Doxey Lab - Research

Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Jonathon D. Kotwa, Briallen Lobb, Ariane Massé, Marianne Gagnier, Patryk Aftanas, Arinjay Banerjee, Andra Banete, Juliette Blais-Savoie, Jeff Bowman, Tore Buchanan, Hsien-Yao Chee, Peter Kruczkiewicz, Kuganya Nirmalarajah, Catherine Soos, Oksana Vernygora, Lily Yip, L. Robbin Lindsay, Allison J. McGeer, Finlay Maguire, Oliver Lung, Andrew C. Doxey, Bradley Pickering, Samira Mubareka

iScience · 01 Oct 2023

Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection

Briallen Lobb, Matthew C. Lee, Christi L. McElheny, Yohei Doi, Kristin Yahner, Alejandro Hoberman, Judith M. Martin, Jeremy A. Hirota, Andrew C. Doxey, Nader Shaikh

BMC Infectious Diseases · 13 Sep 2023

infectious disease genomics antimicrobial resistance

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

Harold P. Hodgins, Pengsheng Chen, Briallen Lobb, Xin Wei, Benjamin J. M. Tremblay, Michael J. Mansfield, Victoria C. Y. Lee, Pyung-Gang Lee, Jeffrey Coffin, Ana T. Duggan, Alexis E. Dolphin, Gabriel Renaud, Min Dong, Andrew C. Doxey

Nature Communications · 06 Sep 2023

phylogenomics pathogens evolution toxins ancient DNA

Cannabis smoke suppresses antiviral immune responses to influenza A in mice

Nadia Milad, Matthew F. Fantauzzi, Joshua J.C. McGrath, Steven P. Cass, Danya Thayaparan, Peiyao Wang, Sam Afkhami, Jennifer A. Aguiar, Kjetil Ask, Andrew C. Doxey, Martin R. Stampfli, Jeremy A. Hirota

ERJ Open Research · 17 Aug 2023

omics lung

Identification of a botulinum neurotoxin-like gene cluster inBacillus toyonensis

Xin Wei, Briallen Lobb, Kang Wang, Min Dong, Andrew C. Doxey

Cold Spring Harbor Laboratory · 25 Jul 2023

toxins evolution pathogens

Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity

Emma Collington, Briallen Lobb, Nooran Abu Mazen, Andrew C Doxey, D Moira Glerum

Genome Biology and Evolution · 22 Jul 2023

phylogenomics pathogens evolution

A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information

Nilanth Yogadasan, Andrew C Doxey, Simon D X Chuong

Genome Biology and Evolution · 01 Jul 2023

machine-learning phylogenomics protein function prediction

Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome

Briallen Lobb, Anson Shapter, Andrew C. Doxey, Jozef I. Nissimov

Viruses · 05 May 2023

phylogenomics viruses

Comparative analysis of adenylate isopentenyl transferase genes in plant growth-promoting bacteria and plant pathogenic bacteria

Xin Wei, Gabriel Moreno-Hagelsieb, Bernard R. Glick, Andrew C. Doxey

Heliyon · 01 Mar 2023

phylogenomics pathogens plant-growth promoting bacteria

Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants

Songhai Tian, Xiaozhe Xiong, Ji Zeng, Siyu Wang, Benjamin Jean-Marie Tremblay, Peng Chen, Baohua Chen, Min Liu, Pengsheng Chen, Kuanwei Sheng, Daniel Zeve, Wanshu Qi, David T. Breault, César Rodríguez, Ralf Gerhard, Rongsheng Jin, Andrew C. Doxey, Min Dong

Nature Communications · 09 Nov 2022

toxins evolution pathogens

Glutamine metabolism mediates sensitivity to respiratory complex II inhibition in acute myeloid leukemia

Alessia Roma, Matthew Tcheng, Nawaz Ahmed, Sarah Walker, Preethi Jayanth, Mark D. Minden, Kristin Hope, Praveen P. Nekkar Rao, Jessica Luc, Andrew C. Doxey, Julie A. Reisz, Rachel Culp-Hill, Angelo D'Alessandro, Paul A. Spagnuolo

Molecular Cancer Research · 22 Aug 2022

cancer proteins

Identification of divergent botulinum neurotoxin homologs in Paeniclostridium ghonii

Xin Wei, Travis Wentz, Briallen Lobb, Michael J Mansfield, William Zhen, Huagang Tan, Zijing Wu, Sabine Pellett, Min Dong, Andrew C Doxey

Cold Spring Harbor Laboratory · 18 Aug 2022

toxins pathogens

Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae

Joseph F.A. Varga, Sascha R. Brunner, Grant Cheng, Daniel Min, Marc G. Aucoin, Andrew Doxey, Brian Dixon

Developmental & Comparative Immunology · 01 Aug 2022

proteins function prediction pathogens

Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways

Daniel Richard, Pushpanathan Muthuirulan, Jennifer Aguiar, Andrew C. Doxey, Arinjay Banerjee, Karen Mossman, Jeremy Hirota, Terence D. Capellini

iScience · 01 Jun 2022

COVID-19 genomics

Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold

Seiji N. Sugiman-Marangos, Shivneet K. Gill, Michael J. Mansfield, Kathleen E. Orrell, Andrew C. Doxey, Roman A. Melnyk

Communications Biology · 19 Apr 2022

toxins function prediction evolution

"From Protein Toxins to Applied Toxicological Testing" virtual workshop identifies the need for a bioinformatic framework to assess novel food protein safety.

Patricia A Bauman, Andrew C Doxey, Ivano Eberini, Emir Islamovic, Florence Jungo, Colton Kessenich, John Kough, Mansi Krishan, Luca Palazzolo, Laura Privalle, Chester E Rodriguez, Karla J F Satchell, Andre Silvanovich, Lucilia Pereira Mouriès

Regulatory toxicology and pharmacology : RTP · 24 Feb 2022

Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster

Travis G. Wentz, Benjamin J. M. Tremblay, Marite Bradshaw, Andrew C. Doxey, Shashi K. Sharma, John-Demian Sauer, Sabine Pellett

Frontiers in Microbiology · 09 Feb 2022

analysis toxins

Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Jonathon D. Kotwa, Briallen Lobb, Ariane Massé, Marianne Gagnier, Patryk Aftanas, Arinjay Banerjee, Andra Banete, Juliette Blais-Savoie, Jeff Bowman, Tore Buchanan, Hsien-Yao Chee, Peter Kruczkiewicz, Finlay Maguire, Allison J. McGeer, Kuganya Nirmalarajah, Catherine Soos, Lily Yip, L. Robbin Lindsay, Andrew C. Doxey, Oliver Lung, Bradley Pickering, Samira Mubareka

Cold Spring Harbor Laboratory · 21 Jan 2022

COVID-19 surveillance pathogens

Potentiation of long-acting β2-agonist and glucocorticoid responses in human airway epithelial cells by modulation of intracellular cAMP

Yechan Kim, Vincent Hou, Ryan D. Huff, Jennifer A. Aguiar, Spencer Revill, Nicholas Tiessen, Quynh Cao, Matthew S. Miller, Mark D. Inman, Kjetil Ask, Andrew C. Doxey, Jeremy A. Hirota

Respiratory Research · 19 Oct 2021

PathFams: statistical detection of pathogen-associated protein domains.

Briallen Lobb, Benjamin Jean-Marie Tremblay, Gabriel Moreno-Hagelsieb, Andrew C Doxey

BMC genomics · 14 Sep 2021

pathogens resource

Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses.

Arinjay Banerjee, Nader El-Sayes, Patrick Budylowski, Rajesh Abraham Jacob, Daniel Richard, Hassaan Maan, Jennifer A Aguiar, Wael L Demian, Kaushal Baid, Michael R D'Agostino, Jann Catherine Ang, Tetyana Murdza, Benjamin J-M Tremblay, Sam Afkhami, Mehran Karimzadeh, Aaron T Irving, Lily Yip, Mario Ostrowski, Jeremy A Hirota, Robert Kozak, Terence D Capellini, Matthew S Miller, Bo Wang, Samira Mubareka, Allison J McGeer, Andrew G McArthur, Andrew C Doxey, Karen Mossman

iScience · 26 Apr 2021

omics COVID-19

Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment.

Sophie M Poznanski, Kanwaldeep Singh, Tyrah M Ritchie, Jennifer A Aguiar, Isabella Y Fan, Ana L Portillo, Eduardo A Rojas, Fatemeh Vahedi, Abdullah El-Sayes, Sansi Xing, Martin Butcher, Yu Lu, Andrew C Doxey, Jonathan D Schertzer, Hal W Hirte, Ali A Ashkar

Cell metabolism · 13 Apr 2021

omics cancer

AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.

Daniel Min, Andrew C Doxey, Joshua D Neufeld

GigaScience · 03 Feb 2021

resource microbial ecology metagenomics

High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress.

Heather Ikert, Michael D J Lynch, Andrew C Doxey, John P Giesy, Mark R Servos, Barbara A Katzenback, Paul M Craig

Frontiers in physiology · 13 Jan 2021

omics

PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling.

Benjamin J-M Tremblay, Briallen Lobb, Andrew C Doxey

Bioinformatics (Oxford, England) · 08 Jan 2021

resource analysis

Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B.

Michael J Mansfield, Benjamin J-M Tremblay, Ji Zeng, Xin Wei, Harold Hodgins, Jay Worley, Lynn Bry, Min Dong, Andrew C Doxey

PLoS pathogens · 28 Dec 2020

pathogens omics resource

Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status.

Matthew F Fantauzzi, Jennifer A Aguiar, Benjamin J-M Tremblay, Michael J Mansfield, Toyoshi Yanagihara, Abiram Chandiramohan, Spencer Revill, Min Hyung Ryu, Chris Carlsten, Kjetil Ask, Martin Stämpfli, Andrew C Doxey, Jeremy A Hirota

ERJ open research · 14 Dec 2020

Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2.

Arinjay Banerjee, Andrew C Doxey, Karen Mossman, Aaron T Irving

Trends in ecology & evolution · 13 Dec 2020

COVID-19

Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell culture inserts

Abiram Chandiramohan, Mohammedhossein Dabaghi, Jennifer A. Aguiar, Nicholas Tiessen, Mary Stewart, Quynh T. Cao, Jenny P. Nguyen, Nima Makhdami, Gerard Cox, Andrew C. Doxey, Jeremy A. Hirota

ERJ Open Research · 10 Dec 2020

Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis.

Ulrich Eckhard, Constantin Blöchl, Benjamin G L Jenkins, Michael J Mansfield, Christian G Huber, Andrew C Doxey, Hans Brandstetter

Scientific reports · 04 Nov 2020

proteins function prediction omics

ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells.

Quynh T Cao, Jennifer A Aguiar, Benjamin J-M Tremblay, Nadin Abbas, Nicholas Tiessen, Spencer Revill, Nima Makhdami, Anmar Ayoub, Gerard Cox, Kjetil Ask, Andrew C Doxey, Jeremy A Hirota

Frontiers in cellular and infection microbiology · 16 Sep 2020

omics lung

Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component.

Sura Ali, Benjamin Jenkins, Jiujun Cheng, Briallen Lobb, Xin Wei, Suhelen Egan, Trevor C Charles, Brendan J McConkey, John Austin, Andrew C Doxey

Molecular microbiology · 15 Sep 2020

proteins function prediction

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus.

Arinjay Banerjee, Andrew C Doxey, Benjamin J-M Tremblay, Michael J Mansfield, Sonu Subudhi, Jeremy A Hirota, Matthew S Miller, Andrew G McArthur, Samira Mubareka, Karen Mossman

The Journal of general virology · 09 Sep 2020

COVID-19 analysis

Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue

Jennifer A. Aguiar, Benjamin J-M. Tremblay, Michael J. Mansfield, Owen Woody, Briallen Lobb, Arinjay Banerjee, Abiram Chandiramohan, Nicholas Tiessen, Quynh Cao, Anna Dvorkin-Gheva, Spencer Revill, Matthew S. Miller, Christopher Carlsten, Louise Organ, Chitra Joseph, Alison John, Paul Hanson, Richard C. Austin, Bruce M. McManus, Gisli Jenkins, Karen Mossman, Kjetil Ask, Andrew C. Doxey, Jeremy A. Hirota

European Respiratory Journal · 16 Jul 2020

COVID-19 analysis

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens.

Briallen Lobb, Rhiannon Hodgson, Michael D J Lynch, Michael J Mansfield, Jiujun Cheng, Trevor C Charles, Josh D Neufeld, Paul M Craig, Andrew C Doxey

mSystems · 28 Apr 2020

omics microbial ecology toxins

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.

Emilie Spasov, Jackson M Tsuji, Laura A Hug, Andrew C Doxey, Laura A Sauder, Wayne J Parker, Josh D Neufeld

The ISME journal · 24 Apr 2020

omics microbial ecology

Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae.

Luca Bano, Matthias Kiel, Gabriele Sales, Andrew C Doxey, Michael J Mansfield, Haleluya T Wami, Marco Schiavone, Ornella Rossetto, Marco Pirazzini, Ulrich Dobrindt, Cesare Montecucco

Microbiology resource announcements · 16 Apr 2020

omics

An assessment of genome annotation coverage across the bacterial tree of life.

Briallen Lobb, Benjamin Jean-Marie Tremblay, Gabriel Moreno-Hagelsieb, Andrew C Doxey

Microbial genomics · 01 Mar 2020

analysis

The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus.

Kathleen E Orrell, Michael J Mansfield, Andrew C Doxey, Roman A Melnyk

Nature communications · 23 Jan 2020

toxins pathogens analysis proteins function prediction

Effect of long-acting β-agonists/glucocorticoids on human airway epithelial cell cytokine, transcriptomic and oxidative stress responses to cannabis smoke.

Ryan D Huff, Jennifer A Aguiar, Wayne Tse, Martin R Stämpfli, Brendan J McConkey, Andrew C Doxey, Jeremy A Hirota

ERJ open research · 20 Jan 2020

Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties.

Lee H Bergstrand, Josh D Neufeld, Andrew C Doxey

Bioinformatics (Oxford, England) · 01 Dec 2019

resource genomics

A study of nitric oxide dynamics in a growing biofilm using a density dependent reaction-diffusion model.

Maryam Ghasemi, Benjamin Jenkins, Andrew C Doxey, Sivabal Sivaloganathan

Journal of theoretical biology · 16 Oct 2019

Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke.

Jennifer A Aguiar, Ryan D Huff, Wayne Tse, Martin R Stämpfli, Brendan J McConkey, Andrew C Doxey, Jeremy A Hirota

Physiological reports · 01 Oct 2019

transcriptomics lung

Metagenomic and chemical characterization of soil cobalamin production.

Xinda Lu, Katherine R Heal, Anitra E Ingalls, Andrew C Doxey, Josh D Neufeld

The ISME journal · 06 Sep 2019

metagenomics microbial ecology

Exploring the Evolution of Virulence Factors through Bioinformatic Data Mining.

Andrew C Doxey, Michael J Mansfield, Briallen Lobb

mSystems · 21 May 2019

pathogens toxins evolution

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Kerrin Mendler, Han Chen, Donovan H Parks, Briallen Lobb, Laura A Hug, Andrew C Doxey

Nucleic acids research · 21 May 2019

resource evolution genomics function prediction

Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins.

Michael James Mansfield, Travis Gwynn Wentz, Sicai Zhang, Elliot Jeon Lee, Min Dong, Shashi Kant Sharma, Andrew Charles Doxey

Scientific reports · 07 Feb 2019

toxins analysis evolution function prediction

The impact of cigarette smoke exposure, COPD, or asthma status on ABC transporter gene expression in human airway epithelial cells.

Jennifer A Aguiar, Andrea Tamminga, Briallen Lobb, Ryan D Huff, Jenny P Nguyen, Yechan Kim, Anna Dvorkin-Gheva, Martin R Stampfli, Andrew C Doxey, Jeremy A Hirota

Scientific reports · 17 Jan 2019

omics analysis disease

Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Peter Brown, , Yaoqi Zhou

Database : the journal of biological databases and curation · 01 Jan 2019

Metagenomic Sequencing of Wastewater from a South African Research Farm.

Briallen Lobb, Anthony A Adegoke, Kesen Ma, Andrew C Doxey, Olayinka A Aiyegoro

Microbiology resource announcements · 25 Oct 2018

metagenomics

Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus.

Michael J Mansfield, Seiji N Sugiman-Marangos, Roman A Melnyk, Andrew C Doxey

FEBS letters · 16 Aug 2018

pathogens toxins evolution

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.

Mobolaji F Adegboye, Briallen Lobb, Olubukola O Babalola, Andrew C Doxey, Kesen Ma

Genome announcements · 28 Jun 2018

Genomic insights into the evolution and ecology of botulinum neurotoxins.

Michael J Mansfield, Andrew C Doxey

Pathogens and disease · 01 Jun 2018

Discovery of novel bacterial toxins by genomics and computational biology.

Andrew C Doxey, Michael J Mansfield, Cesare Montecucco

Toxicon : official journal of the International Society on Toxinology · 10 Feb 2018

Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium.

Sicai Zhang, Francois Lebreton, Michael J Mansfield, Shin-Ichiro Miyashita, Jie Zhang, Julia A Schwartzman, Liang Tao, Geoffrey Masuyer, Markel Martínez-Carranza, Pål Stenmark, Michael S Gilmore, Andrew C Doxey, Min Dong

Cell host & microbe · 27 Jan 2018

toxins pathogens omics function prediction evolution

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses.

Deepak Kumaresan, Jason Stephenson, Andrew C Doxey, Hina Bandukwala, Elliot Brooks, Alexandra Hillebrand-Voiculescu, Andrew S Whiteley, J Colin Murrell

Microbiome · 02 Jan 2018

metagenomics microbial ecology

Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height.

Michael Guo, Zun Liu, Jessie Willen, Cameron P Shaw, Daniel Richard, Evelyn Jagoda, Andrew C Doxey, Joel Hirschhorn, Terence D Capellini

eLife · 05 Dec 2017

Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution.

Christopher Kuc, Daniel J Richard, Samantha Johnson, Leslie Bragg, Mark R Servos, Andrew C Doxey, Paul M Craig

Scientific reports · 04 Dec 2017

evolution function prediction

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in

Maya D'Alessio, Ricardo Nordeste, Andrew C Doxey, Trevor C Charles

mSystems · 12 Sep 2017

omics function prediction

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella.

Ulrich Eckhard, Hina Bandukwala, Michael J Mansfield, Giada Marino, Jiujun Cheng, Iain Wallace, Todd Holyoak, Trevor C Charles, John Austin, Christopher M Overall, Andrew C Doxey

Nature communications · 12 Sep 2017

function prediction proteins

Estrogen Receptor β Is a Novel Target in Acute Myeloid Leukemia.

Sarah-Grace Rota, Alessia Roma, Iulia Dude, Christina Ma, Robert Stevens, Janet MacEachern, Joanna Graczyk, Shaundrei Mabriel G Espiritu, Praveen N Rao, Mark D Minden, Elena Kreinin, David A Hess, Andrew C Doxey, Paul A Spagnuolo

Molecular cancer therapeutics · 23 Aug 2017

cancer function prediction

The Skin Microbiome of Cohabiting Couples.

Ashley A Ross, Andrew C Doxey, Josh D Neufeld

mSystems · 20 Jul 2017

microbial ecology omics

Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk.

Terence D Capellini, Hao Chen, Jiaxue Cao, Andrew C Doxey, Ata M Kiapour, Michael Schoor, David M Kingsley

Nature genetics · 03 Jul 2017

evolution disease omics

Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function.

Jeremy Adams, Michael J Mansfield, Daniel J Richard, Andrew C Doxey

Bioinformatics (Oxford, England) · 01 May 2017

Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences.

Jiujun Cheng, Tatyana Romantsov, Katja Engel, Andrew C Doxey, David R Rose, Josh D Neufeld, Trevor C Charles

PloS one · 08 Mar 2017

metagenomics proteins function prediction

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity.

Sara Coyotzi, Andrew C Doxey, Ian D Clark, David R Lapen, Philippe Van Cappellen, Josh D Neufeld

Environmental microbiology · 01 Feb 2017

Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.

Eleanor Jameson, Andrew C Doxey, Ruth Airs, Kevin J Purdy, J Colin Murrell, Yin Chen

Microbial genomics · 20 Sep 2016

metagenomics microbial ecology toxins

Novel function discovery through sequence and structural data mining.

Briallen Lobb, Andrew C Doxey

Current opinion in structural biology · 10 Jun 2016

function prediction proteins

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.

Pavel Petrenko, Briallen Lobb, Daniel A Kurtz, Josh D Neufeld, Andrew C Doxey

BMC biology · 05 Nov 2015

metagenomics function prediction resource

Remote homology and the functions of metagenomic dark matter.

Briallen Lobb, Daniel A Kurtz, Gabriel Moreno-Hagelsieb, Andrew C Doxey

Frontiers in genetics · 21 Jul 2015

metagenomics proteins function prediction

Botulinum neurotoxin homologs in non-Clostridium species.

Michael J Mansfield, Jeremy B Adams, Andrew C Doxey

FEBS letters · 23 Dec 2014

toxins function prediction evolution

mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens.

Pavel Petrenko, Andrew C Doxey

Bioinformatics (Oxford, England) · 17 Oct 2014

resource proteins pathogens

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.

Andrew C Doxey, Daniel A Kurtz, Michael D J Lynch, Laura A Sauder, Josh D Neufeld

The ISME journal · 15 Aug 2014

function prediction microbial ecology omics

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Harendra Guturu, Andrew C Doxey, Aaron M Wenger, Gill Bejerano

Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 11 Nov 2013

proteins function prediction analysis

Prediction of molecular mimicry candidates in human pathogenic bacteria.

Andrew C Doxey, Brendan J McConkey

Virulence · 28 May 2013

pathogens analysis

Horizontal gene transfer contributed to the evolution of extracellular surface structures: the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth) families.

Angelika Böttger, Andrew C Doxey, Michael W Hess, Kristian Pfaller, Willi Salvenmoser, Rainer Deutzmann, Andreas Geissner, Barbara Pauly, Johannes Altstätter, Sandra Münder, Astrid Heim, Hans-Joachim Gabius, Brendan J McConkey, Charles N David

PloS one · 27 Dec 2012

proteins function prediction evolution