List of works - Shyam Prabhakar

A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.

scientific article published on 23 December 2016

A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

scientific article published on 20 February 2017

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

scientific article

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content

scientific article

Accelerated evolution of conserved noncoding sequences in humans

scientific article

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

scientific article

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

scientific article

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

scientific article published on 01 December 2018

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

scientific article

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

scientific article published on 8 March 2016

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

scientific article published on 03 April 2013

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures

scientific article published on 06 December 2018

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.

scientific article published on 14 April 2018

DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data ⬇️

journal article from 'bioRxiv' published in 2020

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

scientific journal article

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

scientific article published on January 2007

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

scientific article published on 01 April 2020

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.

scientific article

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

scientific article published on 12 June 2020

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

scientific article

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos

scientific article published on September 2015

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish

scientific article

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

scientific article published on 08 September 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

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.

scientific article

Human-specific gain of function in a developmental enhancer

scientific article published on September 2008

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures

scientific article

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column

scientific article

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

scientific article published on 25 September 2020

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

scientific article published on December 2010

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease

scientific article published on 23 April 2019

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

scientific article published on 25 May 2020

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome

scientific article

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.

scientific article published on 9 September 2005

Massive contribution of transposable elements to mammalian regulatory sequences

scientific article published on 9 May 2016

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness

scientific article

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling

scientific article

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming

scientific journal article

Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

scientific article published on 21 September 2015

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

scientific article

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas

scientific article published on 20 August 2019

Primate-specific evolution of an LDLR enhancer

scientific article published on 2 August 2006

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

scientific article

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation

scientific article published on 23 October 2019

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response

scientific article published on 01 April 2019

Robust clustering and interpretation of scRNA-seq data using reference component analysis

scientific article published on 17 February 2021

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

scientific article

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

scientific article

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

scientific article published on 27 May 2015

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

scientific article

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF- effectors

scientific article

Study sequence rules of estrogen receptor α-DNA interactions using dual polarization interferometry and computational modeling

scientific article published on 23 October 2012

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

scientific article

The DNA sequence and comparative analysis of human chromosome 5

scientific article

The PsychENCODE project

scientific article

The sequence and analysis of duplication-rich human chromosome 16

scientific article

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis

scientific article

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles

scientific article published on 16 April 2013

Tumor-derived circulating endothelial cell clusters in colorectal cancer

scientific article

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

scientific article

Uniform, optimal signal processing of mapped deep-sequencing data

scientific article

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data ⬇️

journal article from 'bioRxiv' published in 2020

List of works by Shyam Prabhakar

A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.

A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content

Accelerated evolution of conserved noncoding sequences in humans

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.

DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data ⬇️

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

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

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.

Human-specific gain of function in a developmental enhancer

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.

Massive contribution of transposable elements to mammalian regulatory sequences

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming

Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas

Primate-specific evolution of an LDLR enhancer

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response

Robust clustering and interpretation of scRNA-seq data using reference component analysis

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF- effectors

Study sequence rules of estrogen receptor α-DNA interactions using dual polarization interferometry and computational modeling

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

The DNA sequence and comparative analysis of human chromosome 5

The PsychENCODE project

The sequence and analysis of duplication-rich human chromosome 16

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles

Tumor-derived circulating endothelial cell clusters in colorectal cancer

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Uniform, optimal signal processing of mapped deep-sequencing data

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data ⬇️