Publikationen
Bitte schreiben Sie uns eine E-Mail, sollten Sie Probleme damit haben, die Veröffentlichungen herunterzuladen.
Jahr 2019
-
I Yanai, MJ Lercher
What is the question?
Genome Biol 20, 289 (2019) doi:10.1186/s13059-019-1902-1
-
I Yanai, MJ Lercher
Night science
Genome Biol 20, 179 (2019) doi:10.1186/s13059-019-1800-6
-
D Singh, MJ Lercher
Network reduction methods for genome-scale metabolic models
Cell Mol Life Sci. 2019 Nov 20. doi: 10.1007/s00018-019-03383-z. [Epub ahead of print] Review.
PMID: 31748914
-
NL Gao, J Chen, T Wang, MJ Lercher, WH Chen
Prokaryotic genome expansion is facilitated by phages and plasmids but impaired by CRISPR
Front Microbiol. 2019 Oct 16;10:2254. doi: 10.3389/fmicb.2019.02254. eCollection 2019.
PMID:31681190
-
D Alzoubi, AA Desouki, MJ Lercher
Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast
Sci Rep. 2019 Aug 14;9(1):11837. doi: 10.1038/s41598-019-47935-6.
PMID: 31413270
-
Clarisa E Alvarez, Anastasiia Bovdilova, Astrid Höppner, Christian-Claus Wolff, Mariana Saigo, Felipe Trajtenberg, Tao Zhang, Alejandro Buschiazzo, Luitgard Nagel-Steger, Maria F Drincovich, MJ Lercher, Veronica G Maurino
Molecular adaptations of NADP-malic enzyme for its function in C4 photosynthesis in grasses.
Nat Plants. 2019 Jul;5(7):755-765. doi: 10.1038/s41477-019-0451-7. Epub 2019 Jun 24.
PMID: 31235877
-
B Subramanian, S Gao, MJ Lercher, S Hu, WH Chen
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees
Nucleic Acids Res. 2019 Jul 2;47(W1):W270-W275. doi: 10.1093/nar/gkz357.
PMID: 31114888
-
TY Pang, MJ Lercher
Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment
Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):187-192. doi: 10.1073/pnas.1718997115. Epub 2018 Dec 18.
PMID: 30563853
-
XP Hu, H Dourado, MJ Lercher
An analytical theory of cellular growth
bioRxiv, 802470 (2019)
Jahr 2018
-
David Heckmann, Colton J Lloyd, Nathan Mih, Yuanchi Ha, Daniel C Zielinski, Zachary B Haiman, Abdelmoneim Amer Desouki, M. J. Lercher, Bernhard O Palsson
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Nature communications 9 (1), 5252 (2018)
-
D Alzoubi, AA Desouki, M. J. Lercher
Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations
Scientific reports 8 (1), 17252 (2018)
-
AK Denton, J Maß, C Külahoglu, M. J. Lercher, A Bräutigam, APM Weber
Corrigendum: Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
Journal of experimental botany 69 (15), 3789 (2018)
-
B Pfeifer, M. J. Lercher
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation
Bioinformatics 34 (18), 3205-3207 (2018)
-
E Sundermann, M. J. Lercher, D Heckmann
Modeling Cellular Resource Allocation Reveals Low Phenotypic Plasticity of C4 Plants and Infers Environments of C4 Photosynthesis Evolution
bioRxiv, 371096 (2018)
-
D Hartleb, CJ Fritzemeier, M. J. Lercher
Automated high-quality reconstruction of metabolic networks from high-throughput data
bioRxiv, 282251 (2018)
-
D Alzoubi, AA Desouki, M. J. Lercher
Different alleles of the same gene vary in pleiotropy, often mediated through currency metabolite production
bioRxiv, 144329 (2018)
-
N. Gao, C. Zhang, Z. Zhang, S. Hu, M. J. Lercher, X. Zhao, P. Bork, Z. Liu, W. Chen
MVP: a microbe–phage interaction database
Nucleic acids research, 46(D1): D700-D707 (2018)
Jahr 2017
N. Gao, G. Lu, M. J. Lercher, W. H. Chen
Selection for energy efficiency drives strand-biased gene distribution in prokaryotes
Scientific Reports, 7:10572 (2017)
J. Schmitz, N. V. Srikanth, M. Hüdig, G Poschmann, M. J. Lercher,V. G. Maurino
The ancestors of diatoms evolved a unique mitochondrial dehydrogenase to oxidize photorespiratory glycolate
Photosynthesis Research 132:183-196 (2017)
C. J. Fritzemeier, D. Hartleb, B. Szappanos, B. Papp, M. J. Lercher
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal.
PLoS Computational Biology 13e1005494 (2017)
T. Y. Pang, M. J. Lercher
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.
Scientific Reports 7:40294 (2017)
Y. Li, D. Heckmann, M. J. Lercher, V. G. Maurino
Combining genetic and evolutionary engineering to establish C-4 metabolism in C-3 plants.
Journal of Experimental Botany 48:117-125 (2017)
A. K. Denton, J. Maß, C. Külahoglu, M. J. Lercher, A. Bräutigam, A. P. M. Weber
Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.
Journal of Experimental Botany 48:147-160 (2017)
Jahr 2016
D. Hartleb, F. Jarre, M. J. Lercher
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.
PLoS Computational Biology 12e1005036 (2016)
Z. He, H. Zhang, S. Gao, M. J. Lercher, W. Chen, S. Hu
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees.
Nucleic Acids Research 44:W236-W241 (2016)
B. Szappanos, J. Fritzemeier, B. Csörgő, V. Lázár, X. Lu, G. Fekete, B. Balint, R. Herczeg, I. Nagy, R. A. Notebaart, M. J. Lercher, C. Pál, B. Pap
Adaptive evolution of complex innovations through stepwise metabolic niche expansion.
Nature Communications 7:11607 (2016)
W. Chen, G. Lu, P. Bork, S. Hu, M. J. Lercher
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
Nature Communications 7:11334 (2016)
Jahr 2015
A. Dilthey, M. J. Lercher
Horizontally transferred genes cluster spatially and metabolically.
Biology Direct 10:72 (2015)
- A. A. Desouki, F. Jarre, G. Gelius-Dietrich, M. J. Lercher
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions.
Bioinformatics 31:2159-2165 (2015)
U. Wittelsbürger, B. Pfeifer, M. J. Lercher
WhopGenome: high-speed access to whole-genome variation and sequence data in R.
Bioinformatics 31:413-415 (2015)
Jahr 2014
J. Mallmann, D. Heckmann, A. Bräutigam, M. J. Lercher, A. P. M. Weber, P. Westhoff, U. Gowik
The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria.
eLife 10.7554 /eLife.02478 (2014)
B. Pfeifer, U. Wittelsbürger, S. Ramos-Onsins, M. J. Lercher
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R.
Mol Biol Evol. 31:1929-1936 (2014)
G. Schönknecht, A.P. Weber, M. J. Lercher
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.
Bioessays.36:9-20 (2014)
C. Esser, A. Kuhn, G. Groth, M. J. Lercher, V. G. Maurino
Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases.
Mol Biol Evol. 31:1089-101 (2014)
M. K. Engqvist, C. Eßer, A. Maier, M. J. Lercher, V. G. Maurino
Mitochondrial 2-hydroxyglutarate metabolism.
Mitochondrion (epub. ahead of print)(2014)
G. Gelius-Dietrich, A. A. Desouki, C. J. Fritzemeier, M. J. Lercher
sybil - Efficient constraint-based modelling in R.
BMC Systems Biology 13:125 (2014)
Jahr 2013
D. Heckmann, S. Schulze, A. Denton, U. Gowik, P. Westhoff, A. P. M. Weber, M. J. Lercher
Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape.
Cell 153:1579-1588 (2013)
Ausgezeichnet mit dem "Best-Paper-Preis der Willhelm-Pfeffer Stiftung 2014"
-
G. Schönknecht, W. H. Chen, C. M. Ternes, G. G. Barbier, R. P. Shrestha, M. Stanke, A. Brautigam, B. J. Baker, J. F. Banfield, R. M. Garavito, K. Carr, C. Wilkerson, S. A. Rensing, D. Gagneul, N. E. Dickenson, C. Oesterhelt, M. J. Lercher, A. P. M. Weber
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote.
Science 339:1207-1210 (2013)
Jahr 2012
W. H. Chen, K. Trachana, M. J. Lercher, P. Bork
Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age.
Mol Biol Evol. (2012 – Epub ahead of print)
-
W. H. Chen, P. Minguez, M. J. Lercher, P. Bork
OGEE: an online gene essentiality database.
Nucleic Acids Res. 40 (Database issue):D901-6 (2012)
-
H. Zhang, S. Gao, M. J. Lercher, S. Hu, W. H. Chen
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.
Nucleic Acids Research 40 (Webserver issue): W569-72 (2012)
-
T. Laubach, A. von Haeseler, M. J. Lercher
TreeSnatcher plus: capturing phylogenetic trees from images.
BMC Bioinformatics 13:110 (2012)
-
L. Grassi, M. Caselle, M. J. Lercher, M. C. Lagomarsino
Horizontal gene transfers as metagenomic gene duplications.
Mol Biosyst. 8:790-5 (2012)
Jahr 2011
B. Szappanos, K. Kovács, B. Szamecz, F. Honti, M. Costanzo, A. Baryshnikova, G. Gelius-Dietrich, M. J. Lercher, M. Jelasity, C. L. Myers, B. J. Andrews, C. Boone, S. G. Oliver, C. Pál, B. Papp
An integrated approach to characterize genetic interaction networks in yeast metabolism.
Nat Genet. 43:656-62 (2011)
-
G. Z. Wang, M. J. Lercher
The effects of network neighbours on protein evolution.
PLoS One. 6:e18288 (2011)
-
W. H. Chen, W. Wei, M. J. Lercher
Minimal regulatory spaces in yeast genomes.
BMC Genomics 12:320 (2011)
-
G. Z. Wang, J. Liu, W. Wang, H. Y. Zhang, M. J. Lercher
A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactions.
PLoS One 6e17650 (2011)
-
G. Z. Wang, W. H. Chen, M. J. Lercher
Coexpression of linked gene pairs persists long after their separation.
Genome Biol Evol. 3:565-70 (2011)
-
A. Bräutigam, K. Kajala, J. Wullenweber, M. Sommer, D. Gagneul, K.L. Weber, K. M. Carr, U. Gowik, J. Maß, M. J. Lercher, P. Westhoff, J. M. Hibberd, A. P. Weber
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.
Plant Physiol. 155:142-56 (2011)
-
G.Z. Wang, M. J. Lercher, L. D. Hurst
Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise.
Genome Biol Evol. 3:320-31 (2011)
Jahr 2010
G.Z. Wang, M. J. Lercher
Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes.
BMC Evol Biol. 10:263 (2010)
-
L. Hao, X. Ge, H. Wan, S. Hu, M. J. Lercher, J. Yu, W. H. Chen
Human functional genetic studies are biased against the medically most relevant primate-specific genes.
BMC Evol Biol. 10:316 (2010)
-
F. He, W. H. Chen, S. Collins, C. Acquisti, U. Goebel, S. Ramos-Onsins, M. J. Lercher, J. de Meaux
Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions in Arabidopsis thaliana.
Genetics 185:695-701 (2010)
-
M. Weiss, S. Schrimpf, M.O. Hengartner, M. J. Lercher, C. von Mering
Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.
Proteomics 10:1297-306 (2010)
Jahr 2009
S. P. Schrimpf, M. Weiss, L. Reiter, C. H. Ahrens, M. Jovanovic, J. Malmström, E. Brunner, S. Mohanty, M. J. Lercher, P. E. Hunziker, R. Aebersold, C. von Mering, M. O. Hengartner
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes.
PLoS Biology 7:e48 (2009)
-
W. H. Chen, J. de Meaux, M. J. Lercher
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions.
BMC Genomics 16:178 (2009)
-
T. Warnecke, G.-Z. Wang, M. J. Lercher, L. D. Hurst
Does negative auto-regulation increase gene duplicability?
BMC Evolutionary Biology 9:193 (2009)
-
W. H. Chen, M. J. Lercher
ColorTree: a batch customization tool for phylogenic trees.
BMC Research Notes 2:155 (2009)
Jahr 2008
M. J. Lercher & C. Pál
Integration of horizontally transferred genes into regulatory interaction networks takes many million years.
Molecular Biology & Evolution 25:559-67 (2008)
Jahr 2007
Raes J., Korbel J.O., Lercher M.J., von Mering C., Bork P.
Prediction of effective genome size in metagenomic samples.
Genome Biology 15: R10 (2007)
Jahr 2006
J. Savard, D. Tautz & M. J. Lercher
Phylogenomic Analysis Reveals Bees and Wasps (Hymenoptera) at the Base of the Radiation of Holometabolous Insects.
Genome Research 16: 1334-1338 (2006)
-
M. J. Lercher & L. D. Hurst
Evidence that co-expressed genes cluster but are not regularly spaced.
Journal of Molecular Biology 359: 825-831 (2006)
-
P. Keightley, M. J. Lercher & A. Eyre-Walker
Understanding the degradation of hominid gene control.
PLoS Computational Biology 2: e19 (2006)
-
G. Legube, S. K. McWeeney, M. J. Lercher & A. Akhtar
X-chromosome-wide profiling of MSL-1 distribution &fu dosage compensation in Drosophila.
Genes & Development 20: 871-883 (2006)
-
C. Pál, B. Papp & M. J. Lercher
An integrated view of protein evolution.
Nature Reviews Genetics 7: 337-48 (2006)
-
C. Pál, B. Papp, M. J. Lercher, P. Csermely, S. G. Oliver & L. D. Hurst
Chance and necessity in the evolution of minimal metabolic networks.
Nature 440: 667-670 (2006)
-
I. Yanai, J. Korbel, S. Boue, S. K. McWeeney, P. Bork & M. J. Lercher
Similar gene expression profiles do not imply similar tissue functions.
Trends in Genetics 22: 132-138 (2006)
-
J. Savard, D. Tautz & M. J. Lercher
Genome-wide acceleration of protein evolution in flies (Diptera).
BMC Evolutionary Biology 6: 7 (2006)
Jahr 2005
C. Pál, B. Papp & M. J. Lercher
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.
Nature Genetics 37: 1372-1375 (2005)
-
C. Pál, B. Papp & M. J. Lercher
Horizontal gene transfer depends on gene content of the host
Bioinformatics 21: ii222-ii223 (2005)
-
P. Keightley, M. J. Lercher & A. Eyre-Walker
Evidence for widespread degradation of gene control regions in hominid genomes.
PLoS Biology 3: e42 (2005)
-
M. J. Lercher & L. D. Hurst
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.
BMC Evolutionary Biology 5: 62 (2005)
Jahr 2004
M. T. Webster, N. G. C. Smith, M. J. Lercher & H. Ellegren
Gene Expression, Synteny, and Local Similarity in Human Noncoding Mutation Rates.
Molecular Biology and Evolution 21: 1820-1830 (2004)
-
L. D. Hurst, C. Pál & M. J. Lercher
The dynamics of eukaryotic gene order.
Nature Reviews Genetics 5: 299-310 (2004)
-
M. J. Lercher, J. Chamary & L. D. Hurst
Genomic regionality in rates of evolution is not explained by clustering of genes of
comparable expression profile.Genome Research 14: 1002-1013 (2004)
Jahr 2003
M. J. Lercher, A. O. Urrutia, A. Pavlicek & L. D. Hurst
A unification of mosaic structures in the human genome.
Human Molecular Genetics 12: 2411-2415 (2003)
-
M. J. Lercher & L. D. Hurst
Imprinted chromosomal regions of the human genome have unusually high recombination rates.
Genetics 165: 1629-1632 (2003)
-
M. J. Lercher, A. O. Urrutia & L. D. Hurst
Evidence that the human X chromosome is enriched for male-specific but not female-specific genes.
Molecular Biology and Evolution 20: 1113-1116 (2003)
-
M. J. Lercher, T. Blumenthal & L. D. Hurst
Co-expression of neighbouring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes.
Genome Research 13: 238 - 243 (2003)
Jahr 2002
M. J. Lercher, N. G. C. Smith, A. Eyre-Walker & L. D. Hurst
The evolution of isochores: evidence from SNP frequency distributions.
Genetics 162: 1805 - 1810 (2002)
-
M. J. Lercher & L. D. Hurst
Can mutation or fixation biases explain the allele frequency distribution of human SNPs?
Gene 300: 53 - 58 (2002)
-
M. J. Lercher, A. O. Urrutia & L. D. Hurst
Clustering of housekeeping genes provides a unified model of gene order in the human genome.
Nature Genetics 31: 180 - 183 (2002)
-
M. J. Lercher & L. D. Hurst
Human SNP variability and mutation rate are higher in regions of high recombination.
Trends in Genetics 18: 337 - 340 (2002)
-
N. G. C. Smith & M. J. Lercher
Regional similarities in polymorphism in the human genome extend over many megabases.
Trends in Genetics 18: 281 - 283 (2002)
Jahr 2001
M. J. Lercher, E. J. B. Williams & L. D. Hurst
Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias.
Molecular Biology and Evolution 18: 2032 - 2039 (2001)