Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

Autor: Wincker Patrick, Da Silva Corinne, Casavant Thomas, Scheetz Todd, Bafna Vineet, Soares Marcelo B, Edsall Lee, Gaasterland Terry, Macagno Eduardo R, Tasiemski Aurélie, Salzet Michel

Publikováno v: BMC Genomics, Vol 11, Iss 1, p 407 (2010)

Abstract Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in me

Externí odkaz: https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb

Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome.

Autor: Viel KCMF; Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Parameswaran S; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Donmez OA; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Forney CR; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Hass MR; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Yin C; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Jones SH; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Prosser HK; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Diouf AA; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Gittens OE; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Edsall LE; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Chen X; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Rowden H; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Dunn KA; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Guo R; Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA., VonHandorf A; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Leong MML; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA., Ernst K; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Kaufman KM; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Lawson LP; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Gewurz B; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA., Zhao B; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA., Kottyan LC; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Leah.Kottyan@cchmc.org.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA. Leah.Kottyan@cchmc.org.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Leah.Kottyan@cchmc.org., Weirauch MT; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Matthew.Weirauch@cchmc.org.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA. Matthew.Weirauch@cchmc.org.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Matthew.Weirauch@cchmc.org.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Matthew.Weirauch@cchmc.org.; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Matthew.Weirauch@cchmc.org.

Publikováno v: BMC genomics [BMC Genomics] 2024 Mar 12; Vol. 25 (1), pp. 273. Date of Electronic Publication: 2024 Mar 12.

Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci.

Autor: Hong T; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA., Parameswaran S; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Donmez OA; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Miller D; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Forney C; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Lape M; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Saint Just Ribeiro M; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Liang J; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA., Edsall LE; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Magnusen AF; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Miller W; Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45267, USA., Chepelev I; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA., Harley JB; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA.; US Department of Veterans Affairs Medical Center, Cincinnati, Ohio 45229, USA., Zhao B; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA., Kottyan LC; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA.; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA., Weirauch MT; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA.; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.

Publikováno v: Genome research [Genome Res] 2021 Dec; Vol. 31 (12), pp. 2185-2198. Date of Electronic Publication: 2021 Nov 19.

Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.

Autor: Edsall LE; Center for Genomic and Computational Biology, Duke University.; Division of Medical Genetics, Department of Pediatrics, Duke University.; University Program in Genetics and Genomics, Duke University., Berrio A; Department of Biology, Duke University., Majoros WH; Department of Biostatistics and Bioinformatics, Duke University., Swain-Lenz D; Department of Biology, Duke University., Morrow S; Department of Biology, Duke University., Shibata Y; Center for Genomic and Computational Biology, Duke University.; Division of Medical Genetics, Department of Pediatrics, Duke University., Safi A; Center for Genomic and Computational Biology, Duke University.; Division of Medical Genetics, Department of Pediatrics, Duke University., Wray GA; Center for Genomic and Computational Biology, Duke University.; Department of Biology, Duke University., Crawford GE; Center for Genomic and Computational Biology, Duke University.; Division of Medical Genetics, Department of Pediatrics, Duke University., Allen AS; Department of Biostatistics and Bioinformatics, Duke University.

Publikováno v: Genome biology and evolution [Genome Biol Evol] 2019 Oct 01; Vol. 11 (10), pp. 3035-3053.

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.

Autor: Chen Y; Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Chen C; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA., Zhang Z; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA., Liu CC; Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Johnson ME; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA., Espinoza CA; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA., Edsall LE; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA., Ren B; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA., Zhou XJ; Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA., Grant SF; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA., Wells AD; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA adwells@mail.med.upenn.edu., Chen L; Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA linchen@usc.edu.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2015 Jan; Vol. 43 (2), pp. 1268-82. Date of Electronic Publication: 2015 Jan 07.