A citation-based method for searching scientific literature

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. Cell Rep 2016
Times Cited: 64







List of co-cited articles
594 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
345
42

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
677
37

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
78
23

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
238
23

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
184
20

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
71
18

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
18

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
122
18

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
819
18

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
18


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
135
17

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
76
17


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
485
17

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
15

Photoreceptor cell fate specification in vertebrates.
Joseph A Brzezinski, Thomas A Reh. Development 2015
85
14

Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl.
Shigeo Yoshida, Alan J Mears, James S Friedman, Todd Carter, Shirley He, Edwin Oh, Yuezhou Jing, Rafal Farjo, Gilles Fleury, Carrolee Barlow,[...]. Hum Mol Genet 2004
132
14



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
47
17

Cone-like morphological, molecular, and electrophysiological features of the photoreceptors of the Nrl knockout mouse.
Lauren L Daniele, Concepcion Lillo, Arkady L Lyubarsky, Sergei S Nikonov, Nancy Philp, Alan J Mears, Anand Swaroop, David S Williams, Edward N Pugh. Invest Ophthalmol Vis Sci 2005
162
12

Recapitulation of Human Retinal Development from Human Pluripotent Stem Cells Generates Transplantable Populations of Cone Photoreceptors.
Anai Gonzalez-Cordero, Kamil Kruczek, Arifa Naeem, Milan Fernando, Magdalena Kloc, Joana Ribeiro, Debbie Goh, Yanai Duran, Samuel J I Blackford, Laura Abelleira-Hervas,[...]. Stem Cell Reports 2017
112
12

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

OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness.
Jerome E Roger, Avinash Hiriyanna, Norimoto Gotoh, Hong Hao, Debbie F Cheng, Rinki Ratnapriya, Marie-Audrey I Kautzmann, Bo Chang, Anand Swaroop. J Clin Invest 2014
42
16

Two transcription factors can direct three photoreceptor outcomes from rod precursor cells in mouse retinal development.
Lily Ng, Ailing Lu, Alok Swaroop, David S Sharlin, Anand Swaroop, Douglas Forrest. J Neurosci 2011
57
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
417
10


Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.
Matthew J Brooks, Harsha K Rajasimha, Jerome E Roger, Anand Swaroop. Mol Vis 2011
85
10

Retinopathy and attenuated circadian entrainment in Crx-deficient mice.
T Furukawa, E M Morrow, T Li, F C Davis, C L Cepko. Nat Genet 1999
416
10

Functional architecture of the retina: development and disease.
Mrinalini Hoon, Haruhisa Okawa, Luca Della Santina, Rachel O L Wong. Prog Retin Eye Res 2014
231
10

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
288
10

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research.
Vijender Chaitankar, Gökhan Karakülah, Rinki Ratnapriya, Felipe O Giuste, Matthew J Brooks, Anand Swaroop. Prog Retin Eye Res 2016
34
20

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
59
11

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
153
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
95
10

Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo.
Matthew J Brooks, Holly Y Chen, Ryan A Kelley, Anupam K Mondal, Kunio Nagashima, Natalia De Val, Tiansen Li, Vijender Chaitankar, Anand Swaroop. Stem Cell Reports 2019
47
14

Retinoid X receptor (gamma) is necessary to establish the S-opsin gradient in cone photoreceptors of the developing mouse retina.
Melanie R Roberts, Anita Hendrickson, Christopher R McGuire, Thomas A Reh. Invest Ophthalmol Vis Sci 2005
152
9

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
40
15



Intrinsic control of mammalian retinogenesis.
Mengqing Xiang. Cell Mol Life Sci 2013
63
9


Transformation of cone precursors to functional rod photoreceptors by bZIP transcription factor NRL.
Edwin C T Oh, Naheed Khan, Elena Novelli, Hemant Khanna, Enrica Strettoi, Anand Swaroop. Proc Natl Acad Sci U S A 2007
114
9

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
9

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
73
9

Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL.
Lina Zelinger, Gökhan Karakülah, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J Brooks, Anand Swaroop. Invest Ophthalmol Vis Sci 2017
13
46

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
124
9

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
533
9



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.