A citation-based method for searching scientific literature

Dmitry Velmeshev, Lucas Schirmer, Diane Jung, Maximilian Haeussler, Yonatan Perez, Simone Mayer, Aparna Bhaduri, Nitasha Goyal, David H Rowitch, Arnold R Kriegstein. Science 2019
Times Cited: 266







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



Times Cited
  Times     Co-cited
Similarity


Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism.
F Kyle Satterstrom, Jack A Kosmicki, Jiebiao Wang, Michael S Breen, Silvia De Rubeis, Joon-Yong An, Minshi Peng, Ryan Collins, Jakob Grove, Lambertus Klei,[...]. Cell 2020
683
22

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
20

Transcriptomic analysis of autistic brain reveals convergent molecular pathology.
Irina Voineagu, Xinchen Wang, Patrick Johnston, Jennifer K Lowe, Yuan Tian, Steve Horvath, Jonathan Mill, Rita M Cantor, Benjamin J Blencowe, Daniel H Geschwind. Nature 2011
18

Single-cell transcriptomic analysis of Alzheimer's disease.
Hansruedi Mathys, Jose Davila-Velderrain, Zhuyu Peng, Fan Gao, Shahin Mohammadi, Jennie Z Young, Madhvi Menon, Liang He, Fatema Abdurrob, Xueqiao Jiang,[...]. Nature 2019
742
17

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
Mingfeng Li, Gabriel Santpere, Yuka Imamura Kawasawa, Oleg V Evgrafov, Forrest O Gulden, Sirisha Pochareddy, Susan M Sunkin, Zhen Li, Yurae Shin, Ying Zhu,[...]. Science 2018
300
14

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
Tomasz J Nowakowski, Aparna Bhaduri, Alex A Pollen, Beatriz Alvarado, Mohammed A Mostajo-Radji, Elizabeth Di Lullo, Maximilian Haeussler, Carmen Sandoval-Espinosa, Siyuan John Liu, Dmitry Velmeshev,[...]. Science 2017
388
14

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
551
14

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
14

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.
Neelroop N Parikshak, Vivek Swarup, T Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang,[...]. Nature 2016
345
13

Synaptic, transcriptional and chromatin genes disrupted in autism.
Silvia De Rubeis, Xin He, Arthur P Goldberg, Christopher S Poultney, Kaitlin Samocha, A Erucment Cicek, Yan Kou, Li Liu, Menachem Fromer, Susan Walker,[...]. Nature 2014
13

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.
Michael J Gandal, Pan Zhang, Evi Hadjimichael, Rebecca L Walker, Chao Chen, Shuang Liu, Hyejung Won, Harm van Bakel, Merina Varghese, Yongjun Wang,[...]. Science 2018
478
13

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
13

The contribution of de novo coding mutations to autism spectrum disorder.
Ivan Iossifov, Brian J O'Roak, Stephan J Sanders, Michael Ronemus, Niklas Krumm, Dan Levy, Holly A Stessman, Kali T Witherspoon, Laura Vives, Karynne E Patterson,[...]. Nature 2014
12

Identification of common genetic risk variants for autism spectrum disorder.
Jakob Grove, Stephan Ripke, Thomas D Als, Manuel Mattheisen, Raymond K Walters, Hyejung Won, Jonatan Pallesen, Esben Agerbo, Ole A Andreassen, Richard Anney,[...]. Nat Genet 2019
744
12

Spatio-temporal transcriptome of the human brain.
Hyo Jung Kang, Yuka Imamura Kawasawa, Feng Cheng, Ying Zhu, Xuming Xu, Mingfeng Li, André M M Sousa, Mihovil Pletikos, Kyle A Meyer, Goran Sedmak,[...]. Nature 2011
12

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
12

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
11

Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders.
Donna M Werling, Neelroop N Parikshak, Daniel H Geschwind. Nat Commun 2016
139
11

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.
A Jeremy Willsey, Stephan J Sanders, Mingfeng Li, Shan Dong, Andrew T Tebbenkamp, Rebecca A Muhle, Steven K Reilly, Leon Lin, Sofia Fertuzinhos, Jeremy A Miller,[...]. Cell 2013
548
11

Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons.
Corina Nagy, Malosree Maitra, Arnaud Tanti, Matthew Suderman, Jean-Francois Théroux, Maria Antonietta Davoli, Kelly Perlman, Volodymyr Yerko, Yu Chang Wang, Shreejoy J Tripathy,[...]. Nat Neurosci 2020
99
11

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
11

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
11

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs).
Brett S Abrahams, Dan E Arking, Daniel B Campbell, Heather C Mefford, Eric M Morrow, Lauren A Weiss, Idan Menashe, Tim Wadkins, Sharmila Banerjee-Basu, Alan Packer. Mol Autism 2013
349
11

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism.
Neelroop N Parikshak, Rui Luo, Alice Zhang, Hyejung Won, Jennifer K Lowe, Vijayendran Chandran, Steve Horvath, Daniel H Geschwind. Cell 2013
619
10

Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism.
Simone Gupta, Shannon E Ellis, Foram N Ashar, Anna Moes, Joel S Bader, Jianan Zhan, Andrew B West, Dan E Arking. Nat Commun 2014
301
10

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
941
10

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
10

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
9

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
955
9

De novo mutations revealed by whole-exome sequencing are strongly associated with autism.
Stephan J Sanders, Michael T Murtha, Abha R Gupta, John D Murdoch, Melanie J Raubeson, A Jeremy Willsey, A Gulhan Ercan-Sencicek, Nicholas M DiLullo, Neelroop N Parikshak, Jason L Stein,[...]. Nature 2012
9

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
9

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko,[...]. Nat Biotechnol 2018
406
9

A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function.
John D Cahoy, Ben Emery, Amit Kaushal, Lynette C Foo, Jennifer L Zamanian, Karen S Christopherson, Yi Xing, Jane L Lubischer, Paul A Krieg, Sergey A Krupenko,[...]. J Neurosci 2008
8

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
Jessica Mariani, Gianfilippo Coppola, Ping Zhang, Alexej Abyzov, Lauren Provini, Livia Tomasini, Mariangela Amenduni, Anna Szekely, Dean Palejev, Michael Wilson,[...]. Cell 2015
610
8

Long-term maturation of human cortical organoids matches key early postnatal transitions.
Aaron Gordon, Se-Jin Yoon, Stephen S Tran, Christopher D Makinson, Jin Young Park, Jimena Andersen, Alfredo M Valencia, Steve Horvath, Xinshu Xiao, John R Huguenard,[...]. Nat Neurosci 2021
79
10

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
Damon Polioudakis, Luis de la Torre-Ubieta, Justin Langerman, Andrew G Elkins, Xu Shi, Jason L Stein, Celine K Vuong, Susanne Nichterwitz, Melinda Gevorgian, Carli K Opland,[...]. Neuron 2019
166
8

Transcriptional landscape of the prenatal human brain.
Jeremy A Miller, Song-Lin Ding, Susan M Sunkin, Kimberly A Smith, Lydia Ng, Aaron Szafer, Amanda Ebbert, Zackery L Riley, Joshua J Royall, Kaylynn Aiona,[...]. Nature 2014
719
8

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron, Adrian Veres, Samuel L Wolock, Aubrey L Faust, Renaud Gaujoux, Amedeo Vetere, Jennifer Hyoje Ryu, Bridget K Wagner, Shai S Shen-Orr, Allon M Klein,[...]. Cell Syst 2016
535
8

Neuronal vulnerability and multilineage diversity in multiple sclerosis.
Lucas Schirmer, Dmitry Velmeshev, Staffan Holmqvist, Max Kaufmann, Sebastian Werneburg, Diane Jung, Stephanie Vistnes, John H Stockley, Adam Young, Maike Steindel,[...]. Nature 2019
193
8

Prevalence of Autism Spectrum Disorder Among Children Aged 8 Years - Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2016.
Matthew J Maenner, Kelly A Shaw, Jon Baio, Anita Washington, Mary Patrick, Monica DiRienzo, Deborah L Christensen, Lisa D Wiggins, Sydney Pettygrove, Jennifer G Andrews,[...]. MMWR Surveill Summ 2020
7

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
7

Shank3 mutant mice display autistic-like behaviours and striatal dysfunction.
João Peça, Cátia Feliciano, Jonathan T Ting, Wenting Wang, Michael F Wells, Talaignair N Venkatraman, Christopher D Lascola, Zhanyan Fu, Guoping Feng. Nature 2011
906
7


A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.
Alexandra Grubman, Gabriel Chew, John F Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca K Simmons, Sam Buckberry, Dulce B Vargas-Landin, Daniel Poppe,[...]. Nat Neurosci 2019
269
7

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
532
7

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
352
7

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
7

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
Elizabeth K Ruzzo, Laura Pérez-Cano, Jae-Yoon Jung, Lee-Kai Wang, Dorna Kashef-Haghighi, Chris Hartl, Chanpreet Singh, Jin Xu, Jackson N Hoekstra, Olivia Leventhal,[...]. Cell 2019
158
7

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
7


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.