A citation-based method for searching scientific literature

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, Michael A Beer, Joseph R Ecker, Jeremy Nathans. Elife 2016
Times Cited: 78







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



Times Cited
  Times     Co-cited
Similarity


Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina.
Anand Swaroop, Douglas Kim, Douglas Forrest. Nat Rev Neurosci 2010
347
30

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
48
45

The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis.
Issam Aldiri, Beisi Xu, Lu Wang, Xiang Chen, Daniel Hiler, Lyra Griffiths, Marc Valentine, Abbas Shirinifard, Suresh Thiagarajan, Andras Sablauer,[...]. Neuron 2017
123
28

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.
Joseph C Corbo, Karen A Lawrence, Marcus Karlstetter, Connie A Myers, Musa Abdelaziz, William Dirkes, Karin Weigelt, Martin Seifert, Vladimir Benes, Lars G Fritsche,[...]. Genome Res 2010
137
25

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
482
25

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
679
24

Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals.
Jung-Woong Kim, Hyun-Jin Yang, Adam Phillip Oel, Matthew John Brooks, Li Jia, David Charles Plachetzki, Wei Li, William Ted Allison, Anand Swaroop. Dev Cell 2016
72
25


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
20

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
77
20

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.
Alisa Mo, Eran A Mukamel, Fred P Davis, Chongyuan Luo, Gilbert L Henry, Serge Picard, Mark A Urich, Joseph R Nery, Terrence J Sejnowski, Ryan Lister,[...]. Neuron 2015
365
20

Transcriptional code and disease map for adult retinal cell types.
Sandra Siegert, Erik Cabuy, Brigitte Gross Scherf, Hubertus Kohler, Satchidananda Panda, Yun-Zheng Le, Hans Jörg Fehling, Dimos Gaidatzis, Michael B Stadler, Botond Roska. Nat Neurosci 2012
185
19

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
65
23

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
17


Global epigenomic reconfiguration during mammalian brain development.
Ryan Lister, Eran A Mukamel, Joseph R Nery, Mark Urich, Clare A Puddifoot, Nicholas D Johnson, Jacinta Lucero, Yun Huang, Andrew J Dwork, Matthew D Schultz,[...]. Science 2013
15


Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
14

Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes.
S Chen, Q L Wang, Z Nie, H Sun, G Lennon, N G Copeland, D J Gilbert, N A Jenkins, D J Zack. Neuron 1997
552
14

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
12

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.
Matthew S Wilken, Joseph A Brzezinski, Anna La Torre, Kyle Siebenthall, Robert Thurman, Peter Sabo, Richard S Sandstrom, Jeff Vierstra, Theresa K Canfield, R Scott Hansen,[...]. Epigenetics Chromatin 2015
41
24

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
12

LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation.
Irina Solovei, Audrey S Wang, Katharina Thanisch, Christine S Schmidt, Stefan Krebs, Monika Zwerger, Tatiana V Cohen, Didier Devys, Roland Foisner, Leo Peichl,[...]. Cell 2013
486
12

Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development.
Akihiro Nishida, Akiko Furukawa, Chieko Koike, Yasuo Tano, Shinichi Aizawa, Isao Matsuo, Takahisa Furukawa. Nat Neurosci 2003
419
11

The cis-regulatory logic of the mammalian photoreceptor transcriptional network.
Timothy H-C Hsiau, Claudiu Diaconu, Connie A Myers, Jongwoo Lee, Constance L Cepko, Joseph C Corbo. PLoS One 2007
109
11

Genomic analysis of mouse retinal development.
Seth Blackshaw, Sanjiv Harpavat, Jeff Trimarchi, Li Cai, Haiyan Huang, Winston P Kuo, Griffin Weber, Kyungjoon Lee, Rebecca E Fraioli, Seo-Hee Cho,[...]. PLoS Biol 2004
449
11

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
22
40

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
157
11

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
10

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
10


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
103
10

Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors.
Masayuki Akimoto, Hong Cheng, Dongxiao Zhu, Joseph A Brzezinski, Ritu Khanna, Elena Filippova, Edwin C T Oh, Yuezhou Jing, Jose-Luis Linares, Matthew Brooks,[...]. Proc Natl Acad Sci U S A 2006
239
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.
Michael A White, Connie A Myers, Joseph C Corbo, Barak A Cohen. Proc Natl Acad Sci U S A 2013
125
10

Photoreceptor cell fate specification in vertebrates.
Joseph A Brzezinski, Thomas A Reh. Development 2015
86
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Stage and gene specific signatures defined by histones H3K4me2 and H3K27me3 accompany mammalian retina maturation in vivo.
Evgenya Y Popova, Xuming Xu, Andrew T DeWan, Anna C Salzberg, Arthur Berg, Josephine Hoh, Samuel S Zhang, Colin J Barnstable. PLoS One 2012
41
19

Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors.
Mark M Emerson, Natalia Surzenko, Jillian J Goetz, Jeffrey Trimarchi, Constance L Cepko. Dev Cell 2013
74
10

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
113
10

Cell-specific DNA methylation patterns of retina-specific genes.
Shannath L Merbs, Miriam A Khan, Laszlo Hackler, Verity F Oliver, Jun Wan, Jiang Qian, Donald J Zack. PLoS One 2012
37
21

Conditional knockdown of DNA methyltransferase 1 reveals a key role of retinal pigment epithelium integrity in photoreceptor outer segment morphogenesis.
Igor O Nasonkin, Shannath L Merbs, Kevin Lazo, Verity F Oliver, Matthew Brooks, Krushangi Patel, Raymond A Enke, Jacob Nellissery, Milan Jamrich, Yun Z Le,[...]. Development 2013
54
14

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
59
13

A method to predict the impact of regulatory variants from DNA sequence.
Dongwon Lee, David U Gorkin, Maggie Baker, Benjamin J Strober, Alessandro L Asoni, Andrew S McCallion, Michael A Beer. Nat Genet 2015
242
8


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
8

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.
Lars G Fritsche, Wilmar Igl, Jessica N Cooke Bailey, Felix Grassmann, Sebanti Sengupta, Jennifer L Bragg-Gresham, Kathryn P Burdon, Scott J Hebbring, Cindy Wen, Mathias Gorski,[...]. Nat Genet 2016
727
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
8



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.