A citation-based method for searching scientific literature

Aide Macias-Muñoz, Rabi Murad, Ali Mortazavi. BMC Genomics 2019
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
Eric H Davidson, Jonathan P Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, Chiou-Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, César Arenas-Mena,[...]. Dev Biol 2002
246
100

Parameters of self-organization in Hydra aggregates.
U Technau, C Cramer von Laue, F Rentzsch, S Luft, B Hobmayer, H R Bode, T W Holstein. Proc Natl Acad Sci U S A 2000
93
100

The orphan COUP-TF nuclear receptors are markers for neurogenesis from cnidarians to vertebrates.
Dominique Gauchat, Hector Escriva, Marijana Miljkovic-Licina, Simona Chera, Marie-Claire Langlois, Agnès Begue, Vincent Laudet, Brigitte Galliot. Dev Biol 2004
45
100

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.
Srikar Krishna, Aparna Nair, Sirisha Cheedipudi, Deepak Poduval, Jyotsna Dhawan, Dasaradhi Palakodeti, Yashoda Ghanekar. Nucleic Acids Res 2013
37
100

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
100

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
100


Paullones are potent inhibitors of glycogen synthase kinase-3beta and cyclin-dependent kinase 5/p25.
M Leost, C Schultz, A Link, Y Z Wu, J Biernat, E M Mandelkow, J A Bibb, G L Snyder, P Greengard, D W Zaharevitz,[...]. Eur J Biochem 2000
292
100

Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling.
Mansi Srivastava, Kathleen L Mazza-Curll, Josien C van Wolfswinkel, Peter W Reddien. Curr Biol 2014
93
100

A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration.
Hendrik O Petersen, Stefanie K Höger, Mario Looso, Tobias Lengfeld, Anne Kuhn, Uwe Warnken, Chiemi Nishimiya-Fujisawa, Martina Schnölzer, Marcus Krüger, Suat Özbek,[...]. Mol Biol Evol 2015
60
100

Chromatin Control of Developmental Dynamics and Plasticity.
Matteo Perino, Gert Jan C Veenstra. Dev Cell 2016
67
100

Deep conservation of wrist and digit enhancers in fish.
Andrew R Gehrke, Igor Schneider, Elisa de la Calle-Mustienes, Juan J Tena, Carlos Gomez-Marin, Mayuri Chandran, Tetsuya Nakamura, Ingo Braasch, John H Postlethwait, José Luis Gómez-Skarmeta,[...]. Proc Natl Acad Sci U S A 2015
79
100

Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki.
Arnau Sebé-Pedrós, Alex de Mendoza, B Franz Lang, Bernard M Degnan, Iñaki Ruiz-Trillo. Mol Biol Evol 2011
132
100

Head regeneration in Hydra.
Hans R Bode. Dev Dyn 2003
80
100

A survey of best practices for RNA-seq data analysis.
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang,[...]. Genome Biol 2016
100

Multiple Wnts are involved in Hydra organizer formation and regeneration.
Tobias Lengfeld, Hiroshi Watanabe, Oleg Simakov, Dirk Lindgens, Lydia Gee, Lee Law, Heiko A Schmidt, Suat Ozbek, Hans Bode, Thomas W Holstein. Dev Biol 2009
183
100

Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.
Jack F Cazet, Adrienne Cho, Celina E Juliano. Elife 2021
8
100


An ancient chordin-like gene in organizer formation of Hydra.
Fabian Rentzsch, Corina Guder, Dirk Vocke, Bert Hobmayer, Thomas W Holstein. Proc Natl Acad Sci U S A 2007
45
100

Acoel genome reveals the regulatory landscape of whole-body regeneration.
Andrew R Gehrke, Emily Neverett, Yi-Jyun Luo, Alexander Brandt, Lorenzo Ricci, Ryan E Hulett, Annika Gompers, J Graham Ruby, Daniel S Rokhsar, Peter W Reddien,[...]. Science 2019
59
100

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity.
Federico Gaiti, Katia Jindrich, Selene L Fernandez-Valverde, Kathrein E Roper, Bernard M Degnan, Miloš Tanurdžić. Elife 2017
26
100

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
Davis J McCarthy, Yunshun Chen, Gordon K Smyth. Nucleic Acids Res 2012
100

AP-1cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration.
Keith Z Sabin, Peng Jiang, Micah D Gearhart, Ron Stewart, Karen Echeverri. Commun Biol 2019
20
100

The locus of evolution: evo devo and the genetics of adaptation.
Hopi E Hoekstra, Jerry A Coyne. Evolution 2007
595
100

Genomic approaches towards finding cis-regulatory modules in animals.
Ross C Hardison, James Taylor. Nat Rev Genet 2012
135
100

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
María José Nueda, Sonia Tarazona, Ana Conesa. Bioinformatics 2014
156
100

Blast2GO: A comprehensive suite for functional analysis in plant genomics.
Ana Conesa, Stefan Götz. Int J Plant Genomics 2008
100


Ks1, an epithelial cell-specific gene, responds to early signals of head formation in Hydra.
R Weinziger, L M Salgado, C N David, T C Bosch. Development 1994
42
100

The cellular basis for animal regeneration.
Elly M Tanaka, Peter W Reddien. Dev Cell 2011
321
100

High-throughput functional annotation and data mining with the Blast2GO suite.
Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Tim D Williams, Shivashankar H Nagaraj, María José Nueda, Montserrat Robles, Manuel Talón, Joaquín Dopazo, Ana Conesa. Nucleic Acids Res 2008
100

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
100

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA.
Nicolás Frankel, Deniz F Erezyilmaz, Alistair P McGregor, Shu Wang, François Payre, David L Stern. Nature 2011
133
100

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
Nicholas H Putnam, Mansi Srivastava, Uffe Hellsten, Bill Dirks, Jarrod Chapman, Asaf Salamov, Astrid Terry, Harris Shapiro, Erika Lindquist, Vladimir V Kapitonov,[...]. Science 2007
100

Enhancer evolution across 20 mammalian species.
Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F Rayner, Margus Lukk, Miguel Pignatelli, Thomas J Park, Robert Deaville, Jonathan T Erichsen, Anna J Jasinska,[...]. Cell 2015
357
100

beta-catenin plays a central role in setting up the head organizer in hydra.
Lydia Gee, Julia Hartig, Lee Law, Jörg Wittlieb, Konstantin Khalturin, Thomas C G Bosch, Hans R Bode. Dev Biol 2010
57
100

Deep evolutionary origin of limb and fin regeneration.
Sylvain Darnet, Aline C Dragalzew, Danielson B Amaral, Josane F Sousa, Andrew W Thompson, Amanda N Cass, Jamily Lorena, Eder S Pires, Carinne M Costa, Marcos P Sousa,[...]. Proc Natl Acad Sci U S A 2019
22
100

Autoregulatory and repressive inputs localize Hydra Wnt3 to the head organizer.
Yukio Nakamura, Charisios D Tsiairis, Suat Özbek, Thomas W Holstein. Proc Natl Acad Sci U S A 2011
70
100

The head organizer in Hydra.
Hans R Bode. Int J Dev Biol 2012
29
100

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles. Bioinformatics 2005
100

Budhead, a fork head/HNF-3 homologue, is expressed during axis formation and head specification in hydra.
D E Martinez, M L Dirksen, P M Bode, M Jamrich, R E Steele, H R Bode. Dev Biol 1997
113
100

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
100

BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
100

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Alan P Boyle, Lingyun Song, Bum-Kyu Lee, Darin London, Damian Keefe, Ewan Birney, Vishwanath R Iyer, Gregory E Crawford, Terrence S Furey. Genome Res 2011
225
100


Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
Jay R Hesselberth, Xiaoyu Chen, Zhihong Zhang, Peter J Sabo, Richard Sandstrom, Alex P Reynolds, Robert E Thurman, Shane Neph, Michael S Kuehn, William S Noble,[...]. Nat Methods 2009
410
100

Budding in Hydra attenuata: bud stages and fate map.
J J Otto, R D Campbell. J Exp Zool 1977
91
100


Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.
Shaliu Fu, Qin Wang, Jill E Moore, Michael J Purcaro, Henry E Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje,[...]. Nucleic Acids Res 2018
17
100

WNT signalling molecules act in axis formation in the diploblastic metazoan Hydra.
B Hobmayer, F Rentzsch, K Kuhn, C M Happel, C C von Laue, P Snyder, U Rothbächer, T W Holstein. Nature 2000
382
100


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.