List of works - Bruce Birren

16S rRNA gene survey of microbial communities in Winogradsky columns

scientific article

A catalog of reference genomes from the human microbiome

scientific article

A second generation human haplotype map of over 3.1 million SNPs

scientific article

A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame

scientific article

Analysis of high-throughput sequencing and annotation strategies for phage genomes

scientific article

Analysis of the DNA sequence and duplication history of human chromosome 15

scientific article

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi

scientific article published on August 2005

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

scientific article

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

scientific article

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development

scientific article

Comparative functional genomics of the fission yeasts

scientific article

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

scientific article

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis

scientific article

Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies

scientific article

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus

scientific article

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States

scientific article

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters

scientific article published on 5 June 2012

Correction: The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations.

scientific article published on 15 August 2013

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

DNA sequence and analysis of human chromosome 18

scientific article

DNA sequence and analysis of human chromosome 8

scientific article

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

scientific article

Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum

scientific article

Dynamics of Pseudomonas aeruginosa genome evolution

scientific article

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

scientific article

Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains

scientific article published on 20 August 2013

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia

scientific article

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission

scientific article

Erratum to “Pathogen discovery from human tissue by sequence-based computational subtraction”

scholarly article published in Genomics

Erratum: Corrigendum: DNA sequence and analysis of human chromosome 18

scientific article published in Nature

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes.

scientific article published on 11 October 2010

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

scientific article (publication date: September 2015)

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Evolutionary dynamics of the accessory genome of Listeria monocytogenes

scientific article

Full-length transcriptome assembly from RNA-Seq data without a reference genome

scientific article

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia

scientific article published on 2 July 2011

Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.

scientific article

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

scientific article

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome-wide detection and characterization of positive selection in human populations

scientific article

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

scientific article

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

scientific article published on September 2013

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication

scientific article

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

scientific article published on 9 February 2016

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis.

scientific article

Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments

scientific article

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

scientific article

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

scientific article

Genomics of the fungal kingdom: insights into eukaryotic biology

scientific article

High-quality draft genome sequences of 28 Enterococcus sp. isolates

scientific article

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections

scientific article published on 16 November 2011

Human chromosome 11 DNA sequence and analysis including novel gene identification

scientific article

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

scientific article

Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

scientific article

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

scientific article

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

scientific article

Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene

scientific article published on July 2002

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

scientific article published in January 2004

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

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics

scientific article

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

scientific article (publication date: December 2008)

Pathogen discovery from human tissue by sequence-based computational subtraction

scientific article published in March 2003

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens

scientific article

Patterns of intron gain and loss in fungi

scientific article

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization

scientific article

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

scientific article (publication date: 8 April 2004)

Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies.

scientific article published on 11 October 2010

Sequencing and comparison of yeast species to identify genes and regulatory elements ⬇️

scientific article published on May 15, 2003

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

scientific article

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

scientific article

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

The complete genome and proteome of Mycoplasma mobile

scientific article

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

scientific article (publication date: December 2014)

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults

scientific article

The genome of M. acetivorans reveals extensive metabolic and physiological diversity

scientific article

The genome sequence of the filamentous fungus Neurospora crassa

scientific article

The genome sequence of the rice blast fungus Magnaporthe grisea

scientific article

The role of selection in shaping diversity of natural M. tuberculosis populations

scientific article (publication date: August 2013)

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

Whole genome amplification and de novo assembly of single bacterial cells

scientific article

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

scientific article published on 8 March 2012

List of works by Bruce Birren

16S rRNA gene survey of microbial communities in Winogradsky columns

A catalog of reference genomes from the human microbiome

A second generation human haplotype map of over 3.1 million SNPs

A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame

Analysis of high-throughput sequencing and annotation strategies for phage genomes

Analysis of the DNA sequence and duplication history of human chromosome 15

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development

Comparative functional genomics of the fission yeasts

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis

Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters

Correction: The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

DNA sequence and analysis of human chromosome 18

DNA sequence and analysis of human chromosome 8

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum

Dynamics of Pseudomonas aeruginosa genome evolution

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission

Erratum to “Pathogen discovery from human tissue by sequence-based computational subtraction”

Erratum: Corrigendum: DNA sequence and analysis of human chromosome 18

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes.

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Evolutionary dynamics of the accessory genome of Listeria monocytogenes

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia

Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Genome sequence of Aedes aegypti, a major arbovirus vector

Genome-wide detection and characterization of positive selection in human populations

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis.

Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

Genomics of the fungal kingdom: insights into eukaryotic biology

High-quality draft genome sequences of 28 Enterococcus sp. isolates

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections

Human chromosome 11 DNA sequence and analysis including novel gene identification

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

Initial sequencing and analysis of the human genome

Initial sequencing and comparative analysis of the mouse genome

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

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

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

Pathogen discovery from human tissue by sequence-based computational subtraction

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens

Patterns of intron gain and loss in fungi

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies.

Sequencing and comparison of yeast species to identify genes and regulatory elements ⬇️

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Standardized metadata for human pathogen/vector genomic sequences

The complete genome and proteome of Mycoplasma mobile

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults