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https://www.researchgate.net/profile/Trygve_Bakken

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Scopus Author ID: 35725101200
ResearcherID: R-4622-2017

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United States

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Allen Institute for Brain Science: Seattle, WA, US

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Trygve E Bakken

Works (50 of 55)

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Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system

Nature Neuroscience
2024-12 | Journal article
DOI: 10.1038/s41593-024-01827-9
Contributors: Igor Adameyko; Trygve Bakken; Aparna Bhaduri; Chintan Chhatbar; Mariella G. Filbin; David Gate; Hannah Hochgerner; Chang Nam Kim; Jordan Krull; Gioele La Manno et al.
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Crossref

Transcriptomic diversity of cell types across the adult human brain

Science
2023-10-13 | Journal article
DOI: 10.1126/science.add7046
Contributors: Kimberly Siletti; Rebecca Hodge; Alejandro Mossi Albiach; Ka Wai Lee; Song-Lin Ding; Lijuan Hu; Peter Lönnerberg; Trygve Bakken; Tamara Casper; Michael Clark et al.
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Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Nature Ecology & Evolution
2023-09-04 | Journal article
DOI: 10.1038/s41559-023-02186-7
Contributors: Hamsini Suresh; Megan Crow; Nikolas Jorstad; Rebecca Hodge; Ed Lein; Alexander Dobin; Trygve Bakken; Jesse Gillis
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Oligodendrocyte precursor cells ingest axons in the mouse neocortex

Proceedings of the National Academy of Sciences
2022-11-29 | Journal article
DOI: 10.1073/pnas.2202580119
Contributors: JoAnn Buchanan; Leila Elabbady; Forrest Collman; Nikolas L. Jorstad; Trygve E. Bakken; Carolyn Ott; Jenna Glatzer; Adam A. Bleckert; Agnes L. Bodor; Derrick Brittain et al.
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Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders

Proceedings of the National Academy of Sciences
2022-11-15 | Journal article
DOI: 10.1073/pnas.2203491119
Contributors: Tianyun Wang; Chang N. Kim; Trygve E. Bakken; Madelyn A. Gillentine; Barbara Henning; Yafei Mao; Christian Gilissen; Tomasz J. Nowakowski; Evan E. Eichler; John Acampado et al.
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Transcriptomic diversity of cell types across the adult human brain

2022-10-14 | Preprint
DOI: 10.1101/2022.10.12.511898
Contributors: Kimberly Siletti; Rebecca Hodge; Alejandro Mossi Albiach; Lijuan Hu; Ka Wai Lee; Peter Lönnerberg; Trygve Bakken; Song-Lin Ding; Michael Clark; Tamara Casper et al.
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Conserved coexpression at single cell resolution across primate brains

2022-09-22 | Preprint
DOI: 10.1101/2022.09.20.508736
Contributors: Hamsini Suresh; Megan Crow; Nikolas Jorstad; Rebecca Hodge; Ed Lein; Alexander Dobin; Trygve Bakken; Jesse Gillis
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Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse

Nature
2022-04-07 | Journal article
DOI: 10.1038/s41586-022-04562-y
Contributors: Trygve E. Bakken; Nikolas L. Jorstad; Qiwen Hu; Blue B. Lake; Wei Tian; Brian E. Kalmbach; Megan Crow; Rebecca D. Hodge; Fenna M. Krienen; Staci A. Sorensen et al.
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Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Nature
2022-01-20 | Journal article
DOI: 10.1038/s41586-021-04322-4
Contributors: Jim Berg; Staci A. Sorensen; Jonathan T. Ting; Jeremy A. Miller; Thomas Chartrand; Anatoly Buchin; Trygve E. Bakken; Agata Budzillo; Nick Dee; Song-Lin Ding et al.
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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Nature
2021-10-07 | Journal article
DOI: 10.1038/s41586-021-03465-8
Contributors: Trygve E. Bakken; Nikolas L. Jorstad; Qiwen Hu; Blue B. Lake; Wei Tian; Brian E. Kalmbach; Megan Crow; Rebecca D. Hodge; Fenna M. Krienen; Staci A. Sorensen et al.
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Human neocortical expansion involves glutamatergic neuron diversification

Nature
2021-10-07 | Journal article
DOI: 10.1038/s41586-021-03813-8
Contributors: Jim Berg; Staci A. Sorensen; Jonathan T. Ting; Jeremy A. Miller; Thomas Chartrand; Anatoly Buchin; Trygve E. Bakken; Agata Budzillo; Nick Dee; Song-Lin Ding et al.
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A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

Genome Research
2021-10-04 | Journal article
DOI: 10.1101/gr.275569.121
Contributors: Brian Aevermann; Yun Zhang; Mark Novotny; Mohamed Keshk; Trygve Bakken; Jeremy Miller; Rebecca Hodge; Boudewijn Lelieveldt; Ed Lein; Richard H. Scheuermann
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Integrated gene analyses of de novo mutations from 46,612 trios with autism and developmental disorders

2021-09-16 | Other
DOI: 10.1101/2021.09.15.460398
Contributors: Tianyun Wang; Chang Kim; Trygve E. Bakken; Madelyn A. Gillentine; Barbara Henning; Yafei Mao; Christian Gilissen; Tomasz J. Nowakowski; Evan E. Eichler
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Crossref

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

eLife
2021-09-02 | Journal article
DOI: 10.7554/eLife.64875
Contributors: Trygve E Bakken; Cindy TJ van Velthoven; Vilas Menon; Rebecca D Hodge; Zizhen Yao; Thuc Nghi Nguyen; Lucas T Graybuck; Gregory D Horwitz; Darren Bertagnolli; Jeff Goldy et al.
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Recent ultra-rare inherited variants implicate new autism candidate risk genes

Nature Genetics
2021-08-26 | Journal article
DOI: 10.1038/s41588-021-00899-8
Contributors: Amy B. Wilfert; Tychele N. Turner; Shwetha C. Murali; PingHsun Hsieh; Arvis Sulovari; Tianyun Wang; Bradley P. Coe; Hui Guo; Kendra Hoekzema; Trygve E. Bakken et al.
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Oligodendrocyte precursor cells prune axons in the mouse neocortex

2021-06-29 | Other
DOI: 10.21203/rs.3.rs-581121/v1
Contributors: JoAnn Buchanan; Leila Elabbady; Forrest Collman; Nicholas Jorstad; Trygve Bakken; Carolyn Ott; Jenna Glazer; Adam Bleckert; Agnes Bodor; Derrick Brittain et al.
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Oligodendrocyte precursor cells prune axons in the mouse neocortex

2021-05-29 | Other
DOI: 10.1101/2021.05.29.446047
Contributors: JoAnn Buchanan; Leila Elabbady; Forrest Collman; Nikolas L. Jorstad; Trygve E. Bakken; Carolyn Ott; Jenna Glatzer; Adam A. Bleckert; Agnes L. Bodor; Derrick Brittan et al.
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Structural and cellular transcriptome foundations of human brain disease

2021-05-13 | Preprint
DOI: 10.1101/2021.05.12.443911
Contributors: Yashar Zeighami; Trygve E. Bakken; Thomas Nickl-Jockschat; Zeru Peterson; Anil G. Jegga; Jeremy A. Miller; Alan C. Evans; Ed S. Lein; Michael Hawrylycz
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Common cell type nomenclature for the mammalian brain

eLife
2020-12-29 | Journal article
DOI: 10.7554/eLife.59928
Contributors: Jeremy A Miller; Nathan W Gouwens; Bosiljka Tasic; Forrest Collman; Cindy TJ van Velthoven; Trygve E Bakken; Michael J Hawrylycz; Hongkui Zeng; Ed S Lein; Amy Bernard
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Single-cell RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates and humans

2020-11-06 | Preprint
DOI: 10.1101/2020.11.05.367482
Contributors: Trygve E. Bakken; Cindy T.J. van Velthoven; Vilas Menon; Rebecca D. Hodge; Zizhen Yao; Thuc Nghi Nguyen; Lucas T. Graybuck; Gregory D. Horwitz; Darren Bertagnolli; Jeff Goldy et al.
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A multimodal cell census and atlas of the mammalian primary motor cortex

2020-10-21 | Preprint
DOI: 10.1101/2020.10.19.343129
Contributors: Ricky S. Adkins; Andrew I. Aldridge; Shona Allen; Seth A. Ament; Xu An; Ethan Armand; Giorgio A. Ascoli; Trygve E. Bakken; Anita Bandrowski; Samik Banerjee et al.
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NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing

2020-09-24 | Preprint
DOI: 10.1101/2020.09.23.308932
Contributors: Brian Aevermann; Yun Zhang; Mark Novotny; Trygve Bakken; Jeremy Miller; Rebecca Hodge; Boudewijn Lelieveldt; Ed Lein; Richard H. Scheuermann
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Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type specific lineage patterns in human brain

2020-04-20 | Preprint
DOI: 10.1101/2020.04.19.046904
Contributors: August Yue Huang; Pengpeng Li; Rachel E. Rodin; Sonia N. Kim; Yanmei Dou; Connor J. Kenny; Shyam K. Akula; Rebecca D. Hodge; Trygve E. Bakken; Jeremy A. Miller et al.
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Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

2020-04-02 | Preprint
DOI: 10.1101/2020.03.31.018820
Contributors: Jim Berg; Staci A. Sorensen; Jonathan T. Ting; Jeremy A. Miller; Thomas Chartrand; Anatoly Buchin; Trygve E. Bakken; Agata Budzillo; Nick Dee; Song-Lin Ding et al.
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Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

2020-04-01 | Preprint
DOI: 10.1101/2020.03.31.016972
Contributors: Trygve E. Bakken; Nikolas L. Jorstad; Qiwen Hu; Blue B. Lake; Wei Tian; Brian E. Kalmbach; Megan Crow; Rebecca D. Hodge; Fenna M. Krienen; Staci A. Sorensen et al.
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Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

Nature Communications
2020-03-03 | Journal article
DOI: 10.1038/s41467-020-14952-3
Contributors: Rebecca D. Hodge; Jeremy A. Miller; Mark Novotny; Brian E. Kalmbach; Jonathan T. Ting; Trygve E. Bakken; Brian D. Aevermann; Eliza R. Barkan; Madeline L. Berkowitz-Cerasano; Charles Cobbs et al.
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Conserved cell types with divergent features in human versus mouse cortex

Nature
2019 | Journal article
DOI: 10.1038/s41586-019-1506-7
EID:

2-s2.0-85071326152
Contributors: Hodge, R.D.; Bakken, T.E.; Miller, J.A.; Smith, K.A.; Barkan, E.R.; Graybuck, L.T.; Close, J.L.; Long, B.; Johansen, N.; Penn, O. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity

Nature Genetics
2019 | Journal article
DOI: 10.1038/s41588-018-0288-4
EID:

2-s2.0-85058847706
Contributors: Coe, B.P.; Stessman, H.A.F.; Sulovari, A.; Geisheker, M.R.; Bakken, T.E.; Lake, A.M.; Dougherty, J.D.; Lein, E.S.; Hormozdiari, F.; Bernier, R.A. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

New insights into the development of the human cerebral cortex

Journal of Anatomy
2019 | Journal article
DOI: 10.1111/joa.13055
EID:

2-s2.0-85070062982
Contributors: Molnár, Z.; Clowry, G.J.; Šestan, N.; Alzu'bi, A.; Bakken, T.; Hevner, R.F.; Hüppi, P.S.; Kostović, I.; Rakic, P.; Anton, E.S. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

eLife
2019-11-11 | Journal article
DOI: 10.7554/eLife.47889
Contributors: Stephen J Smith; Uygar Sümbül; Lucas T Graybuck; Forrest Collman; Sharmishtaa Seshamani; Rohan Gala; Olga Gliko; Leila Elabbady; Jeremy A Miller; Trygve E Bakken et al.
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Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas

PLOS ONE
2019-09-04 | Journal article
DOI: 10.1371/journal.pone.0212898
Contributors: Natalie Weed; Joseph Najbauer; Trygve Bakken; Nile Graddis; Nathan Gouwens; Daniel Millman; Michael Hawrylycz; Jack Waters
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Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas

2019-02-14 | Other
DOI: 10.1101/549519
Contributors: Natalie Weed; Trygve Bakken; Nile Graddis; Nathan Gouwens; Daniel Millman; Michael Hawrylycz; Jack Waters
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Crossref

Single-Cell Transcriptomic Evidence for Dense Intracortical Neuropeptide Networks

2019-01-13 | Other
DOI: 10.1101/519694
Contributors: Stephen J Smith; Uygar Sümbül; Lucas Graybuck; Forrest Collman; Sharmishtaa Seshamani; Rohan Gala; Olga Gliko; Leila Elabbady; Jeremy A. Miller; Trygve Bakken et al.
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Crossref

Genetic identification of brain cell types underlying schizophrenia

Nature Genetics
2018 | Journal article
DOI: 10.1038/s41588-018-0129-5
EID:

2-s2.0-85047196309
Contributors: Skene, N.G.; Bryois, J.; Bakken, T.E.; Breen, G.; Crowley, J.J.; Gaspar, H.A.; Giusti-Rodriguez, P.; Hodge, R.D.; Miller, J.A.; Muñoz-Manchado, A.B. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex

Neuron
2018 | Journal article
DOI: 10.1016/j.neuron.2018.10.012
EID:

2-s2.0-85059333690
Contributors: Kalmbach, B.E.; Buchin, A.; Long, B.; Close, J.; Nandi, A.; Miller, J.A.; Bakken, T.E.; Hodge, R.D.; Chong, P.; de Frates, R. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Shared and distinct transcriptomic cell types across neocortical areas

Nature
2018 | Journal article
DOI: 10.1038/s41586-018-0654-5
EID:

2-s2.0-85055855595
Contributors: Tasic, B.; Yao, Z.; Graybuck, L.T.; Smith, K.A.; Nguyen, T.N.; Bertagnolli, D.; Goldy, J.; Garren, E.; Economo, M.N.; Viswanathan, S. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

Nature Neuroscience
2018 | Journal article
DOI: 10.1038/s41593-018-0205-2
EID:

2-s2.0-85052700215
Contributors: Boldog, E.; Bakken, T.E.; Hodge, R.D.; Novotny, M.; Aevermann, B.D.; Baka, J.; Bordé, S.; Close, J.L.; Diez-Fuertes, F.; Ding, S.-L. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

PLOS ONE
2018-12-26 | Journal article
DOI: 10.1371/journal.pone.0209648
Contributors: Trygve E. Bakken; Eduardo Soriano; Rebecca D. Hodge; Jeremy A. Miller; Zizhen Yao; Thuc Nghi Nguyen; Brian Aevermann; Eliza Barkan; Darren Bertagnolli; Tamara Casper et al.
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Cell type discovery using single-cell transcriptomics: implications for ontological representation

Human Molecular Genetics
2018-05-01 | Journal article
DOI: 10.1093/hmg/ddy100
Contributors: Brian D Aevermann; Mark Novotny; Trygve Bakken; Jeremy A Miller; Alexander D Diehl; David Osumi-Sutherland; Roger S Lasken; Ed S Lein; Richard H Scheuermann
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Cell type discovery and representation in the era of high-content single cell phenotyping

BMC Bioinformatics
2017 | Journal article
DOI: 10.1186/s12859-017-1977-1
EID:

2-s2.0-85038899097
Contributors: Bakken, T.; Cowell, L.; Aevermann, B.D.; Novotny, M.; Hodge, R.; Miller, J.A.; Lee, A.; Chang, I.; McCorrison, J.; Pulendran, B. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Erratum: Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation (Neuron (2017) (93) (5)(1035–1048.e5) (S0896627317300983) (10.1016/j.neuron.2017.02.014))

Neuron
2017 | Journal article
DOI: 10.1016/j.neuron.2017.10.024
EID:

2-s2.0-85033686286
Contributors: Close, J.L.; Yao, Z.; Levi, B.P.; Miller, J.A.; Bakken, T.E.; Menon, V.; Ting, J.T.; Wall, A.; Krostag, A.-R.; Thomsen, E.R. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Production of a preliminary quality control pipeline for single nuclei rna-seq and its application in the analysis of cell type diversity of post-mortem human brain neocortex

Pacific Symposium on Biocomputing
2017 | Journal article
DOI: 10.1142/9789813207813_0052
EID:

2-s2.0-85015607256
Contributors: Aevermann, B.; McCorrison, J.; Venepally, P.; Hodge, R.; Bakken, T.; Miller, J.; Novotny, M.; Tran, D.N.; Diez-Fuertes, F.; Christiansen, L. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation

Neuron
2017 | Journal article
DOI: 10.1016/j.neuron.2017.02.014
EID:

2-s2.0-85014804284
Contributors: Close, J.L.; Yao, Z.; Levi, B.P.; Miller, J.A.; Bakken, T.E.; Menon, V.; Ting, J.T.; Wall, A.; Krostag, A.-R.; Thomsen, E.R. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing

2017-12-25 | Other
DOI: 10.1101/239749
Contributors: Trygve E. Bakken; Rebecca D. Hodge; Jeremy M. Miller; Zizhen Yao; Thuc N. Nguyen; Brian Aevermann; Eliza Barkan; Darren Bertagnolli; Tamara Casper; Nick Dee et al.
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A comprehensive transcriptional map of primate brain development

Nature
2016 | Journal article
DOI: 10.1038/nature18637
EID:

2-s2.0-84978173600
Contributors: Bakken, T.E.; Miller, J.A.; Ding, S.-L.; Sunkin, S.M.; Smith, K.A.; Ng, L.; Szafer, A.; Dalley, R.A.; Royall, J.J.; Lemon, T. et al.
Source: Self-asserted source
Trygve E Bakken via Scopus - Elsevier

Spatiotemporal dynamics of the postnatal developing primate brain transcriptome.

2015-05 | Journal article
DOI: 10.1093/hmg/ddv166
PMID: 25954031
Contributors: Bakken TE; Miller JA; Luo R; Bernard A; Bennett JL; Lee CK; Bertagnolli D; Parikshak NN; Smith KA; Sunkin SM et al.
Source: Self-asserted source
Trygve E Bakken via Europe PubMed Central
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Convergent transcriptional specializations in the brains of humans and song-learning birds.

2014-12 | Journal article
DOI: 10.1126/science.1256846
PMID: 25504733
PMC: PMC4385736
Contributors: Pfenning AR; Hara E; Whitney O; Rivas MV; Wang R; Roulhac PL; Howard JT; Wirthlin M; Lovell PV; Ganapathy G et al.
Source: Self-asserted source
Trygve E Bakken via Europe PubMed Central
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Disruptive CHD8 mutations define a subtype of autism early in development.

2014-07 | Journal article
DOI: 10.1016/j.cell.2014.06.017
PMID: 24998929
Contributors: Bernier R; Golzio C; Xiong B; Stessman HA; Coe BP; Penn O; Witherspoon K; Gerdts J; Baker C; Vulto-van Silfhout AT et al.
Source: Self-asserted source
Trygve E Bakken via Europe PubMed Central
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The complete genome sequence of a Neanderthal from the Altai Mountains.

2014-01 | Journal article
DOI: 10.1038/nature12886
PMID: 24352235
PMC: PMC4031459
Contributors: Prüfer K; Racimo F; Patterson N; Jay F; Sankararaman S; Sawyer S; Heinze A; Renaud G; Sudmant PH; de Filippo C et al.
Source: Self-asserted source
Trygve E Bakken via Europe PubMed Central
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Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans.

2012-03 | Journal article
DOI: 10.1073/pnas.1105829109
PMID: 22343285
PMC: PMC3309762
Contributors: Bakken TE; Roddey JC; Djurovic S; Akshoomoff N; Amaral DG; Bloss CS; Casey BJ; Chang L; Ernst TM; Gruen JR et al.
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Trygve E Bakken via Europe PubMed Central
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Page 1 of 2

Peer review (15 reviews for 7 publications/grants)

Review activity for Advanced science. (1)
Review activity for Cell genomics. (1)
Review activity for Current opinion in genetics & development. (1)
Review activity for GigaScience. (2)
Review activity for Nature (7)
Review activity for Nature communications (2)
Review activity for PLoS biology. (1)
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