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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.


  • 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)