Check out these amazing publications from our FAME-ous researchers!
2024
Solving genomic puzzles: computational methods for metagenomic binning
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Hansheng Xue, Bhavya Papudeshi, Susanna R Grigson, George Bouras, Rosa E Prahl, Anubhav Kaphle, Andrey Verich, Berenice Talamantes-Becerra, Elizabeth A Dinsdale, Robert A Edwards (2024), Briefings in Bioinformatics
ICP – could there be a virus in the works?
Sarah K Giles, William M Hague, Robert A Edwards (2024), Obstetric Medicine
Hecatomb: an integrated software platform for viral metagenomics
Michael J Roach, Sarah J Beecroft, Kathie A Mihindukulasuriya, Leran Wang, Anne Paredes, Luis Alberto Chica Cárdenas, Kara Henry-Cocks, Lais Farias Oliveira Lima, Elizabeth A Dinsdale, Robert A Edwards, Scott A Handley (2024), GigaScience
Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies
George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J Roach, Bhavya Papudeshi, Louise M Judd, Anna E Sheppard, Robert A Edwards, Sarah Vreugde (2024), Microbial Genomics
Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics
Enhui Wu, Vijini Mallawaarachchi, Jinzhi Zhao, Yi Yang, Hebin Liu, Xiaoqing Wang, Chengpin Shen, Yu Lin, Liang Qiao (2024), Microbiome
Encoding Unitig-level Assembly Graphs with Heterophilous Constraints for Metagenomic Contigs Binning
Hansheng Xue, Vijini Mallawaarachchi, Lexing Xie, Vaibhav Rajan (2024), Proceedings of the 12th International Conference on Learning Representations
Koverage: Read-coverage analysis for massive (meta) genomics datasets
Michael J Roach, Bradley J Hart, Sarah J Beecroft, Bhavya Papudeshi, Laura K Inglis, Susanna R Grigson, Vijini Mallawaarachchi, George Bouras, Robert A Edwards (2024), Journal of Open Source Software
Prophages: an integral but understudied component of the human microbiome
Laura K. Inglis, Michael J. Roach, Robert A. Edwards (2024), Microbial Genomics
Dnaapler: A tool to reorient circular microbial genomes
George Bouras, Susanna R Grigson, Bhavya Papudeshi, Vijini Mallawaarachchi, Michael J Roach (2024), Journal of Open Source Software
2023
Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
Susanna R Grigson, Sarah K Giles, Robert A Edwards, Bhavya Papudeshi (2023), Clinical Infectious Diseases
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Vijini Mallawaarachchi, Michael J. Roach, Przemyslaw Decewicz, Bhavya Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L. K. Hutton, Elizabeth A. Dinsdale, Robert A. Edwards (2023), Bioinformatics
Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome
Michael Doane, Michael B. Reed, JC McKerral, Laís Farias Oliveira Lima, Megan Morris, Asha Z. Goodman, Shaili Johri, Bhavya Papudeshi, Taylor Dillon, Abigail C. Turnlund … (2023), Scientific Reports
Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale
Laís FO Lima, Amanda T Alker, Bhavya Papudeshi, Megan M Morris, Robert A Edwards, Samantha J De Putron, Elizabeth A Dinsdale (2023), Environmental microbiology
Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii
Bhavya Papudeshi, Douglas B Rusch, David VanInsberghe, Curtis M Lively, Robert A Edwards, Farrah Bashey (2023), American Society for Microbiology
Stingray epidermal microbiomes are species-specific with local adaptations
Emma N Kerr, Bhavya Papudeshi, Miranda Haggerty, Natasha Wild, Asha Z Goodman, Lais FO Lima, Ryan D Hesse, Amber Skye, Vijini Mallawaarachchi, Shaili Johri, Sophia Parker, Elizabeth A Dinsdale (2023), Frontiers in Microbilogy
Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions
Michael P Doane, Martin Ostrowski, Mark Brown, Anna Bramucci, Levente Bodrossy, Jodie van de Kamp, Andrew Bissett, Peter Steinberg, Martina A Doblin, Justin Seymour (2023), Environmental Microbiology
The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time‑points
Michael P Doane, Colton J Johnson, Shaili Johri, Emma N Kerr, Megan M Morris, Ric Desantiago, Abigail C Turnlund, Asha Goodman, Maria Mora, Laís Farias Oliveira Lima, Andrew P Nosal, Elizabeth A Dinsdale (2023), Microbial ecology
The utility of dust for forensic intelligence: Exploring collection methods and detection limits for environmental DNA, elemental and mineralogical analyses of dust samples
Nicole R Foster, Belinda Martin, Jurian Hoogewerff, Michael G Aberle, Patrice de Caritat, Paul Roffey, Robert Edwards, Arif Malik, Priscilla Thwaites, Michelle Waycott, Jennifer Young (2023), Forensic Science International
Plassembler: an automated bacterial plasmid assembly tool
George Bouras, Anna E Sheppard, Vijini Mallawaarachchi, Sarah Vreugde (2023), Bioinformatics
Metaproteomics profiling of the microbial communities in fermentation starters (Daqu) during multi-round production of Chinese liquor
Jinzhi Zhao, Yi Yang, Mengjing Teng, Jianxujie Zheng, Bing Wang, Vijini Mallawaarachchi, Yu Lin, Ziyu Fang, Chengpin Shen, Shaoning Yu, Fan Yang, Liang Qiao, Li Wang (2023), Frontiers in Nutrition
Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters
Jinzhi Zhao, Yi Yang, Liangqiang Chen, Jianxujie Zheng, Xibin Lv, Dandan Li, Ziyu Fang, Chengpin Shen, Vijini Mallawaarachchi, Yu Lin, Shaoning Yu, Fan Yang, Li Wang, Liang Qiao (2023), Frontiers in Microbiology
Biogeochemical Processes and Microbial Dynamics Governing Phosphorus Retention and Release in Sediments: A Case Study in Lower Great Lakes Headwaters
Nicholas Falk, Ian G Droppo, Ken G Drouillard, Christopher G Weisener (2023), Environmental Management
What the protein!? Computational methods for predicting microbial protein functions
Susanna Grigson, Robert Edwards (2023), OSF Preprints
The Promise and Pitfalls of Prophages
Jody C. McKerral, Bhavya Papudeshi, Laura K. Inglis, Michael J. Roach, Przemyslaw Decewicz, Katelyn McNair, Antoni Luque, Elizabeth A. Dinsdale, Robert A. Edwards (2023), BioRxiv
Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2
Bhavya Papudeshi, Alejandro A. Vega, Cole Souza, Sarah K. Giles, Vijini Mallawaarachchi, Michael J. Roach, Michelle An, Nicole Jacobson, Katelyn McNair, Maria Fernanda Mora, Karina Pastrana, Lance Boling, Christopher Leigh, Clarice Harker, Will S. Plewa, Susanna R. Grigson, George Bouras, Przemysław Decewicz, Antoni Luque, Lindsay Droit, Scott A. Handley, David Wang, Anca M. Segall, Elizabeth A. Dinsdale, Robert A. Edwards (2023), Microbial Genomics
Emergent community architecture despite distinct diverity in the global whale shark (Rhincodon typus) epidermal micrbiome
Michael P Doane, Michael B Reed, Jody McKerral, Laís Farias Oliveira Lima, Megan Morris, Asha Z Goodman, Shaili Johri, Bhavya Papudeshi, Taylor Dillon, Abigail C Turnlund, Meredith Peterson, Maria Mora, Rafael de la Parra Venegas, Richard Pillans, Christoph A Rohner, Simon J Pierce, Christine G Legaspi, Gonzalo Araujo, Deni Ramirez-Macias, Robert A Edwards, Elizabeth A Dinsdale (2023), Scientific Reports
Heat-stressed coral microbiomes are stable and potentially beneficial at the level of taxa and functional genes
Laís Farias Oliveira Lima, Amanda Alker, Megan Morris, Robert Edwards, Samantha De Putron, Elizabeth Dinsdale (2023), [Authorea Preprints] (10.22541/au.167542930.03517639/v1){:target=”_blank”}
Compounding Achromobacter Phages for Therapeutic Applications
Ana Georgina Cobián Güemes, Tram Le, Maria Isabel Rojas, Nicole E Jacobson, Helena Villela, Katelyn McNair, Shr-Hau Hung, Lili Han, Lance Boling, Jessica Claire Octavio, Lorena Dominguez, Vito Adrian Cantú, Sinéad Archdeacon, Alejandro A Vega, Michelle A An, Hamza Hajama, Gregory Burkeen, Robert A Edwards, Douglas J Conrad, Forest Rohwer, Anca M Segall (2023), MDPI Viruses
Classification Confidence in Exploratory Learning: A User’s Guide
Peter Salamon, David Salamon, V Adrian Cantu, Michelle An, Tyler Perry, Robert A Edwards, Anca M Segall (2023), Machine Learning and Knowledge Extraction
Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
Evelien M Adriaenssens, Simon Roux, J Rodney Brister, Ilene Karsch-Mizrachi, Jens H Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cédric Lood, Elliot J Lefkowitz, Matthew B Sullivan, Robert A Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E Dutilh (2023), Nature Biotechnology
PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
Katelyn McNair, Peter Salamon, Robert A Edwards, Anca M Segall (2023), Research Square
Statement in Support of:“Virology under the Microscope—a Call for Rational Discourse”
Peter Speck, … Robert Edwards, … April Van Der Kamp, … (2023), ASM mBio
Confidence for exploratory machine learning
Peter Salamon, David Salamon, V Adrian Cantu, Michelle An, Tyler Perry, Robert A Edwards, Anca M Segall (2023), Biophysical Journal
Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
Dann Turner, Andrey N Shkoporov, Cédric Lood, Andrew D Millard, Bas E Dutilh, Poliane Alfenas-Zerbini, Leonardo J van Zyl, Ramy K Aziz, Hanna M Oksanen, Minna M Poranen, Andrew M Kropinski, Jakub Barylski, J Rodney Brister, Nina Chanisvili, Rob A Edwards, François Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtböke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Muñoz, Jānis Rūmnieks, BL Sarkar, Matthew B Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M Adriaenssens (2023), Archives of Virology
Temperate gut phages are prevalent, diverse, and predominantly inactive
Sofia Dahlman, Laura Avellaneda-Franco, Ciaren Kett, Dinesh Subedi, Remy B Young, Jodee A Gould, Emily L Rutten, Emily L Gilliver, Christopher JR Turkington, Neda Nezam-Abadi, Juris A Grasis, Dena Lyras, Robert A Edwards, Samuel C Forster, Jeremy J Barr (2023), bioRxiv
Prophage rates in the human microbiome vary by body site and host health
Laura K Inglis, Michael J Roach, Robert A Edwards (2023), bioRxiv
2022
Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments
Asha Z Goodman, Bhavya Papudeshi, Michael P Doane, Maria Mora, Emma Kerr, Melissa Torres, Jennifer Nero Moffatt, Lais Lima, Andrew P Nosal, Elizabeth Dinsdale (2022), Microorganisms
Win some, lose some: the ecophysiology of Porites astreoides as a key coral species to Caribbean reefs
Lima, LFO, H. Bursch and E. A. Dinsdale (2022), Frontiers in Marine Biology
Making change sustainable: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) meeting review
Toby, I, Williams J, Lu G, Cai C, Crandall KA, Dinsdale EA, Drew J, Edgington NP, Goller CC, Grandgenett NF, Grant BJ, Hauser C, Johnson KA, Jones CJ, Jue NK, Jungck FR, Kerby J, Kleinschmit AJ, Miller KG, Morgan WR, Murdoch B, Noutsios G, Nunez-Castilla J, Pauley M, Pearson WR, Robertson SD, Robic S, Rosenwald A, Seah YM, Shofner M, Sierk M, Siltberg-Liberles J, Smith T, Stover NA, Tapprich W, Triplett EW, Ryder EF. (2022), CourseSource
Ten simple rules and a template for creating workflows-as-applications
Michael J Roach, N Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Papudeshi, Scott A Handley, C Titus Brown, Nathan S Watson-Haigh, Robert A Edwards (2022), Plos Comp. Biol.
Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome
Ryan D Hesse, Michael Roach, Emma N Kerr, Bhavya Papudeshi, Laís FO Lima, Asha Z Goodman, Lisa Hoopes, Mark Scott, Lauren Meyer, Charlie Huveneers, Elizabeth A Dinsdale (2022), Viruses
Single-cell gene expression links SARS-CoV-2 infection and gut serotonin
Alyce M Martin, Michael Roach, Lauren A Jones, Daniel Thorpe, Rosemary A Coleman, Caitlin Allman, Robert Edwards, Damien J Keating (2022), Gut
Hecatomb: An End-to-End Research Platform for Viral Metagenomics
Michael Roach, Sarah Beecroft, Kathie A Mihindukulasuriya, Leran Wang, Lais Farias Oliveira Lima, Elizabeth A Dinsdale, Robert A Edwards, Scott A Handley (2022), BioRxiv
The StkSR Two-Component System Influences Colistin Resistance in Acinetobacter baumannii
Sarah K Giles, Uwe H Stroeher, Bhavya Papudeshi, Robert A Edwards, Jessica AP Carlson-Jones, Michael Roach, Melissa H Brown (2022), Microorganisms
The human gut virome: composition, colonization, interactions, and impacts on human health
Evan Pargin, Michael J Roach, Amber Skye, Bhavya Papudeshi, Laura K Inglis, Vijini Mallawaarachchi, Susanna R Grigson, Clarice Harker, Robert A Edwards, Sarah K Giles (2022), Frontiers in Microbiology
OligoFlow: rapid and sensitive virus quantification using flow cyomerty and oligonucleotide hybridization
James S Paterson, Lisa M Dann, Jessica Carlson-Jones, Sarah Giles, Connor McIvor, Peter G Speck, James G Mitchell (2022), bioRxiv
Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments
Asha Z Goodman, Bhavya Papudeshi, Michael P Doane, Maria Mora, Emma Kerr, Melissa Torres, Jennifer Nero Moffatt, Lais Lima, Andrew P Nosal, Elizabeth Dinsdale (2022), Microorganisms
Analysis of rapid HIT application to touch DNA samples
Belinda Martin, Todd Kaesler, Adrian Linacre (2022), Journal of Forensic Sciences
The influences of dusty environments on the STR typing success of post-detonation touch DNA samples
Belinda Martin, Todd Kaesler, K Paul Kirkbride, Adrian Linacre (2022), Forensic Science International: Genetics
Exploring tapelifts as a method for dual workflow STR amplification
Belinda Martin, Duncan Taylor, Adrian Linacre (2022), Forensic Science International: Genetics
Accurate binning of metagenomic contigs using composition, coverage, and assembly graphs
Vijini Mallawaarachchi, Yu Lin (2022), Journal of Computational Biology
CH-Bin: A convex hull based approach for binning metagenomic contigs
Sunera Chandrasiri, Thumula Perera, Anjala Dilhara, Indika Perera, Vijini Mallawaarachchi (2022), Computational Biology and Chemistry
RepBin: Constraint-based graph representation learning for metagenomic binning
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin (2022), Proceedings of the 36th AAAI Conference on Artificial Intelligence
MetaCoAG: Binning metagenomic contigs via composition, coverage and assembly graphs
Vijini Mallawaarachchi, Yu Lin (2022), International Conference on Research in Computational Molecular Biology
Integrating microbial DNA community analyses into time-integrated suspended sediment sampling methods
Nicholas Falk, Ian G Droppo, Ken G Drouillard, Christopher G Weisener (2022), Journal of Soils and Sediments
Organizing the bacterial annotation space with amino acid sequence embeddings
Susanna R Grigson, Jody C McKerral, James G Mitchell, Robert A Edwards (2022), BMC bioinformatics
Isling: a tool for detecting integration of wild-type viruses and clinical vectors
Suzanne Scott, Claus V Hallwirth, Felix Hartkopf, Susanna Grigson, Yatish Jain, Ian E Alexander, Denis C Bauer, Laurence OW Wilson (2022), Journal of molecular biology
A bioinformatic pipeline for simulating viral integration data
Suzanne Scott, Susanna Grigson, Felix Hartkopf, Claus V Hallwirth, Ian E Alexander, Denis C Bauer, Laurence OW Wilson (2022), Data in Brief
How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research
Laura K. Inglis and Robert A. Edwards (2022), Microorganisms
Win some, lose some: The ecophysiology of Porites astreoides as a key coral species to Caribbean reefs
Lais FO Lima, Hayden Bursch, Elizabeth A Dinsdale (2022), Frontiers in Marince Science
Prophage rates in the human microbiome vary by body site and host health
Laura K Inglis, Michael J Roach, Robert A Edwards (2022), bioRxiv
Programmed ribosomal frameshifts, and how to find them
Katelyn McNair, Peter Salamon, Robert A Edwards, Anca M Segall (2022), bioRxiv
Towards the biogeography of butyrate-producing bacteria
Joel E Brame, Craig Liddicoat, Catherine A Abbott, Robert A Edwards, Jake M Robinson, Nicolas E Gauthier, Martin F Breed (2022), bioRxiv
Estimating Classification Confidence Using Kernel Densities
Peter Salamon, David Salamon, V Adrian Cantu, Michelle An, Tyler Perry, Robert A Edwards, Anca M Segall (2022), arXiv
Taxonomy proposal 2021: Abolish the order Caudovirales and the families Myoviridae, Siphoviridae and Podoviridae (Caudoviricetes)
Evelien Adriaenssens, Andrew M Kropinski, D Turner, Mart Krupovic, Andrew Millard, Bas E Dutilh, Hanna M Oksanen, Cedric Lood, Alejandro Reyes, Cristina Moraru, Ramy K Aziz, Tong Yigang, Jakub Barylski, Malgorzata Lobocka, BL Sarkar, Annika Gillis, Leonardo J van Zyl, Susan M Lehman, Matthew B Sullivan, Johannes Wittmann, Alla I Kushkina, Petar Knezevic, J Rodney Brister, Rob A Edwards, Ipek Kurtboke, Minna Poranen, Rob Lavigne, Andrey N Shkoporov, Jumpei Uchiyama, Andrea I Moreno Switt, François Enault (2022), ICTV Online: International Committee on Taxonomy of Viruses
Predicting the capsid architecture of phages from metagenomic data
Diana Y Lee, Caitlin Bartels, Katelyn McNair, Robert A Edwards, Manal A Swairjo, Antoni Luque (2022), Computational and Structural Biotechnology Journal
2021
Philympics 2021: Prophage Predictions Perplex Programs
MJ Roach, K McNair, SK Giles, LK Inglis, E Pargin, S Roux, P Decewicz, RA Edwards (2021), F1000Research
No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study
M Roach, A Cantu, MK Vieri, M Cotten, P Kellam, M Phan, L Hoek, M Mandro, F Tepage, G Mambandu, G Musinya, A Laudisoit, R Colebunders, R Edwards, JL Mokili (2021), Pathogens
Epidermal Microbiomes of Triakis semifasciata Are Consistent across Captive and Wild Environments
Asha Goodman, Bhavya Papudeshi, Michael P Doane, Colton Johnson, Maria Mora, Emma Kerr, Melissa Torres, Jennifer Nero, Laís Lima, Andrew P Nosel, Elizabeth A Dinsdale (2021), Research square
Elasmobranch microbiomes: emerging patterns and implications for host health and ecology
Cameron T Perry, Zoe A Pratte, Ana Clavere-Graciette, Kim B Ritchie, Robert E Hueter, Alisa L Newton, G Christopher Fischer, Elizabeth A Dinsdale, Michael P Doane, Krystan A Wilkinson, Kim Bassos-Hull, Kady Lyons, Alistair DM Dove, Lisa A Hoopes, Frank J Stewart (2021), Animal Microbiome
Reducing Data Deficiencies: Preliminary Elasmobranch Fisheries Surveys in India, Identify Range Extensions and Large Proportions of Female and Juvenile Landings
Shaili Johri, Isabella Livingston, Anjani Tiwari, Jitesh Solanki, Anissa Busch, Isabel Moreno, Sam R. Fellows, Michael P Doane, Elizabeth A Dinsdale (2021), Frontiers in Marine Science
Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases
María-Eugenia DeCastro, Michael P Doane, Elizabeth Ann Dinsdale, Esther Rodríguez-Belmonte, María-Isabel González-Siso (2021), Scientific Reports
Comparison of six commercially available STR kits for their application to touch DNA using direct PCR
Belinda Martin, Duncan Taylor, Adrian Linacre (2021), Forensic Science International: Reports
How many cells are required for successful DNA profiling?
Piyamas Kanokwongnuwut, Belinda Martin, Duncan Taylor, K Paul Kirkbride, Adrian Linacre (2021), Forensic Science International: Genetics
Evaluating sediment phosphorus exchange in rural Ontario headwaters by paired sequential extraction and sorption isotherms
Nicholas Falk, Matthew Day, Christopher G Weisener (2021), Water, Air, & Soil Pollution
Synergetic impacts of turbulence and fishing reduce ocean biomass
Jody C McKerral, Justin R Seymour, Trish J Lavery, Paul J Rogers, Thomas C Jeffries, James S Paterson, Ben Roudnew, Charlie Huveneers, Kelly Newton, Virginie van Dongen-Vogels, Nardi P Cribb, Karina M Winn, Renee J Smith, Crystal L Beckmann, Eloise Prime, Claire M Charlton, Maria Kleshnina, Susanna R Grigson, Marika Takeuchi, Laurent Seuront, James G Mitchell (2021), bioRxiv
There Is More than Multiple Choice: Crowd-Sourced Assessment Tips for Online, Hybrid, and Face-to-Face Environments
Jennifer C. Drew, Neal Grandgenett, Elizabeth A. Dinsdale, Luis E. Vázquez Quiñones, Sebastian Galindo, William R. Morgan, Mark Pauley, Anne Rosenwald, Eric W. Triplett, William Tapprich, Adam J. Kleinschmit, ASM Journal of Microbiology & Biology Education
Perspective on taxonomic classification of uncultivated viruses
Bas E Dutilh, Arvind Varsani, Yigang Tong, Peter Simmonds, Sead Sabanadzovic, Luisa Rubino, Simon Roux, Alejandro Reyes Munoz, Cédric Lood, Elliot J Lefkowitz, Jens H Kuhn, Mart Krupovic, Robert A Edwards, J Rodney Brister, Evelien M Adriaenssens, Matthew B Sullivan, Current Opinion in Virology
Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
Mart Krupovic, Dann Turner, Vera Morozova, Mike Dyall-Smith, Hanna M Oksanen, Rob Edwards, Bas E Dutilh, Susan M Lehman, Alejandro Reyes, Diana P Baquero, Matthew B Sullivan, Jumpei Uchiyama, Jesca Nakavuma, Jakub Barylski, Mark J Young, Shishen Du, Poliane Alfenas-Zerbini, Alla Kushkina, Andrew M Kropinski, Ipek Kurtböke, J Rodney Brister, Cédric Lood, BL Sarkar, Tong Yigang, Ying Liu, Li Huang, Johannes Wittmann, Nina Chanishvili, Leonardo J van Zyl, Janis Rumnieks, Tomohiro Mochizuki, Matti Jalasvuori, Ramy K Aziz, Małgorzata Łobocka, Kenneth M Stedman, Andrey N Shkoporov, Annika Gillis, Xu Peng, François Enault, Petar Knezevic, Rob Lavigne, Sung-Keun Rhee, Virginija Cvirkaite-Krupovic, Cristina Moraru, Andrea I Moreno Switt, Minna M Poranen, Andrew Millard, David Prangishvili, Evelien M Adriaenssens, Archives in Virology
hafeZ: active prophage identification through read mapping
Christopher JR Turkington, Neda Nezam Abadi, Robert A Edwards, Juris A Grasis, bioRxiv
RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content
Felipe Hernandes Coutinho, Asier Zaragoza-Solas, Mario López-Pérez, Jakub Barylski, Andrzej Zielezinski, Bas E Dutilh, Robert Edwards, Francisco Rodriguez-Valera, Cell Press Patterns
MultiPhATE2: code for functional annotation and comparison of phage genomes
Carol L Ecale Zhou, Jeffrey Kimbrel, Robert Edwards, Katelyn McNair, Brian A Souza, Stephanie Malfatti, Oxford G3
Gut microbiota represent a major thermogenic biomass
Ruth A Riedl, Colin ML Burnett, Nicole A Pearson, John J Reho, Mohamad Mokadem, Robert A Edwards, Tammy L Kindel, John R Kirby, Justin L Grobe, Function
A novel group of promiscuous podophages infecting diverse gammaproteobacteria from river communities exhibits dynamic intergenus host adaptation
Daniel Cazares, Adrian Cazares, Wendy Figueroa, Gabriel Guarneros, Robert A Edwards, Pablo Vinuesa, Msystems
Utilizing amino acid composition and entropy of potential open reading frames to identify protein-coding genes
Katelyn McNair, Carol L Ecale Zhou, Brian Souza, Stephanie Malfatti, Robert A Edwards, Microorganisms
NCBI’s virus discovery codeathon: building “FIVE”—The Federated Index of Viral Experiments API index
Joan Martí-Carreras, Alejandro Rafael Gener, Sierra D Miller, Anderson F Brito, Christiam E Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M Kristensen, Wynn K Meyer, Sejal Modha, Alexis L Norris, Surya Saha, Anna K Belford, Evan Biederstedt, James Rodney Brister, Jan P Buchmann, Nicholas P Cooley, Robert A Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J Tisza, Benjamin J Tully, Bert Vanmechelen, Valerie C Virta, Jake L Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby, MDPI Viruses
Adaptive evolution of sulfite tolerance in Brettanomyces bruxellensis
Caroline Bartel, Michael Roach, Cristobal Onetto, Chris Curtin, Cristian Varela, Anthony Borneman (2021), FEMS Yeast Research
2020
The microbial abundance dynamics of the paediatric oral cavity before and after sleep
Jessica AP Carlson-Jones, Anna Kontos, Declan Kennedy, James Martin, Kurt Lushington, Jody McKerral, James S Paterson, Renee J Smith, Lisa M Dann, Peter Speck, James G Mitchell (2020), Journal of oral microbiology
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
Michael P Doane, Megan M Morris, Bhavya Papudeshi, Lauren Allen, Dnyanada Pande, John M Haggerty, Shaili Johri, Abigail C Turnlund, Meredith Peterson, Dovi Kacev, Andy Nosal, Deni Ramirez, Kevin Hovel, Julia Ledbetter, Amanda Alker, Jackeline Avalos, Kristi Baker, Shruti Bhide, Emma Billings, Steven Byrum, Molly Clemens, Amelia Juliette Demery, Lais Farias Oliveira Lima, Oscar Gomez, Omar Gutierrez, Selena Hinton, Donald Kieu, Angie Kim, Rebeca Loaiza, Alexander Martinez, Jordan McGhee, Kristine Nguyen, Sabrina Parlan, Amanda Pham, Rosalyn Price-Waldman, Robert A Edwards, Elizabeth A Dinsdale, BMC Microbiome
Modeling of the coral microbiome: the influence of temperature and microbial network
Laís FO Lima, Maya Weissman, Micheal Reed, Bhavya Papudeshi, Amanda T Alker, Megan M Morris, Robert A Edwards, Samantha J de Putron, Naveen K Vaidya, Elizabeth A Dinsdale, ASM mBio
Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes
Cynthia B Silveira, Felipe H Coutinho, Giselle S Cavalcanti, Sean Benler, Michael P Doane, Elizabeth A Dinsdale, Robert A Edwards, Ronaldo B Francini-Filho, Cristiane C Thompson, Antoni Luque, Forest L Rohwer, Fabiano Thompson, BMC Genomics
Latitude and chlorophyll a density drive the distribution of carbohydrate‐active enzymes in the planktonic microbial fraction of the epipelagic zone
Michael Doane, John Matthew Haggerty, Cleanto Rodrigo da Silva Lopes, Peter Yates, Rob Edwards, Elizabeth Dinsdale, Fabyano Alvares Cardoso Lopes, Thiago Bruce, Environmental Microbiology Reports
Mitochondrial genome of the silky shark Carcharhinus falciformis from the British Indian Ocean Territory Marine Protected Area
Shaili Johri, Taylor K Chapple, Elizabeth A Dinsdale, Robert Schallert, Barbara A Block, Mitochondrial DNA Part B
Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area
Shaili Johri, Taylor K Chapple, Robert Schallert, Elizabeth A Dinsdale, Barbara A Block, Mitochondrial DNA Part B
Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae)
Nicholas Dunn, Shaili Johri, David Curnick, Chris Carbone, Elizabeth A Dinsdale, Taylor K Chapple, Barbara A Block, Vincent Savolainen, Mitochondrial DNA Part B
Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean
Shaili Johri, Anjani Tiwari, Emma N Kerr, Elizabeth A Dinsdale, Mitochondrial DNA Part B
Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory
Shaili Johri, Nicholas Dunn, Taylor K Chapple, David Curnick, Vincent Savolainen, Elizabeth A Dinsdale, Barbara A Block, Mitochondrial DNA Part B
Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
Elizabeth F Ryder, William R Morgan, Michael Sierk, Samuel S Donovan, Sabrina D Robertson, Hayley C Orndorf, Anne G Rosenwald, Eric W Triplett, Elizabeth Dinsdale, Mark A Pauley, William E Tapprich, Biochemistry and Molecular Biology Education
Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus)
Shaili Johri, Sam R Fellows, Jitesh Solanki, Anissa Busch, Isabella Livingston, Maria Fernanda Mora, Anjani Tiwari, Vito Adrian Cantu, Asha Goodman, Megan M Morris, Michael P Doane, Robert A Edwards, Elizabeth A Dinsdale, MetaGene
Microbial abundance, composition, and function in nectar are shaped by flower visitor identity
Megan M Morris, Natalie J Frixione, Alexander C Burkert, Elizabeth A Dinsdale, Rachel L Vannette, FEMS Microbiology Society
PhANNs, a fast and accurate tool and web server to classify phage structural proteins
Vito Adrian Cantu, Peter Salamon, Victor Seguritan, Jackson Redfield, David Salamon, Robert A Edwards, Anca M Segall, PLoS Computational Biology
Standardized bacteriophage purification for personalized phage therapy
Tiffany Luong, Ann-Charlott Salabarria, Robert A Edwards, Dwayne R Roach, Nature Protocols
A distinct contractile injection system gene cluster found in a majority of healthy adult human microbiomes
Maria I Rojas, Giselle S Cavalcanti, Katelyn McNair, Sean Benler, Amanda T Alker, Ana G Cobián-Güemes, Melissa Giluso, Kyle Levi, Forest Rohwer, Barbara A Bailey, Sinem Beyhan, Robert A Edwards, Nicholas J Shikuma, ASM MSystems