List of works - Fran Supek

A large-scale evaluation of computational protein function prediction

scientific article

A synthesis of bacterial and archaeal phenotypic trait data

scientific article published on 05 June 2020

Accurate models for P-gp drug recognition induced from a cancer cell line cytotoxicity screen

scientific article published on 8 July 2013

Antitumor potential of crown ethers: structure-activity relationships, cell cycle disturbances, and cell death studies of a series of ionophores.

scientific article published on 15 February 2007

Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

scientific article published in July 2017

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

scientific article

Computational structure-activity study directs synthesis of novel antitumor enkephalin analogs.

scientific article published on 29 July 2009

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

scientific article published on 03 August 2020

Differential DNA mismatch repair underlies mutation rate variation across the human genome

scientific article

Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria

scientific article published on 10 February 2017

Enhanced analytical power of SDS-PAGE using machine learning algorithms.

scientific article

Extensive complementarity between gene function prediction methods

scientific article published on 13 August 2016

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

scientific article published on 13 May 2015

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

scientific article published on 03 December 2021

Hydroxymethylated cytosines are associated with elevated C to G transversion rates

scientific article

INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

scientific article published in April 2004

Inferring gene function from evolutionary change in signatures of translation efficiency

scientific article published on 3 March 2014

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

scientific article published on 19 November 2018

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

scientific article

Machine learning prioritizes synthesis of primaquine ureidoamides with high antimalarial activity and attenuated cytotoxicity

scientific article published on 31 January 2018

Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns

scientific article published on 01 July 2020

Mutational signatures are markers of drug sensitivity of cancer cells

scientific article published on 25 May 2022

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli

scientific article published on 26 April 2010

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

scientific article published on 05 February 2020

Passenger mutations accurately classify human tumors

scientific article published on 15 April 2019

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype

scientific article published on 20 December 2019

Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships

scientific article

Proteome sequence features carry signatures of the environmental niche of prokaryotes.

scientific article

Putative mechanisms of antitumor activity of cyano-substituted heteroaryles in HeLa cells.

scientific article published on 3 November 2010

REVIGO summarizes and visualizes long lists of gene ontology terms

scientific article (publication date: 2011)

Signatures of conformational stability and oxidation resistance in proteomes of pathogenic bacteria

scientific article published on 29 May 2014

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

article

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

scientific article

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

article

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

scientific article published on 28 October 2019

The impact of rare germline variants on human somatic mutation processes

scientific article published in 2022

The landscape of microbial phenotypic traits and associated genes

scientific article

The rules and impact of nonsense-mediated mRNA decay in human cancers

scientific article published on 12 September 2016

Translational selection is ubiquitous in prokaryotes

scientific article

Visualizing GO Annotations

scientific article published on January 2017

List of works by Fran Supek

A large-scale evaluation of computational protein function prediction

A synthesis of bacterial and archaeal phenotypic trait data

Accurate models for P-gp drug recognition induced from a cancer cell line cytotoxicity screen

Antitumor potential of crown ethers: structure-activity relationships, cell cycle disturbances, and cell death studies of a series of ionophores.

Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

Computational structure-activity study directs synthesis of novel antitumor enkephalin analogs.

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

Differential DNA mismatch repair underlies mutation rate variation across the human genome

Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria

Enhanced analytical power of SDS-PAGE using machine learning algorithms.

Extensive complementarity between gene function prediction methods

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

Hydroxymethylated cytosines are associated with elevated C to G transversion rates

INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

Inferring gene function from evolutionary change in signatures of translation efficiency

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Machine learning prioritizes synthesis of primaquine ureidoamides with high antimalarial activity and attenuated cytotoxicity

Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns

Mutational signatures are markers of drug sensitivity of cancer cells

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Passenger mutations accurately classify human tumors

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype

Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships

Proteome sequence features carry signatures of the environmental niche of prokaryotes.

Putative mechanisms of antitumor activity of cyano-substituted heteroaryles in HeLa cells.

REVIGO summarizes and visualizes long lists of gene ontology terms

Signatures of conformational stability and oxidation resistance in proteomes of pathogenic bacteria

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

The impact of rare germline variants on human somatic mutation processes

The landscape of microbial phenotypic traits and associated genes

The rules and impact of nonsense-mediated mRNA decay in human cancers

Translational selection is ubiquitous in prokaryotes

Visualizing GO Annotations