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Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast.

Alzoubi D, Desouki AA, Lercher MJ.

Sci Rep. 2019 Aug 14;9(1):11837. doi: 10.1038/s41598-019-47935-6.


Molecular adaptations of NADP-malic enzyme for its function in C4 photosynthesis in grasses.

Alvarez CE, Bovdilova A, Höppner A, Wolff CC, Saigo M, Trajtenberg F, Zhang T, Buschiazzo A, Nagel-Steger L, Drincovich MF, Lercher MJ, Maurino VG.

Nat Plants. 2019 Jul;5(7):755-765. doi: 10.1038/s41477-019-0451-7. Epub 2019 Jun 24.


Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.

Subramanian B, Gao S, Lercher MJ, Hu S, Chen WH.

Nucleic Acids Res. 2019 Jul 2;47(W1):W270-W275. doi: 10.1093/nar/gkz357.


Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment.

Pang TY, Lercher MJ.

Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):187-192. doi: 10.1073/pnas.1718997115. Epub 2018 Dec 18.


Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO.

Nat Commun. 2018 Dec 7;9(1):5252. doi: 10.1038/s41467-018-07652-6.


Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations.

Alzoubi D, Desouki AA, Lercher MJ.

Sci Rep. 2018 Nov 22;8(1):17252. doi: 10.1038/s41598-018-35092-1.


Corrigendum: Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.

Denton AK, Maß J, Külahoglu C, Lercher MJ, Bräutigam A, Weber APM.

J Exp Bot. 2018 Jun 27;69(15):3789. doi: 10.1093/jxb/ery196. No abstract available.


BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation.

Pfeifer B, Lercher MJ.

Bioinformatics. 2018 Sep 15;34(18):3205-3207. doi: 10.1093/bioinformatics/bty299.


MVP: a microbe-phage interaction database.

Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH.

Nucleic Acids Res. 2018 Jan 4;46(D1):D700-D707. doi: 10.1093/nar/gkx1124.


Selection for energy efficiency drives strand-biased gene distribution in prokaryotes.

Gao N, Lu G, Lercher MJ, Chen WH.

Sci Rep. 2017 Sep 5;7(1):10572. doi: 10.1038/s41598-017-11159-3.


Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal.

Fritzemeier CJ, Hartleb D, Szappanos B, Papp B, Lercher MJ.

PLoS Comput Biol. 2017 Apr 18;13(4):e1005494. doi: 10.1371/journal.pcbi.1005494. eCollection 2017 Apr.


The ancestors of diatoms evolved a unique mitochondrial dehydrogenase to oxidize photorespiratory glycolate.

Schmitz J, Srikanth NV, Hüdig M, Poschmann G, Lercher MJ, Maurino VG.

Photosynth Res. 2017 May;132(2):183-196. doi: 10.1007/s11120-017-0355-1. Epub 2017 Feb 28.


Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.

Denton AK, Maß J, Külahoglu C, Lercher MJ, Bräutigam A, Weber AP.

J Exp Bot. 2017 Jan;68(2):147-160. doi: 10.1093/jxb/erw463. Epub 2017 Jan 2. Erratum in: J Exp Bot. 2018 Jun 27;69(15):3789.


Combining genetic and evolutionary engineering to establish C4 metabolism in C3 plants.

Li Y, Heckmann D, Lercher MJ, Maurino VG.

J Exp Bot. 2017 Jan;68(2):117-125. doi: 10.1093/jxb/erw333. Epub 2016 Sep 22.


Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.

Hartleb D, Jarre F, Lercher MJ.

PLoS Comput Biol. 2016 Aug 2;12(8):e1005036. doi: 10.1371/journal.pcbi.1005036. eCollection 2016 Aug. Erratum in: PLoS Comput Biol. 2016 Dec 9;12 (12 ):e1005264.


Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

Szappanos B, Fritzemeier J, Csörgő B, Lázár V, Lu X, Fekete G, Bálint B, Herczeg R, Nagy I, Notebaart RA, Lercher MJ, Pál C, Papp B.

Nat Commun. 2016 May 20;7:11607. doi: 10.1038/ncomms11607.


Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees.

He Z, Zhang H, Gao S, Lercher MJ, Chen WH, Hu S.

Nucleic Acids Res. 2016 Jul 8;44(W1):W236-41. doi: 10.1093/nar/gkw370. Epub 2016 Apr 30.


Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Chen WH, Lu G, Bork P, Hu S, Lercher MJ.

Nat Commun. 2016 Apr 21;7:11334. doi: 10.1038/ncomms11334.


Forty years of The Selfish Gene are not enough.

Yanai I, Lercher MJ.

Genome Biol. 2016 Mar 2;17:39. doi: 10.1186/s13059-016-0910-7. Review. No abstract available.


Horizontally transferred genes cluster spatially and metabolically.

Dilthey A, Lercher MJ.

Biol Direct. 2015 Dec 21;10:72. doi: 10.1186/s13062-015-0102-5.


CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions.

Desouki AA, Jarre F, Gelius-Dietrich G, Lercher MJ.

Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: 10.1093/bioinformatics/btv096. Epub 2015 Feb 19.


WhopGenome: high-speed access to whole-genome variation and sequence data in R.

Wittelsbürger U, Pfeifer B, Lercher MJ.

Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636. Epub 2014 Oct 1.


The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria.

Mallmann J, Heckmann D, Bräutigam A, Lercher MJ, Weber AP, Westhoff P, Gowik U.

Elife. 2014 Jun 16;3:e02478. doi: 10.7554/eLife.02478.


PopGenome: an efficient Swiss army knife for population genomic analyses in R.

Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ.

Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16.


Mitochondrial 2-hydroxyglutarate metabolism.

Engqvist MK, Eßer C, Maier A, Lercher MJ, Maurino VG.

Mitochondrion. 2014 Nov;19 Pt B:275-81. doi: 10.1016/j.mito.2014.02.009. Epub 2014 Feb 21. Review.


Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases.

Esser C, Kuhn A, Groth G, Lercher MJ, Maurino VG.

Mol Biol Evol. 2014 May;31(5):1089-101. doi: 10.1093/molbev/msu041. Epub 2014 Jan 9.


Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.

Schönknecht G, Weber AP, Lercher MJ.

Bioessays. 2014 Jan;36(1):9-20. doi: 10.1002/bies.201300095. Epub 2013 Nov 13.


Sybil--efficient constraint-based modelling in R.

Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ.

BMC Syst Biol. 2013 Nov 13;7:125. doi: 10.1186/1752-0509-7-125.


Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape.

Heckmann D, Schulze S, Denton A, Gowik U, Westhoff P, Weber AP, Lercher MJ.

Cell. 2013 Jun 20;153(7):1579-88. doi: 10.1016/j.cell.2013.04.058.


Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.

Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP.

Science. 2013 Mar 8;339(6124):1207-10. doi: 10.1126/science.1231707.


EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.

Zhang H, Gao S, Lercher MJ, Hu S, Chen WH.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W569-72. doi: 10.1093/nar/gks576. Epub 2012 Jun 13.


TreeSnatcher plus: capturing phylogenetic trees from images.

Laubach T, von Haeseler A, Lercher MJ.

BMC Bioinformatics. 2012 May 24;13:110. doi: 10.1186/1471-2105-13-110.


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.

Chen WH, Trachana K, Lercher MJ, Bork P.

Mol Biol Evol. 2012 Jul;29(7):1703-6. doi: 10.1093/molbev/mss014. Epub 2012 Jan 19.


Horizontal gene transfers as metagenomic gene duplications.

Grassi L, Caselle M, Lercher MJ, Lagomarsino MC.

Mol Biosyst. 2012 Mar;8(3):790-5. doi: 10.1039/c2mb05330f. Epub 2012 Jan 4.


OGEE: an online gene essentiality database.

Chen WH, Minguez P, Lercher MJ, Bork P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D901-6. doi: 10.1093/nar/gkr986. Epub 2011 Nov 10.


Coexpression of linked gene pairs persists long after their separation.

Wang GZ, Chen WH, Lercher MJ.

Genome Biol Evol. 2011;3:565-70. doi: 10.1093/gbe/evr049. Epub 2011 Jul 6.


Minimal regulatory spaces in yeast genomes.

Chen WH, Wei W, Lercher MJ.

BMC Genomics. 2011 Jun 16;12:320. doi: 10.1186/1471-2164-12-320.


An integrated approach to characterize genetic interaction networks in yeast metabolism.

Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pál C, Papp B.

Nat Genet. 2011 May 29;43(7):656-62. doi: 10.1038/ng.846.


The effects of network neighbours on protein evolution.

Wang GZ, Lercher MJ.

PLoS One. 2011 Apr 12;6(4):e18288. doi: 10.1371/journal.pone.0018288.


A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactions.

Wang GZ, Liu J, Wang W, Zhang HY, Lercher MJ.

PLoS One. 2011 Mar 2;6(3):e17650. doi: 10.1371/journal.pone.0017650.


Human functional genetic studies are biased against the medically most relevant primate-specific genes.

Hao L, Ge X, Wan H, Hu S, Lercher MJ, Yu J, Chen WH.

BMC Evol Biol. 2010 Oct 20;10:316. doi: 10.1186/1471-2148-10-316.


Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes.

Wang GZ, Lercher MJ.

BMC Evol Biol. 2010 Aug 31;10:263. doi: 10.1186/1471-2148-10-263.


An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.

Bräutigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Mass J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP.

Plant Physiol. 2011 Jan;155(1):142-56. doi: 10.1104/pp.110.159442. Epub 2010 Jun 11.


Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana.

He F, Chen WH, Collins S, Acquisti C, Goebel U, Ramos-Onsins S, Lercher MJ, de Meaux J.

Genetics. 2010 Jun;185(2):695-701. doi: 10.1534/genetics.110.114629. Epub 2010 Mar 16.


Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions.

Chen WH, de Meaux J, Lercher MJ.

BMC Genomics. 2010 Mar 16;11:178. doi: 10.1186/1471-2164-11-178.


Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.

Weiss M, Schrimpf S, Hengartner MO, Lercher MJ, von Mering C.

Proteomics. 2010 Mar;10(6):1297-306. doi: 10.1002/pmic.200900414.


Does negative auto-regulation increase gene duplicability?

Warnecke T, Wang GZ, Lercher MJ, Hurst LD.

BMC Evol Biol. 2009 Aug 7;9:193. doi: 10.1186/1471-2148-9-193.


ColorTree: a batch customization tool for phylogenic trees.

Chen WH, Lercher MJ.

BMC Res Notes. 2009 Jul 31;2:155. doi: 10.1186/1756-0500-2-155.

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