Neurotree: Graphing the academic genealogy of neuroscience Stephen V. David1, Will Chertoff1, Titipat Achakulvisut2, Daniel Acuna2 1Oregon Health & Science University, 2Northwestern University
1. Overview 3. Example tree 4. Founding ancestors
Neurotree (http://neurotree.org, [1]) is a collaborative, open-access Name N Resarch area Family tree The distance between two nodes can be Johannes Müller 7715 Physiology website that tracks and visualizes the academic genealogy and history P+ William Fitch measured by the number of mentorship Sir Charles Sherrington 4758 Neurophysiology of neuroscience. After 10 years of growth driven by user-generated Allen Hermann von Helmholtz 3048 Psychophysics University of P- steps connecting them through a Sir John Eccles 2998 Synapses content, the site has captured information about the mentorship of over Rudolf Oregon Ludwig Robert Samuel Alexander Sir Charles Medical common ancestor i(below). The list at Karl Lashley 2558 Learning and memory 80,000 neuroscientists. It has become a unique tool for a community of John Friedrich Karl Koch Sir Charles Kinnier Charles Gordon John Scott Sir Charles Harvey Sir Charles Karl Edgar School C+ Louis Agassiz 2241 Anatomy Sir Michael Newport Goltz Virchow Universität Scott Wilson Symonds Holmes Farquhar Sherrington Scott Williams Scott Spencer Wilder Douglas Frederic right shows the 30 most frequent primary researchers, students, journal editors, and the press. Once Foster Langley Kaiser-Wilhelms- Universität Berlin (ID Sherrington National Hospital, Queen National Hospital, Queen National Hospital, Queen Fulton Oxford Sherrington Cushing Sherrington Lashley Penfield Adrian Bremer William James 2183 Psychology C- Cambridge Cambridge Universität Straßburg Berlin Tree) Oxford Square, London Square, London Square, London Yale Oxford Yale Oxford Harvard McGill Cambridge Brussels William K common ancestors in a sample of Edgar Adrian 2123 Physiology linked into the tree, each researcher can be characterized by their Livingston James Angell 2083 Psychology Edward University of + 116,000 random node pairs. These Rudolf Virchow 1961 Pathology mentorship network, defined recursively as their graduate and Sir Charles Scott Derek Ernst G.T. R. Steven John Farquhar Donald Olding Giuseppe Oregon Sherrington Denny-Brown Liddell Creed Fulton Hebb Moruzzi Medical Carl Ludwig 1891 Physiology, anatomy Oxford Boston City Hospital and Harvard Medical School Oxford Oxford Yale McGill University of Pisa School individuals are some of the better known postdoctoral mentors and their mentors' own networks. - Stephen Kuffler 1890 Visual system historical figures in neuroscience. John Langley 1878 Autonomic nervous system Sir John Carew Birger Ronald Wilhelm Wundt 1796 Experimental psychology Recently, we have linked Neurotree researcher profiles to several Eccles Kaada Melzack ? Sir Michael Foster 1583 Neurophysiology ANU UiO McGill publication databases, including PubMed, ProQuest, and Scopus. Henry Bowditch 1403 Physiology Richard Franz Nissl 1212 Anatomy Each researcher can thus be characterized by unique fingerprints Per John G.M. 4500 Rudolf Wagner 1207 Phsyiology Andersen O'Keefe Morris derived from their mentorship network and publication metadata. We University of Oslo UCL Edinburgh Claude Bernard 954 Physiology Johann Clarus 940 Anatomy, surgery 3000 have begun analysis of mentorship network structure and the influence An individual’s mentors and trainees May-Britt Otto Meyerhof 755 Biochemistry Moser Friedrich Goltz 752 Physiology of this network on the research program of trainees. are displayed in a family tree format. Norwegian University of Science and Technology (Options) Pair cont Robert Bunsen 749 Inorganic chemistry 1500 Archibald Hill 747 Biophysics Driven by the enthusiasm of participants, Neurotree has spawned Andrew H. Retsina M Charlotte N Tor Li Richard James Kei M Laura Lee Hiroshi T Christian Heyne 672 Classical philology Bahle Meyer Boccara Stensola Lu Gardner Igarashi Colgin Ito John Fulton 600 Physiology Michigan, Ann Arbor MIT IST Austria Norwegian University of Science and Technology Norwegian University of Science and Technology NTNU UC Irvine UT Austin NTNU parallel sites for other fields that share a common platform and central 0 Rudolf Leuckart 585 Zoology 0 5 10 15 20 25 30 35 Jeffries Wyman 541 Comparative anatomy database under the umbrella of the Academic Family Tree Anita Y Sarah Ann Stephanie P Stephanie H Stanley P Brian J. Kevin Wood Sean Gregory Chenguang Distance through common anscestor Lin Gomez Runkle Chen Chen Gill Shading indicates similarity of publication Gereke Bieri Trettel Zheng Ignaz Döllinger 521 Comparative development MIT MIT MIT Stanford MIT MIT UT Austin (*50% of pairs have no common ancestor, not shown) (http://academictree.org). Future efforts will expand the network metadata (LSA) with the central node. Edward Titchener 513 Structuralism analysis to explore properties of the larger tree and interactions between its constituent fields. Data in the Academic Family Tree is shared via a Creative Commons license. Biographical details 5. Cluster analysis Users can search by name, institution, and/or research area
Ploucquet/Oetinger Clusters were generated by spectral factorization [2], and the medicine NEUROTREE Search Tree Recent Additions Distance Analysis Help REPORT BUG Sign In Connections between 3-10 philosophy(1) clusters 11-25 cluster map was drawn using Graphviz (graphviz.org, [3]). 26+ Each cluster is a box labeled with the two member nodes with Holmes/Virchow Biographical information, anatom y Neuro ree May-Britt Moser, Ph.D. physiology(2) the strongest average connection strength across the whole useful weblinks, etc., if T Affiliations: Norwegian University of Science and Technology tree and by the two most common research areas in that Area: Spatial recognition availble Website: http://www.nobelprize.org/nobel_prizes/medicine/laureates/2014/may-britt-moser-facts.html Denny Brown/Sherrington neurology cluster. Clusters are sorted from top to bottom roughly from Bio: pharmacology(3) The Nobel Prize in Physiology or Medicine 2014 was divided, one half awarded to John O'Keefe, the other half jointly to May-Britt Moser and oldest to youngest. Edvard I. Moser "for their discoveries of cells that constitute a positioning system in the brain".
Eccles/Kandel Jennings/Hecht Mean distance: 8.54 SNBCP Automatically damage & disease biology detected publications plasticity(6 ) marine biology(5)
Tree Distance to... Nearest Nobel Oldest ancestor PubMed Report error are curated by users. Lashley/Hopkins Watson/Freud behavioral neuroendocrinology reading and spelling acquisition and disability neuroendocrinology(7) literacy(4)
Sign in to add mentor Parents Publications (Beta) We are testing a new system for linking publications to authors. Griffin/Marle r Miller/Jarvik Terman/Merrill Per Andersen grad student University of Oslo You can help! If you notice any innacuracies, please sign in evolution motivation damage & disease and mark papers as correct or incorrect matches. development(10) emotion(8) traumatic brain injury(9) 2. Database architecture Richard G.M. Morris post-doc Edinburgh Rowland DC, Roudi Y, Moser MB, Moser EI. (2016) John O'Keefe post-doc UCL Ten Years of Grid Cells. Annual Review of Stevens/Nicholls Bradbury/Tinbergen Solomon/Zandbelt Tolman/Campbell Neuroscience development m athematics anxiety disorders anxiety damage & disease(11) physics(12) assessment(14) anxiety disorders(13) Miao C, Cao Q, Ito HT, Yamahachi H, Witter MP, Moser Sign in to add trainee MB, Moser EI. (2015) Hippocampal Remapping after Children Neurotree has been developed entirely using open-source software. Partial Inactivation of the Medial Entorhinal Cortex. Neuron. 88: 590-603 Lapham/RichardsonJr Tomer/David Grundfest/Lau Monod/Brown Spitzer/Bixby Bower/ThompsonSchill Andrew H. research 2015- Kavli Institute for Systems Neuroscience and Centre for Neural neuropathology marine ecology calcium signaling traditional chinese medicine development memory Data about researchers and the mentor relationships between them damage & disease(24) community ecology(57) neurotransmitter-gated ion channels(16) cancer(18) steroid regulation of ion channels(27) attention(15) Bahle assistant 2016 Computation, NTNU, Trondheim, Norway Lu L, Igarashi KM, Witter MP, Moser EI, Moser MB. (2015) Topography of Place Maps along the CA3-to- are stored in a database (MySQL), and the web interface is Retsina M grad Norwegian University of Science and Technology CA2 Axis of the Hippocampus. Neuron. 87: 1078-92 Meyer student Corwin/Thoreson Sejnowski/Merzenich Postle/Fitts generated dynamically by a scripting system on the web server Kropff E, Carmichael JE, Moser MB, Moser EI. (2015) biomechanics visual syste m natural language processing Charlotte N grad 2006- Kavli Institute for Systems Neuroscience and Centre for Neural traumatic brain injury(52) computation & theory(17) human factors(21) Speed cells in the medial entorhinal cortex. Nature (apache/PHP). Boccara student 2012 Computation, NTNU, Trondheim, Norway Ito HT, Zhang SJ, Witter MP, Moser EI, Moser MB. Tor Stensola grad 2008- Norwegian University of Science and Technology (2015) A prefrontal-thalamo-hippocampal circuit for student 2014 Laughlin/Dickinson Holy/Malm o Thompson/Brown Phillips/Fetz goal-directed spatial navigation. Nature. 522: 50-5 biomechanics behavioral neuroendocrinology behavior motor system neurobiology(39) animal behavior(45) memory(19) spinal cord(22) Li Lu grad 2009- Norwegian University of Science and Technology Moser MB, Rowland DC, Moser EI. (2015) Place cells, student 2014 grid cells, and memory. Cold Spring Harbor Perspectives in Medicine. 5: a021808 Laura Lee post-doc Kavli Institute for Systems Neuroscience and Centre for Neural Lohmann/Ruppersberg Hen/Morris Rauske/Porter Jeffrey/Lawrence Colgin Computation, NTNU, Trondheim, Norway synapses memory motor system personality People Connections Institutions Stensola T, Stensola H, Moser MB, Moser EI. (2015) plasticity(59) behavior(36) locomotion(49) social psychology(20) Richard James post-doc NTNU Shearing-induced asymmetry in entorhinal grid cells. pid (unique #) cid (unique #) instid Gardner Nature. 518: 207-12 Moser MB, Rowland DC, Moser EI. (2015) Place cells, Gabrieli/DEsposito Kei M Igarashi post-doc Norwegian University of Science and Technology visual system first name pid1 name grid cells, and memory. Cold Spring Harbor attention(23) Hiroshi T Ito post-doc 2009- NTNU Perspectives in Biology. 7: a021808 middle name pid2 alias pres last name instid URL Rowland DC, Moser MB. (2015) Neuroscience: A three-dimensional neural compass. Nature. 517: Epel/Gouras Squire/Bartels Gagnon/Wolbers Benton/Kaplan Moody/Graham alzheimer’s disease visual system spatial cognition pediatric psychology damage & disease institution grad/postdoc/etc city/state 156-7 alzheimer disease(28) computation & theory(29) behavioral geography(60) pediatric neuropsychology(25) clinical psychology(26) Sign in to add collaborator research area dissertation title (lon,lat) Collaborators Bjerknes TL, Langston RF, Kruge IU, Moser EI, Moser MB. (2015) Coherence among head direction cells photo URL start/stop year Edvard I Moser collaborator Norwegian University of Science and Technology before eye opening in rat pups. Current Biology : Cb. Miller/Yau Sapolsky/Korol Nicolelis/Coderre Kolb/Rubinstein Blankenship/Kruger Gomes/Ventura Xerri/Stark Montague/Ahn Kleinschmidt/Passingham Erichsen/Jacobs Goodale/Culham Holyoak/Krawczy k Heilman/Landi s StormvanLeeuwen/Cornelissen pain brain development pain child language acquisition s.cerevisiae visual system visual system memory memory aging visual system computation & theory neuropsychology ophthalmology home page 25: 103-8 circadian rhythms(31) nicotine(41) neurophysiology(37) second language acquisition(43) membrane biology(53) ophthalmology(42) m otor system(34) case-based reasoning(50) act-r(38) animal behavior(54) perception and action(35) artificial intelligence(47) damage & disease(30) psychiatry(44)
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Cepko/Schinder Ramoa/Mower Gulyas/Larsson Cools/Holtmaat Publications Keywords pain pain design psychiatry damage & disease(32) plasticity(58) psycholinguistics(55) neurology(48) Added by: wormlikeameba (2013-07-07 15:27:08) - Is someone missing from the tree? Register/sign in to make changes pid pubid Question? Ideas? Want to start a new tree? Contact admin at neurotree dot org - Report bug/error ©2005-2016 The Academic Family Tree - Data licensed for re-use with attribution to this site (CC-BY 3.0). G Chesselet/Olman AstonJones/Grace pubid keyword evolutionary genetics neuroimgaging neurotransmitters bibliograhic info LSA projection population genetics(33 ) neural electrodes(51) damage & disease(40) Creating an account enables users Beam/Sigwort h TahsiliFahadan/Dawson to add new information to the tree damage & disease phonology ion channels(46) phonetics(56)
The database consists of two basic tables, people and connections. Connection analysis Each mentor relationship is stored as a row in the connections table. Pointers (pid1 and pid2) index the two people involved in the Connections between two nodes can be traced by the shortest path through the tree or through the closest common ancestor (below). relationship, and the connection type variable specifies the nature of 6. Mentorship network influences? Acknowledgments the relationship (graduate student, postdoctoral researcher, etc.). Connection from May-Britt Moser to Mike Posner: We thank the several thousand users who continue to We characterized publication metadata with PubMed 1 Auxiliary tables are used to link neuroscientists to affiliated institutions 10 steps: build Neurotree into a resource of increasing value. We MeSH terms and by latent semantic analysis (LSA, and publication metadata. Hermann von Helmholtz (Physikalisch-Technische Reichsanstalt) ** Common ancestor ** 0.8 also thank Henry Cooney for assistance developing and | | [4]) on abstract text, which projects each author’s | (trained research assistant) | (trained research assistant) 0.6 maintaining the web site. | | publications into a 400-dimensional vector. By both 0.4 Max Planck (Friedrich-Wilhelms-Universität zu Berlin)(Physics Tree) Friedrich Goltz (Kaiser-Wilhelms-Universität Straßburg) measures, the similarity of publications for two nodes | | 0.2 Fraction different MeSH terms Funding was provided by the Metaknowledge Network | (trained research assistant) | (trained grad student) is weaker when common ancestor distance is larger. LSA cosine distance | | Publication distance 0 (knowledgelab.org). Wolfgang Köhler (Swarthmore College) Sir Charles Scott Sherrington (University of Oxford) Howeverm LSA may provide better resolution for 0 5 10 15 20 25 | | authors separated by a small distance. Common ancestor distance Fun neurogenealogy facts: Famous cousins | (trained post-doc) | (trained grad student) | | References Leonard Carmichael (University of Rochester) Sir John Carew Eccles (Australian National University) | | In a preliminary study, we measured fecundity 20 trainee [1] S. V David, B.Y. Hayden. (2012) Neurotree: a collaborative, graphical Did you know that the following historical figures are academic cousins? | (trained grad student) | (trained grad student) (number of children + grandchildren, a measure of mentor-matched sibling database of the academic genealogy of neuroscience. PLoS One. 7 (10): Ivan Pavlov and Sigmund Freud (through Johannes Muller) | | professional success [1]) as a function of the common e46608. Paul M Fitts (University of Michigan, Ann Arbor) Per Andersen (University of Oslo) [2] C. Lim, S. Bohacek, J. Hespanha, K. Obraczka. (2005) Hierarchical Donald Hebb and Stephen Kuffler (through Charles Sherrington) | | ancestor distance between an individual’s graduate 10 | (trained grad student) | (trained grad student) max-flow routing In: IEEE GLOBECOM. Max Wertheimer and Alois Alzheimer (through Wilhelm Wundt) | | and postdoctoral mentors. According to this analysis [3] E.R. Gansner, E.R. Gansner, E. Koutsofios, S.C. North, K. Vo. (1993) A Franz Nissl and Karl Lashley (2nd cousins through Wundt) Mike Posner (University of Oregon) May-Britt Moser (Norwegian University of Science and Technology) nodes with more closely related mentors (2-3 steps) Mean fecundity Technique for Drawing Directed Graphs. IEEE Trans Softw Eng. 19 (3): 0 214 – 230. tend to be more successful at producing offspring 0 5 10 15 Distance between mentors [4] S. Deerwester, S. Dumais, G. Fumas, T. Landauer, R. Hirschman. (1990) than nodes with more distantly related mentors. Indexing by latent semantic analysis. J Am Soc Inf Sci. 41 (6): 391.