List of works - Paul Blainey

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

scientific article published on 22 April 2019

A Single-cell genome for Thiovulum sp.

scientific article

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

scientific article

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

scientific article

A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis

scientific article published on 08 December 2020

An immune-cell signature of bacterial sepsis

scientific article published on 17 February 2020

Combinatorial drug discovery in nanoliter droplets

article published in the Proceedings of the National Academy of Sciences of the United States of America

Correction: Digital PCR provides sensitive and absolute calibration for high throughput sequencing

scientific article published on 19 November 2009

DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution

scientific article published on 21 December 2020

Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA†

scientific article published on 06 March 2008

Digital MDA for enumeration of total nucleic acid contamination

scientific article

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

scientific article

Dissecting genomic diversity, one cell at a time

scientific article

FTIR studies of intermolecular hydrogen bonding in halogenated ethanols

scientific article published in December 2001

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis

scientific article

Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13 ⬇️

scientific article published on 31 March 2023

Genomic analysis at the single-cell level

scientific article

Human STING is a proton channel

scientific article published on 03 August 2023

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

scientific article published on 27 February 2019

Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19

scientific article published on 02 September 2020

Laser microdissection of the alveolar duct enables single-cell genomic analysis

scientific article

Massively multiplexed nucleic acid detection using Cas13

scientific article published on 29 April 2020

Massively parallel screening of synthetic microbial communities

scientific article published on 11 June 2019

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012.

scientific article

Mobile genes in the human microbiome are structured from global to individual scales.

scientific article

Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA.

scientific article

Molecular sled sequences are common in mammalian proteins

scientific article published on 8 February 2016

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

scientific article published on 26 September 2019

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

scientific article published on 23 January 2019

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA.

scientific article published on 15 April 2007

Nonspecifically bound proteins spin while diffusing along DNA.

scientific article

Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium

scientific article published on 28 October 2019

Optimal estimation of diffusion coefficients from single-particle trajectories

scientific article published on 28 February 2014

Optofluidic cell selection from complex microbial communities for single-genome analysis

scientific article

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

scientific article published on 9 September 2011

Points of significance: nested designs. For studies with hierarchical noise sources, use a nested analysis of variance approach

scientific article published in October 2014

Pooled genetic perturbation screens with image-based phenotypes

scientific article published in 2022

Positive interactions are common among culturable bacteria

scientific article published on 05 November 2021

Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis

scientific article published on September 2012

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: I. binding to DNA AND to hexon of the precursor to protein VI, pVI, of human adenovirus

scientific article published on 7 October 2012

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction

scientific article published on 7 October 2012

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: IV. viral proteinase slides along DNA to locate and process its substrates

scientific article published on 7 October 2012

Replication

scientific article published on 01 September 2014

Sampling distributions and the bootstrap

scientific article published on June 2015

Self-encapsulation of poly-2,7-fluorenes in a dendrimer matrix

scientific article published in July 2001

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays.

scientific article published on 24 September 2015

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

scientific article published on January 2013

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).

scientific article

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

scientific article

Sliding on DNA: From Peptides to Small Molecules.

scientific article

The future is now: single-cell genomics of bacteria and archaea

scientific article

Tools for the Microbiome: Nano and Beyond

scientific article published on 22 December 2015

Virtual microfluidics for digital quantification and single-cell sequencing

scientific article published on August 2016

What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism? ⬇️

scientific article published on 01 March 2017

List of works by Paul Blainey

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

A Single-cell genome for Thiovulum sp.

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis

An immune-cell signature of bacterial sepsis

Combinatorial drug discovery in nanoliter droplets

Correction: Digital PCR provides sensitive and absolute calibration for high throughput sequencing

DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution

Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA†

Digital MDA for enumeration of total nucleic acid contamination

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

Dissecting genomic diversity, one cell at a time

FTIR studies of intermolecular hydrogen bonding in halogenated ethanols

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis

Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13 ⬇️

Genomic analysis at the single-cell level

Human STING is a proton channel

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19

Laser microdissection of the alveolar duct enables single-cell genomic analysis

Massively multiplexed nucleic acid detection using Cas13

Massively parallel screening of synthetic microbial communities

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012.

Mobile genes in the human microbiome are structured from global to individual scales.

Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA.

Molecular sled sequences are common in mammalian proteins

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA.

Nonspecifically bound proteins spin while diffusing along DNA.

Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium

Optimal estimation of diffusion coefficients from single-particle trajectories

Optofluidic cell selection from complex microbial communities for single-genome analysis

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Points of significance: nested designs. For studies with hierarchical noise sources, use a nested analysis of variance approach

Pooled genetic perturbation screens with image-based phenotypes

Positive interactions are common among culturable bacteria

Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: I. binding to DNA AND to hexon of the precursor to protein VI, pVI, of human adenovirus

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction

Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: IV. viral proteinase slides along DNA to locate and process its substrates

Replication

Sampling distributions and the bootstrap

Self-encapsulation of poly-2,7-fluorenes in a dendrimer matrix

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays.

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

Sliding on DNA: From Peptides to Small Molecules.

The future is now: single-cell genomics of bacteria and archaea

Tools for the Microbiome: Nano and Beyond

Virtual microfluidics for digital quantification and single-cell sequencing

What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism? ⬇️