Expanded microbiome niches of RAG-deficient patients

Autor: Thomas, Jim, Mullikin, James, Young, Alice, Bouffard, Gerry, Barnabas, Betty, Brooks, Shelise, Buchter, Chloe, Crawford, Juyun, Han, Joel, Ho, Shi-ling, Legaspi, Richelle, Maduro, Quino, Marfani, Holly, Montemayor, Casandra, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Black, Sean, Dekhtyar, Mila, Masiello, Cathy, McDowell, Jenny, Park, Morgan, Thomas, Pam, Vemulapalli, Meg, Blaustein, Ryan A., Shen, Zeyang, Kashaf, Sara Saheb, Lee-Lin, ShihQueen, Conlan, Sean, Bosticardo, Marita, Delmonte, Ottavia M., Holmes, Cassandra J., Taylor, Monica E., Banania, Glenna, Nagao, Keisuke, Dimitrova, Dimana, Kanakry, Jennifer A., Su, Helen, Holland, Steven M., Bergerson, Jenna R.E., Freeman, Alexandra F., Notarangelo, Luigi D., Kong, Heidi H., Segre, Julia A.

Publikováno v: In Cell Reports Medicine 17 October 2023 4(10)

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Complete sequencing of ape genomes.

Autor: Yoo D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Rhie A; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Hebbar P; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Antonacci F; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., Logsdon GA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA., Solar SJ; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Antipov D; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Pickett BD; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Safonova Y; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Montinaro F; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.; Institute of Genomics, University of Tartu, Tartu, Estonia., Luo Y; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA., Malukiewicz J; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Storer JM; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA., Lin J; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Sequeira AN; Department of Biology, Penn State University, University Park, PA 16802, USA., Mangan RJ; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA., Hickey G; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Anez GM; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Balachandran P; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Bankevich A; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Beck CR; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA., Biddanda A; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Borchers M; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Bouffard GG; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Brannan E; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Brooks SY; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Carbone L; Department of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA.; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Carrel L; PSU Medical School, Penn State University School of Medicine, Hershey, PA, USA., Chan AP; The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA., Crawford J; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Diekhans M; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Engelbrecht E; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Feschotte C; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA., Formenti G; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA., Garcia GH; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., de Gennaro L; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., Gilbert D; San Diego Biomedical Research Institute, San Diego, CA, USA., Green RE; University of California Santa Cruz, Santa Cruz, CA, USA., Guarracino A; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA., Gupta I; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Haddad D; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Han J; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China., Harris RS; Department of Biology, Penn State University, University Park, PA 16802, USA., Hartley GA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA., Harvey WT; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Hiller M; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany., Hoekzema K; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Houck ML; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Jeong H; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Kamali K; Department of Biology, Penn State University, University Park, PA 16802, USA., Kellis M; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Kille B; Department of Computer Science, Rice University, Houston, TX 77005, USA., Lee C; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA., Lee Y; Laboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea., Lees W; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.; Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel., Lewis AP; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Li Q; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA., Loftus M; Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Loh YHE; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Loucks H; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Ma J; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Mao Y; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.; Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China.; Shanghai Jiao Tong University Chongqing Research Institute, Chongqing, China., Martinez JFI; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Masterson P; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., McCoy RC; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., McGrath B; Department of Biology, Penn State University, University Park, PA 16802, USA., McKinney S; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Meyer BS; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Miga KH; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Mohanty SK; Department of Biology, Penn State University, University Park, PA 16802, USA., Munson KM; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Pal K; Department of Biology, Penn State University, University Park, PA 16802, USA., Pennell M; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Pevzner PA; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Potapova T; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Ringeling FR; Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany., Roha JL; Department of Integrative Biology, University of California, Berkeley, Berkeley, USA., Ryder OA; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Sacco S; University of California Santa Cruz, Santa Cruz, CA, USA., Saha S; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Sasaki T; San Diego Biomedical Research Institute, San Diego, CA, USA., Schatz MC; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA., Schork NJ; The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA., Shanks C; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Smeds L; Department of Biology, Penn State University, University Park, PA 16802, USA., Son DR; Department of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Steiner C; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Sweeten AP; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Tassia MG; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Torres-González E; Department of Biology, Penn State University, University Park, PA 16802, USA., Trivedi M; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Wei W; School of Life Sciences, Westlake University, Hangzhou 310024, China.; National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China., Wertz J; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Yang M; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Zhang P; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA., Zhang S; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China., Zhang Y; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Zhang Z; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Zhao SA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Zhu Y; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Jarvis ED; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Gerton JL; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Rivas-González I; Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany., Paten B; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Szpiech ZA; Department of Biology, Penn State University, University Park, PA 16802, USA., Huber CD; Department of Biology, Penn State University, University Park, PA 16802, USA., Lenz TL; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Konkel MK; Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Yi SV; Department of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Canzar S; Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany., Watson CT; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Sudmant PH; Department of Integrative Biology, University of California, Berkeley, Berkeley, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, USA., Molloy E; Department of Computer Science, University of Maryland, College Park, MD 20742, USA., Garrison E; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA., Lowe CB; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA., Ventura M; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.; Departments of Molecular and Cell Biology, UConn Storrs, CT, USA., Koren S; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Makova KD; Department of Biology, Penn State University, University Park, PA 16802, USA., Phillippy AM; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 05. Date of Electronic Publication: 2024 Oct 05.