List of works by Boris Lenhard

------Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

scientific article published on 25 June 2020

A cladistic model of ACE sequence variation with implications for myocardial infarction, Alzheimer disease and obesity

scientific article published on 14 September 2004

A cohesin-independent role for NIPBL at promoters provides insights in CdLS.

scientific article

A global genomic transcriptional code associated with CNS-expressed genes

article

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

scientific article

A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells

scientific article

A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates

scientific article published on 01 July 2019

A prioritization analysis of disease association by data-mining of functional annotation of human genes

scientific article

A promoter-level mammalian expression atlas

scientific article

Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation

scientific article published on 25 January 2017

Alternative promoter usage of the membrane glycoprotein CD36

scientific article

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

scientific article published on 15 February 2008

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

scientific article

C-terminal truncation of yeast SerRS is toxic for Saccharomyces cerevisiae due to altered mechanism of substrate recognition

scientific article published on 01 November 1998

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

scientific article

CNEr: A toolkit for exploring extreme noncoding conservation

Chromatin and epigenetic features of long-range gene regulation

scientific article published on 13 June 2013

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

scientific article published on 03 September 2013

Complex Loci in human and mouse genomes

scientific article

Computational characterization of modes of transcriptional regulation of nuclear receptor genes

scientific article (publication date: 2014)

ConSite: web-based prediction of regulatory elements using cross-species comparison

scientific article published on July 2004

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Conserved non-coding elements: developmental gene regulation meets genome organization

scientific article

Control of developmentally primed erythroid genes by combinatorial co-repressor actions

scientific article

Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene

scientific article published on 4 September 2015

Core promoters across the genome

scientific article published in February 2017

Correction to 'The mystery of extreme non-coding conservation'.

scientific article published on May 2015

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

scholarly article published in Nature Genetics

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

scientific article published on 06 September 2009

DNA stretching induces Cas9 off-target activity

scientific article published on 25 February 2019

Defining the active site of yeast seryl-tRNA synthetase. Mutations in motif 2 loop residues affect tRNA-dependent amino acid recognition

scientific article published on 01 January 1997

Dissecting genomic regulatory elements in vivo

scientific article published on 07 June 2012

Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions

scientific article

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.

scientific article published on 26 February 2018

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

scientific article published on 10 January 2020

Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development

scientific article published on 13 December 2011

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

scientific article published on 03 September 2013

Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease

scientific article published on 01 April 2022

Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte.

scientific article published on 7 March 2018

Erratum: The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation.

scientific article published in March 2010

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

scientific article

Exploring hepatic hormone actions using a compilation of gene expression profiles

scientific article

Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies

scientific article published on January 2004

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

Gene characterization index: assessing the depth of gene annotation

scientific article

GeneLynx mouse: integrated portal to the mouse genome

scientific article published on June 2003

Genome-wide DNA methylation profiling of non-small cell lung carcinomas

scientific article published on 22 June 2012

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis

scientific article

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos

scientific article

Genomewide DNA methylation analysis identifies novel methylated genes in non-small-cell lung carcinomas

scientific article published in May 2013

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

scientific article published on 26 March 2007

Genomic regulatory blocks underlie extensive microsynteny conservation in insects

scientific article

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

scientific article

Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization

scientific article published on 01 March 2021

HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers

scientific article published on 10 March 2014

HGVbase: a curated resource describing human DNA variation and phenotype relationships

scientific article (publication date: 2004)

Identification of conserved regulatory elements by comparative genome analysis

scientific article

Identification of functional SNPs in the 5-prime flanking sequences of human genes

scientific article

In silico detection of sequence variations modifying transcriptional regulation

scientific article

In vivo live imaging of RNA polymerase II transcription factories in primary cells

scientific article published on April 2013

In vivo live imaging of RNA polymerase II transcription factories in primary cells

article by Alireza Ghamari et al published 1 June 2013 in Genes & Development

In vivo live imaging of RNA polymerase II transcription factories in primary cells.

scientific article

In vivo transcript profiling and phylogenetic analysis identifies suppressor of cytokine signaling 2 as a direct signal transducer and activator of transcription 5b target in liver.

scientific article published on 28 September 2006

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes

scientific article published on 25 June 2003

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Integrator is recruited to promoter-proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors

scientific article published on 19 December 2020

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

scientific article (publication date: 2010)

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

scientific article

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

scientific article

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

scholarly article by Aziz Khan et al published 4 January 2018 in Nucleic Acids Research

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

scientific article published in 2021

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

scientific article published in 2023

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

scientific article

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

scientific article (publication date: 2004)

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome

scientific article

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

scientific article

Making enhancers from spare parts of the genome

scientific article published on 29 December 2011

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

scientific article published on 8 May 2007

Mammalian microRNA prediction through a support vector machine model of sequence and structure

scientific article

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

scientific article

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

scientific article

Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing

scientific article

Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin

scientific article published on 18 May 2021

New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences

scientific article

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.

scientific article

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

scientific article published on 12 March 2013

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

scientific article (publication date: 3 December 2010)

Promoter architecture of mouse olfactory receptor genes

scientific journal article

Promoter architectures and developmental gene regulation

scientific article

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

scientific article published on 24 February 2020

RNAdb 2.0--an expanded database of mammalian non-coding RNAs

scientific article published on December 2006

RNAdb--a comprehensive mammalian noncoding RNA database

scientific article

Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish

scientific article published on 29 December 2009

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus

scientific article published on July 2004

Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes

scientific article

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

scientific article published on 01 March 2019

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes

scientific journal article

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

scientific article published on 12 February 2015

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

scientific article (publication date: 2009)

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.

scientific article published on 12 November 2008

TFBS: Computational framework for transcription factor binding site analysis

scientific article

TFBSTools: an R/bioconductor package for transcription factor binding site analysis.

scientific article

Targeting Aberrant Epigenetic Networks Mediated by PRMT1 and KDM4C in Acute Myeloid Leukemia

scientific article

The C-terminal extension of yeast seryl-tRNA synthetase affects stability of the enzyme and its substrate affinity

scientific article published on 01 February 1996

The DNA-Binding Protein CTCF Limits Proximal Vκ Recombination and Restricts κ Enhancer Interactions to the Immunoglobulin κ Light Chain Locus

article by Claudia Ribeiro de Almeida et al published October 2011 in Immunity

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

scientific article

The accessible chromatin landscape of the human genome

scientific article

The aurora B kinase and the polycomb protein ring1B combine to regulate active promoters in quiescent lymphocytes

scientific journal article

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation

scientific article

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

scientific article published on 18 June 2012

The mystery of extreme non-coding conservation.

scientific article

The random versus fragile breakage models of chromosome evolution: a matter of resolution

scientific article published on 13 September 2007

The transcriptional landscape of the mammalian genome

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

scientific article

Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest.

scientific article published on 17 December 2014

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters

scientific article

Transcriptional features of genomic regulatory blocks

scientific article published on 19 April 2009

Transcriptional memory of cells of origin overrides β-catenin requirement of MLL cancer stem cells

scientific article published on 4 October 2017

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

scientific article published on 15 December 2015

Translog, a web browser for studying the expression divergence of homologous genes

scientific article

Two independent transcription initiation codes overlap on vertebrate core promoters

scientific article published on 16 February 2014

Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks

scientific article published on 15 October 2019

Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer's disease

scientific article published on 18 March 2004

Web-based tools and approaches to study long-range gene regulation in Metazoa

scientific article published on 15 July 2009

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

scientific article published on 27 January 2020

Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish

article

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

scientific article

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