Song-Lin Ding, M.D.
Principal Scientist
Song-Lin Ding joined the Allen Institute in 2010 as a chief neuroanatomist to create reference atlases for the developing and adult human brains. He also generates brain ontology and defines laser microdissection sampling areas for human and macaque brain structures in various stages of development. Ding has over 23 years of experience in neuroanatomy. Prior to joining the Allen Institute, Ding served as a research scientist at the University of Iowa and a Research Assistant Professor at the University of Rochester. In both places, he focused on anatomical organization of adult human and macaque brains. At the University of Iowa he also helped characterize a mouse model for Batten Disease. Prior to this work, Ding was an Associate Professor at the Institute of Neuroscience, Guangzhou Medical College, China where he investigated the development of human visual and hippocampal cortices. His research interests mainly cover connectional, chemical, developmental and comparative aspects of the visual and limbic systems. His postdoctoral work at the Center for Neuroscience at the University of Tennessee, Memphis focused on the development and chemical natures of the corpus callosum connections in the rat and cat visual cortex. Ding received a M.D. from Hunan Medical University in China. He is also a Guest Professor at the Institute of Neuroscience, Guangzhou Medical College, China.
Research
Research Interests
Research Interests Understanding detailed brain organization – including its cell types, chemical/molecular nature, connections and parcellations – is an essential step to revealing the mechanisms underlying different brain functions and related diseases. As a neuroanatomist, I am interested in generating anatomical and molecular atlases for the developing and adult human and macaque brains. We use these atlases to guide our large-scale laser microdissection efforts at the Allen Institute. To create precise and detailed human brain reference atlases I use a combination of cellular and molecular markers in multiple cell types to identify the chemical characterization, molecular signature, and unique developmental changes of each target brain structure. So far we have created the first version of digital reference atlases for one adult and two prenatal human brains. Our ongoing effort is to generate reference atlases with more detailed parcellation of the entire human brain by adding fine cortical and subcortical subdivisions. Anatomical and molecular atlases of developing macaque brains provide exemplary models where there is very limited availability of human brains in various stages of development. To collect large-scale microarray data on macaque brain development we are now trying to define all layers of the visual, somatosensory and anterior cingulate cortices as well as subdivisions of the hippocampal formation, amygdala and basal ganglia at six stages of prenatal development. This dataset, together with the microarray data from prenatal human brains, will significantly fuel our understanding of human brain development and related disease. One of my future goals is to explore comparative neuroanatomy of human, monkey and rodent brains with emphasis on the visual and limbic structures. I aim to compare cell types and their molecular characterization, wiring circuits and developmental changes in different species in order to gain information on similarities and differences among these species. In addition, searching for mouse cortical homologues of human and macaque brains using molecular and connectional neuroanatomy would greatly facilitate the interactive use of the huge datasets created at the Allen Institute for mouse, macaque and human brains.
Expertise
- Neuroanatomy
- Brain development
- Atlasing
- Neurodegenerative disease
Research Programs
- Cell types
- Atlasing
Selected Publications View Publications
Cellular resolution anatomical and molecular atlases for prenatal human brains
The Journal of Comparative Neurology
January 2022
Ding SL, Royall JJ, Lesnar P, Facer BAC, Smith KA, Wei Y, Brouner K, Dalley RA, Dee N, Dolbeare TA, Ebbert A, Glass IA, Keller NH, Lee F, Lemon TA, Nyhus J, Pendergraft J, Reid R, Sarreal M, Shapovalova NV, Szafer A, Phillips JW, Sunkin SM, Hohmann JG, Jones AR, Hawrylycz MJ, Hof PR, Ng L, Bernard A, Lein ES
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Cell
May 17, 2021
Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H.
Anatomical structures, cell types and biomarkers of the Human Reference Atlas
Nature Cell Biology
November 23, 2021
Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.
Frontiers in Neuroscience
November 2, 2021
Chen CH, Hu JM, Zhang SY, Xiang XJ, Chen SQ, Ding SL
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
October 6, 2021
BRAIN Initiative Cell Census Network (BICCN)
Human neocortical expansion involves glutamatergic neuron diversification
Nature
October 6, 2021
Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Nature
October 6, 2021
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES
Cell Reports
May 19, 2020
Ding SL, Yao Z, Hirokawa KE, Nguyen TN, Graybuck LT, Fong O, Bohn P, Ngo K, Smith KA, Koch C, Phillips JW, Lein ES, Harris JA, Tasic B, Zeng H
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas
Cell
May 14, 2020
Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L
Afferent Projections to Area Prostriata of the Mouse
Frontiers in Neuroanatomy
November 27, 2020
Hu JM, Chen CH, Chen SQ, Ding SL.
Frontiers in Neural Circuits
November 13, 2020
Chen CH, Hu JM, Chen SQ, Liu SM, Ding SL.
Conserved cell types with divergent features in human versus mouse cortex
Nature
August 21, 2019
Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES
Localization of area prostriata and its connections with primary visual cortex in rodent
Journal of Comparative Neurology
August 19, 2019
Lu W, Chen S, Chen X, Hu J, Xuan A, Ding SL
Progress update from the hippocampal subfields group
Alzheimers & Dementia
June 13, 2019
Olsen RK, Carr VA, Daugherty AM, La Joie R, Amaral RSC, Amunts K, Augustinack JC, Bakker A, Bender AR, Berron D, Boccardi M, Bocchetta M, Burggren AC, Chakravarty MM8, Chételat G, de Flores R, DeKraker J, Ding SL, Geerlings MI, Huang Y, Insausti R, Johnson EG, Kanel P, Kedo O, Kennedy KM, Keresztes A, Lee JK, Lindenberger U, Mueller SG, Mulligan EM, Ofen N, Palombo DJ, Pasquini L, Pluta J, Raz N, Rodrigue KM, Schlichting ML, Lee Shing Y, Stark CEL, Steve TA, Suthana NA, Wang L, Werkle-Bergner M, Yushkevich PA, Yu Q, Wisse LEM
Human Brain Mapping
April 29, 2019
Xie L, Wisse LEM, Pluta J, de Flores R, Piskin V, Manjón JV, Wang H, Das SR, Ding SL, Wolk DA, Yushkevich PA
Hippocampus
November 1, 2019
de Flores R, Berron D, Ding SL, Ittyerah R, Pluta JB, Xie L, Adler DH, Robinson JL, Schuck T, Trojanowski JQ, Grossman M, Liu W, Pickup S, Das SR, Wolk DA, Yushkevich PA, Wisse LEM
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
Nature Neuroscience
August 27, 2018
Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Jennie L. Close, Diez-Fuertes F, Ding SL, Faragó N, Kocsis AK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G
Journal of Comparative Neurology
December 15, 2013
Ding SL
Neurobiology of Disease
February 2011
Ding SL, Tecedor L, Stein CS, Davidson BL
Human Brain Mapping
September 2010
Ding SL, Van Hoesen GW
Stratum radiatum of CA2 is an additional target of the perforant path in human and monkey
Neuroreport
March 2010
Ding SL, Haber SN, Van Hoesen GW
Journal of Comparative Neurology
June 2009
Ding SL, Van Hoesen GW, Cassell MD, Poremba A