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List of works by Leonard C. Schalkwyk

5-hydroxymethylcytosine is highly dynamic across human fetal brain development

scientific article published on 18 September 2017

A 5× genome coverage bovine BAC library: production, characterization, and distribution

article

A B2 SINE insertion in the Comt1 gene (Comt1(B2i)) results in an overexpressing, behavior modifying allele present in classical inbred mouse strains

scientific article

A bovine YAC library containing four- to five-fold genome equivalents

scientific article

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

scientific article

A data-driven approach to preprocessing Illumina 450K methylation array data

scientific article

A genome-wide association study identifies multiple loci associated with mathematics ability and disability

scientific article

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples

scientific article

A histone acetylome-wide association study of Alzheimer's disease identifies disease-associated H3K27ac differences in the entorhinal cortex

scientific article published on 22 October 2018

A three-stage genome-wide association study of general cognitive ability: hunting the small effects.

scientific article

ATP-binding cassette sub-family F member 1 (ABCF1) is identified as a putative therapeutic target of escitalopram in the inflammatory cytokine pathway

scientific article published on 29 May 2013

Advanced integrated mouse YAC map including BAC framework

scientific article

Advanced paternal age effects in neurodevelopmental disorders-review of potential underlying mechanisms

scientific article published on 31 January 2017

Advanced paternal age is associated with altered DNA methylation at brain-expressed imprinted loci in inbred mice: implications for neuropsychiatric disease.

scientific article published on 26 June 2012

Advancing paternal age is associated with deficits in social and exploratory behaviors in the offspring: a mouse model

scientific article

Allele-specific methylation in the human genome: implications for genetic studies of complex disease

scientific article

Allelic skewing of DNA methylation is widespread across the genome

scientific article

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

scientific article

An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation

scientific article published on 30 August 2016

Antidepressant-dependent mRNA changes in mouse associated with hippocampal neurogenesis in a mouse model of depression

scientific article published on November 2012

Antidepressants and the resilience to early-life stress in inbred mouse strains

scientific article published on December 2011

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

scientific article

Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes

article

Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months

scientific article published on August 2009

Assessing reliability, heritability and general cognitive ability in a battery of cognitive tasks for laboratory mice

scientific article

Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms.

scientific article published in April 2005

Behavioral characterization of wild derived male mice (Mus musculus musculus) of the PWD/Ph inbred strain: high exploration compared to C57BL/6J.

scientific article

Behavioural battery testing: evaluation and behavioural outcomes in 8 inbred mouse strains

scientific article published on 2 December 2009

Bigmelon: tools for analysing large DNA methylation datasets

scientific article published on 01 March 2019

Chapter 15 Halobacterial genes and genomes

article

Comparative mRNA analysis of behavioral and genetic mouse models of aggression

scientific article published on 17 February 2016

Complex probes for high-throughput parallel genetic mapping of genomic mouse BAC clones

scientific article

Construction and characterisation of a gridded chicken cosmid library with four-fold genomic coverage.

scientific article

Construction and characterization of a 10-genome equivalent yeast artificial chromosome library for the laboratory rat, Rattus norvegicus

scientific article published on February 1997

Convergent animal and human evidence suggests a role of PPM1A gene in response to antidepressants

scientific article

Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain.

scientific article

DNA methylation aging clocks: challenges and recommendations

scientific article published on 25 November 2019

DNA methylation at the Igf2/H19 imprinting control region is associated with cerebellum mass in outbred mice

scientific article published on 6 December 2012

DNA methylation in interleukin-11 predicts clinical response to antidepressants in GENDEP

scientific article published on 03 September 2013

DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy

scientific article

Depression-Related Behavioral Tests

scientific article published on June 2012

Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2

article

Differential methylation of the TRPA1 promoter in pain sensitivity

scientific article published on January 2014

Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder

scientific article

Dynamic and sex-specific changes in DNA methylation during human fetal brain development

ETn insertion in the mouse Adcy1 gene: transcriptional and phylogenetic analyses

scientific article published in February 2000

Effect of chronic valproic Acid treatment on hepatic gene expression profile in wfs1 knockout mouse.

scientific article published on April 2014

Effects of advanced paternal age on trajectories of social behavior in offspring.

scientific article published on July 2015

Efficient high-resolution genetic mapping of mouse interspersed repetitive sequence PCR products, toward integrated genetic and physical mapping of the mouse genome

scientific article

Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology

article

Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain

scientific article

Erratum to: Variation in 5-hydroxymethylcytosine across human cortex and cerebellum

scientific article published on 17 June 2016

Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

scientific article

Gene expression profiling reveals upregulation of Tlr4 receptors in Cckb receptor deficient mice

article

Gene set enrichment; a problem of pathways

scientific article

Genes and gene networks implicated in aggression related behaviour

scientific article published on 22 August 2014

Genetic analysis of the mouse brain proteome

scientific article published on 25 March 2002

Genetic and environmental (inter)actions in male mouse lines selected for aggressive and nonaggressive behavior

scientific article published on 01 April 2004

Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice

scientific article published on February 2017

Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains

scientific article

Genetics of behavioural domains across the neuropsychiatric spectrum; of mice and men.

scientific article

Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource.

scientific article published on 10 November 2009

Genome mapping in halobacteria

scientific article published in January 1989

Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans

scientific article published on 21 March 2016

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

scientific article published on 01 July 2019

Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs

scientific article

Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits.

scientific article

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans

scientific article

High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe.

scientific article published on April 1993

High-throughput scanning of the rat genome using interspersed repetitive sequence-PCR markers

scientific article

Highly polygenic architecture of antidepressant treatment response: Comparative analysis of SSRI and NRI treatment in an animal model of depression

scientific article

Hippocampal gene expression profiling across eight mouse inbred strains: towards understanding the molecular basis for behaviour

scientific article published in May 2004

Home-cage activity in heterogeneous stock (HS) mice as a model of baseline activity

scientific article published in August 2002

Hypothalamic gene expression profile indicates a reduction in G protein signaling in the Wfs1 mutant mice

scientific article

IRS-PCR-based genetic mapping of the huntingtin interacting protein gene (HIP1) on mouse Chromosome 5

article

ISH51: a large, degenerate family of insertion sequence-like elements in the genome of the archaebacterium, Halobacterium volcanii

scientific article

Identification of genes and gene pathways associated with major depressive disorder by integrative brain analysis of rat and human prefrontal cortex transcriptomes

scientific article published on 3 March 2015

Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain

scientific article

Integrative mouse and human mRNA studies using WGCNA nominates novel candidate genes involved in the pathogenesis of major depressive disorder.

scientific article published in December 2013

Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes

scientific article published on 12 October 2015

Intermediate DNA methylation is a conserved signature of genome regulation

scientific article

Interpretation of knockout experiments: the congenic footprint.

scientific article published on 26 February 2007

Interspecies comparisons of functional genetic variations and their implications in neuropsychiatry

scientific article published on April 2009

Interspersed repetitive sequence (IRS)-PCR for typing of whole genome radiation hybrid panels

scientific article

Introduction to mammalian genome special issue: genetics of behavior

article

Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits

article

Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits

article

Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea ⬇️

scientific article published on March 1, 1992

Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats

scientific article

Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder

scientific article

Longitudinal changes of telomere length and epigenetic age related to traumatic stress and post-traumatic stress disorder.

scientific article published on 23 July 2014

Loss of adenylyl cyclase I activity disrupts patterning of mouse somatosensory cortex

scientific journal article

Maternal separation is associated with strain-specific responses to stress and epigenetic alterations to Nr3c1, Avp, and Nr4a1 in mouse

scientific article

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

scientific article

Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits

scientific article published on 23 April 2013

Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease

scientific article

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia

scientific article

Methylomic trajectories across human fetal brain development

scientific article

Microarrays

article

Mitochondrial genes are altered in blood early in Alzheimer's disease

scientific article

Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism

scientific article

Molecular and biochemical characterisation of DNA-dependent protein kinase-defective rodent mutant irs-20

scientific article

Mood-stabilizers differentially affect housekeeping gene expression in human cells.

scientific article published on 12 February 2014

New tools for the high throughput characterization of rat genomic DNA samples

article published in 2000

P.1.31 Gene expression analyses of mouse fibroblast cell line L929 after antidepressant treatment

article

P.1.a.015 Strain differences in susceptibility to unpredictable chronic mild stress as assessed by hippocampal gene expression profiling

article

P.1.d.016 The effects of a selective serotonin reuptake inhibitor and a tricyclic antidepressant on the behaviour of chronically stressed 129SvemJ and C57BL/6J mice in the hole board and forced swim test

scholarly article by E. Binder et al published January 2006 in European Neuropsychopharmacology

P.2.07 Selecting over-active extremes in outbred heterogeneous stock (HS) mice for gene expression profiling: nominating novel candidate genes for over-activity

article

Panel of microsatellite markers for whole-genome scans and radiation hybrid mapping and a mouse family tree.

scientific article published on September 1999

Paternal Age Alters Social Development in Offspring

scientific article

Performance deficit of alpha7 nicotinic receptor knockout mice in a delayed matching-to-place task suggests a mild impairment of working/episodic-like memory

scientific journal article

Peripheral blood RNA expression profiling in illicit methcathinone users reveals effect on immune system

scientific article

Peripheral blood RNA gene expression profiling in patients with bacterial meningitis

scientific article published on 18 March 2013

Pervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains

scientific article published on 3 April 2015

Pharmacoproteomic investigation into antidepressant response in two mouse inbred strains

scientific article

Progress in developing the genetics of the halobacteria

scientific article published on January 1, 1992

Putative transcriptomic biomarkers in the inflammatory cytokine pathway differentiate major depressive disorder patients from control subjects and bipolar disorder patients

scientific article

Quantitative trait locus association scan of early reading disability and ability using pooled DNA and 100K SNP microarrays in a sample of 5760 children

scientific article

Quantitative traits for the tail suspension test: automation, optimization, and BXD RI mapping

scientific article

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation

scientific article published on 07 November 2019

Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex

scientific article published on 29 October 2020

Reduced anxiety and depression-like behaviours in the circadian period mutant mouse afterhours

scientific article

Refined radiation hybrid map of mouse chromosome 17.

scientific article published in October 1998

Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue

scientific article

Response to comment by Stuart Macgregor

S.16.02 Depression: the GENDEP study

SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children

scientific article published on 30 March 2005

Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions

scientific article published on 22 December 2016

Stochastic choice of allelic expression in human neural stem cells

scientific article

Systematic underestimation of the epigenetic clock and age acceleration in older subjects

scientific article published on 17 December 2019

TCF4 (e2-2; ITF2): a schizophrenia-associated gene with pleiotropic effects on human disease

scientific article

Techniques in mammalian genome mapping

scientific article published on February 1995

Technology development at the interface of proteome research and genomics: Mapping nonpolymorphic proteins on the physical map of mouse chromosomes

Technology development at the interface of proteome research and genomics: Mapping nonpolymorphic proteins on the physical map of mouse chromosomes

scientific article published on 01 April 1999

Technology development at the interface of proteome research and genomics: Mapping nonpolymorphic proteins on the physical map of mouse chromosomes

Tetraodon fluviatilis, a new puffer fish model for genome studies

scientific article published on April 1997

The 21st International Mammalian Genome Conference meeting report

scientific article published in September 2008

The Collaborative Cross, a community resource for the genetic analysis of complex traits

article

The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations

scientific article published on 13 October 2020

The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays

scientific article

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

scientific article

The differential transcriptome and ontology profiles of floating and cumulus granulosa cells in stimulated human antral follicles

scientific article

The endogenous and reactive depression subtypes revisited: integrative animal and human studies implicate multiple distinct molecular mechanisms underlying major depressive disorder

scientific article

The inflammatory cytokines: molecular biomarkers for major depressive disorder?

scientific article published on 14 February 2014

The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation

scientific journal article

The nature and identification of quantitative trait loci: a community's view

scientific article published in November 2003

The role of nicotinic receptor alpha 7 subunits in nicotine discrimination

scientific article published in March 2004

Tissue-specific patterns of allelically-skewed DNA methylation

scientific article published on 19 January 2016

To What Extent is Blood a Reasonable Surrogate for Brain in Gene Expression Studies: Estimation from Mouse Hippocampus and Spleen

scientific article

Transcriptome analysis of genes and gene networks involved in aggressive behavior in mouse and zebrafish

scientific article published on 19 April 2016

Transcriptomic changes in the frontal cortex associated with paternal age.

scientific article published on 23 March 2014

Transformation methods for halophilic archaebacteria

scientific article published in January 1989

Transformation of the archaebacterium Halobacterium volcanii with genomic DNA.

scientific article

Tumor necrosis factor and its targets in the inflammatory cytokine pathway are identified as putative transcriptomic biomarkers for escitalopram response

scientific article

Using hippocampal microRNA expression differences between mouse inbred strains to characterise miRNA function

scientific article published on 02 July 2008

Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

scientific article

Variation in 5-hydroxymethylcytosine across human cortex and cerebellum.

scientific article published on 16 February 2016

ViPAR: a software platform for the Virtual Pooling and Analysis of Research Data

scientific article

Wfs1 gene deletion causes growth retardation in mice and interferes with the growth hormone pathway

scientific journal article

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