Literature DB >> 30254541

The Allen Brain Atlas as a Resource for Teaching Undergraduate Neuroscience.

Terri L Gilbert1.   

Abstract

The open science movement has resulted in a growing field of data- and tool-sharing platforms that serve as a resource not only for sharing data and results in the field of brain science but has allowed students and researchers to learn neuroscientific skills and concepts. For over a decade, the Allen Institute for Brain Science has been meticulously collecting high quality data mapping gene expression, connectivity and, more recently, functional data from the brains of mice, macaques and humans. These open data have been paired with unique navigation and visualization tools such that the neuroscience researcher can explore, utilize and even incorporate these data into their publications. The tools created to explore and analyze the Allen Brain Atlas datasets have also been widely utilized to teach neuroscientific concepts to undergraduate and graduate students. This article aims to outline how to use the Allen Brain Atlas resources as teaching tools to impart neuroanatomic concepts to undergraduate and graduate neuroscience students.

Entities:  

Keywords:  Allen Brain Atlas; Allen Mouse Brain Atlas; Gene Expression; In Situ Hybridization (ISH)

Year:  2018        PMID: 30254541      PMCID: PMC6153011     

Source DB:  PubMed          Journal:  J Undergrad Neurosci Educ        ISSN: 1544-2896


  14 in total

1.  Genome-wide atlas of gene expression in the adult mouse brain.

Authors:  Ed S Lein; Michael J Hawrylycz; Nancy Ao; Mikael Ayres; Amy Bensinger; Amy Bernard; Andrew F Boe; Mark S Boguski; Kevin S Brockway; Emi J Byrnes; Lin Chen; Li Chen; Tsuey-Ming Chen; Mei Chi Chin; Jimmy Chong; Brian E Crook; Aneta Czaplinska; Chinh N Dang; Suvro Datta; Nick R Dee; Aimee L Desaki; Tsega Desta; Ellen Diep; Tim A Dolbeare; Matthew J Donelan; Hong-Wei Dong; Jennifer G Dougherty; Ben J Duncan; Amanda J Ebbert; Gregor Eichele; Lili K Estin; Casey Faber; Benjamin A Facer; Rick Fields; Shanna R Fischer; Tim P Fliss; Cliff Frensley; Sabrina N Gates; Katie J Glattfelder; Kevin R Halverson; Matthew R Hart; John G Hohmann; Maureen P Howell; Darren P Jeung; Rebecca A Johnson; Patrick T Karr; Reena Kawal; Jolene M Kidney; Rachel H Knapik; Chihchau L Kuan; James H Lake; Annabel R Laramee; Kirk D Larsen; Christopher Lau; Tracy A Lemon; Agnes J Liang; Ying Liu; Lon T Luong; Jesse Michaels; Judith J Morgan; Rebecca J Morgan; Marty T Mortrud; Nerick F Mosqueda; Lydia L Ng; Randy Ng; Geralyn J Orta; Caroline C Overly; Tu H Pak; Sheana E Parry; Sayan D Pathak; Owen C Pearson; Ralph B Puchalski; Zackery L Riley; Hannah R Rockett; Stephen A Rowland; Joshua J Royall; Marcos J Ruiz; Nadia R Sarno; Katherine Schaffnit; Nadiya V Shapovalova; Taz Sivisay; Clifford R Slaughterbeck; Simon C Smith; Kimberly A Smith; Bryan I Smith; Andy J Sodt; Nick N Stewart; Kenda-Ruth Stumpf; Susan M Sunkin; Madhavi Sutram; Angelene Tam; Carey D Teemer; Christina Thaller; Carol L Thompson; Lee R Varnam; Axel Visel; Ray M Whitlock; Paul E Wohnoutka; Crissa K Wolkey; Victoria Y Wong; Matthew Wood; Murat B Yaylaoglu; Rob C Young; Brian L Youngstrom; Xu Feng Yuan; Bin Zhang; Theresa A Zwingman; Allan R Jones
Journal:  Nature       Date:  2006-12-06       Impact factor: 49.962

2.  Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain.

Authors:  Lydia Ng; Sayan Pathak; Chihchau Kuan; Chris Lau; Hong-Wei Dong; Andrew Sodt; Chinh Dang; Brian Avants; Paul Yushkevich; James Gee; David Haynor; Ed Lein; Allan Jones; Mike Hawrylycz
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2007 Jul-Sep       Impact factor: 3.710

3.  Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas.

Authors:  Philip Chu; Joshua Peck; Joshua C Brumberg
Journal:  J Undergrad Neurosci Educ       Date:  2015-03-15

4.  Neuropathological and transcriptomic characteristics of the aged brain.

Authors:  Jeremy A Miller; Angela Guillozet-Bongaarts; Laura E Gibbons; Nadia Postupna; Anne Renz; Allison E Beller; Susan M Sunkin; Lydia Ng; Shannon E Rose; Kimberly A Smith; Aaron Szafer; Chris Barber; Darren Bertagnolli; Kristopher Bickley; Krissy Brouner; Shiella Caldejon; Mike Chapin; Mindy L Chua; Natalie M Coleman; Eiron Cudaback; Christine Cuhaciyan; Rachel A Dalley; Nick Dee; Tsega Desta; Tim A Dolbeare; Nadezhda I Dotson; Michael Fisher; Nathalie Gaudreault; Garrett Gee; Terri L Gilbert; Jeff Goldy; Fiona Griffin; Caroline Habel; Zeb Haradon; Nika Hejazinia; Leanne L Hellstern; Steve Horvath; Kim Howard; Robert Howard; Justin Johal; Nikolas L Jorstad; Samuel R Josephsen; Chihchau L Kuan; Florence Lai; Eric Lee; Felix Lee; Tracy Lemon; Xianwu Li; Desiree A Marshall; Jose Melchor; Shubhabrata Mukherjee; Julie Nyhus; Julie Pendergraft; Lydia Potekhina; Elizabeth Y Rha; Samantha Rice; David Rosen; Abharika Sapru; Aimee Schantz; Elaine Shen; Emily Sherfield; Shu Shi; Andy J Sodt; Nivretta Thatra; Michael Tieu; Angela M Wilson; Thomas J Montine; Eric B Larson; Amy Bernard; Paul K Crane; Richard G Ellenbogen; C Dirk Keene; Ed Lein
Journal:  Elife       Date:  2017-11-09       Impact factor: 8.140

5.  Teaching with Big Data: Report from the 2016 Society for Neuroscience Teaching Workshop.

Authors:  William Grisham; Joshua C Brumberg; Terri Gilbert; Linda Lanyon; Robert W Williams; Richard Olivo
Journal:  J Undergrad Neurosci Educ       Date:  2017-11-15

6.  Teaching bioinformatics and neuroinformatics by using free web-based tools.

Authors:  William Grisham; Natalie A Schottler; Joanne Valli-Marill; Lisa Beck; Jackson Beatty
Journal:  CBE Life Sci Educ       Date:  2010       Impact factor: 3.325

7.  A mesoscale connectome of the mouse brain.

Authors:  Seung Wook Oh; Julie A Harris; Lydia Ng; Brent Winslow; Nicholas Cain; Stefan Mihalas; Quanxin Wang; Chris Lau; Leonard Kuan; Alex M Henry; Marty T Mortrud; Benjamin Ouellette; Thuc Nghi Nguyen; Staci A Sorensen; Clifford R Slaughterbeck; Wayne Wakeman; Yang Li; David Feng; Anh Ho; Eric Nicholas; Karla E Hirokawa; Phillip Bohn; Kevin M Joines; Hanchuan Peng; Michael J Hawrylycz; John W Phillips; John G Hohmann; Paul Wohnoutka; Charles R Gerfen; Christof Koch; Amy Bernard; Chinh Dang; Allan R Jones; Hongkui Zeng
Journal:  Nature       Date:  2014-04-02       Impact factor: 49.962

8.  An anatomically comprehensive atlas of the adult human brain transcriptome.

Authors:  Michael J Hawrylycz; Ed S Lein; Angela L Guillozet-Bongaarts; Elaine H Shen; Lydia Ng; Jeremy A Miller; Louie N van de Lagemaat; Kimberly A Smith; Amanda Ebbert; Zackery L Riley; Chris Abajian; Christian F Beckmann; Amy Bernard; Darren Bertagnolli; Andrew F Boe; Preston M Cartagena; M Mallar Chakravarty; Mike Chapin; Jimmy Chong; Rachel A Dalley; Barry David Daly; Chinh Dang; Suvro Datta; Nick Dee; Tim A Dolbeare; Vance Faber; David Feng; David R Fowler; Jeff Goldy; Benjamin W Gregor; Zeb Haradon; David R Haynor; John G Hohmann; Steve Horvath; Robert E Howard; Andreas Jeromin; Jayson M Jochim; Marty Kinnunen; Christopher Lau; Evan T Lazarz; Changkyu Lee; Tracy A Lemon; Ling Li; Yang Li; John A Morris; Caroline C Overly; Patrick D Parker; Sheana E Parry; Melissa Reding; Joshua J Royall; Jay Schulkin; Pedro Adolfo Sequeira; Clifford R Slaughterbeck; Simon C Smith; Andy J Sodt; Susan M Sunkin; Beryl E Swanson; Marquis P Vawter; Derric Williams; Paul Wohnoutka; H Ronald Zielke; Daniel H Geschwind; Patrick R Hof; Stephen M Smith; Christof Koch; Seth G N Grant; Allan R Jones
Journal:  Nature       Date:  2012-09-20       Impact factor: 49.962

9.  Novel in silico Method for Teaching Cytoarchitecture, Cellular Diversity, and Gene Expression in the Mammalian Brain.

Authors:  Raddy L Ramos; Phoebe T Smith; Joshua C Brumberg
Journal:  J Undergrad Neurosci Educ       Date:  2007-10-15

10.  Transcriptional landscape of the prenatal human brain.

Authors:  Jeremy A Miller; Song-Lin Ding; Susan M Sunkin; Kimberly A Smith; Lydia Ng; Aaron Szafer; Amanda Ebbert; Zackery L Riley; Joshua J Royall; Kaylynn Aiona; James M Arnold; Crissa Bennet; Darren Bertagnolli; Krissy Brouner; Stephanie Butler; Shiella Caldejon; Anita Carey; Christine Cuhaciyan; Rachel A Dalley; Nick Dee; Tim A Dolbeare; Benjamin A C Facer; David Feng; Tim P Fliss; Garrett Gee; Jeff Goldy; Lindsey Gourley; Benjamin W Gregor; Guangyu Gu; Robert E Howard; Jayson M Jochim; Chihchau L Kuan; Christopher Lau; Chang-Kyu Lee; Felix Lee; Tracy A Lemon; Phil Lesnar; Bergen McMurray; Naveed Mastan; Nerick Mosqueda; Theresa Naluai-Cecchini; Nhan-Kiet Ngo; Julie Nyhus; Aaron Oldre; Eric Olson; Jody Parente; Patrick D Parker; Sheana E Parry; Allison Stevens; Mihovil Pletikos; Melissa Reding; Kate Roll; David Sandman; Melaine Sarreal; Sheila Shapouri; Nadiya V Shapovalova; Elaine H Shen; Nathan Sjoquist; Clifford R Slaughterbeck; Michael Smith; Andy J Sodt; Derric Williams; Lilla Zöllei; Bruce Fischl; Mark B Gerstein; Daniel H Geschwind; Ian A Glass; Michael J Hawrylycz; Robert F Hevner; Hao Huang; Allan R Jones; James A Knowles; Pat Levitt; John W Phillips; Nenad Sestan; Paul Wohnoutka; Chinh Dang; Amy Bernard; John G Hohmann; Ed S Lein
Journal:  Nature       Date:  2014-04-02       Impact factor: 49.962

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  5 in total

1.  Pandemic Teaching: Using the Allen Cell Types Database for Final Semester Projects in an Undergraduate Neurophysiology Lab Course.

Authors:  Yi-Yun Ho; Andrea Roeser; Gwenda Law; Bruce R Johnson
Journal:  J Undergrad Neurosci Educ       Date:  2021-12-24

2.  Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei.

Authors:  Jing Ren; Alina Isakova; Drew Friedmann; Jiawei Zeng; Sophie M Grutzner; Albert Pun; Grace Q Zhao; Sai Saroja Kolluru; Ruiyu Wang; Rui Lin; Pengcheng Li; Anan Li; Jennifer L Raymond; Qingming Luo; Minmin Luo; Stephen R Quake; Liqun Luo
Journal:  Elife       Date:  2019-10-24       Impact factor: 8.140

3.  Introducing immunohistochemistry to the molecular biology laboratory.

Authors:  Audrey Chen; Eric Tarapore; Allisen G To; Davis M Catolico; Kelly C Nguyen; Melissa J Coleman; Rory D Spence
Journal:  Biochem Mol Biol Educ       Date:  2022-02-18       Impact factor: 1.369

Review 4.  Generative Models of Brain Dynamics.

Authors:  Mahta Ramezanian-Panahi; Germán Abrevaya; Jean-Christophe Gagnon-Audet; Vikram Voleti; Irina Rish; Guillaume Dumas
Journal:  Front Artif Intell       Date:  2022-07-15

5.  BrainWiki-A Wiki-Style, User Driven, Comparative Brain Anatomy Tool.

Authors:  Linda Forsell; Esther Naomi Vos; Keerthi Jayaraman; Axel Edman; S Abid Hussaini
Journal:  Front Neuroanat       Date:  2020-10-19       Impact factor: 3.856

  5 in total

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