Submissions from 2019

Machine learning approaches to predict lupus disease activity from gene expression data, Brian Kegerreis, Michelle D. Catalina, Prathyusha Bachali, Nicholas S. Geraci, Adam C. Labonte, Chen Zeng, Nathaniel Stearrett, Keith A. Crandall, Peter E. Lipsky, and Amrie C. Grammer

Baseline human gut microbiota profile in healthy people and standard reporting template, Charles H. King, Hiral Desai, Allison C. Sylvetsky, Jonathan LoTempio, Shant Ayanyan, Jill Carrie, Keith A. Crandall, Brian C. Fochtman, Lusine Gasparyan, Naila Gulzar, Paul Howell, Najy Issa, Konstantinos Krampis, Lopa Mishra, Hiroki Morizono, Joseph R. Pisegna, Shuyun Rao, Yao Ren, Vahan Simonyan, Krista Smith, Sharanjit VedBrat, Michael D. Yao, and Raja Mazumder


Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses, Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, and Marcos E. Perez-Losada


Closed testing of each group versus the others combined in a multiple group analysis, J. M. Lachin and I Bebu


Rationale and Design for a GRADE Substudy of Continuous Glucose Monitoring., Mary E. Larkin, David M. Nathan, Ionut Bebu, Heidi Krause-Steinrauf, William H. Herman, John M. Higgins, Margaret Tiktin, Robert M. Cohen, Claire Lund, Richard M. Bergenstal, Mary L. Johnson, and Valerie Arends


The Kronos Early Estrogen Prevention Study (KEEPS): what have we learned?, Virginia M Miller, Fredrick Naftolin, Sanjay Asthana, Dennis M. Black, Eliot A. Brinton, Matthew J. Budoff, Marcelle I. Cedars, N Maritza Dowling, Carey E. Gleason, Howard N. Hodis, Muthuvel Jayachandran, Kejal Kantarci, Rogerio A. Lobo, JoAnn E. Manson, Lubna Pal, Nanette F. Santoro, Hugh S. Taylor, and S Mitchell Harman


Applying Risk-Benefit Analysis to Outcomes in TB Clinical Trials., Sachiko Miyahara, Ritesh Ramchandani, Soyeon Kim, Scott R. Evans, Amita Gupta, Susan Swindells, Richard E. Chaisson, and Grace Montepiedra


Does diabetes prevention translate into reduced long-term vascular complications of diabetes?, David M. Nathan, Peter H. Bennett, Jill P. Crandall, Sharon L. Edelstein, Ronald B. Goldberg, Steven E. Kahn, William C. Knowler, Kieren J. Mather, Sunder Mudaliar, Trevor J. Orchard, Marinella Temprosa, and Neil H. White


Myelomeningocele sac associated with worse lower extremity neurologic sequela: evidence for prenatal neural stretch injury?, E R. Oliver, G G. Heuer, E A. Thom, P K. Burrows, R A. Didier, S E. DeBari, J S. Martin-Saavedra, J S. Moldenhauer, J Jatres, L J. Howell, N S. Adzick, and B G. Coleman


Optimising treatment decision rules through generated effect modifiers: a precision medicine tutorial, Eva Petkova, Hyung Park, Adam Ciarleglio, R. Todd Ogden, and Thaddeus Tarpey


Recombinant Opisthorchis viverrini tetraspanin expressed in Pichia pastoris as a potential vaccine candidate for opisthorchiasis, L T. Phung, S Chaiyadet, N Hongsrichan, J Sotillo, H D T Dieu, C Q. Tran, P J. Brindley, A Loukas, and T Laha


Diabetes Care Editors' Expert Forum 2018: Managing Big Data for Diabetes Research and Care, M C. Riddle, L Blonde, H C. Gerstein, E W. Gregg, R R. Holman, J M. Lachin, G A. Nichols, A Turchin, and W T. Cefalu


Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)., Daniela Rosado, Raquel Xavier, Ricardo Severino, Fernando Tavares, Jo Cable, and Marcos Pérez-Losada

Transcriptome patterns in hidradenitis suppurativa: support for the role of antimicrobial peptides and interferon pathways in disease pathogenesis, V. K. Shanmugam, D. Jones, S. McNish, M. L. Bendall, and K. A. Crandall


Cancer Incidence and Mortality in Firefighters: A State-of-the-Art Review and Meta-َAnalysis, E. S. Soteriades, J. Kim, C. A. Christophi, and S. N. Kales


ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data, Liam Spurr, Nawaf Alomran, Pavlos Bousounis, Dacian Reece-Stremtan, NM Prashant, Honguy Liu, Piotr Slowinski, Muzi Li, Qianqian Zhang, Justin Sein, Gabriel Asher, Keith A. Crandall, Krasimira Tsaneva-Atanasova, and Anelia Horvath


Modern clinician-initiated clinical trials to determine optimal therapy for multi-drug resistant Gram-negative infections, A G. Stewart, P N A Harris, M Chatfield, S R. Evans, D van Duin, and D L. Paterson


2276. Clinical Epidemiology of the Carbapenem-Resistant Enterobacteriaceae (CRE) Epidemic in Colombia: A Multicenter Prospective Study, Sandra Liliana Valderrama-Beltran, Lauren Komarow, Soraya Salcedo, Laura Mora, Adriana Marin, Karen M. Ordonez Diaz, Edilberto Cristancho Quintero, Beatriz Elena Ariza, Gloria Cortes, De la Hoz Alejandro, Jose Onate, Elsa Yasmin Vente, Viviana Mendez, Jairo Figueroa, Luz Osorio, Carlos Moreno, Jinnethe Reyes, Luis Dulcey, Pallares Christian, Henry Chambers, Vance G. Fowler, Scott R. Evans, Barry Kreiswirth, Maria Virginia Villegas, Robert A. Bonomo, David van Duin, and Cesar A. Arias


Randomization tests for multiarmed randomized clinical trials., Yanying Wang, William F. Rosenberger, and Diane Uschner


Acinetobacter infections, B. M. Wilson, F. Perez, Q. Pan, Y. Jiang, S. Evans, and R. A. Bonomo

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans, Joanna M. Wolfe, Jesse W. Breinholt, Keith A. Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, Laura E. Timm, Mark E. Siddall, and Heather D. Bracken-Grissom


The Consortium of Metabolomics Studies (COMETS): Metabolomics in 47 Prospective Cohort Studies., Bing Yu, Krista A. Zanetti, Marinella Temprosa, Demetrius Albanes, Nathan Appel, Clara Barrios Barrera, Yoav Ben-Shlomo, Eric Boerwinkle, Juan P. Casas, Clary Clish, Caroline Dale, Abbas Dehghan, Andriy Derkach, A Heather Eliassen, Paul Elliott, Eoin Fahy, Christian Gieger, Marc J. Gunter, Sei Harada, Tamara Harris, Deron R. Herr, David Herrington, Joel N. Hirschhorn, Elise Hoover, Ann W. Hsing, Mattias Johansson, Rachel S. Kelly, Chin Meng Khoo, Mika Kivimäki, Bruce S. Kristal, Claudia Langenberg, Jessica Lasky-Su, Deborah A. Lawlor, Luca A. Lotta, Massimo Mangino, Loïc Le Marchand, Ewy Mathé, Charles E. Matthews, Cristina Menni, Lorelei A. Mucci, Rachel Murphy, Matej Oresic, Eric Orwoll, Jennifer Ose, Alexandre C. Pereira, Mary C. Playdon, Lucilla Poston, Jackie Price, Qibin Qi, Kathryn Rexrode, Adam Risch, Joshua Sampson, Wei Jie Seow, Howard D. Sesso, Svati H. Shah, Xiao-Ou Shu, Gordon C S Smith, Ulla Sovio, Victoria L. Stevens, Rachael Stolzenberg-Solomon, Toru Takebayashi, Therese Tillin, Ruth Travis, Ioanna Tzoulaki, Cornelia M. Ulrich, Ramachandran S. Vasan, Mukesh Verma, Ying Wang, Nick J. Wareham, Andrew Wong, Naji Younes, Hua Zhao, Wei Zheng, and Steven C. Moore

Submissions from 2018


Properties of composite time to first event versus joint marginal analyses of multiple outcomes, Ionut Bebu and John M. Lachin


Long-Term Benefit of Empagliflozin on Life Expectancy in Patients With Type 2 Diabetes Mellitus and Established Cardiovascular Disease., Brian Claggett, John M. Lachin, Stefan Hantel, David Fitchett, Silvio E. Inzucchi, Hans J. Woerle, Jyothis T. George, and Bernard Zinman

Invasion by non-indigenous freshwater decapods of Malta and Sicily, central Mediterranean Sea, Alan Deidun, Arnold Sciberras, Justin Formosa, Bruno Zava, Gianni Insacco, Maria Corsini-Foka, and Keith A. Crandall


Multigene phylogeny reveals two new isolated and relic earthworm genera (Oligochaeta: Lumbricidae), Jorge Dominguez, Manuel Aira, Pablo G. Porto, Dario J. Diaz Cosin, and Marcos Perez-Losada

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

Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity, Andrea Hahn, Aszia Burrell, Hani Fanous, Hollis Chaney, Iman Sami, Geovanny F. Perez, Anastassios C. Koumbourlis, Robert J. Freishtat, and Keith A. Crandall

Microbial diversity within the airway microbiome in chronic pediatric lung diseases, Andrea Hahn, Stephanie Warnken, Marcos Pérez-Losada, Robert J. Freishtat, and Keith A. Crandall

De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: Narrowing the US origin(s) of the invasive kudzu, Matthew S. Haynsen, Mohammad Vatanparast, Gouri Mahadwar, Dennis Zhu, Roy Z. Moger-Reischer, Jeff J. Doyle, Keith A. Crandall, and Ashley N. Egan


Comparing neurodevelopmental outcomes at 30 months by presence of hydrocephalus and shunt status among children enrolled in the MOMS trial, A J. Houtrow, P K. Burrows, and E A. Thom

Seminal simian immunodeficiency virus in chronically infected cynomolgus macaques is dominated by virus originating from multiple genital organs, Laurent Houzet, Marcos Pérez-Losada, Giulia Matusali, Claire Deleage, Nathalie Dereuddre-Bosquet, Anne Pascale Satie, Florence Aubry, Emmanuelle Becker, Bernard Jégou, Roger Le Grand, Brandon F. Keele, Keith A. Crandall, and Nathalie Dejucq-Rainsford

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, Richard Durbin, Scott V. Edwards, Félix Forest, M. Thomas P. Gilbert, Melissa M. Goldstein, Igor V. Grigoriev, Kevin J. Hackett, David Haussler, Erich D. Jarvis, Warren E. Johnson, Aristides Patrinos, Stephen Richards, Juan Carlos Castilla-Rubio, Marie Anne Van Sluys, Pamela S. Soltis, Xun Xu, Huanming Yang, and Guojie Zhang


Identification of Burkholderia fungorum in the urine of an individual with spinal cord injury and augmentation cystoplasty using 16S sequencing: copathogen or innocent bystander?, Emma Nally, Suzanne L. Groah, Marcos Perez-Losada, Ljubica Caldovic, Inger Ljungberg, Neel J. Chandel, Bruce Sprague, Michael H. Hsieh, and Hans G. Pohl

Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas, Marcos Pérez-Losada, Kayla J. Authelet, Claire E. Hoptay, Christine Kwak, Keith A. Crandall, and Robert J. Freishtat

Systematic pan-cancer analysis of somatic allele frequency, Liam Spurr, Muzi Li, Nawaf Alomran, Qianqian Zhang, Paula Restrepo, Mercedeh Movassagh, Chris Trenkov, Nerissa Tunnessen, Tatiyana Apanasovich, Keith A. Crandall, Nathan Edwards, and Anelia Horvath


Characterization of mucoid and serous middle ear effusions from patients with chronic otitis media: implication of different biological mechanisms?, Val Stephanie, Marian Poley, Anna Krueger, Gustavo Nino, Kristy Brown, Marcos Perez-Losada, Heather Gordish-Dressman, and Diego Preciado

Phototransduction gene expression and evolution in cave and surface crayfishes, David B. Stern and Keith A. Crandall

The evolution of gene expression underlying vision loss in cave animals, David B. Stern and Keith A. Crandall

Kisspeptin/GPR54 System: What Do We Know about Its Role in Human Reproduction?, Camila M. Trevisan, Erik Montagna, Renato De Oliveira, Denise M. Christofolini, Caio P. Barbosa, Keith A. Crandall, and Bianca Bianco

Phylogeography reveals unexpectedly low genetic diversity in a widely distributed species: The case of the freshwater crab Aegla platensis (Decapoda: Anomura), Bianca L. Zimmermann, Marcelo S. Crivellaro, Caroline B. Hauschild, Marlise L. Bartholomei-Santos, Keith A. Crandall, Marcos Pérez-Losada, Federico Giri, Pablo Collins, and Sandro Santos

Submissions from 2017

An updated classification of the freshwater crayfishes (Decapoda: Astacidea) of the world, with a complete species list, Keith A. Crandall and Sammy De Grave


Looks can be deceiving: species delimitation reveals hidden diversity in the freshwater crab Aegla longirostri (Decapoda: Anomura), Marcelo S. Crivellaro, Bianca L. Zimmermann, Marlise L. Bartholomei-Santos, Keith A. Crandall, Marcos Perez-Losada, Georgina Bond-Buckup, and Sandro Santos

Genome polymorphism detection through relaxed de bruijn graph construction, M. Stanley Fujimoto, Cole Lyman, Anton Suvorov, Paul Bodily, Quinn Snell, Keith Crandall, Seth Bybee, and Mark Clement

Whole genome phylogenetic tree reconstruction using colored de bruijn graphs, Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, and Mark J. Clement

Nasopharyngeal microbiome diversity changes over time in children with asthma, Marcos Pérez-Losada, Lamia Alamri, Keith A. Crandall, and Robert J. Freishtat

Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC, Marcos Pérez-Losada, Amanda D. Castel, Brittany Lewis, Michael Kharfen, Charles P. Cartwright, Bruce Huang, Taylor Maxwell, Alan E. Greenberg, and Keith A. Crandall

Overexpressed somatic alleles are enriched in functional elements in Breast Cancer, Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, and Anelia Horvath

Images are not and should not ever be type specimens: A rebuttal to Garraffoni & Freitas, D. Christopher Rogers, Shane T. Ahyong, Christopher B. Boyko, Cédric D.Udekem D'Acoz, Akira Asakura, Joanmei An, Bonnie A. Bain, Paul Bartels, Lynda Beladjal, Richard C. Brusca, Stephen D. Cairns, Peter Castro, Caroline Chaboo, Tin Yam Chan, Joel Cracraft, Keith Crandall, Neil Cumberlidge, Peter J.F. Davie, Peter C. Dworschak, Michael S. Engel, Raquel A. Fagundo, Darryl L. Felder, Laszlo Forro, Charles H.J.M. Fransen, Stuart R. Gelder, Sarah Gerken, Chris Glasby, Fredric R. Govedich, Danièle Guinot, Brenda J. Hann, Richard W. Heard, and Eric P. Hoberg

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 B. Stern, Eduardo Castro Nallar, Jason Rathod, and Keith A. Crandall

Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA), Christian R. Voolstra, Marcin Adamski, Shobhit Agrawal, Agostinho Antunes, Manuel Aranda, Andy Baxevanis, Mark Blaxter, Thomas Bosch, Heather Bracken-Grissom, Jonathan Coddington, Timothy Collins, Keith Crandall, Mikael Dahl, Daniel Distel, Casey Dunn, Michael Eitel, Jean Francois Flot, Gonzalo Giribet, Fabrizio Ghiselli, Steven H.D. Haddock, Kevin Kocot, Yi Jin Liew, Audrey Majeske, Bernhard Misof, Christopher Mungal, Stephen J. O'Brien, Timothy Ravasi, Mauro de Freitas Rebelo, Ana Riesgo, Christine Schnitzler, Anja Schulze, and Billie Swalla

Corrigendum to: Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA) (Invertebrate Systematics (2017) 31: 1 (1-7) DOI: 10.1071/IS16059), Christian R. Voolstra, Marcin Adamski, Shobhit Agrawal, Agostinho Antunes, Manuel Aranda, Andy Baxevanis, Mark Blaxter, Thomas Bosch, Heather Bracken-Grissom, Jonathan Coddington, Timothy Collins, Keith Crandall, Mikael Dahl, Daniel Distel, Casey Dunn, Michael Eitel, Jean Francois Flot, Gonzalo Giribet, Fabrizio Ghiselli, Steven H.D. Haddock, Kevin Kocot, Yi Jin Liew, Audrey Majeske, Bernhard Misof, Christopher Mungal, Stephen J. O'Brien, Timothy Ravasi, Mauro de Freitas Rebelo, Ana Riesgo, Christine Schnitzler, Anja Schulze, and Billie Swalla

Submissions from 2016

Collecting and processing freshwater crayfishes, Keith A. Crandall

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 A. Crandall

Global diversity and conservation of freshwater crayfish (Crustacea: Decapoda: Astacoidea), Tadashi Kawai and Keith A. Crandall

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children, Marcos Pérez-Losada, Keith A. Crandall, and Robert J. Freishtat

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-scale transcriptome data for fish evolution studies, Ying Sun, Yu Huang, Xiaofeng Li, Carole C. Baldwin, Zhuocheng Zhou, Zhixiang Yan, Keith A. Crandall, Yong Zhang, Xiaomeng Zhao, Min Wang, Alex Wong, Chao Fang, Xinhui Zhang, Hai Huang, Jose V. Lopez, Kirk Kilfoyle, Yong Zhang, Guillermo Ortí, Byrappa Venkatesh, and Qiong Shi

Submissions from 2015


Recombination in viruses: mechanisms, methods of study, and evolutionary consequences., Marcos Pérez-Losada, Miguel Arenas, Juan Carlos Galán, Ferran Palero, and Fernando González-Candelas