List of works - C. Titus Brown

A Missense Mutation in the Vacuolar Protein Sorting 11 () Gene Is Associated with Neuroaxonal Dystrophy in Rottweiler Dogs

article

A Missense Variant in ALDH5A1 Associated with Canine Succinic Semialdehyde Dehydrogenase Deficiency (SSADHD) in the Saluki Dog

scientific article published on 02 September 2020

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

scientific article

A genomic regulatory network for development

scientific article (publication date: March 2002)

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

scientific article published on 18 May 2020

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

scientific article

A thermogenic secondary sexual character in male sea lamprey

scientific article published on July 2013

A virtual training module for introducing the use of Amazon Web Services

scientific article published in 2022

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

scientific article

Abundance-distributions in artificial life and stochastic models: “age and area” revisited

article

Advancing the microbiome research community

scientific article

Anaerobic regulation by an atypical Arc system in Shewanella oneidensis.

scientific article published in June 2005

Author Correction: Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull

scientific article published on 01 February 2020

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Best practices for scientific computing ⬇️

scientific article

Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis.

scientific article published on 11 December 2017

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

scientific article published on 21 February 2017

Cephalopod genomics: A plan of strategies and organization

scientific article (publication date: 10 October 2012)

Changing computational research. The challenges ahead

scientific article (publication date: 2012)

Channeling Community Contributions to Scientific Software: A Sprint Experience

scientific article

Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

scientific article published on 05 October 2021

Computational approaches to finding and analyzing cis-regulatory elements

scientific article published on January 2008

Correction to: Transcriptome of the caribbean stony coral Porites astreoides from three developmental stages

scientific article published on 01 November 2019

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

Differentially-Expressed Pseudogenes in HIV-1 Infection

scientific article

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

scientific article

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

scholarly article

Draft genome of tule elk Cervus canadensis nannodes

scientific article published on 11 December 2017

Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600.

scientific article

Efficient cardinality estimation for k-mers in large DNA sequencing data sets

Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli

scientific article

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

scientific article

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

scientific article published on 06 July 2020

FGF4 Retrogene On CFA12 Is Responsible For Chondrodystrophy And Intervertebral Disc Disease In Dogs

FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs

scientific article published on 11 October 2017

FunGene: the functional gene pipeline and repository

scientific article published on October 2013

Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus.

scientific article

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull

scientific article published on 07 October 2019

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

scientific article published on 28 September 2020

Genomic resources for the study of sea urchin development

scientific article

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms

scientific article (publication date: April 2014)

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

scientific article published on 20 January 2016

High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution

scientific article (publication date: December 2006)

How open science helps researchers succeed ⬇️

scientific article

Hsp90 and hepatobiliary transformation during sea lamprey metamorphosis.

scientific article published in December 2015

Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development

scientific article published on 22 August 2006

Identification of long non-coding RNA in the horse transcriptome

scientific article

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

scholarly article published 1 June 2018

Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq.

scientific article published on 05 June 2013

Keeping it light: (re)analyzing community-wide datasets without major infrastructure.

scientific article

Large-scale sequence comparisons with sourmash

scientific article published on 04 July 2019

METHODS TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH.

scientific article published on January 2016

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Metagenomics: The Paths Forward

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

scientific article

Microbial metabolites in the marine carbon cycle

scientific article published in 2022

New computational approaches for analysis of cis-regulatory networks.

scientific article published in June 2002

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

scientific article

Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin

scientific article published in June 2002

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

scientific article

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

article published in 2018

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

scientific article published on 01 April 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

scientific article published on 15 October 2019

Ribosomal Database Project: data and tools for high throughput rRNA analysis

scientific article

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

scientific article

Sea urchin Forkhead gene family: phylogeny and embryonic expression

scientific article published on 22 September 2006

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

scientific article

Space-efficient read indexing and retrieval based on compressed de Bruijn graphs

Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

scientific article

Strain recovery from metagenomes

scientific article published in October 2015

Streamlining data-intensive biology with workflow systems

scientific article published on 19 January 2021

Sustainable computational science: the ReScience initiative ⬇️

article

Tackling soil diversity with the assembly of large, complex metagenomes

scientific article

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

scientific article

The genome of the sea urchin Strongylocentrotus purpuratus

scientific article

The khmer software package: enabling efficient nucleotide sequence analysis

scientific article published on 25 September 2015

The principles of tomorrow's university

The sea lamprey has a primordial accessory olfactory system

scientific article

These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure

scientific article

Third Report on Chicken Genes and Chromosomes 2015.

scientific article published on 14 July 2015

Tissue Resolved, Gene Structure Refined Equine Transcriptome

article

Tissue resolved, gene structure refined equine transcriptome

scientific article

Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages

scientific article

Virtual training on virtual environments: an online open-source introduction to conda

scientific article published in 2021

Visualizing Evolutionary Activity of Genotypes

scientific article published on 01 January 1999

Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

scientific article

Whole genome sequencing for mutation discovery in a single case of lysosomal storage disease (MPS type 1) in the dog

scientific article published on 16 April 2020

Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds

scientific article published on 06 December 2018

Workshop: Graph compression approaches in assembly

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

scientific article published on 5 August 2015

List of works by C. Titus Brown

A Missense Mutation in the Vacuolar Protein Sorting 11 () Gene Is Associated with Neuroaxonal Dystrophy in Rottweiler Dogs

A Missense Variant in ALDH5A1 Associated with Canine Succinic Semialdehyde Dehydrogenase Deficiency (SSADHD) in the Saluki Dog

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

A genomic regulatory network for development

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

A thermogenic secondary sexual character in male sea lamprey

A virtual training module for introducing the use of Amazon Web Services

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Abundance-distributions in artificial life and stochastic models: “age and area” revisited

Advancing the microbiome research community

Anaerobic regulation by an atypical Arc system in Shewanella oneidensis.

Author Correction: Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Best practices for scientific computing ⬇️

Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis.

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

Cephalopod genomics: A plan of strategies and organization

Changing computational research. The challenges ahead

Channeling Community Contributions to Scientific Software: A Sprint Experience

Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

Computational approaches to finding and analyzing cis-regulatory elements

Correction to: Transcriptome of the caribbean stony coral Porites astreoides from three developmental stages

Critical Assessment of Metagenome Interpretation: the second round of challenges

Differentially-Expressed Pseudogenes in HIV-1 Infection

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

Draft genome of tule elk Cervus canadensis nannodes

Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600.

Efficient cardinality estimation for k-mers in large DNA sequencing data sets

Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

FGF4 Retrogene On CFA12 Is Responsible For Chondrodystrophy And Intervertebral Disc Disease In Dogs

FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs

FunGene: the functional gene pipeline and repository

Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus.

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

Genomic resources for the study of sea urchin development

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution

How open science helps researchers succeed ⬇️

Hsp90 and hepatobiliary transformation during sea lamprey metamorphosis.

Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development

Identification of long non-coding RNA in the horse transcriptome

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq.

Keeping it light: (re)analyzing community-wide datasets without major infrastructure.

Large-scale sequence comparisons with sourmash

METHODS TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH.

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

Metagenomics: The Paths Forward

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

Microbial metabolites in the marine carbon cycle

New computational approaches for analysis of cis-regulatory networks.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

Ribosomal Database Project: data and tools for high throughput rRNA analysis

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Sea urchin Forkhead gene family: phylogeny and embryonic expression

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Space-efficient read indexing and retrieval based on compressed de Bruijn graphs

Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

Strain recovery from metagenomes

Streamlining data-intensive biology with workflow systems

Sustainable computational science: the ReScience initiative ⬇️

Tackling soil diversity with the assembly of large, complex metagenomes

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

The genome of the sea urchin Strongylocentrotus purpuratus