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Devine J, Vidal-García M, Liu W, Neves A, Lo Vercio LD, Green RM, Richbourg HA, Marchini M, Unger CM, Nickle AC, Radford B, Young NM, Gonzalez PN, Schuler RE, Bugacov A, Rolian C, Percival CJ, Williams T, Niswander L, Calof AL, Lander AD, Visel A, Jirik FR, Cheverud JM, Klein OD, Birnbaum RY, Merrill AE, Ackermann RR, Graf D, Hemberger M, Dean W, Forkert ND, Murray SA, Westerberg H, Marcucio RS, Hallgrímsson B. Author Correction: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2023; 10:420. [PMID: 37380661 DOI: 10.1038/s41597-023-02320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Affiliation(s)
- Jay Devine
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Marta Vidal-García
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Wei Liu
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Amanda Neves
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4L8, Canada
| | - Lucas D Lo Vercio
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Rebecca M Green
- School of Dental Medicine, University of Pittsburgh, 3501 Terrace St, Pittsburgh, PA, 15213, USA
| | - Heather A Richbourg
- Orthopaedic Trauma Institute, ZSFG, UCSF, 2550 23rd St, San Francisco, CA, 94110, USA
| | - Marta Marchini
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Colton M Unger
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Audrey C Nickle
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, 2250 Alcazar St, Los Angeles, CA, 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 1975 Zonal Ave, Los Angeles, CA, 90033, USA
| | - Bethany Radford
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Nathan M Young
- Orthopaedic Trauma Institute, ZSFG, UCSF, 2550 23rd St, San Francisco, CA, 94110, USA
| | - Paula N Gonzalez
- Institute for Studies in Neuroscience and Complex Systems (ENyS) CONICET, Av. Calchaquí, 5402, Florencio Varela, Buenos Aires, Argentina
| | - Robert E Schuler
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Alejandro Bugacov
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Campbell Rolian
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Christopher J Percival
- Department of Anthropology, Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, 12801 East 17th Ave, Aurora, CO, 80045, USA
| | - Lee Niswander
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Anne L Calof
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Arthur D Lander
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, 5200 Lake Rd, Merced, CA, 95343, USA
| | - Frank R Jirik
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - James M Cheverud
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL, 60660, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, David Ben Gurion Blvd 1, Be'er Sheva, Israel
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, 2250 Alcazar St, Los Angeles, CA, 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 1975 Zonal Ave, Los Angeles, CA, 90033, USA
| | - Rebecca R Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Daniel Graf
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, T6G 2R3, Canada
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Myriam Hemberger
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Wendy Dean
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Nils D Forkert
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | | | - Henrik Westerberg
- Department of Bioimaging Informatics, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Ralph S Marcucio
- Orthopaedic Trauma Institute, ZSFG, UCSF, 2550 23rd St, San Francisco, CA, 94110, USA
| | - Benedikt Hallgrímsson
- Alberta Children's Hospital Research Institute, University of Calgary, 28 Oki Dr NW, Calgary, AB, T3B 6A8, Canada.
- The McCaig Institute for Bone and Joint Health, University of Calgary, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, Canada.
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada.
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3
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Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, Fisher S, Gonzalez-Reiche AS, Hacia JG, Hallgrimsson B, Hansen K, Harris MP, Ho TV, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Leslie EJ, Li H, Liao EC, Long H, Lu N, Maas RL, Marazita ML, Mohammed J, Prescott S, Schuler R, Selleri L, Spritz RA, Swigut T, van Bakel H, Visel A, Welsh I, Williams C, Williams TJ, Wysocka J, Yuan Y, Chai Y. FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. Development 2020; 147:dev191213. [PMID: 32958507 PMCID: PMC7522026 DOI: 10.1242/dev.191213] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.
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Affiliation(s)
- Bridget D Samuels
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Robert Aho
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - James F Brinkley
- Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Alejandro Bugacov
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Shannon Fisher
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, and McCaig Bone and Joint Institute, University of Calgary, Alberta, Canada
| | - Karissa Hansen
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Harris
- Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Hong Li
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Eric C Liao
- Massachusetts General Hospital, Plastic and Reconstructive Surgery, Boston, MA 02114, USA
| | - Hannah Long
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Na Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard L Maas
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jaaved Mohammed
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara Prescott
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert Schuler
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Tomek Swigut
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
| | - Ian Welsh
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cristina Williams
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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7
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Resch R, Baur C, Bugacov A, Koel BE, Echternach PM, Madhukar A, Montoya N, Requicha AAG, Will P. Linking and Manipulation of Gold Multinanoparticle Structures Using Dithiols and Scanning Force Microscopy. J Phys Chem B 1999. [DOI: 10.1021/jp984508o] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roland Resch
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Christof Baur
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Alejandro Bugacov
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Bruce E. Koel
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Pierre M. Echternach
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Anupam Madhukar
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Nicolas Montoya
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Aristides A. G. Requicha
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
| | - Peter Will
- Laboratory for Molecular Robotics, University of Southern California, 947 West 37th Place, Los Angeles, California 90089-0781, Departments of Chemistry, Materials Science, and Computer Science, University of Southern California, Los Angeles, California, and Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109
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