specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.
Autorzy:
Darcy JL; Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA. . Amend AS; School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA.; Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA. Swift SOI; School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA. Sommers PS; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, USA. LozuponeCA; Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
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Źródło:
Environmental microbiome [Environ Microbiome] 2022 Jun 25; Vol. 17 (1), pp. 34. Date of Electronic Publication: 2022 Jun 25.
CANTARE: finding and visualizing network-based multi-omic predictive models.
Autorzy:
Siebert JC; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. . Saint-Cyr M; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. Borengasser SJ; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. Wagner BD; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA. LozuponeCA; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. Görg C; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 Feb 19; Vol. 22 (1), pp. 80. Date of Electronic Publication: 2021 Feb 19.
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data.
Autorzy:
Shaffer M; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Thurimella K; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Quinn K; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 80045CO, Aurora, USA. Doenges K; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 80045CO, Aurora, USA. Zhang X; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 80045CO, Aurora, USA.; Present address: BioElectron Technology Corporation, Mountain View, CA, 94043, USA. Bokatzian S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 80045CO, Aurora, USA. Reisdorph N; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 80045CO, Aurora, USA. LozuponeCA; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. catherine.lozupone@cuanschutz.edu.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2019 Nov 28; Vol. 20 (1), pp. 614. Date of Electronic Publication: 2019 Nov 28.
VOLARE: visual analysis of disease-associated microbiome-immune system interplay.
Autorzy:
Siebert JC; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .; CytoAnalytics, Denver, CO, 80113, USA. . Neff CP; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Schneider JM; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Regner EH; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Ohri N; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Kuhn KA; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Palmer BE; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. LozuponeCA; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. Görg C; CytoAnalytics, Denver, CO, 80113, USA.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2019 Aug 20; Vol. 20 (1), pp. 432. Date of Electronic Publication: 2019 Aug 20.
Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection.
Autorzy:
Li SX; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Sen S; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Schneider JM; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Xiong KN; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Nusbacher NM; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Moreno-Huizar N; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Shaffer M; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Armstrong AJS; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America.; Department of Immunology and Microbiology, University of Colorado Anschutz, Aurora, Colorado, United States of America. Severs E; Division of Rheumatology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Kuhn K; Division of Rheumatology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Neff CP; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. McCarter M; Division of Colorectal Surgery, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Campbell T; Division of Infectious Diseases, University of Colorado Anschutz, Aurora, Colorado, United States of America. LozuponeCA; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America. Palmer BE; Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America.
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Źródło:
PLoS pathogens [PLoS Pathog] 2019 Apr 04; Vol. 15 (4), pp. e1007611. Date of Electronic Publication: 2019 Apr 04 (Print Publication: 2019).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
The UniFrac significance test is sensitive to tree topology.
Autorzy:
LozuponeCA; Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA. Catherine.Lozupone@ucdenver.edu. Knight R; Departments of Pediatrics and Computer Science & Engineering, University of California San Diego, La Jolla, CA, 92093, USA. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2015 Jul 07; Vol. 16, pp. 211. Date of Electronic Publication: 2015 Jul 07.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
Roy MG; 1] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2]. Livraghi-Butrico A; 1] University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA [2]. Fletcher AA; 1] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2]. McElwee MM; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Evans SE; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Boerner RM; University of Texas Health Science Center-Houston Medical School, 6431 Fannin Street, Houston, Texas 77030, USA. Alexander SN; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Bellinghausen LK; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Song AS; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Petrova YM; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Tuvim MJ; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Adachi R; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Romo I; 1] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Instituto Tecnológico y de Estudios Superiores de Monterrey, Avenida Eugenio Garza Sada 2501 Sur Colonia Tecnológico, Monterrey, Nuevo León 64849, Mexico. Bordt AS; Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, USA. Bowden MG; 1] Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, USA [2] University of Houston-Downtown, 1 Main Street, Houston, Texas 77002, USA. Sisson JH; University of Nebraska Medical Center, 985910 Nebraska Medical Center, Omaha, Nebraska 68198, USA. Woodruff PG; University of California San Francisco, 505 Parnassus Avenue, San Francisco, California 27599, USA. Thornton DJ; University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. Rousseau K; University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. De la Garza MM; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Moghaddam SJ; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Karmouty-Quintana H; University of Texas Health Science Center-Houston Medical School, 6431 Fannin Street, Houston, Texas 77030, USA. Blackburn MR; University of Texas Health Science Center-Houston Medical School, 6431 Fannin Street, Houston, Texas 77030, USA. Drouin SM; University of Texas Health Science Center-Houston Medical School, 6431 Fannin Street, Houston, Texas 77030, USA. Davis CW; University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. Terrell KA; University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. Grubb BR; University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. O'Neal WK; University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. Flores SC; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Cota-Gomez A; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. LozuponeCA; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Donnelly JM; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Watson AM; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Hennessy CE; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Keith RC; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Yang IV; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Barthel L; 1] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2] National Jewish Health, Denver, Colorado 80206, USA. Henson PM; 1] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2] National Jewish Health, Denver, Colorado 80206, USA. Janssen WJ; 1] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2] National Jewish Health, Denver, Colorado 80206, USA. Schwartz DA; University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Boucher RC; University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. Dickey BF; University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. Evans CM; 1] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA.
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Źródło:
Nature [Nature] 2014 Jan 16; Vol. 505 (7483), pp. 412-6. Date of Electronic Publication: 2013 Dec 08.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework.
Autorzy:
Faith DP; The Australian Museum, 6 College St., Sydney, NSW, 2010, Australia. LozuponeCA; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA. Nipperess D; Department of Biological Sciences, Macquarie University, NSW, 2109, Australia. Knight R; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
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