List of works by Thomas R. Gingeras

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A genome-wide survey of sexually dimorphic expression of Drosophila miRNAs identifies the steroid hormone-induced miRNA let-7 as a regulator of sexual identity.

scientific article

A limited set of transcriptional programs define major cell types

scientific article published on 29 July 2020

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

scientific article

A promoter-level mammalian expression atlas

scientific article

Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop.

scientific article published on 5 April 2018

An effort to make sense of antisense transcription in bacteria

scientific article published on August 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

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

scholarly article

Author Correction: Perspectives on ENCODE

scholarly article

Beyond expression profiling: next generation uses of high density oligonucleotide arrays

scientific article published in April 2003

Biological function of unannotated transcription during the early development of Drosophila melanogaster

scientific article published on 3 September 2006

Blunt-end and single-strand ligations by Escherichia coli ligase: influence on an in vitro amplication scheme

scientific article published on 01 April 1990

Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays

scientific article published on November 1998

Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: Causes of signal variation and false positive signals

Comparative analysis of the transcriptome across distant species

scientific article

Comparative transcriptomics in human and mouse.

scientific article published on 8 May 2017

Comparing genomes within the species Mycobacterium tuberculosis

scientific article

Comparison of the transcriptional landscapes between human and mouse tissues

scientific article

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development.

scientific article published on 20 December 2017

Considerations when investigating lncRNA function in vivo.

scientific article

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

scientific article published on 28 June 2013

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

scientific article

Defining functional DNA elements in the human genome

scientific article

Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data.

scientific article

Differential analysis for high density tiling microarray data

scientific article

Diversity and dynamics of the Drosophila transcriptome

scientific article

Dynamics of microRNA expression during mouse prenatal development

scientific article published on 23 October 2019

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

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

scientific article

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

scientific article

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

scientific article published on 23 October 2011

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

scientific article

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Expression of the lacZ gene from two methanol-regulated promoters in Pichia pastoris

scientific article published on May 1987

Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays.

scientific article published in July 1996

Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA

scientific article

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

Fifty years of molecular (DNA/RNA) diagnostics.

scientific article published on 13 January 2005

Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation

scientific article

From identification to validation to gene count.

scientific article

Gene-specific patterns of expression variation across organs and species

scientific article published on 08 July 2016

Genome-wide analysis of estrogen receptor binding sites

scientific article (publication date: November 2006)

Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function

scientific article published on 14 August 2019

Genome-wide antisense transcription drives mRNA processing in bacteria

scientific article published on 28 November 2011

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo

scientific article

Global transcription in pluripotent embryonic stem cells.

scientific article published on May 2008

HIV regulation of the IL-7R: a viral mechanism for enhancing HIV-1 replication in human macrophages in vitro

scientific article

HIV-1 infectability of CD4+ lymphocytes with relation to beta-chemokines and the CCR5 coreceptor

scientific article published on March 1999

High density synthetic oligonucleotide arrays

scientific article (publication date: 1999)

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

scientific article published on 24 September 2009

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

scientific article

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

scientific article

Hybridization properties of immobilized nucleic acids

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

Implications of chimaeric non-co-linear transcripts

scientific article published on September 2009

Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells

scientific article published on October 1986

Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

article by Kerstin Lindblad-Toh et al published April 2000 in Nature Genetics

Large-scale transcriptional activity in chromosomes 21 and 22

scientific article (publication date: 3 May 2002)

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

scientific article

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

scientific article published on 31 March 2020

Mapping RNA-seq Reads with STAR

scientific article

Mapping the strand-specific transcriptome of fission yeast

Microarray-based DNA methylation profiling: technology and applications

scientific article

Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field

scientific article

Missing lincs in the transcriptome

scientific article published in April 2009

Modeling gene expression using chromatin features in various cellular contexts

scientific article (publication date: 13 June 2012)

Molecular biology: RNA discrimination

scientific article published in Nature

Multiplicity of 5' cap structures present on short RNAs

scientific article

MyD88 primes macrophages for full-scale activation by interferon-gamma yet mediates few responses to Mycobacterium tuberculosis

scientific article

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

scientific article published on 29 April 2013

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22

scientific article

Novel Transcribed Regions in the Human Genome

article

Optimizing RNA-Seq Mapping with STAR.

scientific article

Origin of phenotypes: genes and transcripts

scientific article

Perspectives on ENCODE

scientific article published on 29 July 2020

Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment

scientific article published on 01 July 2020

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

RAMPAGE: promoter activity profiling by paired-end sequencing of 5'-complete cDNAs.

scientific article published on 11 November 2013

RNA Reference Materials for Gene Expression Studies: Point: Difficult First Steps

article

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments

scientific article

Reduced HIV-1 infectability of CD4+ lymphocytes from exposed-uninfected individuals: association with low expression of CCR5 and high production of beta-chemokines

scientific article published on April 1998

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells

scientific article published on November 2006

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase

scientific article

STAR: ultrafast universal RNA-seq aligner

scientific article (publication date: 2013)

ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris

scientific article

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

scientific article published on 30 December 2020

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

Synthetic spike-in standards for RNA-seq experiments

scientific article

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

scientific article published on 7 February 2008

TUF love for "junk" DNA.

scientific article

Temporal gene regulation during HIV-1 infection of human CD4+ T cells

scientific article

Temporal profile of replication of human chromosomes

scientific article

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

scientific article

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

scientific article

The fractured landscape of RNA-seq alignment: The default in our STARs

scholarly article published 16 November 2017

The fractured landscape of RNA-seq alignment: the default in our STARs.

scientific article published in May 2018

The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene

scientific article published on February 1983

The long noncoding RNA regulates inflammatory gene expression

article

The multitasking genome

The reality of pervasive transcription

scientific article

The transcriptional diversity of 25 Drosophila cell lines

scientific article

The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies

scientific article published on December 2000

Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.

scientific article published in January 2006

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

scientific article

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

scientific article (publication date: 20 February 2004)

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

scientific article

Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls

scientific article published on September 2009

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

scientific article

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