List of works - Gill Bejerano

"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements

scientific article published on 06 January 2016

A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species

scientific article published on 27 September 2012

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

scientific article (publication date: 4 May 2006)

A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.

scientific article published on 25 March 2015

A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals

scientific article published on 02 July 2020

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

scientific article published on 30 September 2019

A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb

scientific article

A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae

scientific article

A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human

scientific article published on 6 March 2018

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints

scholarly article by Joseph M Paggi & Gill Bejerano published December 2018 in RNA

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

scientific article published on 01 May 2020

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

scientific article published on 30 August 2019

Algorithms for variable length Markov chain modeling.

scientific article published on 29 January 2004

An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease

scientific article published on 07 August 2018

Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data

scientific article

Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome

scientific article published on 01 April 2018

Branch and bound computation of exact p-values

scientific article published on 7 August 2006

CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells

scientific article published on 04 May 2019

Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network

scientific article

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

scientific article

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis

scientific article published on 05 December 2018

Coding exons function as tissue-specific enhancers of nearby genes

scientific article

Comparative Genomic Analysis Using the UCSC Genome Browser

Comparative genomic analysis using the UCSC genome browser

scientific article published in January 2007

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology

scientific article published on 06 September 2019

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

scientific article published on 27 June 2013

Computational screening of conserved genomic DNA in search of functional noncoding elements

scientific article published in July 2005

Control of pelvic girdle development by genes of the Pbx family and Emx2.

scientific article

Deriving genomic diagnoses without revealing patient genomes

scientific article published in August 2017

Dispensability of mammalian DNA

scientific article published on 02 October 2008

Efficient Exact p -Value Computation for Small Sample, Sparse, and Surprising Categorical Data

scholarly article by Gill Bejerano published in October 2004

Efficient exact p-value computation for small sample, sparse, and surprising categorical data

scientific article

Emergent high fatality lung disease in systemic juvenile arthritis

scientific article published on 27 September 2019

Endangered species hold clues to human evolution

scientific article (publication date: 2010)

Enhancers: five essential questions

scientific article

Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories

scientific article published on 4 February 2016

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

scientific article

Evolutionary biology for the 21st century

scientific article

Forces Shaping the Fastest Evolving Regions in the Human Genome

Forces shaping the fastest evolving regions in the human genome

scientific article

Human developmental enhancers conserved between deuterostomes and protostomes

scientific article (publication date: 2012)

Human genome ultraconserved elements are ultraselected

scientific article

Human-specific loss of regulatory DNA and the evolution of human-specific traits

scientific article published on 10 March 2011

Hundreds of conserved non-coding genomic regions are independently lost in mammals

scientific article published on 5 October 2012

Identification and classification of conserved RNA secondary structures in the human genome

scientific article

Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts

article

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

scientific article published on 03 June 2019

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors

scientific article published on 06 July 2021

Into the heart of darkness: large-scale clustering of human non-coding DNA.

scientific article published in August 2004

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

scientific article

MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis.

scientific article published in August 2017

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

scientific article

Morphogenesis is transcriptionally coupled to neurogenesis during peripheral olfactory organ development

scientific article published on 03 November 2020

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.

scientific article published in October 2017

Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales

scientific article published on 15 June 2015

Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging

scientific article (publication date: 2011)

PRISM offers a comprehensive genomic approach to transcription factor function prediction

scientific article published on 4 February 2013

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization

scientific article published on 12 July 2018

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing

scientific article published on 25 February 2019

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

scientific article

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers.

scientific article

TBR1 regulates autism risk genes in the developing neocortex

scientific article published on 20 June 2016

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option

scientific article (publication date: August 2013)

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

scientific article (publication date: 8 May 2007)

Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes

scientific article published on 18 September 2020

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

scientific article

List of works by Gill Bejerano

"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements

A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.

A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb

A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae

A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

Algorithms for variable length Markov chain modeling.

An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease

Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data

Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome

Branch and bound computation of exact p-values

CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells

Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis

Coding exons function as tissue-specific enhancers of nearby genes

Comparative Genomic Analysis Using the UCSC Genome Browser

Comparative genomic analysis using the UCSC genome browser

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

Computational screening of conserved genomic DNA in search of functional noncoding elements

Control of pelvic girdle development by genes of the Pbx family and Emx2.

Deriving genomic diagnoses without revealing patient genomes

Dispensability of mammalian DNA

Efficient Exact p -Value Computation for Small Sample, Sparse, and Surprising Categorical Data

Efficient exact p-value computation for small sample, sparse, and surprising categorical data

Emergent high fatality lung disease in systemic juvenile arthritis

Endangered species hold clues to human evolution

Enhancers: five essential questions

Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Evolutionary biology for the 21st century

Forces Shaping the Fastest Evolving Regions in the Human Genome

Forces shaping the fastest evolving regions in the human genome

Human developmental enhancers conserved between deuterostomes and protostomes

Human genome ultraconserved elements are ultraselected

Human-specific loss of regulatory DNA and the evolution of human-specific traits

Hundreds of conserved non-coding genomic regions are independently lost in mammals

Identification and classification of conserved RNA secondary structures in the human genome

Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors

Into the heart of darkness: large-scale clustering of human non-coding DNA.

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis.

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

Morphogenesis is transcriptionally coupled to neurogenesis during peripheral olfactory organ development

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.

Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales

Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging

PRISM offers a comprehensive genomic approach to transcription factor function prediction

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers.

TBR1 regulates autism risk genes in the developing neocortex

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing