List of works - Chad Nusbaum

A catalog of reference genomes from the human microbiome

scientific article

A cellular memory of developmental history generates phenotypic diversity in C. elegans

scientific article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

scientific article published on 30 August 2012

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

scientific article

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

scientific article

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

scientific article published on October 2009

ALLPATHS: de novo assembly of whole-genome shotgun microreads

scientific article

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries ⬇️

scientific article published on February 21, 2011

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi

scientific article published on August 2005

Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract

scientific article published on May 2015

Characterizing and measuring bias in sequence data

scientific article

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

scientific article

Closing gaps in the human genome using sequencing by synthesis

scientific article published on 02 June 2009

Comparative functional genomics of the fission yeasts

scientific article

Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate

scientific article

Comprehensive comparative analysis of strand-specific RNA sequencing methods

scientific article

Comprehensive variation discovery in single human genomes

scientific article

Correction: Closing gaps in the human genome using sequencing by synthesis.

scientific article published on 19 April 2011

DNA sequence analysis of the conserved region around the SOD1 gene locus in recessively inherited ALS.

scientific article published on 9 July 2009

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

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica

scientific article

Draft Genome Sequence of Cercospora arachidicola, Causal Agent of Early Leaf Spot in Peanuts

scientific article

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

scientific article published in November 2017

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

Erratum: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

scholarly article published in Nature Biotechnology

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

scientific article published in Nature

Finished bacterial genomes from shotgun sequence data

scientific article

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

scientific article

Genome Sequence of Spizellomyces punctatus

scientific article published on 18 August 2016

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 evolution following host jumps in the Irish potato famine pathogen lineage

scientific article published in December 2010

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome-scale DNA methylation maps of pluripotent and differentiated cells

scientific article

Genome-wide identification and characterization of replication origins by deep sequencing

scientific article

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

scientific article

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

scientific article published in October 2008

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

scientific article published on 6 February 2012

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

scientific article

High-resolution description of antibody heavy-chain repertoires in humans

scientific article

High-resolution mapping of copy-number alterations with massively parallel sequencing

scientific article

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

scientific article

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

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach ⬇️

scientific article published on July 1, 2008

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

Integrative analysis of the melanoma transcriptome

scientific article

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing

scientific article

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

scientific article

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

scientific article

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

scientific article

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

scientific article

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species

scientific article published on 10 March 2015

Model-based analysis of ChIP-Seq (MACS)

scientific article

Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA.

scientific article

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

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)

Pacific biosciences sequencing technology for genotyping and variation discovery in human data ⬇️

scientific article published on August 5, 2012

Paired-end sequencing of Fosmid libraries by Illumina

scientific article

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

scientific article

Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis

scientific article published on 01 October 2019

Quality scores and SNP detection in sequencing-by-synthesis systems ⬇️

scientific article published on 22 January 2008

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

scientific article

RNA-Seq methods for imperfect samples: development, evaluation and applications

scientific article published on 19 September 2011

Regulated aggregative multicellularity in a close unicellular relative of metazoa

scientific article published on 24 December 2013

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

scientific article

Semiconductor-based DNA sequencing of histone modification states

scientific article published on January 2013

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

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

scientific article

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

scientific article

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

scientific article

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq

scientific article

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

scientific article

The Capsaspora genome reveals a complex unicellular prehistory of animals

scientific article

The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats

scientific article

The complete genome and proteome of Mycoplasma mobile

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 immune cell landscape in kidneys of patients with lupus nephritis

scientific article published on 17 June 2019

Transcriptomics in a high throughput world.

scientific article

Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system".

scientific article published on 11 March 2016

Yeast Sterol Regulatory Element-binding Protein (SREBP) Cleavage Requires Cdc48 and Dsc5, a Ubiquitin Regulatory X Domain-containing Subunit of the Golgi Dsc E3 Ligase ⬇️

scientific article published on November 15, 2011

List of works by Chad Nusbaum

A catalog of reference genomes from the human microbiome

A cellular memory of developmental history generates phenotypic diversity in C. elegans

A high-resolution map of human evolutionary constraint using 29 mammals

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

ALLPATHS: de novo assembly of whole-genome shotgun microreads

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

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

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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries ⬇️

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi

Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract

Characterizing and measuring bias in sequence data

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

Closing gaps in the human genome using sequencing by synthesis

Comparative functional genomics of the fission yeasts

Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Comprehensive variation discovery in single human genomes

Correction: Closing gaps in the human genome using sequencing by synthesis.

DNA sequence analysis of the conserved region around the SOD1 gene locus in recessively inherited ALS.

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

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica

Draft Genome Sequence of Cercospora arachidicola, Causal Agent of Early Leaf Spot in Peanuts

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

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

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

Erratum: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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

Finished bacterial genomes from shotgun sequence data

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

Genome Sequence of Spizellomyces punctatus

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

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

Genome evolution following host jumps in the Irish potato famine pathogen lineage

Genome sequence of Aedes aegypti, a major arbovirus vector

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Genome-wide identification and characterization of replication origins by deep sequencing

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

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

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

High-resolution description of antibody heavy-chain repertoires in humans

High-resolution mapping of copy-number alterations with massively parallel sequencing

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

Human chromosome 11 DNA sequence and analysis including novel gene identification

Hybrid selection for sequencing pathogen genomes from clinical samples

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach ⬇️

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

Integrative analysis of the melanoma transcriptome

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

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

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species

Model-based analysis of ChIP-Seq (MACS)

Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA.

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

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

Pacific biosciences sequencing technology for genotyping and variation discovery in human data ⬇️

Paired-end sequencing of Fosmid libraries by Illumina

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis

Quality scores and SNP detection in sequencing-by-synthesis systems ⬇️

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

RNA-Seq methods for imperfect samples: development, evaluation and applications

Regulated aggregative multicellularity in a close unicellular relative of metazoa

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

Semiconductor-based DNA sequencing of histone modification states

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

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing

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