List of works - Martin J. Lercher

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

scientific article

A unification of mosaic structures in the human genome

scientific article published on 29 July 2003

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

scientific article

Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

scientific article

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

scientific article published in Scientific Reports

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

scientific article

An analytical theory of balanced cellular growth

scientific article published on 06 March 2020

An integrated approach to characterize genetic interaction networks in yeast metabolism

scientific article

An integrated view of protein evolution

scientific article

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

article

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

scientific article

Can mutation or fixation biases explain the allele frequency distribution of human single nucleotide polymorphisms (SNPs)?

article

Chance and necessity in the evolution of minimal metabolic networks

scientific article

Clustering of housekeeping genes provides a unified model of gene order in the human genome

scientific article

Co-expressed yeast genes cluster over a long range but are not regularly spaced

scientific article published on 06 April 2006

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

scientific article

Coexpression of linked gene pairs persists long after their separation

scientific article

Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes

scientific article

ColorTree: a batch customization tool for phylogenic trees

scientific article

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

scientific article published on 22 September 2016

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

scientific article

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

scientific article

Deep learning allows genome-scale prediction of Michaelis constants from structural features

scientific article published on 21 October 2021

Does negative auto-regulation increase gene duplicability?

scientific article

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

article

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

scientific article

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

scientific article published on 18 April 2017

Evidence for widespread degradation of gene control regions in hominid genomes

scientific article

Evidence that the human X chromosome is enriched for male-specific but not female-specific genes

scientific article published on 30 May 2003

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

scientific article

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

scientific article

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

scientific article published on 14 August 2019

Forty years of The Selfish Gene are not enough

scientific article

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

scientific article

Gene expression, synteny, and local similarity in human noncoding mutation rates

scientific article published on 2 June 2004

Genome-wide acceleration of protein evolution in flies (Diptera).

scientific article

Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile

scientific article

HOTAIR rs7958904 polymorphism is associated with increased cervical cancer risk in a Chinese population

scientific article

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

scientific article

Horizontal gene transfer depends on gene content of the host.

scientific article

Horizontal gene transfers as metagenomic gene duplications

article

Horizontally transferred genes cluster spatially and metabolically

scientific article published on 21 December 2015

Human SNP variability and mutation rate are higher in regions of high recombination

scientific article

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

scientific article

Imprinted chromosomal regions of the human genome have unusually high recombination rates

scientific article published on November 2003

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

scientific article

Integration of horizontally transferred genes into regulatory interaction networks takes many million years

scientific article published on 24 December 2007

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

scientific article published on 08 September 2021

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

scientific article published in November 2001

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

scholarly article by David Heckmann et al published 7 December 2018 in Nature Communications

Magnetic bilayer coupling inYBa2Cu3O7

scientific article published on 01 January 1994

Minimal regulatory spaces in yeast genomes

scientific article published on 16 June 2011

Mitochondrial 2-hydroxyglutarate metabolism.

scientific article published on 21 February 2014

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

scientific article published on 24 June 2019

Network reduction methods for genome-scale metabolic models

scientific article published on 20 November 2019

OGEE: an online gene essentiality database

scientific article published on 10 November 2011

On the optimality of the enzyme–substrate relationship in bacteria

scientific article published in 2021

PET measurement of cerebral acetylcholine esterase activity without blood sampling

scientific article

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects

scientific article (publication date: November 2006)

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

scientific article published on 9 January 2014

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

scientific article published on 16 April 2014

Positron-emission tomography of vector-mediated gene expression in gene therapy for gliomas

scientific article

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

scientific article

Prediction of effective genome size in metagenomic samples

scientific article published on January 2007

Quantitative kinetics of [124I]FIAU in cat and man.

scientific article

Regional similarities in polymorphism in the human genome extend over many megabases

scientific article published on 01 June 2002

Scatter correction in 3-D PET.

scientific article

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

scientific article

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

scientific article

Similar gene expression profiles do not imply similar tissue functions

scientific article

The effects of network neighbours on protein evolution

scientific article

The evolution of isochores: evidence from SNP frequency distributions

scientific article published on December 2002

The evolutionary dynamics of eukaryotic gene order

scientific article

The protein translation machinery is expressed for maximal efficiency in Escherichia coli

scientific article published on 16 October 2020

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

scientific article

Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise

scientific article published on 14 March 2011

TreeSnatcher plus: capturing phylogenetic trees from images

scientific article

Umklapp scattering from spin fluctuations in copper oxides

scientific article published on 01 September 1995

Understanding the degradation of hominid gene control

scientific article published in March 2006

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome

scientific article

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

scientific article

X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila

scientific article

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.

scientific article published on 19 January 2012

sybil – Efficient constraint-based modelling in R

scientific article (publication date: 13 November 2013)

List of works by Martin J. Lercher

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

A unification of mosaic structures in the human genome

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

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

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

An analytical theory of balanced cellular growth

An integrated approach to characterize genetic interaction networks in yeast metabolism

An integrated view of protein evolution

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

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

Can mutation or fixation biases explain the allele frequency distribution of human single nucleotide polymorphisms (SNPs)?

Chance and necessity in the evolution of minimal metabolic networks

Clustering of housekeeping genes provides a unified model of gene order in the human genome

Co-expressed yeast genes cluster over a long range but are not regularly spaced

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

Coexpression of linked gene pairs persists long after their separation

Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes

ColorTree: a batch customization tool for phylogenic trees

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

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

Deep learning allows genome-scale prediction of Michaelis constants from structural features

Does negative auto-regulation increase gene duplicability?

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

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

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

Evidence for widespread degradation of gene control regions in hominid genomes

Evidence that the human X chromosome is enriched for male-specific but not female-specific genes

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

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

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

Forty years of The Selfish Gene are not enough

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

Gene expression, synteny, and local similarity in human noncoding mutation rates

Genome-wide acceleration of protein evolution in flies (Diptera).

Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile

HOTAIR rs7958904 polymorphism is associated with increased cervical cancer risk in a Chinese population

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

Horizontal gene transfer depends on gene content of the host.

Horizontal gene transfers as metagenomic gene duplications

Horizontally transferred genes cluster spatially and metabolically

Human SNP variability and mutation rate are higher in regions of high recombination

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

Imprinted chromosomal regions of the human genome have unusually high recombination rates

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

Integration of horizontally transferred genes into regulatory interaction networks takes many million years

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

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

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

Magnetic bilayer coupling inYBa2Cu3O7

Minimal regulatory spaces in yeast genomes

Mitochondrial 2-hydroxyglutarate metabolism.

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

Network reduction methods for genome-scale metabolic models

OGEE: an online gene essentiality database

On the optimality of the enzyme–substrate relationship in bacteria

PET measurement of cerebral acetylcholine esterase activity without blood sampling

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects

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

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

Positron-emission tomography of vector-mediated gene expression in gene therapy for gliomas

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

Prediction of effective genome size in metagenomic samples

Quantitative kinetics of [124I]FIAU in cat and man.

Regional similarities in polymorphism in the human genome extend over many megabases

Scatter correction in 3-D PET.

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

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

Similar gene expression profiles do not imply similar tissue functions

The effects of network neighbours on protein evolution

The evolution of isochores: evidence from SNP frequency distributions

The evolutionary dynamics of eukaryotic gene order

The protein translation machinery is expressed for maximal efficiency in Escherichia coli

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

Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise

TreeSnatcher plus: capturing phylogenetic trees from images

Umklapp scattering from spin fluctuations in copper oxides

Understanding the degradation of hominid gene control