Submissions from 2019
Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model., Pavel Avdeyev, Shuai Jiang, and Max A Alekseyev
Submissions from 2018
Diversity, structure and sources of bacterial communities in earthworm cocoons., Manuel Aira, Marcos Pérez-Losada, and Jorge Domínguez
Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity, Andrea Hahn, Matthew L. Bendall, Keylie M. Gibson, Hollis Chaney, Iman Sami, Geovanny F. Perez, Anastassios C. Koumbourlis, Timothy A. McCaffrey, Robert J. Freishtat, and Keith A Crandall
Earth BioGenome Project: Sequencing life for the future of life., Harris A Lewin, Gene E Robinson, W John Kress, William J Baker, Jonathan Coddington, Keith A Crandall, and +several additional authors
Glucocorticoids modulate gastrointestinal microbiome in a wild bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, and Alberto Velando
Submissions from 2017
Estimation of the true evolutionary distance under the fragile breakage model., Nikita Alexeev and Max A Alekseyev
Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes), Lily Hughes, Gustavo Somoza, Bryan Nguyen, James Bernot, Mariano Gonzalez-Castro, Juan Martin Diaz de Astarloa, and Guillermo Orti
Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma, Marcos Pérez-Losada, Lamia Alamri, Keith Crandall, and Robert J. Freishtat
Microbial sequence typing in the genomic era., Marcos Pérez-Losada, Miguel Arenas, and Eduardo Castro-Nallar
The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections., Marcos Pérez-Losada, Robert J Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Robert J Freishtat, and Jonathan M Mansbach
Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end., David B Stern, Jesse Breinholt, Carlos Pedraza-Lara, Marilú López-Mejía, Christopher L Owen, Heather Bracken-Grissom, James W Fetzner, and Keith A Crandall
DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants, David Stern, Eduardo Castro Nallar, Jason Rathod, and Keith A. Crandall
Transcriptomic effects of dispersed oil in a non-model decapod crustacean, Hernan Vazquez-Miranda, Brent Thoma, Juliet Wong, Darryl Felder, Keith A. Crandall, and Heather Bracken-Grissom
RNAseq Analysis of the Drosophila Response to the Entomopathogenic Nematode Steinernema., Shruti Yadav, Sean Daugherty, Amol Carl Shetty, and Ioannis Eleftherianos
Submissions from 2016
Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology., Sarah K. Hilton, Eduardo Castro-Nallar, Marcos Pérez-Losada, Ian Toma, Timothy A. McCaffrey, Eric P. Hoffman, Marc O. Siegel, Gary L. Simon, W. Evan Johnson, and Keith Crandall
Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children., Marcos Pérez-Losada, Keith A. Crandall, and Robert J. Freishtat
DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories, J Rombke, M. Aira, T Backeljau, K Breugelmans, J Dominguez, E Funke, and Marcos Perez-Losada
Submissions from 2015
A quick guide for building a successful bioinformatics community., Aidan Budd, Manuel Corpas, Michelle D Brazas, Jonathan C Fuller, Jeremy Goecks, Nicola J Mulder, Magali Michaut, B F Francis Ouellette, Aleksandra Pawlik, and Niklas Blomberg
Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls., Eduardo Castro-Nallar, Matthew L Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G Severance, Faith B Dickerson, Jennifer R Schroeder, Robert H Yolken, and Keith A Crandall
Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities., Eduardo Castro-Nallar, Ying Shen, Robert J. Freishtat, Marcos Pérez-Losada, Solaiappan Manimaran, and et al.
Underground evolution: New roots for the old tree of lumbricid earthworms, Jorge Dominguez, Manuel Aira, Jesse Breinholt, Mirjana Stojanovic, Samuel James, and Marcos Pérez-Losada
Phylogeography of six codistributed New Zealand cicadas and their relationship to multiple biogeographical boundaries suggest a re-evaluation of the Taupo Line, E. Ellis, D. Marshall, K. Hill, Christopher L. Owen, P. Kamp, and C. Simon
Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency, Felix Forest, Keith A. Crandall, Mark W. Chase, and Daniel P. Faith
A synthetic phylogeny of freshwater crayfish: insights for conservation., Christopher L Owen, Heather Bracken-Grissom, David Stern, and Keith A Crandall
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma., Marcos Pérez-Losada, Eduardo Castro-Nallar, Matthew L. Bendall, Robert J. Freishtat, and Keith A. Crandall
Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)., Nadia I Richman, Monika Böhm, Susan B Adams, Fernando Alvarez, Elizabeth A Bergey, Keith A Crandall, and +several additional authors
TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response., Dmitri Rozanov, Anton Cheltsov, Eduard Sergienko, Stefan Vasile, Vladislav Golubkov, Alexander E Aleshin, Trevor Levin, Elie Traer, Byron Hann, Julia Freimuth, Nikita Alexeev, Max A Alekseyev, Sergey P Budko, Hans Peter Bächinger, and Paul Spellman
Submissions from 2014
Clinical PathoScope: Rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data, Allyson L. Byrd, Joseph F. Perez-Rogers, Solaiappan Manimaran, Eduardo Castro-Nallar, Ian Toma, Timothy A. McCaffrey, Marc O. Siegel, Gary Benson, Keith Crandall, and William Evan Johnson
Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes, William J. Faison, Alexandre Rostovtsev, Eduardo Castro-Nallar, Keith Crandall, Konstantin Chumakov, Vahan Simonyan, and Raja Mazumder
PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples., Changjin Hong, Solaiappan Manimaran, Ying Shen, Joseph F Perez-Rogers, Allyson L Byrd, Eduardo Castro-Nallar, Keith A Crandall, and William Evan Johnson
Characteristics and prediction of RNA structure., Hengwu Li, Daming Zhu, Caiming Zhang, Huijian Han, and Keith A Crandall
Single-molecule long read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia, Ian Toma, Marc O. Siegel, John F. Keiser, Anna Yakovleva, Alvin Kim, Joseph Devaney, Eric P. Hoffman, Rami Alsubail, Keith Crandall, Eduardo Castro-Nallar, Marcos Perez-Losada, Sarah Hilton, Lakhmir S. Chawla, Timothy A. McCaffrey, and Gary L. Simon
Submissions from 2013
Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae), B. Ainscough, J. Breinholt, H. Robinson, and Keith A. Crandall
A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)., Heather D Bracken-Grissom, Maren E Cannon, Patricia Cabezas, Rodney M Feldmann, Carrie E Schweitzer, Shane T Ahyong, Darryl L Felder, Rafael Lemaitre, and Keith A Crandall
Pathoscope: species identification and strain attribution with unassembled sequencing data., Owen E Francis, Matthew Bendall, Solaiappan Manimaran, Changjin Hong, Nathan L Clement, Eduardo Castro-Nallar, Quinn Snell, G Bruce Schaalje, Mark J Clement, Keith A Crandall, and W Evan Johnson
Pathogen typing in the genomics era: MLST and the future of molecular epidemiology., Marcos Pérez-Losada, Patricia Cabezas, Eduardo Castro-Nallar, and Keith A Crandall
Tat exon 1 exhibits functional diversity during HIV-1 subtype C primary infection, R. Rossenkhan, I. MacLeod, T. Sebunya, Eduardo Castro-Nallar, M. McLane, and +several additional authors
Phage cluster relationships identified through single gene analysis., Kyle C Smith, Eduardo Castro-Nallar, Joshua Nb Fisher, Donald P Breakwell, Julianne H Grose, and Sandra H Burnett
Submissions from 2012
Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada, A. Andonov, M. Coutthart, Marcos Perez-Losada, Keith A. Crandall, D. Posada, and +several additional authors
Phylogenetics links monster larva to deep-sea shrimp., Heather D Bracken-Grissom, Darryl L Felder, Nicole L Vollmer, Joel W Martin, and Keith A Crandall
Testing phylogenetic hypotheses of the subgenera of the freshwater crayfish genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, and Keith A Crandall
A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement., P Scott Chandry, Simon Gladman, Sean C Moore, Torsten Seemann, Keith A Crandall, and Narelle Fegan
Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae), C. Pedraza-Lara, I. Doadrio, J. Breinholt, and Keith A. Crandall
Phylogenetic search through partial tree mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, and Keith Crandall