. 2012..Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. OGEE is freely available at http://ogeedb.embl.de... - Chance and necessity in the evolution of minimal metabolic networksCsaba Pal
European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
Nature 440:667-70. 2006..We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle... - Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profileMartin J Lercher
Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
Genome Res 14:1002-13. 2004..As regards K4, our results appear consistent with the notion that local similarity is due to processes associated with meiotic recombination... - Evidence for widespread degradation of gene control regions in hominid genomesPeter D Keightley
School of Biological Sciences, University of Edinburgh, United Kingdom
PLoS Biol 3:e42. 2005..This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees... - Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genomeLaurence D Hurst
Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
BMC Evol Biol 5:62. 2005..Here we ask whether ligands are more closely linked to their receptors than expected by chance... - Prediction of effective genome size in metagenomic samplesJeroen Raes
European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Genome Biol 8:R10. 2007..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects... - Genome-wide acceleration of protein evolution in flies (Diptera)Joel Savard
Institut für Genetik der Universität zu Köln, 50674 Koln, Germany
BMC Evol Biol 6:7. 2006..To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we assess the rate variation between insect lineages for a large number of orthologous genes... - Similar gene expression profiles do not imply similar tissue functionsItai Yanai
Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
Trends Genet 22:132-8. 2006..Ectopic expression is possibly explained as expression leakage, caused by spreading of chromatin modifications or the transcription apparatus into neighboring genes... - Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insectsJoel Savard
Abteilung für Evolutionsgenetik, Institut fur Genetik, Universitat zu Koln, Köln 50674, Germany
Genome Res 16:1334-8. 2006..We validate our results by meticulous examination of potential confounding factors. Phylogenomic approaches are thus able to resolve long-standing questions about the phylogeny of insects... - The evolution of isochores: evidence from SNP frequency distributionsMartin J Lercher
Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
Genetics 162:1805-10. 2002..The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions...