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

FEMS microbiology reviews, 2013-05, Vol.37 (3), p.407-427

Blainey, Paul C.

2013

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

Proceedings of the National Academy of Sciences - PNAS, 2019-03, Vol.116 (11), p.5037-5044

2019

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

PloS one, 2011-02, Vol.6 (2), p.e16626-e16626

2011

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Massively parallel screening of synthetic microbial communities

Proceedings of the National Academy of Sciences - PNAS, 2019-06, Vol.116 (26), p.12804-12809

2019

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Combinatorial drug discovery in nanoliter droplets

Proceedings of the National Academy of Sciences - PNAS, 2018-06, Vol.115 (26), p.6685-6690

2018

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Dissecting genomic diversity, one cell at a time

Nature methods, 2014-01, Vol.11 (1), p.19-21

2014

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Pooled genetic screens with image‐based profiling

Molecular systems biology, 2022-11, Vol.18 (11), p.e10768-n/a

2022

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High-throughput automated microfluidic sample preparation for accurate microbial genomics

Nature communications, 2017-01, Vol.8 (1), p.13919-13919, Article 13919

2017

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

Nature communications, 2023-03, Vol.14 (1), p.1803-1803, Article 1803

2023

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Nonspecifically bound proteins spin while diffusing along DNA

Nature structural & molecular biology, 2009-12, Vol.16 (12), p.1224-1229

2009

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Digital PCR provides sensitive and absolute calibration for high throughput sequencing

BMC genomics, 2009-03, Vol.10 (1), p.116-116, Article 116

2009

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

Nature communications, 2016-01, Vol.7 (1), p.10220-10220, Article 10220

2016

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Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

Nature communications, 2019-09, Vol.10 (1), p.4377-14, Article 4377

2019

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A Base-Excision DNA-Repair Protein Finds Intrahelical Lesion Bases by Fast Sliding in Contact with DNA

Proceedings of the National Academy of Sciences - PNAS, 2006-04, Vol.103 (15), p.5752-5757

2006

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

Nature communications, 2013, Vol.4 (1), p.1854-1854, Article 1854

2013

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

Science translational medicine, 2012-09, Vol.4 (153), p.153ra130

2012

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Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

eLife, 2017-07, Vol.6

2017

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

Genome research, 2012-06, Vol.22 (6), p.1107-1119

2012

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Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis

Methods in Enzymology, 2013, Vol.531, p.61-90

2013

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Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)

Applied and Environmental Microbiology, 2011-11, Vol.77 (21), p.7804-7814

2011

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CloneSifter: enrichment of rare clones from heterogeneous cell populations

BMC biology, 2020-11, Vol.18 (1), p.177-177, Article 177

2020

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Positive interactions are common among culturable bacteria

Science advances, 2021-11, Vol.7 (45), p.eabi7159

2021

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Quantification of somatic mutation flow across individual cell division events by lineage sequencing

Genome research, 2018-12, Vol.28 (12), p.1901-1918

2018

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

Nature communications, 2016-02, Vol.7 (1), p.10202-10202, Article 10202

2016

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Optimal estimation of diffusion coefficients from single-particle trajectories

Physical review. E, Statistical, nonlinear, and soft matter physics, 2014-02, Vol.89 (2), p.022726-022726, Article 022726

2014

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

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

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

Massively parallel screening of synthetic microbial communities

Combinatorial drug discovery in nanoliter droplets

Dissecting genomic diversity, one cell at a time

Pooled genetic screens with image‐based profiling

High-throughput automated microfluidic sample preparation for accurate microbial genomics

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

Nonspecifically bound proteins spin while diffusing along DNA

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

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

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

A Base-Excision DNA-Repair Protein Finds Intrahelical Lesion Bases by Fast Sliding in Contact with DNA

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

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

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

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

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)

CloneSifter: enrichment of rare clones from heterogeneous cell populations

Positive interactions are common among culturable bacteria

Quantification of somatic mutation flow across individual cell division events by lineage sequencing

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

Optimal estimation of diffusion coefficients from single-particle trajectories

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