List of works - Robi D Mitra

'Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins.

scientific article published in January 2008

A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis

scientific article published on 22 February 2016

A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis

scientific article published on March 2016

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples.

scientific article published on 13 November 2007

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs.

scientific article published on 27 March 2012

A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

scientific article published on 16 April 2020

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

scientific article published on 08 June 2013

Accurate multiplex polony sequencing of an evolved bacterial genome

scientific article

Advanced sequencing technologies: methods and goals

scientific article

Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes.

scientific article

An optimized, broadly applicable piggyBac transposon induction system

scientific article

Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the Drosophila eye.

scientific article

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

scientific article

Calling Card Analysis in Budding Yeast

scientific article published on 01 February 2016

Calling cards for DNA-binding proteins.

scientific article published on 10 July 2007

Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease

scientific article

Clinical genomicist workstation

scientific article published on 18 March 2013

Correction: Rare Variants in APP, PSEN1 and PSEN2 Increase Risk for AD in Late-Onset Alzheimer's Disease Families

scientific article published on 10 May 2012

Detection of rare genomic variants from pooled sequencing using SPLINTER.

scientific article

Digital genotyping and haplotyping with polymerase colonies

scientific article

Digital quantitative measurements of gene expression

scientific article published on April 2004

Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks

scientific article

Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses

scientific article published on 14 February 2020

Erratum to “Fluorescent in situ sequencing on polymerase colonies” [Anal. Biochem. 320 (2003) 55–65]

scholarly article published in Analytical Biochemistry

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.

scientific article published on 7 September 2016

Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein.

scientific article published on January 1996

Fluorescent in situ sequencing on polymerase colonies

scientific article

From karyotypes to precision genomics in 9p deletion and duplication syndromes

scientific article published on 24 December 2021

Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon

scientific article (publication date: 2 January 2013)

GENE-16. Brd4-BOUND STRETCH/SUPER ENHANCER USAGE UNDERLIES SEXUAL DIMORPHISM IN GLIOBLASTOMA

article by Najla Kfoury et al published 6 November 2017 in Neuro-Oncology

Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin

scientific article published on 09 July 2013

Global gene deletion analysis exploring yeast filamentous growth

scientific article published on 01 September 2012

HGG-25. Targeting KLF5 reduces tumorigenic phenotype in a murine glioblastoma (GBM) model

scientific article published in 2022

High-throughput discovery of rare insertions and deletions in large cohorts

scientific article

High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation

scientific article published on 04 September 2020

Homotypic cooperativity and collective binding are determinants of bHLH specificity and function

scientific article published on 24 July 2019

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis

scientific article published on 28 July 2020

IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes

scientific article

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

scientific article

Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing

scientific article published on 03 June 2009

Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.

scientific article

Long-range polony haplotyping of individual human chromosome molecules

scientific article published on 19 February 2006

Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine

scientific article

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes

scientific article published in 2022

Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors.

scientific article

Nanogel surface coatings for improved single-molecule imaging substrates.

scientific article

Nested Patch PCR for highly multiplexed amplification of genomic loci.

scientific article published in July 2009

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

scientific article published on 22 April 2007

Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret

scientific article

Origin and consequences of the relationship between protein mean and variance

scientific article

PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells

scientific article

Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies

scientific article

Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data

scientific article

Polony analysis of gene expression in ES cells and blastocysts.

scientific article

Protein quantification in complex mixtures by solid phase single-molecule counting

scientific article

Quantification of rare allelic variants from pooled genomic DNA

scientific article

Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays

scientific article published on 05 March 2020

Rapid and extraction-free detection of SARS-CoV-2 from saliva by colorimetric reverse-transcription loop-mediated isothermal amplification

scientific article published on 24 October 2020

Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP

scientific article published on 11 May 2020

Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence.

scientific article published on 31 October 2011

Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families

scientific article (publication date: 2012)

Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex

scientific article

Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells

scientific article published on 18 July 2020

Sensitive single-molecule protein quantification and protein complex detection in a microarray format

scientific article

Sequencing of idiopathic pulmonary fibrosis-related genes reveals independent single gene associations

scientific article

Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome

scientific article

Single molecule profiling of alternative pre-mRNA splicing

scientific article

Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia

scientific article published on 01 September 2018

Synonymous ABCA3 variants do not increase risk for neonatal respiratory distress syndrome

scientific article

TATA is a modular component of synthetic promoters

scientific article

The qBED track: a novel genome browser visualization for point processes

scientific article published on 17 September 2020

Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue

scientific article

Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations

scientific article published on 23 June 2012

Transcription factor regulation and chromosome dynamics during pseudohyphal growth

scientific article

Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

scientific article published on 6 November 2018

Transposon Calling Cards

scientific article published on 01 February 2016

Ultralow protein adsorbing coatings from clickable PEG nanogel solutions: benefits of attachment under salt-induced phase separation conditions and comparison with PEG/albumin nanogel coatings

scientific article published on 11 March 2013

Validation of a next-generation sequencing assay for clinical molecular oncology.

scientific article published on 6 November 2013

List of works by Robi D Mitra

'Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins.

A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis

A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples.

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs.

A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

Accurate multiplex polony sequencing of an evolved bacterial genome

Advanced sequencing technologies: methods and goals

Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes.

An optimized, broadly applicable piggyBac transposon induction system

Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the Drosophila eye.

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

Calling Card Analysis in Budding Yeast

Calling cards for DNA-binding proteins.

Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease

Clinical genomicist workstation

Correction: Rare Variants in APP, PSEN1 and PSEN2 Increase Risk for AD in Late-Onset Alzheimer's Disease Families

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Digital genotyping and haplotyping with polymerase colonies

Digital quantitative measurements of gene expression

Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks

Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses

Erratum to “Fluorescent in situ sequencing on polymerase colonies” [Anal. Biochem. 320 (2003) 55–65]

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.

Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein.

Fluorescent in situ sequencing on polymerase colonies

From karyotypes to precision genomics in 9p deletion and duplication syndromes

Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon

GENE-16. Brd4-BOUND STRETCH/SUPER ENHANCER USAGE UNDERLIES SEXUAL DIMORPHISM IN GLIOBLASTOMA

Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin

Global gene deletion analysis exploring yeast filamentous growth

HGG-25. Targeting KLF5 reduces tumorigenic phenotype in a murine glioblastoma (GBM) model

High-throughput discovery of rare insertions and deletions in large cohorts

High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation

Homotypic cooperativity and collective binding are determinants of bHLH specificity and function

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis

IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing

Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.

Long-range polony haplotyping of individual human chromosome molecules

Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes

Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors.

Nanogel surface coatings for improved single-molecule imaging substrates.

Nested Patch PCR for highly multiplexed amplification of genomic loci.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret

Origin and consequences of the relationship between protein mean and variance

PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells

Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies

Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data

Polony analysis of gene expression in ES cells and blastocysts.

Protein quantification in complex mixtures by solid phase single-molecule counting

Quantification of rare allelic variants from pooled genomic DNA

Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays

Rapid and extraction-free detection of SARS-CoV-2 from saliva by colorimetric reverse-transcription loop-mediated isothermal amplification

Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP

Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence.

Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families

Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex

Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells

Sensitive single-molecule protein quantification and protein complex detection in a microarray format

Sequencing of idiopathic pulmonary fibrosis-related genes reveals independent single gene associations

Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome

Single molecule profiling of alternative pre-mRNA splicing

Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia

Synonymous ABCA3 variants do not increase risk for neonatal respiratory distress syndrome

TATA is a modular component of synthetic promoters

The qBED track: a novel genome browser visualization for point processes

Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue

Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations

Transcription factor regulation and chromosome dynamics during pseudohyphal growth

Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

Transposon Calling Cards

Ultralow protein adsorbing coatings from clickable PEG nanogel solutions: benefits of attachment under salt-induced phase separation conditions and comparison with PEG/albumin nanogel coatings

Validation of a next-generation sequencing assay for clinical molecular oncology.