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List of works by Martin Vingron

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift

scientific article published in January 2004

A clustering approach to Generalized Tree Alignment with application to Alu repeats

A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes

scientific article

A joint model of regulatory and metabolic networks

scientific article published on 4 July 2006

A naturally occurring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms.

scientific article

A new statistical model to select target sequences bound by transcription factors.

scientific article published in January 2006

A physical model for tiling array analysis

scientific article published in July 2007

A polyhedral approach to sequence alignment problems

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts

scientific article published on 12 January 2009

A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ.

scientific article

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk

scientific article published on 8 September 2010

About the interrelation of evolutionary rate and protein age.

scientific article published in January 2006

An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets

article

An entropic characterization of protein interaction networks and cellular robustness

scientific article published in December 2006

An improved compound Poisson model for the number of motif hits in DNA sequences

scientific article published on 28 August 2017

An inventory of yeast proteins associated with nucleolar and ribosomal components

scientific article published on 26 October 2006

Analysis of CREM-dependent gene expression during mouse spermatogenesis

scientific article

Annotating regulatory DNA based on man-mouse genomic comparison

scientific article published in January 2002

Annotating significant pairs of transcription factor binding sites in regulatory DNA.

scientific article

BLUEPRINT to decode the epigenetic signature written in blood.

scientific article

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

scientific article published in February 2012

CD74-NRG1 fusions in lung adenocarcinoma

scientific article published on 27 January 2014

CRUP: a comprehensive framework to predict condition-specific regulatory units

scientific article published on 08 November 2019

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

scientific article published on 26 February 2015

Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast

scientific article

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

scientific article published on 6 December 2016

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development

scientific article

Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines

scientific article

Comparative analysis of cell cycle regulated genes in eukaryotes.

scientific article

Comparative promoter analysis in vertebrate genomes with the CORG workbench

scientific article published in January 2006

Comparative promoter region analysis powered by CORG ⬇️

scientific article

Comparison of sequence-dependent tiling array normalization approaches

scientific article

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog).

scientific article

Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands

scientific article published on July 2008

Comprehensive genomic profiles of small cell lung cancer

scientific article published on 13 July 2015

Condition-specific target prediction from motifs and expression.

scientific article

Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression

scientific article

Correlating Protein–DNA and Protein–Protein Interaction Networks ⬇️

scientific article published on October 10, 2003

Corrigendum to “Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate” [FEBS Lett. 580 (2006) 455-462]

scholarly article published in FEBS Letters

Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

scientific article published on 22 November 2016

CpG deamination creates transcription factor-binding sites with high efficiency

scientific article published on 19 October 2011

CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses

scientific article published on 06 September 2009

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach ⬇️

scientific article published on June 23, 2011

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

scientific article published on 24 August 2009

Design and statistical properties of robust functional networks: a model study of biological signal transduction

scientific article published on 19 January 2007

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

scientific article

Detection of interacting transcription factors in human tissues using predicted DNA binding affinity ⬇️

scientific article published on January 17, 2012

Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series

scientific article

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

scientific article published on 27 September 2018

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

scientific article published on 14 July 2008

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

scientific article published on 7 July 2009

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

scientific article

Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts ⬇️

scientific article published on January 12, 2012

Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions

scientific article

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

scientific article

Exact Score Distribution Computation for Similarity Searches in Ontologies

Exonization of active mouse L1s: a driver of transcriptome evolution?

scientific article

Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse

scientific article

Family specific rates of protein evolution

scientific article published in March 2006

Finding associations among histone modifications using sparse partial correlation networks

scientific article

Formation of new chromatin domains determines pathogenicity of genomic duplications

scientific article

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids

scientific article

Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters

scientific article

Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

scientific article published on 29 July 2019

Functional inference from non-random distributions of conserved predicted transcription factor binding sites

scientific article published in August 2004

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis

scientific article published on 31 January 2003

Genome-scale design of PCR primers and long oligomers for DNA microarrays

scientific article published on October 2003

Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange

scientific article

Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells

scientific article published on 7 February 2013

Genome-wide array analysis of normal and malformed human hearts

scientific article published on 12 May 2003

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

scientific article

Genome-wide kinase-chromatin interactions reveal the regulatory network of ERK signaling in human embryonic stem cells

scientific article published on 30 May 2013

Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts

scientific article published on 27 January 2018

Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts

scientific article published on 19 February 2018

Haplotype-resolved sweet potato genome traces back its hexaploidization history

scientific article published on 21 August 2017

Histone modification levels are predictive for gene expression

scientific article

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

scientific article

Horizontal gene transfer in aminoacyl-tRNA synthetases including leucine-specific subtypes

scientific article published on 4 September 2006

ISCB/SPRINGER series in computational biology.

scientific article

Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters

scientific article published on 15 December 2005

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

scientific article

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

scientific article

Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis

scientific article published on 11 September 2007

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

scientific article published on 15 July 2009

Incorporating evolution of transcription factor binding sites into annotated alignments

scientific article published in August 2007

Increase of functional diversity by alternative splicing

scientific article

Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling

scientific article

Inferring nucleosome positions with their histone mark annotation from ChIP data

scientific article

Inferring the paths of somatic evolution in cancer

scientific article

IntAct: an open source molecular interaction database

scientific article

Integer linear programming approaches for non-unique probe selection

Integrating sequence, evolution and functional genomics in regulatory genomics

scientific article published on 30 January 2009

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.

scientific article published on 13 March 2018

Large scale hierarchical clustering of protein sequences

scientific article

Mammalian mitochondrial nitric oxide synthase: characterization of a novel candidate

scientific journal article

Mapping translocation breakpoints by next-generation sequencing

scientific article published on 7 March 2008

Maximum similarity: a new formulation of phylogenetic reconstruction

scientific article published in July 2009

Microarray data representation, annotation and storage

scientific article

Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis

scientific article

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Modeling read counts for CNV detection in exome sequencing data

scientific article

Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays ⬇️

scientific article published on December 17, 2001

NOA1 is an essential GTPase required for mitochondrial protein synthesis

scientific journal article

Natural similarity measures between position frequency matrices with an application to clustering

scientific article published on 2 January 2008

Natural variation of histone modification and its impact on gene expression in the rat genome

scientific article

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes

scientific article

Normalization and quantification of differential expression in gene expression microarrays

scientific article published on 7 March 2006

On the power of profiles for transcription factor binding site detection

scientific article published on 29 November 2003

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

scientific article

Optimal robust non-unique probe selection using Integer Linear Programming

scientific article published in August 2004

P53 Binding Sites in Transposons ⬇️

scientific article published on March 20, 2012

PASTAA: identifying transcription factors associated with sets of co-regulated genes

scientific article published on 09 December 2008

Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression

scientific article published on 8 March 2009

Parameter estimation for the calibration and variance stabilization of microarray data

scientific article

Polymer physics predicts the effects of structural variants on chromatin architecture

scientific article published on 16 April 2018

Predicting enhancers in mammalian genomes using supervised hidden Markov models

Predicting the outcome of renal transplantation

scientific article

Predicting transcription factor affinities to DNA from a biophysical model

scientific article published on 10 November 2006

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

scientific article

Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes

scientific article

Prioritization of gene regulatory interactions from large-scale modules in yeast

scientific article

Quantifying the effect of sequence variation on regulatory interactions

scientific article

R2KS: A Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists ⬇️

scientific article published on June 1, 2012

Ranbow: A fast and accurate method for polyploid haplotype reconstruction

scientific article published on 29 May 2020

Reconstruction of gene networks using prior knowledge

scientific article published on 20 November 2015

Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana

scientific article published on 13 June 2014

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

scientific article

SITEBLAST--rapid and sensitive local alignment of genomic sequences employing motif anchors

scientific article published on 14 December 2004

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein

scientific article published on January 2002

Self-correcting networks: function, robustness, and motif distributions in biological signal processing

scientific article published in June 2008

Sequence-dependent nucleosome positioning

scientific article

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

scientific article published on September 2016

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

article

Simultaneous alignment and annotation of cis-regulatory regions

scientific article published in January 2007

Soluble epoxide hydrolase is a susceptibility factor for heart failure in a rat model of human disease

scientific article published in May 2008

Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient

scientific article

Special RECOMB 2008 Issue. Preface

scientific article published in August 2009

Statistical detection of cooperative transcription factors with similarity adjustment

scientific article

Statistical modeling of transcription factor binding affinities predicts regulatory interactions

scientific article

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

scientific article

Studying the Evolution of Promoter Sequences: A Waiting Time Problem ⬇️

scientific article published on December 1, 2010

Support Vector Machines for Protein Fold Class Prediction

article published in 2003

Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma

scientific article published on 4 June 2013

T cells become licensed in the lung to enter the central nervous system

scientific article published in August 2012

T-Reg Comparator: an analysis tool for the comparison of position weight matrices

scientific article

T-STAG: resource and web-interface for tissue-specific transcripts and genes

scientific article

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

scientific article (publication date: March 2002)

The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle

scientific article

The Distance Precision Matrix: computing networks from non-linear relationships.

scientific article published in March 2019

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data ⬇️

scientific article published on December 29, 2010

The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2.

scientific article published on 6 October 2010

The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF

scientific article

The SYSTERS Protein Family Database in 2005 ⬇️

scientific article

The deferred path heuristic for the generalized tree alignment problem

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality

scientific article

Theoretical analysis of alternative splice forms using computational methods

scientific article published in January 2002

This special issue comprises the papers accepted for presentationat the 19th Annual International Conference on Intelligent Systemsfor Molecular Biology, joint with the 10th European Conference onComputational Biology, an official conference of the I

scholarly article by Terry Gaasterland published in July 2011

Time-Dependent Gene Network Modelling by Sequential Monte Carlo

scientific article published on 30 October 2015

TransFind--predicting transcriptional regulators for gene sets

scientific article

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

scientific article

Transcriptional autoregulatory loops are highly conserved in vertebrate evolution

scientific article

Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

scientific article published on 30 August 2017

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