A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity


Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
Qun Pan, Ofer Shai, Leo J Lee, Brendan J Frey, Benjamin J Blencowe. Nat Genet 2008
25

Alternative isoform regulation in human tissue transcriptomes.
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
24

The neurogenetics of alternative splicing.
Celine K Vuong, Douglas L Black, Sika Zheng. Nat Rev Neurosci 2016
127
23

A highly conserved program of neuronal microexons is misregulated in autistic brains.
Manuel Irimia, Robert J Weatheritt, Jonathan D Ellis, Neelroop N Parikshak, Thomas Gonatopoulos-Pournatzis, Mariana Babor, Mathieu Quesnel-Vallières, Javier Tapial, Bushra Raj, Dave O'Hanlon,[...]. Cell 2014
273
19

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
18

Precise temporal regulation of alternative splicing during neural development.
Sebastien M Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffié, Qinghong Yan, Martin Jacko, Jose C Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst,[...]. Nat Commun 2018
49
34

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.
Xiaochang Zhang, Ming Hui Chen, Xuebing Wu, Andrew Kodani, Jean Fan, Ryan Doan, Manabu Ozawa, Jacqueline Ma, Nobuaki Yoshida, Jeremy F Reiter,[...]. Cell 2016
128
14

Alternative splicing as a regulator of development and tissue identity.
Francisco E Baralle, Jimena Giudice. Nat Rev Mol Cell Biol 2017
339
14

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders.
Mathieu Quesnel-Vallières, Zahra Dargaei, Manuel Irimia, Thomas Gonatopoulos-Pournatzis, Joanna Y Ip, Mingkun Wu, Timothy Sterne-Weiler, Shinichi Nakagawa, Melanie A Woodin, Benjamin J Blencowe,[...]. Mol Cell 2016
58
22

The evolutionary landscape of alternative splicing in vertebrate species.
Nuno L Barbosa-Morais, Manuel Irimia, Qun Pan, Hui Y Xiong, Serge Gueroussov, Leo J Lee, Valentina Slobodeniuc, Claudia Kutter, Stephen Watt, Recep Colak,[...]. Science 2012
538
12

A compendium of RNA-binding motifs for decoding gene regulation.
Debashish Ray, Hilal Kazan, Kate B Cook, Matthew T Weirauch, Hamed S Najafabadi, Xiao Li, Serge Gueroussov, Mihai Albu, Hong Zheng, Ally Yang,[...]. Nature 2013
771
11

Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins.
Dietmar Schreiner, Thi-Minh Nguyen, Giancarlo Russo, Steffen Heber, Andrea Patrignani, Erik Ahrné, Peter Scheiffele. Neuron 2014
104
11

Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing.
Elisabetta Furlanis, Peter Scheiffele. Annu Rev Cell Dev Biol 2018
43
25

Variation in alternative splicing across human tissues.
Gene Yeo, Dirk Holste, Gabriel Kreiman, Christopher B Burge. Genome Biol 2004
352
11

RNA mis-splicing in disease.
Marina M Scotti, Maurice S Swanson. Nat Rev Genet 2016
462
10

SAM68 regulates neuronal activity-dependent alternative splicing of neurexin-1.
Takatoshi Iijima, Karen Wu, Harald Witte, Yoko Hanno-Iijima, Timo Glatter, Stéphane Richard, Peter Scheiffele. Cell 2011
178
10

An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.
Ye Zhang, Kenian Chen, Steven A Sloan, Mariko L Bennett, Anja R Scholze, Sean O'Keeffe, Hemali P Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch,[...]. J Neurosci 2014
10

The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function.
Lauren T Gehman, Pratap Meera, Peter Stoilov, Lily Shiue, Janelle E O'Brien, Miriam H Meisler, Manuel Ares, Thomas S Otis, Douglas L Black. Genes Dev 2012
132
10

Landscape of ribosome-engaged transcript isoforms reveals extensive neuronal-cell-class-specific alternative splicing programs.
Elisabetta Furlanis, Lisa Traunmüller, Geoffrey Fucile, Peter Scheiffele. Nat Neurosci 2019
36
27

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.
Sebastien M Weyn-Vanhentenryck, Aldo Mele, Qinghong Yan, Shuying Sun, Natalie Farny, Zuo Zhang, Chenghai Xue, Margaret Herre, Pamela A Silver, Michael Q Zhang,[...]. Cell Rep 2014
200
9

RNA protein interaction in neurons.
Robert B Darnell. Annu Rev Neurosci 2013
109
9

The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation.
Qin Li, Sika Zheng, Areum Han, Chia-Ho Lin, Peter Stoilov, Xiang-Dong Fu, Douglas L Black. Elife 2014
87
10

Control of neuronal synapse specification by a highly dedicated alternative splicing program.
Lisa Traunmüller, Andrea M Gomez, Thi-Minh Nguyen, Peter Scheiffele. Science 2016
70
12

Alternative Splicing in Neurogenesis and Brain Development.
Chun-Hao Su, Dhananjaya D, Woan-Yuh Tarn. Front Mol Biosci 2018
43
20

Rbfox1 Mediates Cell-type-Specific Splicing in Cortical Interneurons.
Brie Wamsley, Xavier Hubert Jaglin, Emilia Favuzzi, Giulia Quattrocolo, Maximiliano José Nigro, Nusrath Yusuf, Alireza Khodadadi-Jamayran, Bernardo Rudy, Gord Fishell. Neuron 2018
34
26

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.
Shihao Shen, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D Henry, Ying Nian Wu, Qing Zhou, Yi Xing. Proc Natl Acad Sci U S A 2014
631
9

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.
Jason Merkin, Caitlin Russell, Ping Chen, Christopher B Burge. Science 2012
493
9


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.
Javier Tapial, Kevin C H Ha, Timothy Sterne-Weiler, André Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez,[...]. Genome Res 2017
104
8

Widespread intron retention in mammals functionally tunes transcriptomes.
Ulrich Braunschweig, Nuno L Barbosa-Morais, Qun Pan, Emil N Nachman, Babak Alipanahi, Thomas Gonatopoulos-Pournatzis, Brendan Frey, Manuel Irimia, Benjamin J Blencowe. Genome Res 2014
333
8

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
280
8

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development.
Mathieu Quesnel-Vallières, Manuel Irimia, Sabine P Cordes, Benjamin J Blencowe. Genes Dev 2015
61
13

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.
Yang I Li, Luis Sanchez-Pulido, Wilfried Haerty, Chris P Ponting. Genome Res 2015
86
9


An RNA map predicting Nova-dependent splicing regulation.
Jernej Ule, Giovanni Stefani, Aldo Mele, Matteo Ruggiu, Xuning Wang, Bahar Taneri, Terry Gaasterland, Benjamin J Blencowe, Robert B Darnell. Nature 2006
379
8


Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function.
Yuhki Saito, Yuan Yuan, Ilana Zucker-Scharff, John J Fak, Saša Jereb, Yoko Tajima, Donny D Licatalosi, Robert B Darnell. Neuron 2019
19
42

Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing.
Barbara Treutlein, Ozgun Gokce, Stephen R Quake, Thomas C Südhof. Proc Natl Acad Sci U S A 2014
157
8

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
328
8

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
715
7

Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly.
Martin Jacko, Sebastien M Weyn-Vanhentenryck, John W Smerdon, Rui Yan, Huijuan Feng, Damian J Williams, Joy Pai, Ke Xu, Hynek Wichterle, Chaolin Zhang. Neuron 2018
37
18

RNA splicing is a primary link between genetic variation and disease.
Yang I Li, Bryce van de Geijn, Anil Raj, David A Knowles, Allegra A Petti, David Golan, Yoav Gilad, Jonathan K Pritchard. Science 2016
251
7

An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus.
Thi-Minh Nguyen, Dietmar Schreiner, Le Xiao, Lisa Traunmüller, Caroline Bornmann, Peter Scheiffele. Elife 2016
42
16

Expansion of the eukaryotic proteome by alternative splicing.
Timothy W Nilsen, Brenton R Graveley. Nature 2010
7

A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons.
Paul L Boutz, Peter Stoilov, Qin Li, Chia-Ho Lin, Geetanjali Chawla, Kristin Ostrow, Lily Shiue, Manuel Ares, Douglas L Black. Genes Dev 2007
362
7

Tissue-specific alternative splicing remodels protein-protein interaction networks.
Jonathan D Ellis, Miriam Barrios-Rodiles, Recep Colak, Manuel Irimia, Taehyung Kim, John A Calarco, Xinchen Wang, Qun Pan, Dave O'Hanlon, Philip M Kim,[...]. Mol Cell 2012
233
7

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility.
Towfique Raj, Yang I Li, Garrett Wong, Jack Humphrey, Minghui Wang, Satesh Ramdhani, Ying-Chih Wang, Bernard Ng, Ishaan Gupta, Vahram Haroutunian,[...]. Nat Genet 2018
119
7

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics.
Mathieu Quesnel-Vallières, Robert J Weatheritt, Sabine P Cordes, Benjamin J Blencowe. Nat Rev Genet 2019
54
12

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism.
Jennifer C Darnell, Sarah J Van Driesche, Chaolin Zhang, Ka Ying Sharon Hung, Aldo Mele, Claire E Fraser, Elizabeth F Stone, Cynthia Chen, John J Fak, Sung Wook Chi,[...]. Cell 2011
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.