List of works - Jennifer Harrow

A conditional knockout resource for the genome-wide study of mouse gene function

scientific article

AnnoTrack - a tracking system for genome annotation ⬇️

scientific article (publication date: 5 October 2010)

Assessment of transcript reconstruction methods for RNA-seq

scientific article

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

scientific article

Comparative analysis of pseudogenes across three phyla

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

scientific article

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

scientific article published on 18 June 2015

Creating reference gene annotation for the mouse C57BL6/J genome assembly

scientific article

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

scientific article

Defining the human reference protein-coding gene set.

scientific article published on 11 October 2010

Determination and validation of principal gene products.

scientific article

Devising a Consensus Framework for Validation of Novel Human Coding Loci

scientific article published on 14 September 2015

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin

scientific article

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

ELIXIR Software Management Plan for Life Sciences

ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future

scientific article published on 15 March 2021

ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale

scientific article

Efficient targeted transcript discovery via array-based normalization of RACE libraries

scientific article

Ensembl 2012

scientific article

Ensembl 2013

scientific article

Ensembl 2014

scientific article

Ensembl 2015

scientific article (publication date: 2015)

Ensembl 2016

scientific article

Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

scientific article published in Nature

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

scientific article published on 03 March 2020

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

scientific article

From identification to validation to gene count.

scientific article

Functional transcriptomics in the post-ENCODE era

scientific article published on 30 October 2013

GENCODE pseudogenes

scientific article published in January 2014

GENCODE: producing a reference annotation for ENCODE

scientific article

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Gene inactivation and its implications for annotation in the era of personal genomics

scientific article (publication date: 2011)

Genome annotation for clinical genomic diagnostics: strengths and weaknesses

scientific article

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

scientific article

Genomic anatomy of the Tyrp1 (brown) deletion complex

scholarly article

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

scientific article

Identifying protein-coding genes in genomic sequences

scientific article published on 30 January 2009

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

scientific article

MHC-linked and un-linked class I genes in the wallaby

scientific article published on 14 July 2009

Measuring outcomes and impact from the BioHackathon Europe

Meeting report: a workshop on Best Practices in Genome Annotation

scientific article

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

scientific article (publication date: 15 November 2014)

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

scientific article published on 7 August 2006

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions

scientific article

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

scientific article

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

RNAcentral: an international database of ncRNA sequences

scientific article

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

scientific article published on 02 December 2019

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

scientific article

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

scientific article published on 01 October 2018

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article

The DNA sequence and biological annotation of human chromosome

scientific article

The GENCODE pseudogene resource

scientific article

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

scientific article

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The importance of identifying alternative splicing in vertebrate genome annotation

scientific article

The origins, evolution, and functional potential of alternative splicing in vertebrates

scientific article

The tammar wallaby major histocompatibility complex shows evidence of past genomic instability

scientific article

Towards FAIR principles for research software

article published in 2019

Tracking and coordinating an international curation effort for the CCDS Project

scientific article

Transcriptional activity and strain-specific history of mouse pseudogenes

scientific article published on 29 July 2020

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

scientific article

List of works by Jennifer Harrow

A conditional knockout resource for the genome-wide study of mouse gene function

AnnoTrack - a tracking system for genome annotation ⬇️

Assessment of transcript reconstruction methods for RNA-seq

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

Comparative analysis of pseudogenes across three phyla

Comparative analysis of the transcriptome across distant species

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Creating reference gene annotation for the mouse C57BL6/J genome assembly

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Defining the human reference protein-coding gene set.

Determination and validation of principal gene products.

Devising a Consensus Framework for Validation of Novel Human Coding Loci

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin

EGASP: the human ENCODE Genome Annotation Assessment Project

ELIXIR Software Management Plan for Life Sciences

ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future

ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale

Efficient targeted transcript discovery via array-based normalization of RACE libraries

Ensembl 2012

Ensembl 2013

Ensembl 2014

Ensembl 2015

Ensembl 2016

Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Evidence for transcript networks composed of chimeric RNAs in human cells

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

From identification to validation to gene count.

Functional transcriptomics in the post-ENCODE era

GENCODE pseudogenes

GENCODE: producing a reference annotation for ENCODE

GENCODE: the reference human genome annotation for The ENCODE Project

Gene inactivation and its implications for annotation in the era of personal genomics

Genome annotation for clinical genomic diagnostics: strengths and weaknesses

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

Genomic anatomy of the Tyrp1 (brown) deletion complex

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Identifying protein-coding genes in genomic sequences

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

MHC-linked and un-linked class I genes in the wallaby

Measuring outcomes and impact from the BioHackathon Europe

Meeting report: a workshop on Best Practices in Genome Annotation

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

RNAcentral: A vision for an international database of RNA sequences

RNAcentral: an international database of ncRNA sequences

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Systematic evaluation of spliced alignment programs for RNA-seq data

The DNA sequence and biological annotation of human chromosome

The GENCODE pseudogene resource

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

The implications of alternative splicing in the ENCODE protein complement

The importance of identifying alternative splicing in vertebrate genome annotation

The origins, evolution, and functional potential of alternative splicing in vertebrates

The tammar wallaby major histocompatibility complex shows evidence of past genomic instability

Towards FAIR principles for research software

Tracking and coordinating an international curation effort for the CCDS Project

Transcriptional activity and strain-specific history of mouse pseudogenes

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene