Literature DB >> 32958507

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.

Bridget D Samuels1, Robert Aho2, James F Brinkley3, Alejandro Bugacov4, Eleanor Feingold5, Shannon Fisher6, Ana S Gonzalez-Reiche7, Joseph G Hacia8, Benedikt Hallgrimsson9, Karissa Hansen2, Matthew P Harris10, Thach-Vu Ho1, Greg Holmes7, Joan E Hooper11, Ethylin Wang Jabs7, Kenneth L Jones12, Carl Kesselman4, Ophir D Klein13, Elizabeth J Leslie14, Hong Li15, Eric C Liao16, Hannah Long17, Na Lu7, Richard L Maas18, Mary L Marazita5,19,20, Jaaved Mohammed17, Sara Prescott17, Robert Schuler4, Licia Selleri2, Richard A Spritz21, Tomek Swigut17, Harm van Bakel7, Axel Visel22,23,24, Ian Welsh2, Cristina Williams4, Trevor J Williams15, Joanna Wysocka17, Yuan Yuan1, Yang Chai25.   

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.
© 2020. Published by The Company of Biologists Ltd.

Entities:  

Keywords:  Craniofacial development; Data resource; FaceBase Consortium; Human; Mouse; Zebrafish

Mesh：

Year:  2020        PMID： 32958507      PMCID： PMC7522026          DOI： 10.1242/dev.191213

Source DB:  PubMed          Journal:  Development        ISSN： 0950-1991            Impact factor:   6.868


  54 in total

1.  The role of TGF-beta signaling in regulating chondrogenesis and osteogenesis during mandibular development.

Authors:  Kyoko Oka; Shoji Oka; Tomoyo Sasaki; Yoshihiro Ito; Pablo Bringas; Kazuaki Nonaka; Yang Chai
Journal:  Dev Biol       Date:  2006-11-21       Impact factor: 3.582

Review 2.  Recent advances in craniofacial morphogenesis.

Authors:  Yang Chai; Robert E Maxson
Journal:  Dev Dyn       Date:  2006-09       Impact factor: 3.780

3.  The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution.

Authors:  Hong Li; Kenneth L Jones; Joan E Hooper; Trevor Williams
Journal:  Development       Date:  2019-06-17       Impact factor: 6.868

4.  Closing the Gap: Genetic and Genomic Continuum from Syndromic to Nonsyndromic Craniosynostoses.

Authors:  Yann Heuzé; Gregory Holmes; Inga Peter; Joan T Richtsmeier; Ethylin Wang Jabs
Journal:  Curr Genet Med Rep       Date:  2014-09-01

5.  Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form.

Authors:  Katrin Henke; Jacob M Daane; M Brent Hawkins; Christopher M Dooley; Elisabeth M Busch-Nentwich; Derek L Stemple; Matthew P Harris
Journal:  Genetics       Date:  2017-08-23       Impact factor: 4.562

6.  Genome-wide mapping of global-to-local genetic effects on human facial shape.

Authors:  Peter Claes; Jasmien Roosenboom; Julie D White; Tomek Swigut; Dzemila Sero; Jiarui Li; Myoung Keun Lee; Arslan Zaidi; Brooke C Mattern; Corey Liebowitz; Laurel Pearson; Tomás González; Elizabeth J Leslie; Jenna C Carlson; Ekaterina Orlova; Paul Suetens; Dirk Vandermeulen; Eleanor Feingold; Mary L Marazita; John R Shaffer; Joanna Wysocka; Mark D Shriver; Seth M Weinberg
Journal:  Nat Genet       Date:  2018-02-19       Impact factor: 38.330

7.  Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest.

Authors:  Alvaro Rada-Iglesias; Ruchi Bajpai; Sara Prescott; Samantha A Brugmann; Tomek Swigut; Joanna Wysocka
Journal:  Cell Stem Cell       Date:  2012-09-13       Impact factor: 24.633

8.  Unique and non-redundant function of csf1r paralogues in regulation and evolution of post-embryonic development of the zebrafish.

Authors:  Joana Caetano-Lopes; Katrin Henke; Katia Urso; Jeffrey Duryea; Julia F Charles; Matthew L Warman; Matthew P Harris
Journal:  Development       Date:  2020-01-22       Impact factor: 6.862

9.  Fully Automatic Landmarking of Syndromic 3D Facial Surface Scans Using 2D Images.

Authors:  Jordan J Bannister; Sebastian R Crites; J David Aponte; David C Katz; Matthias Wilms; Ophir D Klein; Francois P J Bernier; Richard A Spritz; Benedikt Hallgrímsson; Nils D Forkert
Journal:  Sensors (Basel)       Date:  2020-06-03       Impact factor: 3.576

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444
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  9 in total

Review 1.  FaceBase: A Community-Driven Hub for Data-Intensive Research.

Authors:  R E Schuler; A Bugacov; J G Hacia; T V Ho; J Iwata; L Pearlman; B D Samuels; C Williams; Z Zhao; C Kesselman; Y Chai
Journal:  J Dent Res       Date:  2022-07-31       Impact factor: 8.924

2.  Spatiotemporal MicroRNA-Gene Expression Network Related to Orofacial Clefts.

Authors:  F Yan; L M Simon; A Suzuki; C Iwaya; P Jia; J Iwata; Z Zhao
Journal:  J Dent Res       Date:  2022-06-30       Impact factor: 8.924

Review 3.  A Roadmap for the Human Oral and Craniofacial Cell Atlas.

Authors:  A J Caetano; I Sequeira; K M Byrd
Journal:  J Dent Res       Date:  2022-10       Impact factor: 8.924

4.  Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse.

Authors:  William Dempsey; Ian Foster; Scott Fraser; Carl Kesselman
Journal:  Harv Data Sci Rev       Date:  2022-07-28

5.  Marsupials and Multi-Omics: Establishing New Comparative Models of Neural Crest Patterning and Craniofacial Development.

Authors:  Axel H Newton
Journal:  Front Cell Dev Biol       Date:  2022-06-23

6.  MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.

Authors:  Jay Devine; Marta Vidal-García; Wei Liu; Amanda Neves; Lucas D Lo Vercio; Rebecca M Green; Heather A Richbourg; Marta Marchini; Colton M Unger; Audrey C Nickle; Bethany Radford; Nathan M Young; Paula N Gonzalez; Robert E Schuler; Alejandro Bugacov; Campbell Rolian; Christopher J Percival; Trevor Williams; Lee Niswander; Anne L Calof; Arthur D Lander; Axel Visel; Frank R Jirik; James M Cheverud; Ophir D Klein; Ramon Y Birnbaum; Amy E Merrill; Rebecca R Ackermann; Daniel Graf; Myriam Hemberger; Wendy Dean; Nils D Forkert; Stephen A Murray; Henrik Westerberg; Ralph S Marcucio; Benedikt Hallgrímsson
Journal:  Sci Data       Date:  2022-05-25       Impact factor: 8.501

7.  A landmark-free morphometrics pipeline for high-resolution phenotyping: application to a mouse model of Down syndrome.

Authors:  Nicolas Toussaint; Yushi Redhead; Marta Vidal-García; Lucas Lo Vercio; Wei Liu; Elizabeth M C Fisher; Benedikt Hallgrímsson; Victor L J Tybulewicz; Julia A Schnabel; Jeremy B A Green
Journal:  Development       Date:  2021-03-12       Impact factor: 6.862

8.  Single-cell analysis identifies a key role for Hhip in murine coronal suture development.

Authors:  Greg Holmes; Ana S Gonzalez-Reiche; Madrikha Saturne; Susan M Motch Perrine; Xianxiao Zhou; Ana C Borges; Bhavana Shewale; Joan T Richtsmeier; Bin Zhang; Harm van Bakel; Ethylin Wang Jabs
Journal:  Nat Commun       Date:  2021-12-08       Impact factor: 17.694

9.  Technological scouting of bi-material face masks: simulation of adherence using 3D Facial Norms.

Authors:  Elisa Ficarella; Angelo Natalicchio; Roberto Spina; Luigi Maria Galantucci
Journal:  Procedia CIRP       Date:  2022-07-08
  9 in total

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