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Tytuł :
A high-quality bonobo genome refines the analysis of hominid evolution.
Autorzy :
Mao Y; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Catacchio CR; Department of Biology, University of Bari, Bari, Italy.
Hillier LW; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Li R; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Sulovari A; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Fernandes JD; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Montinaro F; Department of Biology, University of Bari, Bari, Italy.; Estonian Biocentre, Institute of Genomics, Tartu, Estonia.
Gordon DS; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Storer JM; Institute for Systems Biology, Seattle, WA, USA.
Haukness M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Fiddes IT; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Murali SC; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Dishuck PC; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Hsieh P; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Harvey WT; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Audano PA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Mercuri L; Department of Biology, University of Bari, Bari, Italy.
Piccolo I; Department of Biology, University of Bari, Bari, Italy.
Antonacci F; Department of Biology, University of Bari, Bari, Italy.
Munson KM; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Lewis AP; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Baker C; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Underwood JG; Pacific Biosciences (PacBio) of California, Menlo Park, CA, USA.
Hoekzema K; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Huang TH; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Sorensen M; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Walker JA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
Hoffman J; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Salama SR; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Pang AWC; Bionano Genomics, San Diego, CA, USA.
Lee J; Bionano Genomics, San Diego, CA, USA.
Hastie AR; Bionano Genomics, San Diego, CA, USA.
Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Batzer MA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
Diekhans M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Ventura M; Department of Biology, University of Bari, Bari, Italy. .
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. .
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Źródło :
Nature [Nature] 2021 Jun; Vol. 594 (7861), pp. 77-81. Date of Electronic Publication: 2021 May 05.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets.
Autorzy :
Beale HC; UC Santa Cruz, Molecular, Cell and Developmental Biology, 1156 High Street, Santa Cruz, CA 95064, USA.; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Roger JM; UC Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.
Cattle MA; UC Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.
McKay LT; UC Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.
Thompson DKA; UC Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.
Learned K; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Lyle AG; UC Santa Cruz, Molecular, Cell and Developmental Biology, 1156 High Street, Santa Cruz, CA 95064, USA.; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Kephart ET; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Currie R; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Lam DL; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Sanders L; UC Santa Cruz, Molecular, Cell and Developmental Biology, 1156 High Street, Santa Cruz, CA 95064, USA.
Pfeil J; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Vivian J; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Bjork I; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Salama SR; UC Santa Cruz, Department of Biomolecular Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Haussler D; UC Santa Cruz, Department of Biomolecular Engineering, 1156 High Street, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Vaske OM; UC Santa Cruz, Molecular, Cell and Developmental Biology, 1156 High Street, Santa Cruz, CA 95064, USA.; UC Santa Cruz, Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
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Źródło :
GigaScience [Gigascience] 2021 Mar 13; Vol. 10 (3).
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Autorzy :
Warren WC; Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. .; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.; Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
Harris RA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Haukness M; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Fiddes IT; Inscripta Inc., Boulder, CO 80301, USA.
Murali SC; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Fernandes J; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Dishuck PC; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Storer JM; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.; Institue for Systems Biology, Seattle, WA 98109, USA.
Raveendran M; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Hillier LW; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Porubsky D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Mao Y; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Gordon D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Vollger MR; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Lewis AP; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Munson KM; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
DeVogelaere E; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Armstrong J; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Diekhans M; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Walker JA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Tomlinson C; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Graves-Lindsay TA; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Kremitzki M; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Salama SR; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Audano PA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Escalona M; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Maurer NW; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Antonacci F; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Mercuri L; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Maggiolini FAM; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Catacchio CR; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Underwood JG; Pacific Biosciences of California, Seattle, WA 94025, USA.
O'Connor DH; Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA.
Sanders AD; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
Korbel JO; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
Ferguson B; Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
Kubisch HM; Tulane National Primate Research Center, Covington, LA 70433, USA.
Picker L; Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA.
Kalin NH; Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA.
Rosene D; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA.
Levine J; Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.
Abbott DH; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.; Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA.
Gray SB; The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA.
Sanchez MM; Yerkes National Primate Research Center, Atlanta, GA 30329, USA.; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA.
Kovacs-Balint ZA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA.
Kemnitz JW; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.; Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
Thomasy SM; Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.; Department of Ophthalmology and Vision Science, School of Medicine, University of California-Davis, Davis, CA 95817, USA.
Roberts JA; California National Primate Research Center, Davis, CA 95616, USA.
Kinnally EL; California National Primate Research Center, Davis, CA 95616, USA.; Department of Psychology, University of California, Davis, CA 95616, USA.
Capitanio JP; California National Primate Research Center, Davis, CA 95616, USA.; Department of Psychology, University of California, Davis, CA 95616, USA.
Skene JHP; Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
Platt M; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Cole SA; Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA.
Green RE; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Ventura M; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Wiseman RW; Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA.
Paten B; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Batzer MA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Rogers J; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. .
Eichler EE; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. .; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Źródło :
Science (New York, N.Y.) [Science] 2020 Dec 18; Vol. 370 (6523).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Genetic Predisposition to Disease*
Genome*
Polymorphism, Single Nucleotide*
Macaca mulatta/*genetics
Animals ; Genetic Variation ; Humans ; Molecular Sequence Annotation ; Whole Genome Sequencing
Czasopismo naukowe
Tytuł :
Identification of a differentiation stall in epithelial mesenchymal transition in histone H3-mutant diffuse midline glioma.
Autorzy :
Sanders LM; Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Cheney A; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Seninge L; Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
van den Bout A; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Chen M; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Beale HC; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Kephart ET; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Pfeil J; Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Learned K; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Lyle AG; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Bjork I; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Haussler D; Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Salama SR; Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Vaske OM; University of California Santa Cruz Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.; Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Źródło :
GigaScience [Gigascience] 2020 Dec 15; Vol. 9 (12).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Czasopismo naukowe
Tytuł :
ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy.
Autorzy :
Rao AA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.; Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.
Madejska AA; Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.; Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, Santa Cruz, CA, United States.
Pfeil J; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.; Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.
Paten B; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.; Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.
Salama SR; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.
Haussler D; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.; Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.
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Źródło :
Frontiers in immunology [Front Immunol] 2020 Nov 10; Vol. 11, pp. 483296. Date of Electronic Publication: 2020 Nov 10 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Antigens, Neoplasm*/genetics
Antigens, Neoplasm*/immunology
Epitopes, T-Lymphocyte*/genetics
Epitopes, T-Lymphocyte*/immunology
Immunotherapy*
Neoplasms*/genetics
Neoplasms*/immunology
Neoplasms*/therapy
Software*
T-Lymphocytes, Cytotoxic/*immunology
Humans ; Predictive Value of Tests
Czasopismo naukowe
Tytuł :
Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature.
Autorzy :
Levinson A; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Lee AG; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Martell HJ; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Breese MR; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Zaloudek C; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.; Department of Pathology, University of California, San Francisco, San Francisco, CA.
Van Ziffle J; Department of Pathology, University of California, San Francisco, San Francisco, CA.
Laguna B; Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA.
Leung SG; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Chen MD; Department of Obstetrics and Gynecology, Sutter Health, San Francisco, CA.
Chen LM; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.; Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA.
Pfeil J; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA.
Ladwig NR; Department of Pathology, University of California, San Francisco, San Francisco, CA.
Shah AT; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Behroozfard I; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.
Rao AA; Department of Pathology, University of California, San Francisco, San Francisco, CA.
Salama SR; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA.
Sweet-Cordero EA; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.
Stieglitz E; Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.
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Źródło :
JCO precision oncology [JCO Precis Oncol] 2020 Nov 02; Vol. 4. Date of Electronic Publication: 2020 Nov 02 (Print Publication: 2020).
Typ publikacji :
Case Reports
Raport
Tytuł :
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.
Autorzy :
Okhovat M; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239; .
Nevonen KA; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239.
Davis BA; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239.
Michener P; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239.
Ward S; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239.
Milhaven M; Department of Ecology and Evolution, Institute for Advance Computational Science, Stony Brook University, Stony Brook, NY 11794.
Harshman L; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.; Institute for Human Genetics, University of California, San Francisco, CA 94158.
Sohota A; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.; Institute for Human Genetics, University of California, San Francisco, CA 94158.
Fernandes JD; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064.; University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064.
Salama SR; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064.; University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064.; Howard Hughes Medical Institute, University of California, Santa Cruz, CA 96064.
O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269.
Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.; Institute for Human Genetics, University of California, San Francisco, CA 94158.
Veeramah KR; Department of Ecology and Evolution, Institute for Advance Computational Science, Stony Brook University, Stony Brook, NY 11794.
Carbone L; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239; .; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239.; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006.; Department of Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239.
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Źródło :
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2020 Aug 11; Vol. 117 (32), pp. 19328-19338. Date of Electronic Publication: 2020 Jul 20.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Genome*
Retroelements*
Hylobates/*genetics
Animals ; Chromatin/genetics ; Evolution, Molecular ; Gene Expression Regulation ; Hylobates/classification ; Mutagenesis, Insertional ; Regulatory Sequences, Nucleic Acid ; Species Specificity
Czasopismo naukowe
Tytuł :
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.
Autorzy :
Pfeil J; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Sanders LM; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Anastopoulos I; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Lyle AG; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Weinstein AS; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Xue Y; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Blair A; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Beale HC; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Lee A; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Leung SG; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Dinh PT; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Shah AT; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Breese MR; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Devine WP; Department of Anatomic Pathology, University of California, San Francisco, California, San Francisco, United States of America.
Bjork I; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Salama SR; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Sweet-Cordero EA; Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America.
Haussler D; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.
Vaske OM; Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.; Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America.
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Źródło :
PLoS computational biology [PLoS Comput Biol] 2020 Apr 10; Vol. 16 (4), pp. e1007753. Date of Electronic Publication: 2020 Apr 10 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Expression Profiling/*methods
Neoplasms/*genetics
Transcriptome/*genetics
Biomarkers, Tumor ; Child ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Models, Statistical ; Neuroblastoma/genetics ; Precision Medicine/methods ; Tumor Microenvironment/genetics
Czasopismo naukowe
Tytuł :
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families.
Autorzy :
Fernandes JD; 1Genomics Institute, University of California, Santa Cruz, USA.; 2Department of Biomolecular Engineering, University of California, Santa Cruz, USA.; 3Howard Hughes Medical Institute, University of California, Santa Cruz, USA.
Zamudio-Hurtado A; 1Genomics Institute, University of California, Santa Cruz, USA.; Big Data to Knowledge Program, California State University, Monterey Bay, USA.
Clawson H; 1Genomics Institute, University of California, Santa Cruz, USA.
Kent WJ; 1Genomics Institute, University of California, Santa Cruz, USA.
Haussler D; 1Genomics Institute, University of California, Santa Cruz, USA.; 2Department of Biomolecular Engineering, University of California, Santa Cruz, USA.; 3Howard Hughes Medical Institute, University of California, Santa Cruz, USA.
Salama SR; 1Genomics Institute, University of California, Santa Cruz, USA.; 2Department of Biomolecular Engineering, University of California, Santa Cruz, USA.; 3Howard Hughes Medical Institute, University of California, Santa Cruz, USA.
Haeussler M; 1Genomics Institute, University of California, Santa Cruz, USA.
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Źródło :
Mobile DNA [Mob DNA] 2020 Mar 31; Vol. 11, pp. 13. Date of Electronic Publication: 2020 Mar 31 (Print Publication: 2020).
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.
Autorzy :
Sanders LM; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Rangaswami A; Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California 94305, USA.
Bjork I; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Lam DL; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Beale HC; Department of Molecular, Cell and Developmental Biology, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Kephart ET; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Durbin A; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Learned K; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Currie R; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Lyle AG; Department of Molecular, Cell and Developmental Biology, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Pfeil J; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
Shah AT; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Lee AG; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Leung SG; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Behroozfard IH; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Breese MR; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Peralez J; Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California 94305, USA.
Hazard FK; Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California 94305, USA.
Lacayo N; Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California 94305, USA.
Spunt SL; Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California 94305, USA.
Haussler D; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Salama SR; Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Sweet-Cordero EA; Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California 94143, USA.
Vaske OM; Department of Molecular, Cell and Developmental Biology, UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.
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Źródło :
Cold Spring Harbor molecular case studies [Cold Spring Harb Mol Case Stud] 2019 Oct 23; Vol. 5 (5). Date of Electronic Publication: 2019 Oct 23 (Print Publication: 2019).
Typ publikacji :
Case Reports; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Peritoneal Neoplasms/*diagnosis
Peritoneal Neoplasms/*genetics
Teratoma/*diagnosis
Base Sequence/genetics ; Child ; Female ; Glioma/diagnosis ; Glioma/genetics ; Humans ; Ovarian Neoplasms/diagnosis ; Ovarian Neoplasms/genetics ; Prognosis ; RNA-Seq/methods ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Sequence Analysis, RNA/methods ; Teratoma/genetics ; Whole Exome Sequencing
SCR Disease Name :
Teratoma, Ovarian
Czasopismo naukowe
Tytuł :
Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.
Autorzy :
Vaske OM; Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz.; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Bjork I; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Salama SR; University of California, Santa Cruz Genomics Institute, Santa Cruz.; Howard Hughes Medical Institute, University of California, Santa Cruz.
Beale H; Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz.; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Tayi Shah A; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Sanders L; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Pfeil J; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Lam DL; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Learned K; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Durbin A; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Kephart ET; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Currie R; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Newton Y; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Swatloski T; University of California, Santa Cruz Genomics Institute, Santa Cruz.
McColl D; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Vivian J; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Zhu J; University of California, Santa Cruz Genomics Institute, Santa Cruz.
Lee AG; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Leung SG; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Spillinger A; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Liu HY; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Liang WS; Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona.
Byron SA; Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona.
Berens ME; Cancer and Cell Biology Division, TGen, Phoenix, Arizona.
Resnick AC; Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Lacayo N; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California.
Spunt SL; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California.
Rangaswami A; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California.
Huynh V; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Torno L; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Plant A; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Kirov I; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Zabokrtsky KB; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Rassekh SR; British Columbia Children's Hospital Research Institute, British Columbia Children's Hospital, Vancouver, British Columbia, Canada.
Deyell RJ; British Columbia Children's Hospital Research Institute, British Columbia Children's Hospital, Vancouver, British Columbia, Canada.
Laskin J; BC Cancer, Vancouver, British Columbia, Canada.
Marra MA; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
Sender LS; CHOC Children's Hospital, Hyundai Cancer Institute, Orange, California.
Mueller S; Department of Neurology, University of California, San Francisco.; Department of Neurosurgery, University of California, San Francisco.; Department of Pediatrics, University of California, San Francisco.
Sweet-Cordero EA; Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco.
Goldstein TC; University of California, Santa Cruz Genomics Institute, Santa Cruz.; Now with Anthem, Inc, Palo Alto, California.
Haussler D; University of California, Santa Cruz Genomics Institute, Santa Cruz.; Howard Hughes Medical Institute, University of California, Santa Cruz.
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Źródło :
JAMA network open [JAMA Netw Open] 2019 Oct 02; Vol. 2 (10), pp. e1913968. Date of Electronic Publication: 2019 Oct 02.
Typ publikacji :
Comparative Study; Journal Article; Multicenter Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Sequence Analysis, RNA*
Neoplasms/*genetics
RNA, Neoplasm/*analysis
Canada ; Child ; Child, Preschool ; Female ; Gene Expression ; Humans ; Infant ; Infant, Newborn ; Male ; Precision Medicine ; United States ; Young Adult
Czasopismo naukowe
Tytuł :
Barriers to accessing public cancer genomic data.
Autorzy :
Learned K; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA. .
Durbin A; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Currie R; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Kephart ET; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Beale HC; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Sanders LM; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Pfeil J; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Goldstein TC; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Salama SR; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Haussler D; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Vaske OM; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA.
Bjork IM; UC Santa Cruz, 1156 High Street, Mailstop: Genomics Institute, Santa Cruz, CA, 95064, USA. .
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Źródło :
Scientific data [Sci Data] 2019 Jun 20; Vol. 6 (1), pp. 98. Date of Electronic Publication: 2019 Jun 20.
Typ publikacji :
Journal Article
MeSH Terms :
Information Dissemination*
Neoplasms/*genetics
Datasets as Topic ; Genomics ; Humans
Czasopismo naukowe
Tytuł :
Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.
Autorzy :
Field AR; Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Jacobs FMJ; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Fiddes IT; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Phillips APR; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Reyes-Ortiz AM; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
LaMontagne E; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Whitehead L; Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Meng V; Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Rosenkrantz JL; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Olsen M; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Hauessler M; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Katzman S; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Salama SR; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. Electronic address: .
Haussler D; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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Źródło :
Stem cell reports [Stem Cell Reports] 2019 Feb 12; Vol. 12 (2), pp. 245-257. Date of Electronic Publication: 2019 Jan 10.
Typ publikacji :
Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Cell Differentiation/*genetics
Cerebral Cortex/*physiology
Gene Expression Regulation/*genetics
RNA, Long Noncoding/*genetics
Animals ; Cell Line ; Gene Expression Profiling/methods ; HEK293 Cells ; Humans ; Organoids/physiology ; Pluripotent Stem Cells/physiology ; Primates ; Sequence Analysis, RNA ; Transcriptome/genetics
Czasopismo naukowe
Tytuł :
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
Autorzy :
Pollen AA; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA. Electronic address: .
Bhaduri A; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Andrews MG; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Nowakowski TJ; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Anatomy, UCSF, San Francisco, CA, USA.
Meyerson OS; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Mostajo-Radji MA; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Di Lullo E; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Alvarado B; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Bedolli M; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Dougherty ML; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Fiddes IT; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Kronenberg ZN; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Shuga J; New Technologies, Fluidigm, South San Francisco, CA, USA.
Leyrat AA; New Technologies, Fluidigm, South San Francisco, CA, USA.
West JA; New Technologies, Fluidigm, South San Francisco, CA, USA.
Bershteyn M; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Lowe CB; Department of Developmental Biology, Stanford University, Stanford, CA, USA.
Pavlovic BJ; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
Salama SR; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Haussler D; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, 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.
Kriegstein AR; Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA. Electronic address: .
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Źródło :
Cell [Cell] 2019 Feb 07; Vol. 176 (4), pp. 743-756.e17.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Cerebral Cortex/*cytology
Organoids/*metabolism
Animals ; Biological Evolution ; Brain/cytology ; Cell Culture Techniques/methods ; Cell Differentiation/genetics ; Cerebral Cortex/metabolism ; Gene Regulatory Networks/genetics ; Humans ; Induced Pluripotent Stem Cells/cytology ; Macaca ; Neurogenesis/genetics ; Organoids/growth & development ; Pan troglodytes ; Pluripotent Stem Cells/cytology ; Single-Cell Analysis ; Species Specificity ; Transcriptome/genetics
Czasopismo naukowe
Tytuł :
Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
Autorzy :
Fiddes IT; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Lodewijk GA; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands.
Mooring M; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Bosworth CM; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Ewing AD; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Mantalas GL; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Molecular, Cell and Developmental Biology Department, UC Santa Cruz, Santa Cruz, CA, USA.
Novak AM; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
van den Bout A; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands.
Bishara A; Department of Computer Science, Stanford University, Stanford, CA, USA.
Rosenkrantz JL; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA.
Lorig-Roach R; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Field AR; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Molecular, Cell and Developmental Biology Department, UC Santa Cruz, Santa Cruz, CA, USA.
Haeussler M; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Russo L; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands.
Bhaduri A; Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA.
Nowakowski TJ; Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA.
Pollen AA; Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA.
Dougherty ML; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Nuttle X; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA.
Addor MC; Service de génétique médicale, Lausanne, Switzerland.
Zwolinski S; Department of Cytogenetics, Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
Katzman S; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Kriegstein A; Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, 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.
Salama SR; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA.
Jacobs FMJ; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands. Electronic address: .
Haussler D; UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA. Electronic address: .
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Źródło :
Cell [Cell] 2018 May 31; Vol. 173 (6), pp. 1356-1369.e22. Date of Electronic Publication: 2018 May 31.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Signal Transduction*
Brain/*embryology
Cerebral Cortex/*physiology
Neurogenesis/*physiology
Receptor, Notch2/*metabolism
Animals ; Cell Differentiation ; Embryonic Stem Cells/metabolism ; Female ; Gene Deletion ; Genes, Reporter ; Gorilla gorilla ; HEK293 Cells ; Humans ; Neocortex/cytology ; Neural Stem Cells/metabolism ; Neuroglia/metabolism ; Neurons/metabolism ; Pan troglodytes ; Receptor, Notch2/genetics ; Sequence Analysis, RNA
Czasopismo naukowe

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