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1

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

Lein, Ed S., Hawrylycz, Michael J., Ao, Nancy, Ayres, Mikael, Bensinger, Amy, Bernard, Amy, Boe, Andrew F., Boguski, Mark S., Brockway, Kevin S., Byrnes, Emi J.

Journal:

Year:

2006

Language:

english

File:

PDF, 2.89 MB

english, 2006

2

An anatomically comprehensive atlas of the adult human brain transcriptome

Hawrylycz, Michael J., Lein, Ed S., Guillozet-Bongaarts, Angela L., Shen, Elaine H., Ng, Lydia, Miller, Jeremy A., van de Lagemaat, Louie N., Smith, Kimberly A., Ebbert, Amanda, Riley, Zackery L., Aba

Journal:

Year:

2012

Language:

english

File:

PDF, 5.33 MB

english, 2012

3

Differential connectivity and response dynamics of excitatory and inhibitory neurons in visual cortex

Hofer, Sonja B, Ko, Ho, Pichler, Bruno, Vogelstein, Joshua, Ros, Hana, Zeng, Hongkui, Lein, Ed, Lesica, Nicholas A, Mrsic-Flogel, Thomas D

Journal:

Nature Neuroscience

Year:

2011

Language:

english

File:

PDF, 1.58 MB

english, 2011

4

Functional organization of the hippocampal longitudinal axis

Strange, Bryan A., Witter, Menno P., Lein, Ed S., Moser, Edvard I.

Journal:

Nature Reviews Neuroscience

Year:

2014

Language:

english

File:

PDF, 1.31 MB

english, 2014

5

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

Lein, Ed, Borm, Lars E., Linnarsson, Sten

Journal:

Year:

2017

Language:

english

File:

PDF, 594 KB

english, 2017

6

Preparation of Acute Brain Slices Using an Optimized N-Methyl-D-glucamine Protective Recovery Method

Ting, Jonathan T., Lee, Brian R., Chong, Peter, Soler-Llavina, Gilberto, Cobbs, Charles, Koch, Christof, Zeng, Hongkui, Lein, Ed

Journal:

Journal of Visualized Experiments

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

7

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

Coe, Bradley P., Stessman, Holly A. F., Sulovari, Arvis, Geisheker, Madeleine R., Bakken, Trygve E., Lake, Allison M., Dougherty, Joseph D., Lein, Ed S., Hormozdiari, Fereydoun, Bernier, Raphael A., E

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 2.49 MB

english, 2018

8

Cell-type-specific consequences of reelin deficiency in the mouse neocortex, hippocampus, and amygdala

Maureen P. Boyle, Amy Bernard, Carol L. Thompson, Lydia Ng, Andrew Boe, Marty Mortrud, Michael J. Hawrylycz, Allan R. Jones, Robert F. Hevner, Ed S. Lein

Journal:

The Journal of Comparative Neurology

Year:

2011

Language:

english

File:

PDF, 19.15 MB

english, 2011

9

Cell-type-specific consequences of reelin deficiency in the mouse neocortex, hippocampus, and amygdala

Maureen P. Boyle, Amy Bernard, Carol L. Thompson, Lydia Ng, Andrew Boe, Marty Mortrud, Michael J. Hawrylycz, Allan R. Jones, Robert F. Hevner, Ed S. Lein

Journal:

The Journal of Comparative Neurology

Year:

2011

File:

PDF, 411 KB

2011

10

Areal and laminar differentiation in the mouse neocortex using large scale gene expression data

Mike Hawrylycz, Amy Bernard, Chris Lau, Susan M. Sunkin, M. Mallar Chakravarty, Ed S. Lein, Allan R. Jones, Lydia Ng

Journal:

Year:

2010

Language:

english

File:

PDF, 1.95 MB

english, 2010

11

Shifting the paradigm: new approaches for characterizing and classifying neurons

Amy Bernard, Staci A Sorensen, Ed S Lein

Journal:

Current Opinion in Neurobiology

Year:

2009

Language:

english

File:

PDF, 267 KB

english, 2009

12

Multi-scale correlation structure of gene expression in the brain

Mike Hawrylycz, Lydia Ng, Damon Page, John Morris, Chris Lau, Sky Faber, Vance Faber, Susan Sunkin, Vilas Menon, Ed Lein, Allan Jones

Journal:

Neural Networks

Year:

2011

Language:

english

File:

PDF, 2.58 MB

english, 2011

13

Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex

Lydia Ng, Chris Lau, Susan M. Sunkin, Amy Bernard, M. Mallar Chakravarty, Ed S. Lein, Allan R. Jones, Michael Hawrylycz

Journal:

Year:

2010

Language:

english

File:

PDF, 1.44 MB

english, 2010

14

Patches of Disorganization in the Neocortex of Children with Autism

Stoner, Rich, Chow, Maggie L., Boyle, Maureen P., Sunkin, Susan M., Mouton, Peter R., Roy, Subhojit, Wynshaw-Boris, Anthony, Colamarino, Sophia A., Lein, Ed S., Courchesne, Eric

Journal:

New England Journal of Medicine

Year:

2014

Language:

english

File:

PDF, 517 KB

english, 2014

15

The Genetic Geography of the Brain

Lein, Ed, Hawrylycz, Mike

Journal:

Scientific American

Year:

2014

Language:

english

File:

PDF, 10.50 MB

english, 2014

16

Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging

Ouyang, Austin, Jeon, Tina, Sunkin, Susan M., Pletikos, Mihovil, Sedmak, Goran, Sestan, Nenad, Lein, Ed S., Huang, Hao

Journal:

Year:

2015

Language:

english

File:

PDF, 3.21 MB

english, 2015

17

Cortical fast-spiking parvalbumin interneurons enwrapped in the perineuronal net express the metallopeptidases Adamts8, Adamts15 and Neprilysin

Rossier, J, Bernard, A, Cabungcal, J-H, Perrenoud, Q, Savoye, A, Gallopin, T, Hawrylycz, M, Cuénod, M, Do, K, Urban, A, Lein, Ed S

Journal:

Molecular Psychiatry

Year:

2015

Language:

english

File:

PDF, 612 KB

english, 2015

18

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq

Miller, Jeremy A, Menon, Vilas, Goldy, Jeff, Kaykas, Ajamete, Lee, Chang-Kyu, Smith, Kimberly A, Shen, Elaine H, Phillips, John W, Lein, Ed S, Hawrylycz, Mike J

Journal:

Year:

2014

File:

PDF, 2.68 MB

2014

19

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq

Miller, Jeremy A, Menon, Vilas, Goldy, Jeff, Kaykas, Ajamete, Lee, Chang-Kyu, Smith, Kimberly A, Shen, Elaine H, Phillips, John W, Lein, Ed S, Hawrylycz, Mike J

Journal:

Year:

2014

Language:

english

File:

PDF, 2.68 MB

english, 2014

20

SPIE Proceedings [SPIE SPIE Medical Imaging - Lake Buena Vista, FL (Saturday 7 February 2009)] Medical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging - Gene expression based mouse brain parcellation using Markov random field regularized non-negative matrix factorization

Pathak, Sayan D., Hu, Xiaoping P., Clough, Anne V., Haynor, David R., Thompson, Carol L., Lein, Ed, Hawrylycz, Michael

Year:

2009

Language:

english

File:

PDF, 15.55 MB

english, 2009

21

SPIE Proceedings [SPIE Medical Imaging - San Diego, CA (Saturday 12 February 2005)] Medical Imaging 2005: Image Processing - Gene expression detection and expression visualization in in situ hybridized cross-sectional images of the mouse brain

Pathak, Sayan, Fitzpatrick, J. Michael, Reinhardt, Joseph M., Lein, Ed, Smith, Simon, Haynor, David R., Hawrylycz, Michael

Year:

2005

Language:

english

File:

PDF, 772 KB

english, 2005

22

Transcriptomic Perspectives on Neocortical Structure, Development, Evolution, and Disease

Lein, Ed S., Belgard, T. Grant, Hawrylycz, Michael, Molnár, Zoltán

Journal:

Annual Review of Neuroscience

Year:

2017

Language:

english

File:

PDF, 6.24 MB

english, 2017

23

Neural mechanisms of functional impairment across the lifespan

van Thriel, Christoph, Levin, Ed, Lein, Pam, Costa, Lucio G., Westerink, Remco H.S.

Journal:

NeuroToxicology

Year:

2017

Language:

english

File:

PDF, 169 KB

english, 2017

24

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Long, Brian, Zhou, Zhi, Cetin, Ali, Ting, Jonathan, Gwinn, Ryder, Tasic, Bosiljka, Daigle, Tanya, Lein, Ed, Zeng, Hongkui, Saggau, Peter, Hawrylycz, Michael, Peng, Hanchuan

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.75 MB

english, 2017

25

Big data and single cell transcriptomics: implications for ontological representation

Aevermann, Brian D, Novotny, Mark, Bakken, Trygve, Miller, Jeremy A, Diehl, Alexander D, Osumi-Sutherland, David, Lasken, Roger S, Lein, Ed S, Scheuermann, Richard H

Journal:

Human Molecular Genetics

Year:

2018

Language:

english

File:

PDF, 625 KB

english, 2018

26

Comments and General Discussion on “The Anatomical Problem Posed by Brain Complexity and Size: A Potential Solution”

DeFelipe, Javier, Douglas, Rodney J., Hill, Sean L., Lein, Ed S., Martin, Kevan A. C., Rockland, Kathleen S., Segev, Idan, Shepherd, Gordon M., Tamás, Gábor

Journal:

Frontiers in Neuroanatomy

Year:

2016

Language:

english

File:

PDF, 616 KB

english, 2016

27

Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections

Iglesias, Juan Eugenio, Modat, Marc, Peter, Loïc, Stevens, Allison, Annunziata, Roberto, Vercauteren, Tom, Lein, Ed, Fischl, Bruce, Ourselin, Sebastien

Journal:

Medical Image Analysis

Year:

2018

Language:

english

File:

PDF, 9.95 MB

english, 2018

28

Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain

Huang, August Yue, Li, Pengpeng, Rodin, Rachel E., Kim, Sonia N., Dou, Yanmei, Kenny, Connor J., Akula, Shyam K., Hodge, Rebecca D., Bakken, Trygve E., Miller, Jeremy A., Lein, Ed S., Park, Peter J.,

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.79 MB

2020

29

Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis

Ding, Song-Lin, Yao, Zizhen, Hirokawa, Karla E., Nguyen, Thuc Nghi, Graybuck, Lucas T., Fong, Olivia, Bohn, Phillip, Ngo, Kiet, Smith, Kimberly A., Koch, Christof, Phillips, John W., Lein, Ed S., Harr

Journal:

Year:

2020

File:

PDF, 8.84 MB

2020

30

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

Gyllborg, Daniel, Langseth, Christoffer Mattsson, Qian, Xiaoyan, Choi, Eunkyoung, Salas, Sergio Marco, Hilscher, Markus M, Lein, Ed S, Nilsson, Mats

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 6.60 MB

2020

31

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the FriedmanâRafsky non-parametric test

Zhang, Yun, Aevermann, Brian D, Bakken, Trygve E, Miller, Jeremy A, Hodge, Rebecca D, Lein, Ed S, Scheuermann, Richard H

Journal:

Briefings in Bioinformatics

Year:

2020

File:

PDF, 2.52 MB

2020