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List of works by Len A. Pennacchio

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions

scientific article published on 25 March 2012

52 Genetic Loci Influencing Myocardial Mass

scientific article

A Cryptochrome 2 mutation yields advanced sleep phase in humans

scientific article

A PYY Q62P variant linked to human obesity

scientific article published on 20 December 2005

A common allele on chromosome 9 associated with coronary heart disease

scientific article

A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis

scientific article (publication date: 2011)

A high-resolution enhancer atlas of the developing telencephalon

scientific article published on 31 January 2013

A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

scientific article published on 20 February 2015

A noncoding single-nucleotide polymorphism at 8q24 drives -mutant glioma formation

scientific article published on 7 October 2022

A restricted spectrum of NRAS mutations causes Noonan syndrome

scientific article

ATAC-seq Reveals an Isl1 Enhancer that Regulates Sinoatrial Node Development and Function

scientific article published on 12 October 2020

Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome

scientific article

An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 29 July 2020

An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects.

scientific article published on 16 January 2014

Analysis of apolipoprotein A5, c3, and plasma triglyceride concentrations in genetically engineered mice

scientific article

Apoa5 Q139X truncation predisposes to late-onset hyperchylomicronemia due to lipoprotein lipase impairment

scientific article

Apolipoprotein A-V deficiency results in marked hypertriglyceridemia attributable to decreased lipolysis of triglyceride-rich lipoproteins and removal of their remnants

scientific journal article

Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators

scientific article (publication date: 16 May 2003)

Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice

scientific article (publication date: April 2003)

Apolipoprotein AIV Gene Variant S347 Is Associated With Increased Risk of Coronary Heart Disease and Lower Plasma Apolipoprotein AIV Levels

article

Apolipoprotein AV accelerates plasma hydrolysis of triglyceride-rich lipoproteins by interaction with proteoglycan-bound lipoprotein lipase.

scientific article

Array comparative genomic hybridization in patients with congenital diaphragmatic hernia: mapping of four CDH-critical regions and sequencing of candidate genes at 15q26.1-15q26.2.

scientific article

Association of common variants in the Joubert syndrome gene (AHI1) with autism

scientific article published on 09 September 2008

Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study

scientific article published on 17 December 2008

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 10 October 2020

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 04 January 2021

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

scholarly article

Author Correction: Perspectives on ENCODE

scholarly article

Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

scientific article published in March 2018

Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma.

scientific article

Brg1 modulates enhancer activation in mesoderm lineage commitment.

scientific article

Cathepsin B but not cathepsins L or S contributes to the pathogenesis of Unverricht-Lundborg progressive myoclonus epilepsy (EPM1)

scientific article (publication date: 15 September 2003)

Cathepsin L is required for endothelial progenitor cell-induced neovascularization

scientific article

ChIP-Seq identification of weakly conserved heart enhancers

scientific article

ChIP-seq accurately predicts tissue-specific activity of enhancers

scientific article (publication date: 12 February 2009)

Characterization of the human neurocan gene, CSPG3 ⬇️

scientific article published on October 23, 1998

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

scientific article

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

scientific article

Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors

scientific article

Comparative Genomics: A Tool to Functionally Annotate Human DNA

Comparative and functional analysis of cardiovascular-related genes

scientific article

Comparative genomic analysis as a tool for biological discovery

scientific article published on January 2004

Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene

scientific article published in February 2005

Comparative genomic tools and databases: providing insights into the human genome

scientific article

Comparative genomics: a tool to functionally annotate human DNA.

scientific article published in January 2007

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains

scientific article

Complete genome sequence of Desulfurispirillum indicum strain S5(T).

scientific article

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

scientific article published on 25 February 2013

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

scientific article

Complete genome sequence of Rahnella aquatilis CIP 78.65

scientific article

Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil

scientific article published in April 2012

Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5

scientific article

Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae

scientific article

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

scientific article published on 12 March 2020

Comprehensive identification and analysis of human accelerated regulatory DNA

scientific article

Congenital heart defects in patients with deletions upstream of SOX9.

scientific article published on 18 October 2013

Contrasting patterns of sequence evolution at the functionally redundant bric à brac paralogs in Drosophila melanogaster

scientific article published on 29 July 2009

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites

scientific article

De novoIdentification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

scientific article

Deletion of ultraconserved elements yields viable mice

scientific article published in September 2007

Dicer, Drosha, and outcomes in patients with ovarian cancer

scientific article published on December 2008

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

scientific article

Differential Etv2 threshold requirement for endothelial and erythropoietic development

scientific article published on 01 May 2022

Directed evolution of ionizing radiation resistance in Escherichia coli

scientific article published on 05 June 2009

Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip

scientific article

Dlx1&2-dependent expression of Zfhx1b (Sip1, Zeb2) regulates the fate switch between cortical and striatal interneurons

scientific article published on January 2013

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

scientific article published on 05 July 2019

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

scientific article

Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease

scientific article published on 28 September 2016

Enhancer identification through comparative genomics

scientific article published on 5 January 2007

Enhancer redundancy provides phenotypic robustness in mammalian development

scientific article published on 31 January 2018

Enhancers: five essential questions

scientific article

Erratum: Corrigendum: Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome

scholarly article published in Nature Genetics

Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair

scientific article published on January 2014

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Fine tuning of craniofacial morphology by distant-acting enhancers

scientific article

Function-based identification of mammalian enhancers using site-specific integration

scientific article

Functional autonomy of distant-acting human enhancers

scientific article published on 05 March 2009

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

scientific article published on 19 August 2014

Gain-of-function R225W mutation in human AMPKgamma(3) causing increased glycogen and decreased triglyceride in skeletal muscle

scientific article

Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy

scientific article

Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome

scientific article published on 13 December 2006

Generation of long insert pairs using a Cre-LoxP Inverse PCR approach

scientific article

Genetic and functional analyses identify DISC1 as a novel callosal agenesis candidate gene

scientific article published on 7 July 2011

Genetic dissection of the α-globin super-enhancer in vivo

scientific article published on 04 July 2016

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

scientific article published on 3 August 2012

Genome sequence of "Candidatus Frankia datiscae" Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata

scientific article

Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores

scientific article

Genome sequence of the mercury-methylating and pleomorphic Desulfovibrio africanus Strain Walvis Bay.

scientific article

Genome-wide compendium and functional assessment of in vivo heart enhancers

scientific article published on 05 October 2016

Genomic Patterns of De Novo Mutation in Simplex Autism.

scientific article published on 27 September 2017

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

scientific article published on 01 August 2019

Genomic strategies to identify mammalian regulatory sequences

scientific article

Genomic views of distant-acting enhancers

scientific article

Germline Chd8 haploinsufficiency alters brain development in mouse.

scientific article published on 26 June 2017

Glucose regulates the expression of the apolipoprotein A5 gene

scientific article

Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11.

scientific article published on May 2004

Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons

scientific article published on 25 March 2004

High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes

scientific article

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

scientific article

Human cathepsin L rescues the neurodegeneration and lethality in cathepsin B/L double-deficient mice

scientific article published in July 2006

Human-specific gain of function in a developmental enhancer

scientific article published on September 2008

Identification and characterization of novel Fgf17 enhancers active in the rostral forebrain signaling center

Identification of a novel enhancer of brain expression near the apoE gene cluster by comparative genomics

scientific article published in January 2004

Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence

scientific article

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

scientific article published on 13 February 2017

In vivo characterization of a vertebrate ultraconserved enhancer

scientific article

In vivo characterization of human APOA5 haplotypes

scientific article published on 23 October 2007

Insights from human/mouse genome comparisons

scientific article

Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor

scientific article

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers

scientific article

Lack of MEF2A mutations in coronary artery disease

scientific article

Lack of support for the association between GAD2 polymorphisms and severe human obesity

scientific article published on 30 August 2005

Large-scale discovery of enhancers from human heart tissue

scientific article published on 4 December 2011

Large-scale identification of tissue-specific enhancers in vivo

Large-scale identification of tissue-specific enhancers in vivo.

scientific article published on 11 October 2010

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.

scientific article published on 21 August 2017

Limits of sequence and functional conservation

scientific article

Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia

scientific article published on 09 October 2003

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

scientific article published on 18 November 2021

Massively parallel functional dissection of mammalian enhancers in vivo

scientific article

Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy ⬇️

scientific article

Mechanism of triglyceride lowering in mice expressing human apolipoprotein A5

scientific article

Medical sequencing at the extremes of human body mass

scientific article published on 5 March 2007

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

scientific article (publication date: 28 January 2011)

Most rare missense alleles are deleterious in humans: implications for complex disease and association studies

scientific article published on 8 March 2007

Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair

scientific article

Neuropathological changes in a mouse model of progressive myoclonus epilepsy: cystatin B deficiency and Unverricht-Lundborg disease

scientific article

Noncoding deletions reveal a gene that is critical for intestinal function

scientific article published on 19 June 2019

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

scientific article published on 23 April 2015

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

scientific article

Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

scholarly article published 1 April 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

scientific article published on 22 January 2004

Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL.

scientific article published on 25 February 2007

Predicting tissue-specific enhancers in the human genome

scientific article published on 8 January 2007

Presynaptic Homeostasis Opposes Disease Progression in Mouse Models of ALS-Like Degeneration: Evidence for Homeostatic Neuroprotection

scientific article published on 30 April 2020

Principles of regulatory information conservation between mouse and human

scientific article

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

scientific article published on October 2016

Progressive ataxia, myoclonic epilepsy and cerebellar apoptosis in cystatin B-deficient mice

scientific journal article

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development

scientific article published on December 2013

Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans.

scientific article published on 15 December 2008

Reactivation of a developmentally silenced embryonic globin gene

scientific article published on 21 July 2021

Relationship between Genetic Variation at PPP1R3B and Liver Glycogen and Triglyceride Levels

scientific article published on 21 December 2017

Relative contribution of variation within the APOC3/A4/A5 gene cluster in determining plasma triglycerides

scientific article

Response to Wang et al.

scientific article

SNP-VISTA: an interactive SNP visualization tool

scientific article

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

scientific article published on 07 October 2013

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

scientific article published on 12 February 2018

Somatic mutations of GUCY2F, EPHA3, and NTRK3 in human cancers

scientific article

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

scientific article published on 29 July 2020

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

scientific article published on 15 July 2019

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

scientific article published on 29 July 2020

TIMELESS mutation alters phase responsiveness and causes advanced sleep phase

scientific article published on 28 May 2019

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

scientific article

The DNA sequence and biology of human chromosome 19

scientific article

The DNA sequence and comparative analysis of human chromosome 5

scientific article

The Epigenomic Landscape of Prokaryotes

scientific article

The INSIG2 rs7566605 genetic variant does not play a major role in obesity in a sample of 24,722 individuals from four cohorts

scientific article

The amphioxus genome and the evolution of the chordate karyotype

scientific article

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

scientific article

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

scientific article published on 29 July 2020

The liver X receptor ligand T0901317 down-regulates APOA5 gene expression through activation of SREBP-1c

scientific article published on 17 August 2004

The sequence and analysis of duplication-rich human chromosome 16

scientific article

Tissue-specific RNA expression marks distant-acting developmental enhancers

scientific article

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis

scientific article

Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

scientific article published on 02 September 2009

Transcriptional regulation of apolipoprotein A5 gene expression by the nuclear receptor RORalpha

scientific article

Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex

scientific article

Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels

scientific article (publication date: 15 November 2002)

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

scientific article

Ultraconserved Enhancers Are Required for Normal Development.

scientific article

Ultraconserved enhancer function does not require perfect sequence conservation

scientific article published on 29 March 2021

Use of "MGE enhancers" for labeling and selection of embryonic stem cell-derived medial ganglionic eminence (MGE) progenitors and neurons

scientific article

VISTA Enhancer Browser--a database of tissue-specific human enhancers

scientific article

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