C. T. Brown

发表

These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure

Qingpeng Zhang, J. Pell, Rosangela Canino-Koning, 2013, PloS one.

The khmer software package: enabling efficient nucleotide sequence analysis

Daniel Standage, Qingpeng Zhang, C. Titus Brown, 2015, F1000Research.

Tackling soil diversity with the assembly of large, complex metagenomes

S. Tringe, J. Yates, J. Tiedje, 2014, Proceedings of the National Academy of Sciences.

Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

C. T. Brown, E. Lowe, B. Swalla, 2014 .

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Tim H. Brom, A. Howe, C. T. Brown, 2012, 1203.4802.

FunGene: the functional gene pipeline and repository

Jordan A. Fish, J. Tiedje, C. T. Brown, 2013, Front. Microbiol..

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

James R. Cole, James M. Tiedje, Yanni Sun, 2019, Front. Genet..

Comparing faster evolving rplB and rpsC versus SSU rRNA for improved microbial community resolution

J. Tiedje, C. T. Brown, Jiarong Guo, 2018, bioRxiv.

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

C. Brown, C. T. Brown, Sherine Awad, 2017, bioRxiv.

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

J. Tiedje, C. T. Brown, Jiarong Guo, 2015, Applied and Environmental Microbiology.

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

Jordan A. Fish, C. Brown, J. Tiedje, 2015, Microbiome.

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

Abdul Jabbar, Andreas Hofmann, Jason Pell, 2013, Genome Biology.

Third Report on Chicken Genes and Chromosomes 2015

Bronwen L. Aken, Hans H. Cheng, Andrew J. Oler, 2015, Cytogenetic and Genome Research.

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

C. T. Brown, E. Lowe, B. Swalla, 2014, eLife.

The Genome of the Sea Urchin Strongylocentrotus purpuratus

Andrew R. Jackson, R. F. Gray, Wendy S. Beane, 2006, Science.

RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates

Hans H. Cheng, C. T. Brown, A. B. Pyrkosz, 2013, 1303.2411.

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Hans H. Cheng, T. Graves, Valerie A. Schneider, 2016, G3: Genes, Genomes, Genetics.

PhyloSift: phylogenetic analysis of genomes and metagenomes

Henry C. M. Leung, Brian C. Thomas, Ocn, 2014, PeerJ.

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

Rick L. Stevens, James R. Knight, J. Raes, 2010, Standards in genomic sciences.

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

Alexander S. Garruss, Alexander S Garruss, Bronwen L. Aken, 2013, Nature Genetics.

How open science helps researchers succeed

Brian A. Nosek, Jeffrey R. Spies, Kara H. Woo, 2016, eLife.

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

J. Eisen, C. T. Brown, D. Sumner, 2020, The ISME Journal.

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

S. Goffredi, C. T. Brown, Qingpeng Zhang, 2013, The ISME Journal.

Making Common Fund data more findable: catalyzing a data ecosystem

Daniel J. B. Clarke, Robert E. Schuler, K. Chard, 2021, bioRxiv.

CAREER : ABI : Assembling Extremely Large Metagenomes C

C. T. Brown, 2012 .

CAREER : ABI : Scaling and Improving de Bruijn graph assembly

C. T. Brown, 2011 .

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

B. Weimer, C. T. Brown, Bihua C. Huang, 2020, bioRxiv.

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish

A. Whitehead, C. T. Brown, L. Froenicke, 2020, GigaScience.

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

A. Whitehead, C. T. Brown, L. Froenicke, 2019, bioRxiv.

Supplementary Information Differentially Expressed Pseudogenes in HIV-1 Infection

C. Adami, Aditi Gupta, C. T. Brown, 2015 .

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

Timothy A. Whitehead, D. Burton, C. T. Brown, 2015, bioRxiv.

Streamlining data-intensive biology with workflow systems

Shannon E. K. Joslin, C. T. Brown, L. Irber, 2020, bioRxiv.

Data Carpentry Python Ecology lesson v2017.04.0

Ming Tang, Greg Wilson, Mateusz Kuzak, 2017 .

Session Introduction

J. Ioannidis, K. Karczewski, N. Tatonetti, 2016, PSB.

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

A. Ghezzi, C. T. Brown, R. Croll, 2017, BMC Research Notes.

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

C. T. Brown, T. Mansour, C. Ettinger, 2017, Proceedings of the National Academy of Sciences.

The principles of tomorrow's university

Kyle E. Niemeyer, Jeffrey R. Spies, Devin R. Berg, 2018, F1000Research.

Continental subsurface waters support unique but diverse C-acquisition strategies

Sharon L. Grim, C. T. Brown, T. Kieft, 2013 .

Biogeographic Distribution of Five Antarctic Cyanobacteria Using Large-Scale k-mer Searching with sourmash branchwater

C. T. Brown, L. Irber, D. Sumner, 2022, bioRxiv.

Ten simple rules to cultivate transdisciplinary collaboration in data science

Tracy K. Teal, Nirav C. Merchant, S. Kobourov, 2021, PLoS Comput. Biol..

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease

Blair D. Sullivan, Dominik Moritz, C. T. Brown, 2022, bioRxiv.

The sea lamprey has a primordial accessory olfactory system

C. T. Brown, Kaben G. Nanlohy, M. Kiupel, 2013, BMC Evolutionary Biology.

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

James R. Cole, Qiong Wang, Benli Chai, 2013, Nucleic Acids Res..

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

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

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

Hans H. Cheng, C. T. Brown, H. Kung, 2013, Journal of Virology.

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

William A. Walters, Ahmad Turan Naimey, Lasse Buur Rasmussen, 2019, Nature Biotechnology.

MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata

C. Titus Brown, Moustafa Shokrof, Tamer A. Mansour, 2020, BMC Bioinformatics.

Crossing the streams: a framework for streaming analysis of short DNA sequencing reads

C. Titus Brown, Sherine Awad, Qingpeng Zhang, 2015, PeerJ Prepr..

BIGDATA: Small: DA: DCM: Low-memory Streaming Prefilters for Biological Sequencing Data

C. Titus Brown, C. T. Brown, 2012 .

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

Frédéric Delsuc, Patrick Lemaire, Kenta Nakai, 2017, Nucleic Acids Res..

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Frédéric Delsuc, Patrick Lemaire, Mathieu Gineste, 2015, Nucleic Acids Res..

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

C. T. Brown, Rachel Montpetit, Ron C. Runnebaum, 2021, mBio.

Cephalopod genomics: A plan of strategies and organization

C. W. Ragsdale, S. V. Nyholm, M. Martindale, 2012, Standards in genomic sciences.

Mapping global shifts in Saccharomyces cerevisiae gene expression across asynchronous time trajectories with diffusion maps

C. T. Brown, Rachel Montpetit, Ron C. Runnebaum, 2021, bioRxiv.

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

Francesco Asnicar, Mingxun Wang, Pieter C. Dorrestein, 2018 .

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

Daniel S. Standage, Fereydoun Hormozdiari, C. Titus Brown, 2019, bioRxiv.

Identification of long non-coding RNA in the horse transcriptome

C. T. Brown, T. Mansour, J. Murray, 2017, BMC Genomics.

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

Tamer A. Mansour, Joshua J. C. Rosenthal, C. Titus Brown, 2016, GigaScience.

Tissue resolved, gene structure refined equine transcriptome

C. T. Brown, T. Mansour, J. Murray, 2016, bioRxiv.

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

C. T. Brown, T. Mansour, C. Drögemüller, 2020, Genes.

The Degenerate Tale of Ascidian Tails.

C. T. Brown, E. Lowe, B. Swalla, 2021, Integrative and comparative biology.

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

Harriet Alexander, C Titus Brown, Lisa K Johnson, 2018, bioRxiv.

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

C. T. Brown, T. Mansour, R. Rebhun, 2018, PLoS genetics.

Advancing the Microbiome Research Community

Rob Knight, Dan Knights, J. Gregory Caporaso, 2014, Cell.

Differentially-Expressed Pseudogenes in HIV-1 Infection

C. Adami, Aditi Gupta, C. T. Brown, 2015, Viruses.

Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom

C. T. Brown, C. Kvaal, B. Goodner, 2021, Frontiers in Microbiology.

An Open, FAIRified Data Commons: Proposal for NIH Data Commons Pilot

Brian A. Nosek, Jeffrey R. Spies, Sara D. Bowman, 2017 .

Hsp90 and hepatobiliary transformation during sea lamprey metamorphosis

S. Whyard, C. T. Brown, Kaben G. Nanlohy, 2015, BMC Developmental Biology.

Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR

J. Leadbetter, C. T. Brown, D. Newman, 2021, Microbiology Resource Announcements.

Whole-genome assembly of Culex tarsalis

Bradley J. Main, C. Barker, C. T. Brown, 2020, bioRxiv.

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

C. T. Brown, S. Maheshwari, L. Comai, 2017, Genome research.

Strain recovery from metagenomes

C. T. Brown, C Titus Brown, 2015, Nature Biotechnology.

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

Faye D. Schilkey, Sharon L. Grim, C. T. Brown, 2014, Front. Microbiol..

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

Blair D. Sullivan, Dominik Moritz, C. T. Brown, 2020, Genome Biology.

Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity

Blair D. Sullivan, Dominik Moritz, C. Titus Brown, 2018 .

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Arend Hintze, James M. Tiedje, C. Titus Brown, 2011, Proceedings of the National Academy of Sciences.

Microbial metabolites in the marine carbon cycle

S. Doney, M. Covert, R. Braakman, 2022, Nature Microbiology.

Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets

Janet Jansson, Jason Pell, Rosangela Canino-Koning, 2012, 1212.0159.

Ten simple rules and a template for creating workflows-as-applications

C. T. Brown, M. Roach, Radosław Suchecki, 2022, PLoS Comput. Biol..

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

J. Eisen, C. T. Brown, D. Sumner, 2018, bioRxiv.

sourmash: a library for MinHash sketching of DNA

Luiz Irber, C. Titus Brown, C. T. Brown, 2016, J. Open Source Softw..

Large-scale sequence comparisons with sourmash

Luiz Irber, C. Titus Brown, N. Tessa Pierce, 2019, bioRxiv.

Standing Genetic Variation in Contingency Loci Drives the Rapid Adaptation of Campylobacter jejuni to a Novel Host

Jeffrey E. Barrick, John P. Jerome, J. Barrick, 2011, PloS one.

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

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Single-cell transcriptomics for the 99.9% of species without reference genomes

Venkata. N. P. Vemuri, O. Botvinnik, Camille Ezran, 2021, bioRxiv.

Metagenomics: The Paths Forward

James M. Tiedje, C. Titus Brown, C. T. Brown, 2011 .

Research Statement -c. Titus Brown Current Research: Data Intensive Biology

C. T. Brown, 2013 .

Best Practices for Scientific Computing

Ian M. Mitchell, Mark D. Plumbley, Neil P. Chue Hong, 2012, PLoS biology.

Identification of long non-coding RNA in the horse transcriptome

C. T. Brown, T. Mansour, M. Mienaltowski, 2017, BMC Genomics.

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

Alison L. Van Eenennaam, C. T. Brown, T. Mansour, 2019, Nature Biotechnology.

Erratum

C. T. Brown, J. Rosenthal, T. Mansour, 2020, Arthritis care & research.

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

C. T. Brown, J. Rosenthal, T. Mansour, 2019, GigaScience.

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

Alison L. Van Eenennaam, Tamer A. Mansour, C. Titus Brown, 2019, Nature Biotechnology.

A thermogenic secondary sexual character in male sea lamprey

Jongeun Choi, C. T. Brown, Kaben G. Nanlohy, 2013, Journal of Experimental Biology.

Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates, NW and D2600

Jeffrey E. Barrick, John P. Jerome, J. Barrick, 2012, Journal of bacteriology.

Sustainable computational science: the ReScience initiative pdf

Cyrille Rossant, Xavier Hinaut, Thomas Arildsen, 2017, PeerJ Comput. Sci..

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

Daniel J Cooper, Kathleen M Jagodnik, Denis Torre, 2019, Cell systems.

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

Michel Dumontier, Denis Torre, Avi Ma'ayan, 2019, bioRxiv.

A Missense Mutation in the Vacuolar Protein Sorting 11 (VPS11) Gene Is Associated with Neuroaxonal Dystrophy in Rottweiler Dogs

C. T. Brown, T. Mansour, J. Mickelson, 2018, G3: Genes, Genomes, Genetics.

Large-scale sequence comparisons with sourmash [version 1; peer review: 2 approved]

C. T. Brown, L. Irber, N. Pierce, 2021 .

khmer: Working with Big Data in Bioinformatics pdf

C. Titus Brown, Eric McDonald, C. T. Brown, 2013, ArXiv.

Author response: How open science helps researchers succeed

Brian A. Nosek, Jeffrey R. Spies, Kara H. Woo, 2016 .

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

C. T. Brown, D. Portik, N. T. Pierce-Ward, 2022, bioRxiv.

Sequencing data discovery with MetaSeek

C Titus Brown, Nick Brown, Adrienne Hoarfrost, 2019, Bioinform..

VA-Store: A Virtual Approximate Store Approach to Supporting Repetitive Big Data in Genome Sequence Analyses

Sakti Pramanik, Qiang Zhu, Xianying Liu, 2020, IEEE Transactions on Knowledge and Data Engineering.

Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search

C. T. Brown, L. Irber, N. T. Pierce-Ward, 2022, bioRxiv.

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

C. T. Brown, E. Lowe, B. Swalla, 2017, EvoDevo.

Assembling large, complex environmental metagenomes

S. Tringe, J. Tiedje, A. Howe, 2012, 1212.2832.

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

J. Tiedje, C. T. Brown, Jiarong Guo, 2015, Applied and Environmental Microbiology.