A citation-based method for searching scientific literature

Issam Aldiri, Beisi Xu, Lu Wang, Xiang Chen, Daniel Hiler, Lyra Griffiths, Marc Valentine, Abbas Shirinifard, Suresh Thiagarajan, Andras Sablauer, Marie-Elizabeth Barabas, Jiakun Zhang, Dianna Johnson, Sharon Frase, Xin Zhou, John Easton, Jinghui Zhang, Elaine R Mardis, Richard K Wilson, James R Downing, Michael A Dyer. Neuron 2017
Times Cited: 95







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



Times Cited
  Times     Co-cited
Similarity


Molecular Anatomy of the Developing Human Retina.
Akina Hoshino, Rinki Ratnapriya, Matthew J Brooks, Vijender Chaitankar, Matthew S Wilken, Chi Zhang, Margaret R Starostik, Linn Gieser, Anna La Torre, Mario Nishio,[...]. Dev Cell 2017
89
33


Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina.
Anand Swaroop, Douglas Kim, Douglas Forrest. Nat Rev Neurosci 2010
319
18

Epigenomic landscapes of retinal rods and cones.
Alisa Mo, Chongyuan Luo, Fred P Davis, Eran A Mukamel, Gilbert L Henry, Joseph R Nery, Mark A Urich, Serge Picard, Ryan Lister, Sean R Eddy,[...]. Elife 2016
69
24

Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks.
Rossukon Kaewkhaw, Koray Dogan Kaya, Matthew Brooks, Kohei Homma, Jizhong Zou, Vijender Chaitankar, Mahendra Rao, Anand Swaroop. Stem Cells 2015
84
17


Self-formation of optic cups and storable stratified neural retina from human ESCs.
Tokushige Nakano, Satoshi Ando, Nozomu Takata, Masako Kawada, Keiko Muguruma, Kiyotoshi Sekiguchi, Koichi Saito, Shigenobu Yonemura, Mototsugu Eiraku, Yoshiki Sasai. Cell Stem Cell 2012
711
14

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.
Brian S Clark, Genevieve L Stein-O'Brien, Fion Shiau, Gabrielle H Cannon, Emily Davis-Marcisak, Thomas Sherman, Clayton P Santiago, Thanh V Hoang, Fatemeh Rajaii, Rebecca E James-Esposito,[...]. Neuron 2019
92
15

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
13

Nrl is required for rod photoreceptor development.
A J Mears, M Kondo, P K Swain, Y Takada, R A Bush, T L Saunders, P A Sieving, A Swaroop. Nat Genet 2001
647
13

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
13

Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors.
Andrew E O Hughes, Jennifer M Enright, Connie A Myers, Susan Q Shen, Joseph C Corbo. Sci Rep 2017
38
31

Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs.
Xiufeng Zhong, Christian Gutierrez, Tian Xue, Christopher Hampton, M Natalia Vergara, Li-Hui Cao, Ann Peters, Tea Soon Park, Elias T Zambidis, Jason S Meyer,[...]. Nat Commun 2014
388
12

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
12

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
11

Self-organizing optic-cup morphogenesis in three-dimensional culture.
Mototsugu Eiraku, Nozomu Takata, Hiroki Ishibashi, Masako Kawada, Eriko Sakakura, Satoru Okuda, Kiyotoshi Sekiguchi, Taiji Adachi, Yoshiki Sasai. Nature 2011
11

Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution.
Irina Solovei, Moritz Kreysing, Christian Lanctôt, Süleyman Kösem, Leo Peichl, Thomas Cremer, Jochen Guck, Boris Joffe. Cell 2009
442
10

A novel retinoblastoma therapy from genomic and epigenetic analyses.
Jinghui Zhang, Claudia A Benavente, Justina McEvoy, Jacqueline Flores-Otero, Li Ding, Xiang Chen, Anatoly Ulyanov, Gang Wu, Matthew Wilson, Jianmin Wang,[...]. Nature 2012
308
10

Comprehensive analysis of gene expression in human retina and supporting tissues.
Mingyao Li, Cheng Jia, Krista L Kazmierkiewicz, Anita S Bowman, Lifeng Tian, Yichuan Liu, Neel A Gupta, Harini V Gudiseva, Stephanie S Yee, Mijin Kim,[...]. Hum Mol Genet 2014
79
12

NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors.
Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker,[...]. Cell Rep 2016
55
18

Stimulation of functional neuronal regeneration from Müller glia in adult mice.
Nikolas L Jorstad, Matthew S Wilken, William N Grimes, Stefanie G Wohl, Leah S VandenBosch, Takeshi Yoshimatsu, Rachel O Wong, Fred Rieke, Thomas A Reh. Nature 2017
164
10


Epigenetic control of gene regulation during development and disease: A view from the retina.
Ximena Corso-Díaz, Catherine Jaeger, Vijender Chaitankar, Anand Swaroop. Prog Retin Eye Res 2018
37
27

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Emily Welby, Jorn Lakowski, Valentina Di Foggia, Dimitri Budinger, Anai Gonzalez-Cordero, Aaron T L Lun, Michael Epstein, Aara Patel, Elisa Cuevas, Kamil Kruczek,[...]. Stem Cell Reports 2017
47
21

Cell fate determination in the vertebrate retina.
C L Cepko, C P Austin, X Yang, M Alexiades, D Ezzeddine. Proc Natl Acad Sci U S A 1996
745
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

Ezh2 maintains retinal progenitor proliferation, transcriptional integrity, and the timing of late differentiation.
Jianmin Zhang, Russell J Taylor, Anna La Torre, Matthew S Wilken, Kristen E Cox, Thomas A Reh, Monica L Vetter. Dev Biol 2015
32
28

Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina.
Ratnesh K Singh, Ramya K Mallela, Abigail Hayes, Nicholas R Dunham, Morgan E Hedden, Raymond A Enke, Robert N Fariss, Hal Sternberg, Michael D West, Igor O Nasonkin. Exp Eye Res 2017
20
45

Roles of histone H3K27 trimethylase Ezh2 in retinal proliferation and differentiation.
Atsumi Iida, Toshiro Iwagawa, Yukihiro Baba, Shinya Satoh, Yujin Mochizuki, Hiromitsu Nakauchi, Takahisa Furukawa, Haruhiko Koseki, Akira Murakami, Sumiko Watanabe. Dev Neurobiol 2015
30
30

Cell fate determination in the vertebrate retina.
Erin A Bassett, Valerie A Wallace. Trends Neurosci 2012
156
9

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
9

Optic vesicle-like structures derived from human pluripotent stem cells facilitate a customized approach to retinal disease treatment.
Jason S Meyer, Sara E Howden, Kyle A Wallace, Amelia D Verhoeven, Lynda S Wright, Elizabeth E Capowski, Isabel Pinilla, Jessica M Martin, Shulan Tian, Ron Stewart,[...]. Stem Cells 2011
264
9

Photoreceptor Outer Segment-like Structures in Long-Term 3D Retinas from Human Pluripotent Stem Cells.
Karl J Wahlin, Julien A Maruotti, Srinivasa R Sripathi, John Ball, Juan M Angueyra, Catherine Kim, Rhonda Grebe, Wei Li, Bryan W Jones, Donald J Zack. Sci Rep 2017
88
10

Thyroid hormone signaling specifies cone subtypes in human retinal organoids.
Kiara C Eldred, Sarah E Hadyniak, Katarzyna A Hussey, Boris Brenerman, Ping-Wu Zhang, Xitiz Chamling, Valentin M Sluch, Derek S Welsbie, Samer Hattar, James Taylor,[...]. Science 2018
65
13

Coexpression of normally incompatible developmental pathways in retinoblastoma genesis.
Justina McEvoy, Jacqueline Flores-Otero, Jiakun Zhang, Katie Nemeth, Rachel Brennan, Cori Bradley, Fred Krafcik, Carlos Rodriguez-Galindo, Matthew Wilson, Shunbin Xiong,[...]. Cancer Cell 2011
81
9

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8


Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
8

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
8

Intrinsic control of mammalian retinogenesis.
Mengqing Xiang. Cell Mol Life Sci 2013
55
14

Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis.
Hong Hao, Douglas S Kim, Bernward Klocke, Kory R Johnson, Kairong Cui, Norimoto Gotoh, Chongzhi Zang, Janina Gregorski, Linn Gieser, Weiqun Peng,[...]. PLoS Genet 2012
72
11

The Polycomb complex PRC2 and its mark in life.
Raphaël Margueron, Danny Reinberg. Nature 2011
8

Retinal Organoids from Pluripotent Stem Cells Efficiently Recapitulate Retinogenesis.
Manuela Völkner, Marlen Zschätzsch, Maria Rostovskaya, Rupert W Overall, Volker Busskamp, Konstantinos Anastassiadis, Mike O Karl. Stem Cell Reports 2016
121
8

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman,[...]. Cell 2016
440
8

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
938
8

Generation of a ciliary margin-like stem cell niche from self-organizing human retinal tissue.
Atsushi Kuwahara, Chikafumi Ozone, Tokushige Nakano, Koichi Saito, Mototsugu Eiraku, Yoshiki Sasai. Nat Commun 2015
130
8

An integrated transcriptional analysis of the developing human retina.
Carla B Mellough, Roman Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David W P Dolan, Carl M Jones, Osagie G Izuogu, Min Yu, Dean Hallam,[...]. Development 2019
29
27



GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
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.