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List of works by 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 genome-wide map of diversity in Plasmodium falciparum

scientific article published on 10 December 2006

A high-density single nucleotide polymorphism map for Neurospora crassa

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

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

scientific article (publication date: March 2011)

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 Balto, a famous historic dog, captures lost diversity of 1920s sled dogs ⬇️

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

Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum

scientific article

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage

scientific article published on 3 March 2016

Dynamics of Pseudomonas aeruginosa genome evolution

scientific article

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity

scientific article published in December 2011

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

scientific article

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

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

Enabling a community to dissect an organism: overview of the Neurospora functional genomics project

scientific article published in January 2007

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

scientific article

Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986–2007 ⬇️

scientific article published on January 1, 2011

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

scientific article

Environmental vs. Genetic Influence on the Intestinal Microbiome of Monozygotic and Dizygotic Twins

scholarly article published in May 2011

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

Erratum: Disruption of the nuclear hormone receptor RORα in staggerer mice

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 extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa

scholarly article by Keira A. Cohen et al published March 2015 in International journal of mycobacteriology

Evolution of invasion in a diverse set of Fusobacterium species ⬇️

scientific article

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Evolutionary constraint and innovation across hundreds of placental mammals

scientific article published on 28 April 2023

Evolutionary dynamics of the accessory genome of Listeria monocytogenes

scientific article

Extensive global movement of multidrug-resistantM. tuberculosis strains revealed by whole-genome analysis

scientific article published on 02 May 2019

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment

scientific article

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

scientific article

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

scientific article published on 10 October 2013

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

scientific article published on 2 July 2011

Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).

scientific article

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

scientific article

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

scientific article published on 22 February 2016

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 SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

scientific article published on 15 December 2008

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 globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

scientific article

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

scientific article

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

scientific article published on 11 April 2016

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

scientific article published on 6 February 2012

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 published on 26 May 2006

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 sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).

scientific article published on 30 December 2011

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

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data ⬇️

scientific article published on March 15, 2012

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? ⬇️

scientific article published on December 27, 2012

Human chromosome 11 DNA sequence and analysis including novel gene identification

scientific article

Hybrid selection for sequencing pathogen genomes from clinical samples

scientific article published on 11 August 2011

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

Insights into mammalian TE diversity through the curation of 248 genome assemblies ⬇️

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters ⬇️

scientific article published in July 2014

Integrating gene annotation with orthology inference at scale ⬇️

scientific article published on 28 April 2023

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

scientific article

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

scientific article (publication date: 28 April 2017)

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand

scientific article published on 2 November 2016

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

Mapping of Myxococcus xanthus social motility dsp mutations to the dif genes

scientific article

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

Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999–2008 ⬇️

scientific article published on August 15, 2011

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks

scientific article published on 17 January 2017

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

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

scientific article

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax

scientific article published on 27 June 2016

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

scientific article

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes ⬇️

scientific article published on November 9, 2010

Probing Plasmodium falciparum sexual commitment at the single-cell level

scientific article published in 2018

Probing sexual commitment at the single-cell level

scientific article published on 17 October 2018

Probing sexual commitment at the single-cell level

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

scientific article (publication date: 8 April 2004)

Reemergence and Decline of Dengue Virus Serotype 3 in Puerto Rico ⬇️

scientific article published on June 27, 2012

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

scientific article

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

scientific article published on 11 October 2010

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing

scientific article published on 14 December 2008

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

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment

scientific article

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Staphylococcal enterotoxin P predicts bacteremia in hospitalized patients colonized with methicillin-resistant Staphylococcus aureus

scientific article published on 16 September 2013

Structure and architecture of the maize genome.

scientific article published in December 2005

Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs.

scientific article published on May 2002

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

scientific article

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

scientific article published on 17 February 2016

TBCAP; tuberculosis annotation project

scientific article published on 16 January 2013

The "most wanted" taxa from the human microbiome for whole genome sequencing

scientific article

The Fungal Genome Initiative and Lessons Learned from Genome Sequencing

scientific article published on 01 March 2010

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

scientific article

The Human Microbiome Project: a community resource for the healthy human microbiome

scientific article

The complete genome and proteome of Mycoplasma mobile

scientific article

The contribution of historical processes to contemporary extinction risk in placental mammals ⬇️

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 functional and evolutionary impacts of human-specific deletions in conserved elements ⬇️

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 malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum

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

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

Three-dimensional genome rewiring in loci with human accelerated regions ⬇️

scientific article published on 28 April 2023

Uneven chromosome contraction and expansion in the maize genome.

scientific article

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

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

scientific article published on 6 November 2012

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

scientific article

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