A citation-based method for searching scientific literature

Zizhen Yao, Cindy T J van Velthoven, Thuc Nghi Nguyen, Jeff Goldy, Adriana E Sedeno-Cortes, Fahimeh Baftizadeh, Darren Bertagnolli, Tamara Casper, Megan Chiang, Kirsten Crichton, Song-Lin Ding, Olivia Fong, Emma Garren, Alexandra Glandon, Nathan W Gouwens, James Gray, Lucas T Graybuck, Michael J Hawrylycz, Daniel Hirschstein, Matthew Kroll, Kanan Lathia, Changkyu Lee, Boaz Levi, Delissa McMillen, Stephanie Mok, Thanh Pham, Qingzhong Ren, Christine Rimorin, Nadiya Shapovalova, Josef Sulc, Susan M Sunkin, Michael Tieu, Amy Torkelson, Herman Tung, Katelyn Ward, Nick Dee, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng. Cell 2021
Times Cited: 80







List of co-cited articles
567 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Shared and distinct transcriptomic cell types across neocortical areas.
Bosiljka Tasic, Zizhen Yao, Lucas T Graybuck, Kimberly A Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N Economo, Sarada Viswanathan,[...]. Nature 2018
542
47

Conserved cell types with divergent features in human versus mouse cortex.
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Nelson Johansen, Osnat Penn,[...]. Nature 2019
460
26

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
26

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.
Bosiljka Tasic, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, Lucas T Gray, Staci A Sorensen, Tim Dolbeare,[...]. Nat Neurosci 2016
800
23

Molecular Architecture of the Mouse Nervous System.
Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars E Borm, Gioele La Manno,[...]. Cell 2018
885
21

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
18

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
17

Genome-wide atlas of gene expression in the adult mouse brain.
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,[...]. Nature 2007
16

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.
Arpiar Saunders, Evan Z Macosko, Alec Wysoker, Melissa Goldman, Fenna M Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Laura Bortolin, Shuyu Wang,[...]. Cell 2018
542
16

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells.
Nathan W Gouwens, Staci A Sorensen, Fahimeh Baftizadeh, Agata Budzillo, Brian R Lee, Tim Jarsky, Lauren Alfiler, Katherine Baker, Eliza Barkan, Kyla Berry,[...]. Cell 2020
77
15

The neocortical circuit: themes and variations.
Kenneth D Harris, Gordon M G Shepherd. Nat Neurosci 2015
450
13


A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality.
Tanya L Daigle, Linda Madisen, Travis A Hage, Matthew T Valley, Ulf Knoblich, Rylan S Larsen, Marc M Takeno, Lawrence Huang, Hong Gu, Rachael Larsen,[...]. Cell 2018
222
12

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
12

A community-based transcriptomics classification and nomenclature of neocortical cell types.
Rafael Yuste, Michael Hawrylycz, Nadia Aalling, Argel Aguilar-Valles, Detlev Arendt, Ruben Armañanzas, Giorgio A Ascoli, Concha Bielza, Vahid Bokharaie, Tobias Borgtoft Bergmann,[...]. Nat Neurosci 2020
70
14

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.
Quanxin Wang, Song-Lin Ding, Yang Li, Josh Royall, David Feng, Phil Lesnar, Nile Graddis, Maitham Naeemi, Benjamin Facer, Anh Ho,[...]. Cell 2020
166
11


Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
303
11

Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex.
Giorgio A Ascoli, Lidia Alonso-Nanclares, Stewart A Anderson, German Barrionuevo, Ruth Benavides-Piccione, Andreas Burkhalter, György Buzsáki, Bruno Cauli, Javier Defelipe, Alfonso Fairén,[...]. Nat Rev Neurosci 2008
959
11

From Louvain to Leiden: guaranteeing well-connected communities.
V A Traag, L Waltman, N J van Eck. Sci Rep 2019
439
11

A mesoscale connectome of the mouse brain.
Seung Wook Oh, Julie A Harris, Lydia Ng, Brent Winslow, Nicholas Cain, Stefan Mihalas, Quanxin Wang, Chris Lau, Leonard Kuan, Alex M Henry,[...]. Nature 2014
10

Development and Functional Diversification of Cortical Interneurons.
Lynette Lim, Da Mi, Alfredo Llorca, Oscar Marín. Neuron 2018
218
10

Phenotypic variation of transcriptomic cell types in mouse motor cortex.
Federico Scala, Dmitry Kobak, Matteo Bernabucci, Yves Bernaerts, Cathryn René Cadwell, Jesus Ramon Castro, Leonard Hartmanis, Xiaolong Jiang, Sophie Laturnus, Elanine Miranda,[...]. Nature 2021
39
20

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
10

Neural networks of the mouse neocortex.
Brian Zingg, Houri Hintiryan, Lin Gou, Monica Y Song, Maxwell Bay, Michael S Bienkowski, Nicholas N Foster, Seita Yamashita, Ian Bowman, Arthur W Toga,[...]. Cell 2014
389
8

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
8

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
696
8

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
600
8

Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity.
Anirban Paul, Megan Crow, Ricardo Raudales, Miao He, Jesse Gillis, Z Josh Huang. Cell 2017
203
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits.
Robin Tremblay, Soohyun Lee, Bernardo Rudy. Neuron 2016
712
8

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
800
8

A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons.
D Gowanlock R Tervo, Bum-Yeol Hwang, Sarada Viswanathan, Thomas Gaj, Maria Lavzin, Kimberly D Ritola, Sarah Lindo, Susan Michael, Elena Kuleshova, David Ojala,[...]. Neuron 2016
525
7

Hierarchical organization of cortical and thalamic connectivity.
Julie A Harris, Stefan Mihalas, Karla E Hirokawa, Jennifer D Whitesell, Hannah Choi, Amy Bernard, Phillip Bohn, Shiella Caldejon, Linzy Casal, Andrew Cho,[...]. Nature 2019
126
7

Classification of electrophysiological and morphological neuron types in the mouse visual cortex.
Nathan W Gouwens, Staci A Sorensen, Jim Berg, Changkyu Lee, Tim Jarsky, Jonathan Ting, Susan M Sunkin, David Feng, Costas A Anastassiou, Eliza Barkan,[...]. Nat Neurosci 2019
129
7

The logic of single-cell projections from visual cortex.
Yunyun Han, Justus M Kebschull, Robert A A Campbell, Devon Cowan, Fabia Imhof, Anthony M Zador, Thomas D Mrsic-Flogel. Nature 2018
131
7

The diversity of GABAergic neurons and neural communication elements.
Z Josh Huang, Anirban Paul. Nat Rev Neurosci 2019
71
8

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
176
7

The origin and evolution of cell types.
Detlev Arendt, Jacob M Musser, Clare V H Baker, Aviv Bergman, Connie Cepko, Douglas H Erwin, Mihaela Pavlicev, Gerhard Schlosser, Stefanie Widder, Manfred D Laubichler,[...]. Nat Rev Genet 2016
272
7

Molecular logic of cellular diversification in the mouse cerebral cortex.
Daniela J Di Bella, Ehsan Habibi, Robert R Stickels, Gabriele Scalia, Juliana Brown, Payman Yadollahpour, Sung Min Yang, Catherine Abbate, Tommaso Biancalani, Evan Z Macosko,[...]. Nature 2021
33
18

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.
Jeffrey R Moffitt, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac,[...]. Science 2018
344
7

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldridge, Seth A Ament, Anna Bartlett, M Margarita Behrens, Koen Van den Berge,[...]. Nature 2021
27
22

Distinct descending motor cortex pathways and their roles in movement.
Michael N Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T Graybuck, Thuc Nghi Nguyen, Kimberly A Smith, Zizhen Yao,[...]. Nature 2018
137
7

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
758
7

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
6

Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population.
Euiseok J Kim, Zhuzhu Zhang, Ling Huang, Tony Ito-Cole, Matthew W Jacobs, Ashley L Juavinett, Gokhan Senturk, Mo Hu, Manching Ku, Joseph R Ecker,[...]. Neuron 2020
38
13

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain.
Johan Winnubst, Erhan Bas, Tiago A Ferreira, Zhuhao Wu, Michael N Economo, Patrick Edson, Ben J Arthur, Christopher Bruns, Konrad Rokicki, David Schauder,[...]. Cell 2019
136
6

Rabies Virus CVS-N2c(ΔG) Strain Enhances Retrograde Synaptic Transfer and Neuronal Viability.
Thomas R Reardon, Andrew J Murray, Gergely F Turi, Christoph Wirblich, Katherine R Croce, Matthias J Schnell, Thomas M Jessell, Attila Losonczy. Neuron 2016
133
6

Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons.
Bernardo Rudy, Gordon Fishell, SooHyun Lee, Jens Hjerling-Leffler. Dev Neurobiol 2011
759
6

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
6


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.