A citation-based method for searching scientific literature

Lauren E Blake, Julien Roux, Irene Hernando-Herraez, Nicholas E Banovich, Raquel Garcia Perez, Chiaowen Joyce Hsiao, Ittai Eres, Claudia Cuevas, Tomas Marques-Bonet, Yoav Gilad. Genome Res 2020
Times Cited: 53







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



Times Cited
  Times     Co-cited
Similarity


limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
15

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Athma A Pai, Jordana T Bell, John C Marioni, Jonathan K Pritchard, Yoav Gilad. PLoS Genet 2011
139
15

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
13

Dynamics of DNA methylation in recent human and great ape evolution.
Irene Hernando-Herraez, Javier Prado-Martinez, Paras Garg, Marcos Fernandez-Callejo, Holger Heyn, Christina Hvilsom, Arcadi Navarro, Manel Esteller, Andrew J Sharp, Tomas Marques-Bonet. PLoS Genet 2013
79
13




Primate transcript and protein expression levels evolve under compensatory selection pressures.
Zia Khan, Michael J Ford, Darren A Cusanovich, Amy Mitrano, Jonathan K Pritchard, Yoav Gilad. Science 2013
147
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
11

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species.
Dafni Anastasiadi, Anna Esteve-Codina, Francesc Piferrer. Epigenetics Chromatin 2018
157
11


The evolution of gene expression levels in mammalian organs.
David Brawand, Magali Soumillon, Anamaria Necsulea, Philippe Julien, Gábor Csárdi, Patrick Harrigan, Manuela Weier, Angélica Liechti, Ayinuer Aximu-Petri, Martin Kircher,[...]. Nature 2011
736
9

The interplay between DNA methylation and sequence divergence in recent human evolution.
Irene Hernando-Herraez, Holger Heyn, Marcos Fernandez-Callejo, Enrique Vidal, Hugo Fernandez-Bellon, Javier Prado-Martinez, Andrew J Sharp, Manel Esteller, Tomas Marques-Bonet. Nucleic Acids Res 2015
37
13

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.
Antoine Molaro, Emily Hodges, Fang Fang, Qiang Song, W Richard McCombie, Gregory J Hannon, Andrew D Smith. Cell 2011
253
9

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
368
9

High-resolution comparative analysis of great ape genomes.
Zev N Kronenberg, Ian T Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S Meyerson, Jason G Underwood, Bradley J Nelson, Mark J P Chaisson, Max L Dougherty,[...]. Science 2018
164
9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues.
Bryan J Pavlovic, Lauren E Blake, Julien Roux, Claudia Chavarria, Yoav Gilad. Sci Rep 2018
28
17

Great ape genetic diversity and population history.
Javier Prado-Martinez, Peter H Sudmant, Jeffrey M Kidd, Heng Li, Joanna L Kelley, Belen Lorente-Galdos, Krishna R Veeramah, August E Woerner, Timothy D O'Connor, Gabriel Santpere,[...]. Nature 2013
473
9

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
9

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
9

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
9

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
9

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
9

A comparative study of endoderm differentiation in humans and chimpanzees.
Lauren E Blake, Samantha M Thomas, John D Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad, Bryan J Pavlovic. Genome Biol 2018
14
28

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
7

Comparative studies of gene expression and the evolution of gene regulation.
Irene Gallego Romero, Ilya Ruvinsky, Yoav Gilad. Nat Rev Genet 2012
254
7

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
7

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
7

Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates.
Genevieve Housman, Ellen E Quillen, Anne C Stone. Am J Phys Anthropol 2020
8
50


Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.
Ittai E Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E Blake, Yoav Gilad. PLoS Genet 2019
33
12

Chimpanzee genomic diversity reveals ancient admixture with bonobos.
Marc de Manuel, Martin Kuhlwilm, Peter Frandsen, Vitor C Sousa, Tariq Desai, Javier Prado-Martinez, Jessica Hernandez-Rodriguez, Isabelle Dupanloup, Oscar Lao, Pille Hallast,[...]. Science 2016
119
7

The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences.
Cheng Xue, Muthuswamy Raveendran, R Alan Harris, Gloria L Fawcett, Xiaoming Liu, Simon White, Mahmoud Dahdouli, David Rio Deiros, Jennifer E Below, William Salerno,[...]. Genome Res 2016
68
7

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.
Jia Zeng, Genevieve Konopka, Brendan G Hunt, Todd M Preuss, Dan Geschwind, Soojin V Yi. Am J Hum Genet 2012
103
7

Differential DNA methylation of vocal and facial anatomy genes in modern humans.
David Gokhman, Malka Nissim-Rafinia, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Esther Lizano, Olivia Cheronet, Swapan Mallick, Maria A Nieves-Colón, Heng Li,[...]. Nat Commun 2020
24
16

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
653
7

Conservation and divergence of methylation patterning in plants and animals.
Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G Goll, Jonathan Hetzel, Jayati Jain, Steven H Strauss, Marnie E Halpern,[...]. Proc Natl Acad Sci U S A 2010
767
7

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
7

Dynamic DNA methylation: In the right place at the right time.
Chongyuan Luo, Petra Hajkova, Joseph R Ecker. Science 2018
266
7

Chromatin-state discovery and genome annotation with ChromHMM.
Jason Ernst, Manolis Kellis. Nat Protoc 2017
263
7

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
7

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.
Jason Merkin, Caitlin Russell, Ping Chen, Christopher B Burge. Science 2012
558
5

REVIGO summarizes and visualizes long lists of gene ontology terms.
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
5

Intra- and interspecific variation in primate gene expression patterns.
Wolfgang Enard, Philipp Khaitovich, Joachim Klose, Sebastian Zöllner, Florian Heissig, Patrick Giavalisco, Kay Nieselt-Struwe, Elaine Muchmore, Ajit Varki, Rivka Ravid,[...]. Science 2002
561
5

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.
Irene Gallego Romero, Bryan J Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C Ward, Nicholas E Banovich, Courtney L Kagan, Jonathan E Burnett, Constance H Huang, Amy Mitrano,[...]. Elife 2015
68
5


Epigenetic modifications are associated with inter-species gene expression variation in primates.
Xiang Zhou, Carolyn E Cain, Marsha Myrthil, Noah Lewellen, Katelyn Michelini, Emily R Davenport, Matthew Stephens, Jonathan K Pritchard, Yoav Gilad. Genome Biol 2014
45
6

Sex-specific and lineage-specific alternative splicing in primates.
Ran Blekhman, John C Marioni, Paul Zumbo, Matthew Stephens, Yoav Gilad. Genome Res 2010
183
5


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.