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List of works by Patrick S Chain

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.

scientific article published in January 2013

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

scientific article

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

scientific article

ADEPT, a dynamic next generation sequencing data error-detection program with trimming

scientific article

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

scientific article published on 12 March 2015

Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm.

scientific article

Anoxybacillusgeothermalis sp. nov., a facultatively anaerobic, endospore-forming bacterium isolated from mineral deposits in a geothermal station

scientific article

Artificial polyploidy improves bacterial single cell genome recovery

scientific article

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 12 November 2020

Bacterial Genome Annotation ⬇️

scientific article published on January 1, 2012

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

scholarly article

CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA.

scientific article published on 25 August 2015

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia.

scientific article

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

scientific article (publication date: 2015)

Combining compositional data sets introduces error in covariance network reconstruction

scientific article published in 2024

Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing.

scientific article

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing <i>Escherichia coli</i> O145:H28

scientific article published on 21 April 2022

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7

scientific article published on 10 January 2014

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000

scientific article

Complete Genome Sequence of Francisella philomiragia ATCC 25017 ⬇️

scientific article published on June 1, 2012

Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens

scientific article published on January 2013

Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens

scientific article published on 14 March 2013

Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

scientific article

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP).

scientific article

Complete genome sequence of Actinosynnema mirum type strain (101).

scientific article

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA)

scientific article

Complete genome sequence of Anaerococcus prevotii type strain (PC1).

scientific article

Complete genome sequence of Archaeoglobus profundus type strain (AV18)

scientific article

Complete genome sequence of Atopobium parvulum type strain (IPP 1246)

scientific article

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).

scientific article

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).

scientific article

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).

scientific article

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).

scientific article

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).

scientific article

Complete genome sequence of Conexibacter woesei type strain (ID131577).

scientific article

Complete genome sequence of Cryptobacterium curtum type strain (12-3)

scientific article

Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).

scientific article

Complete genome sequence of Desulfomicrobium baculatum type strain (X)

scientific article

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575)

scientific article

Complete genome sequence of Dyadobacter fermentans type strain (NS114)

scientific article

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).

scientific article

Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production

scientific article (publication date: 20 December 2013)

Complete genome sequence of Gordonia bronchialis type strain (3410).

scientific article

Complete genome sequence of Halogeometricum borinquense type strain (PR3)

scientific article

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2)

scientific article

Complete genome sequence of Halorhabdus utahensis type strain (AX-2)

scientific article

Complete genome sequence of Haloterrigena turkmenica type strain (4k)

scientific article

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134)

scientific article

Complete genome sequence of Kangiella koreensis type strain (SW-125).

scientific article

Complete genome sequence of Kribbella flavida type strain (IFO 14399).

scientific article

Complete genome sequence of Kytococcus sedentarius type strain (541).

scientific article

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).

scientific article

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

scientific article published on 4 April 2008

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377)

scientific article

Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum

scientific article

Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers

scientific article (publication date: 15 June 2010)

Complete genome sequence of Rhodothermus marinus type strain (R-10).

scientific article

Complete genome sequence of Saccharomonospora viridis type strain (P101).

scientific article

Complete genome sequence of Sanguibacter keddieii type strain (ST-74)

scientific article

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1)

scientific article

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022)

scientific article

Complete genome sequence of Spirosoma linguale type strain (1)

scientific article

Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21).

scientific article

Complete genome sequence of Streptobacillus moniliformis type strain (9901)

scientific article

Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

scientific article

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).

scientific article

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).

scientific article

Complete genome sequence of Veillonella parvula type strain (Te3)

scientific article

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07)

scientific article

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

scientific article (publication date: 28 January 2010)

Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea

scientific article

Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade

scientific article published on 04 October 2013

Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

scientific article

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

scientific article published on 15 August 2015

Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.

scientific article

Complete genome sequences for 35 biothreat assay-relevant bacillus species

scientific article

Complete genome sequences for 59 burkholderia isolates, both pathogenic and near neighbor

scientific article published on 30 April 2015

Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T

scientific article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Correction for Johnson et al., Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor

scientific article published on 21 April 2016

Culture-Independent Diagnostics for Health Security.

scientific article published on May 2016

Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

scientific article published in 2022

Draft Genome Assembly of Acinetobacter baumannii ATCC 19606

scientific article

Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium

scientific article

Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46 ⬇️

scientific article published on April 18, 2013

Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis

scientific article published on 14 March 2013

Draft genome sequence of Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida

scientific article published on 21 March 2013

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.

scientific article

Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246).

scientific article published on 15 June 2010

Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377)

scientific article

Facile, high quality sequencing of bacterial genomes from small amounts of DNA.

scientific article

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

scientific article published in March 2014

Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium

scientific article

Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T)

scientific article published on 15 April 2013

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

scientific article

Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide

scientific article

Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment

scientific article

Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece

scientific article

Genome sequence of Kingella kingae septic arthritis isolate PYKK081.

scientific article

Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade

scientific article published on 30 July 2013

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis

scientific article published on 03 October 2013

Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

scientific article

Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements

scientific article published on 30 July 2013

Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B

scientific article

Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037

scientific article

Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255.

scientific article

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565

scientific article (publication date: 20 December 2013)

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943

scientific article (publication date: 20 December 2013)

Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.).

scientific article published on 30 July 2013

Genome sequencing of 18 francisella strains to aid in assay development and testing

scientific article published on 30 April 2015

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres

scientific article published on 17 April 2014

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans

scientific article

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

scientific article

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

scientific article published on 28 July 2017

Illinois Workshop. Dental Prepayment

scientific article published on 01 June 1966

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.

scientific article

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

scientific article

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

scientific article published on 21 October 2015

Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics ⬇️

scientific article published on June 3, 2013

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Molecular Dissection of Induced Platinum Resistance through Functional and Gene Expression Analysis in a Cell Culture Model of Bladder Cancer

scientific article

Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies

scientific article

Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments ⬇️

scholarly article

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

scientific article

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

scientific article

Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4

scientific article published on 30 July 2013

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics.

scientific article

Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58

scientific article

Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria.

scientific article

Rapid evaluation and quality control of next generation sequencing data with FaQCs.

scientific article

Recruiting human microbiome shotgun data to site-specific reference genomes

scientific article

Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 08 June 2020

Saliva microbiomes distinguish caries-active from healthy human populations ⬇️

scientific article published on June 30, 2011

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

scientific article

Standards for sequencing viral genomes in the era of high-throughput sequencing

scientific article published on 17 June 2014

The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice

scientific article published on 24 December 2020

The United States of America and scientific research

scientific article

The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes

scientific article

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

scientific article

The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica

scientific article published on 30 April 2015

Toward unrestricted use of public genomic data:

scientific article

Under-detection of endospore-forming Firmicutes in metagenomic data

scientific article

Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei

scientific article

Widespread bacterial diversity within the bacteriome of fungi

scientific article published on 07 October 2021

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