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List of works by Peter V Kharchenko

"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts

scientific article published on 31 October 2013

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA.

scientific article published on 20 July 2017

A region of the human HOXD cluster that confers polycomb-group responsiveness

scientific article published on January 2010

A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome

scientific article published on August 2008

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

An assessment of histone-modification antibody quality

scientific article

An atlas of healthy and injured cell states and niches in the human kidney ⬇️

Analysis of primary structure of chromatin with next-generation sequencing

scientific article published on April 2010

Analysis of somatic retrotransposition in human cancers.

scientific article

Author Correction: Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis

scientific article published on 19 November 2020

Bayesian approach to single-cell differential expression analysis

scientific article

BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes

scientific article

Cell Kinetics in the Adult Neurogenic Niche and Impact of Diet-Induced Accelerated Aging

scientific article published on 08 February 2019

Cell type ontologies of the Human Cell Atlas

peer-reviewed article published in November 2021

Cell types and ontologies of the Human Cell Atlas ⬇️

journal article published in 2021

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.

scientific article published on August 2016

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Challenges and emerging directions in single-cell analysis

scientific article published on 8 May 2017

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

scientific article published on 18 January 2016

Chromatin proteins captured by ChIP–mass spectrometry are linked to dosage compensation in Drosophila ⬇️

scientific article published on January 6, 2013

Chromatin signatures of the Drosophila replication program

scientific article

Chromosomal periodicity of evolutionarily conserved gene pairs

scholarly article

Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate.

scientific article published on 13 January 2017

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

scientific article published on 26 February 2009

Comparative analysis of metazoan chromatin organization

scientific article

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

scientific article

Correction: Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context

scientific article published on 20 January 2014

DAZL regulates Tet1 translation in murine embryonic stem cells

scientific article published on 15 June 2015

Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth

scientific article published on 23 September 2020

Design and analysis of ChIP-seq experiments for DNA-binding proteins

scientific article

Differential H3K4 methylation identifies developmentally poised hematopoietic genes

scientific article

Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

scientific article published on 01 September 2020

Diversity of developing peripheral glia revealed by single cell RNA sequencing

scientific article

Dosage compensation in drosophila: Sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome

article

Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma

scientific article published on 8 May 2017

Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain

scientific article

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

scientific article

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.

scientific article

Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes

scientific article

Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A.

scientific article published on 16 December 2013

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.

scientific article published on 28 October 2013

Epstein-Barr virus oncoprotein super-enhancers control B cell growth

scientific article

Estimating enrichment of repetitive elements from high-throughput sequence data

scientific article

Evidence for dosage compensation between the X chromosome and autosomes in mammals ⬇️

scientific article published on November 28, 2011

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

scientific article published in April 2020

Expression dynamics of a cellular metabolic network

scientific article published on 2 August 2005

Filling gaps in a metabolic network using expression information

scientific article published in August 2004

From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting ⬇️

scientific article published on January 1, 2003

Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming

scientific article published on 9 May 2013

Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs

scientific article

Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes.

scientific article published on 15 February 2012

How to perform quantitative single cell proteomics with SCoPE2

scientific article published on 01 August 2020

Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis

scientific article published on 07 October 2020

Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner

Identifying metabolic enzymes with multiple types of association evidence

scientific article published on 29 March 2006

Influence of metabolic network structure and function on enzyme evolution

scientific article published on 9 May 2006

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

scientific article published on 5 July 2017

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.

scientific article published on 11 December 2017

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

scientific article published on 15 July 2019

Landscape of somatic retrotransposition in human cancers

scientific article (publication date: 24 August 2012)

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

scientific article published on 13 June 2018

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia

scientific article

Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X

scientific article published on October 2009

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.

scientific article

Nature and function of insulator protein binding sites in the Drosophila genome.

scientific article

Nucleosome positioning in human HOX gene clusters

scientific article published on 22 August 2008

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

scientific article

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

scientific article

Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators

scientific article

RNA velocity of single cells

scientific article published in Nature

Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell

scientific article

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification

scientific article published on 03 February 2014

Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

scientific article

Single-cell mass-spectrometry quantifies the emergence of macrophage heterogeneity

scientific article published on 9 June 2019

Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors

scientific article published on 07 September 2021

Spatiotemporal structure of cell fate decisions in murine neural crest

scientific article

The genomic binding sites of a noncoding RNA.

scientific article published on 5 December 2011

The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains.

scientific article published in July 2015

Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin

scientific article

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

scientific article published on 28 October 2016

UBiT2: a client-side web-application for gene expression data analysis

article

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

scientific article published on 24 November 2014

Upper cortical layer–driven network impairment in schizophrenia

scientific article published in 2022

Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters ⬇️

scientific article published on June 17, 2013

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila ⬇️

scientific article published on March 3, 2011

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.

scientific article published on 19 June 2018

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