A citation-based method for searching scientific literature

Daniel P Murphy, Andrew Eo Hughes, Karen A Lawrence, Connie A Myers, Joseph C Corbo. Elife 2019
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


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
126
87

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
41
62


CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites.
Philip A Ruzycki, Xiaodong Zhang, Shiming Chen. Epigenetics Chromatin 2018
13
50

Single-base pair differences in a shared motif determine differential Rhodopsin expression.
Jens Rister, Ansa Razzaq, Pamela Boodram, Nisha Desai, Cleopatra Tsanis, Hongtao Chen, David Jukam, Claude Desplan. Science 2015
24
37

Functional roles of Otx2 transcription factor in postnatal mouse retinal development.
Chieko Koike, Akihiro Nishida, Shinji Ueno, Hiromitsu Saito, Rikako Sanuki, Shigeru Sato, Akiko Furukawa, Shinichi Aizawa, Isao Matsuo, Noboru Suzuki,[...]. Mol Cell Biol 2007
129
37

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
468
37

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
37


MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers.
Milena M Andzelm, Timothy J Cherry, David A Harmin, Annabel C Boeke, Charlotte Lee, Martin Hemberg, Basil Pawlyk, Athar N Malik, Steven W Flavell, Michael A Sandberg,[...]. Neuron 2015
41
37

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
73
37

CHX10 targets a subset of photoreceptor genes.
Kimberley M Dorval, Brian P Bobechko, Hiroki Fujieda, Shiming Chen, Don J Zack, Rod Bremner. J Biol Chem 2006
44
25

Rax Homeoprotein Regulates Photoreceptor Cell Maturation and Survival in Association with Crx in the Postnatal Mouse Retina.
Shoichi Irie, Rikako Sanuki, Yuki Muranishi, Kimiko Kato, Taro Chaya, Takahisa Furukawa. Mol Cell Biol 2015
23
25


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
66
25

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
25


A single amino acid can determine the DNA binding specificity of homeodomain proteins.
J Treisman, P Gönczy, M Vashishtha, E Harris, C Desplan. Cell 1989
455
25


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
107
25

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
25


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
25

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
25

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
25

Electroporation and RNA interference in the rodent retina in vivo and in vitro.
Takahiko Matsuda, Constance L Cepko. Proc Natl Acad Sci U S A 2004
716
25

The major cell populations of the mouse retina.
C J Jeon, E Strettoi, R H Masland. J Neurosci 1998
884
25

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
402
25

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
25

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
25

Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression.
A Kimura, D Singh, E F Wawrousek, M Kikuchi, M Nakamura, T Shinohara. J Biol Chem 2000
114
25

A new GFP-tagged line reveals unexpected Otx2 protein localization in retinal photoreceptors.
Nicolas Fossat, Coralie Le Greneur, Francis Béby, Stéphane Vincent, Pierre Godement, Gilles Chatelain, Thomas Lamonerie. BMC Dev Biol 2007
45
25

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
25

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
25

Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina.
Alexander Samuel, Michael Housset, Bruno Fant, Thomas Lamonerie. PLoS One 2014
34
25

A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors.
Michael A White, Jamie C Kwasnieski, Connie A Myers, Susan Q Shen, Joseph C Corbo, Barak A Cohen. Cell Rep 2016
26
25

Transcription factors: from enhancer binding to developmental control.
François Spitz, Eileen E M Furlong. Nat Rev Genet 2012
947
25


Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor.
C L Freund, C Y Gregory-Evans, T Furukawa, M Papaioannou, J Looser, L Ploder, J Bellingham, D Ng, J A Herbrick, A Duncan,[...]. Cell 1997
435
25

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
38
25

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration.
Jie Wang, Cristina Zibetti, Peng Shang, Srinivasa R Sripathi, Pingwu Zhang, Marisol Cano, Thanh Hoang, Shuli Xia, Hongkai Ji, Shannath L Merbs,[...]. Nat Commun 2018
48
25

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
72
25

Transcripts within rod photoreceptors of the Zebrafish retina.
Chi Sun, Carlos Galicia, Deborah L Stenkamp. BMC Genomics 2018
16
25

Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina.
Anand Swaroop, Douglas Kim, Douglas Forrest. Nat Rev Neurosci 2010
325
25

Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids.
Haohuan Xie, Wen Zhang, Mei Zhang, Tasneem Akhtar, Young Li, Wenyang Yi, Xiao Sun, Zuqi Zuo, Min Wei, Xin Fang,[...]. Sci Adv 2020
18
25

Chromatin accessibility and the regulatory epigenome.
Sandy L Klemm, Zohar Shipony, William J Greenleaf. Nat Rev Genet 2019
297
25

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
118
25

Low affinity binding site clusters confer hox specificity and regulatory robustness.
Justin Crocker, Namiko Abe, Lucrezia Rinaldi, Alistair P McGregor, Nicolás Frankel, Shu Wang, Ahmad Alsawadi, Philippe Valenti, Serge Plaza, François Payre,[...]. Cell 2015
164
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
658
25

NeuroD regulates multiple functions in the developing neural retina in rodent.
E M Morrow, T Furukawa, J E Lee, C L Cepko. Development 1999
279
25


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.