OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures

Autor: Leo Lahti, Lejzerowicz F, Shi Huang, Jack A. Gilbert, Pedro Belda-Ferre, Qiyun Zhu, Daniel McDonald, Das P, Sepich-Poore Gd, Justin P. Shaffer, Yu J, Guillaume Méric, Rob Knight, Niina Haiminen, Hyun-Chul Kim, Teemu J. Niiranen, Michael Inouye, Aki S. Havulinna, Antonio Gonzalez, George Armstrong, Yoshiki Vázquez-Baeza, Austin D. Swafford, McGrath I, Salomaa, Kuczynski J, Miten Jain

We introduce Operational Genomic Unit (OGU), a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0d7498c3e8eb9b49f8542a933bfc83d8
https://doi.org/10.1101/2021.04.04.438427

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

Autor: Guccione C; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA.; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Patel L; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Medical Scientist Training Program, University of California, San Diego, La Jolla, California, USA., Tomofuji Y; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan., McDonald D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Gonzalez A; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Sepich-Poore GD; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Sonehara K; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan., Zakeri M; Department of Computer Science, Johns Hopkins University., Chen Y; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.; Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA., Dilmore AH; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA., Damle N; Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.; Department of Cognitive Science, University of California San Diego, La Jolla, CA, USA., Baranzini SE; Weill Institute for Neurosciences. Department of Neurology. University of California, San Francisco (UCSF), San Francisco, CA 94158, USA., Nakatsuji T; Department of Dermatology, University of California San Diego, La Jolla, CA, USA., Gallo RL; Department of Dermatology, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Langmead B; Department of Computer Science, Johns Hopkins University., Okada Y; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan.; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita 565-0871, Japan., Curtius K; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA.; VA San Diego Healthcare System, San Diego, CA, USA., Knight R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan.; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Publikováno v: Research square [Res Sq] 2024 Oct 23. Date of Electronic Publication: 2024 Oct 23.

Robustness of cancer microbiome signals over a broad range of methodological variation.

Autor: Sepich-Poore GD; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.; Micronoma, San Diego, CA, USA.; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA., McDonald D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Kopylova E; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Clarity Genomics, Antwerp, Belgium., Guccione C; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Zhu Q; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; School of Life Sciences, Arizona State University, Tempe, AZ, USA., Austin G; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.; Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA., Carpenter C; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Fraraccio S; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Micronoma, San Diego, CA, USA., Wandro S; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Micronoma, San Diego, CA, USA., Kosciolek T; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland., Janssen S; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany., Metcalf JL; Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA., Song SJ; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Kanbar J; Department of Medicine, University of California San Diego, La Jolla, CA, USA., Miller-Montgomery S; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.; Micronoma, San Diego, CA, USA., Heaton R; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA., Mckay R; Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA., Patel SP; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA., Swafford AD; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Korem T; Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.; Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA., Knight R; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.

Publikováno v: Oncogene [Oncogene] 2024 Apr; Vol. 43 (15), pp. 1127-1148. Date of Electronic Publication: 2024 Feb 23.

Reuniting philosophy and science to advance cancer research.

Autor: Pradeu T; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France.; CNRS UMR8590, Institut d'Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris, 75006, France., Daignan-Fornier B; CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux, 33077, France., Ewald A; Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA., Germain PL; Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich, 8092, Switzerland.; Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich, 8057, Switzerland., Okasha S; Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK., Plutynski A; Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO, 63105, USA., Benzekry S; Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille, 13005, France., Bertolaso M; Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Álvaro del Portillo, 21-00128, Rome, Italy.; Centre for Cancer Biomarkers, University of Bergen, Bergen, 5007, Norway., Bissell M; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Brown JS; Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA., Chin-Yee B; Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada.; Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada., Chin-Yee I; Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada., Clevers H; Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, 4070, Switzerland.; Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands., Cognet L; CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence, 33400, France., Darrason M; Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France.; Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon, 69007, France., Farge E; Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d'apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris, 75005, France., Feunteun J; INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France., Galon J; INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l'École de Médecine, Paris, 75006, France., Giroux E; Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon, 69007, France., Green S; Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen, 2200, Denmark., Gross F; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Jaulin F; INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France., Knight R; Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA, 92093, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA., Laconi E; Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari, 09124, Italy., Larmonier N; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Maley C; Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA.; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA.; Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85287, USA.; Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85287, USA.; Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA., Mantovani A; Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy.; Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan, 20089, Italy.; The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK., Moreau V; INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076, France., Nassoy P; CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence, 33400, France., Rondeau E; INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d'Italie, Lyon, 69007, France., Santamaria D; Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, 37007, Spain., Sawai CM; INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076, France., Seluanov A; Department of Biology and Medicine, University of Rochester, Rochester, NY, 14627, USA., Sepich-Poore GD; Micronoma, 6342 Ferris Square, San Diego, CA, 92121, USA., Sisirak V; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Solary E; INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Département d'hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre, 94270, France., Yvonnet S; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, DK-2200, Denmark., Laplane L; CNRS UMR8590, Institut d'Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris, 75006, France.; INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ, 85281, USA.

Publikováno v: Biological reviews of the Cambridge Philosophical Society [Biol Rev Camb Philos Soc] 2023 Oct; Vol. 98 (5), pp. 1668-1686. Date of Electronic Publication: 2023 May 08.

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis.

Autor: Brewer RC; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Lanz TV; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.; Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68167, Germany., Hale CR; Rockefeller University, New York City, NY 10065, USA., Sepich-Poore GD; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA., Martino C; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA., Swafford AD; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA., Carroll TS; Bioinformatics Resource Center, Rockefeller University, 1230 York Ave., New York, NY 10065, USA., Kongpachith S; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Blum LK; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Elliott SE; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Blachere NE; Rockefeller University, New York City, NY 10065, USA.; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA., Parveen S; Rockefeller University, New York City, NY 10065, USA., Fak J; Rockefeller University, New York City, NY 10065, USA., Yao V; Department of Computer Science, Rice University, Houston, TX 77005, USA.; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA., Troyanskaya O; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.; Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.; Flatiron Institute, Simons Foundation, New York, NY 10010, USA., Frank MO; Rockefeller University, New York City, NY 10065, USA., Bloom MS; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Jahanbani S; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Gomez AM; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Iyer R; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Ramadoss NS; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Sharpe O; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Chandrasekaran S; Division of Rheumatology, University of Colorado Denver, Aurora, CO 80045, USA., Kelmenson LB; Division of Rheumatology, University of Colorado Denver, Aurora, CO 80045, USA., Wang Q; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Wong H; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Torres HL; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Wiesen M; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Graves DT; Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA., Deane KD; Division of Rheumatology, University of Colorado Denver, Aurora, CO 80045, USA., Holers VM; Division of Rheumatology, University of Colorado Denver, Aurora, CO 80045, USA., Knight R; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA., Darnell RB; Rockefeller University, New York City, NY 10065, USA.; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA., Robinson WH; Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.; VA Palo Alto Health Care System, Palo Alto, CA 94304, USA., Orange DE; Rockefeller University, New York City, NY 10065, USA.; Hospital for Special Surgery, New York City, NY 10075, USA.

Publikováno v: Science translational medicine [Sci Transl Med] 2023 Feb 22; Vol. 15 (684), pp. eabq8476. Date of Electronic Publication: 2023 Feb 22.