List of works - Joel Rozowsky

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

scientific article

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

scientific article

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

scientific article

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

scientific article published on 18 April 2016

ACT: aggregation and correlation toolbox for analyses of genome tracks.

scientific article

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

scientific article published in Science

AlleleSeq: analysis of allele-specific expression and binding in a network framework

scientific article published on 2 August 2011

An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

scientific article published on 21 October 2009

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

scientific article

An integrative ENCODE resource for cancer genomics

scientific article published on 29 July 2020

Analyzing the ’t Hooft model on a light-cone lattice

article

Annotating non-coding regions of the genome

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Assessing the need for sequence-based normalization in tiling microarray experiments

scientific article published on 25 March 2007

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

scientific article published on 21 November 2006

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

scholarly article

Author Correction: Perspectives on ENCODE

scholarly article

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

scientific article

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

scientific article

Comparative analysis of pseudogenes across three phyla

scientific article

Comparative analysis of regulatory information and circuits across distant species

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

scientific article

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data

scientific article

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

scientific article published on 28 October 2014

Design optimization methods for genomic DNA tiling arrays

scientific article

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources

scientific article

Divergence of transcription factor binding sites across related yeast species

scientific article

Diverse human extracellular RNAs are widely detected in human plasma.

scientific article published on 26 April 2016

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches

scientific article

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

scientific article

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

scientific article published on 28 April 2016

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Extending gene ontology in the context of extracellular RNA and vesicle communication

scientific article published on 12 April 2016

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies

scientific article published on January 2006

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

scientific article (publication date: 2010)

Global identification of human transcribed sequences with genome tiling arrays

scientific article (publication date: 24 December 2004)

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

scientific article published in June 2007

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

scientific article

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

scientific article published on August 2005

Loregic: a method to characterize the cooperative logic of regulatory factors

scientific article

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

scientific article

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function

scientific article published in June 2004

Mapping accessible chromatin regions using Sono-Seq

scientific article

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

scientific article

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

scientific article

Modeling ChIP sequencing in silico with applications

scientific article

Non-Abelian monopoles and dyons in a modified Einstein-Yang-Mills-Higgs system

Novel Transcribed Regions in the Human Genome

article

OrthoClust: an orthology-based network framework for clustering data across multiple species

scientific article

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

scientific article

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

scientific article

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

scientific article

Spontaneous symmetry breaking at infinite momentum without P+ zero modes

scientific article (publication date: 21 August 2000)

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

scientific article published on 29 July 2020

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

scientific article published on 3 January 2008

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

scientific article published on 7 February 2008

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

scientific article

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

scientific article

The real cost of sequencing: scaling computation to keep pace with data generation

scientific article

The reality of pervasive transcription

scientific article

Tilescope: online analysis pipeline for high-density tiling microarray data

scientific article

Tiling array data analysis: a multiscale approach using wavelets

scientific article

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

scientific article

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

scientific article published on 19 July 2007

Two-loop N=4 supersymmetric amplitudes and QCD

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

scientific article

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

scientific article

Variation in transcription factor binding among humans

scientific article

List of works by Joel Rozowsky

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

ACT: aggregation and correlation toolbox for analyses of genome tracks.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

AlleleSeq: analysis of allele-specific expression and binding in a network framework

An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

An integrative ENCODE resource for cancer genomics

Analyzing the ’t Hooft model on a light-cone lattice

Annotating non-coding regions of the genome

Architecture of the human regulatory network derived from ENCODE data

Assessing the need for sequence-based normalization in tiling microarray experiments

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

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

Author Correction: Perspectives on ENCODE

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

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Comparative analysis of pseudogenes across three phyla

Comparative analysis of regulatory information and circuits across distant species

Comparative analysis of the transcriptome across distant species

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

Design optimization methods for genomic DNA tiling arrays

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources

Divergence of transcription factor binding sites across related yeast species

Diverse human extracellular RNAs are widely detected in human plasma.

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Extending gene ontology in the context of extracellular RNA and vesicle communication

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

Global identification of human transcribed sequences with genome tiling arrays

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

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

Loregic: a method to characterize the cooperative logic of regulatory factors

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function

Mapping accessible chromatin regions using Sono-Seq

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

Modeling ChIP sequencing in silico with applications

Non-Abelian monopoles and dyons in a modified Einstein-Yang-Mills-Higgs system

Novel Transcribed Regions in the Human Genome

OrthoClust: an orthology-based network framework for clustering data across multiple species

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

Spontaneous symmetry breaking at infinite momentum without P+ zero modes

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

The real cost of sequencing: scaling computation to keep pace with data generation

The reality of pervasive transcription

Tilescope: online analysis pipeline for high-density tiling microarray data

Tiling array data analysis: a multiscale approach using wavelets

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

Two-loop N=4 supersymmetric amplitudes and QCD

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

Variation in transcription factor binding among humans