A citation-based method for searching scientific literature

Daehwan Kim, Steven L Salzberg. Genome Biol 2011
Times Cited: 530







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



Times Cited
  Times     Co-cited
Similarity


Diverse alternative back-splicing and alternative splicing landscape of circular RNAs.
Xiao-Ou Zhang, Rui Dong, Yang Zhang, Jia-Lin Zhang, Zheng Luo, Jun Zhang, Ling-Ling Chen, Li Yang. Genome Res 2016
508
27

Complementary sequence-mediated exon circularization.
Xiao-Ou Zhang, Hai-Bin Wang, Yang Zhang, Xuhua Lu, Ling-Ling Chen, Li Yang. Cell 2014
27

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
25

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
24

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
20

Natural RNA circles function as efficient microRNA sponges.
Thomas B Hansen, Trine I Jensen, Bettina H Clausen, Jesper B Bramsen, Bente Finsen, Christian K Damgaard, Jørgen Kjems. Nature 2013
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
16

Circular RNAs are a large class of animal RNAs with regulatory potency.
Sebastian Memczak, Marvin Jens, Antigoni Elefsinioti, Francesca Torti, Janna Krueger, Agnieszka Rybak, Luisa Maier, Sebastian D Mackowiak, Lea H Gregersen, Mathias Munschauer,[...]. Nature 2013
16


Circular RNAs are abundant, conserved, and associated with ALU repeats.
William R Jeck, Jessica A Sorrentino, Kai Wang, Michael K Slevin, Christin E Burd, Jinze Liu, William F Marzluff, Norman E Sharpless. RNA 2013
15

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Brian J Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev. Genome Biol 2019
186
13

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
13

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
12


HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
11

JAFFA: High sensitivity transcriptome-focused fusion gene detection.
Nadia M Davidson, Ian J Majewski, Alicia Oshlack. Genome Med 2015
89
12

The Biogenesis, Functions, and Challenges of Circular RNAs.
Xiang Li, Li Yang, Ling-Ling Chen. Mol Cell 2018
11

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
11

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G F Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk,[...]. PLoS Comput Biol 2011
387
10

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
10

Comprehensive identification of internal structure and alternative splicing events in circular RNAs.
Yuan Gao, Jinfeng Wang, Yi Zheng, Jinyang Zhang, Shuai Chen, Fangqing Zhao. Nat Commun 2016
178
9


Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
8

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data.
Shailesh Kumar, Angie Duy Vo, Fujun Qin, Hui Li. Sci Rep 2016
91
8

Ballgown bridges the gap between transcriptome assembly and expression analysis.
Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek. Nat Biotechnol 2015
397
8

Circular RNA identification based on multiple seed matching.
Yuan Gao, Jinyang Zhang, Fangqing Zhao. Brief Bioinform 2018
286
8

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Kai Wang, Darshan Singh, Zheng Zeng, Stephen J Coleman, Yan Huang, Gleb L Savich, Xiaping He, Piotr Mieczkowski, Sara A Grimm, Charles M Perou,[...]. Nucleic Acids Res 2010
681
8

The biogenesis, biology and characterization of circular RNAs.
Lasse S Kristensen, Maria S Andersen, Lotte V W Stagsted, Karoline K Ebbesen, Thomas B Hansen, Jørgen Kjems. Nat Rev Genet 2019
8

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.
Qingsong Gao, Wen-Wei Liang, Steven M Foltz, Gnanavel Mutharasu, Reyka G Jayasinghe, Song Cao, Wen-Wei Liao, Sheila M Reynolds, Matthew A Wyczalkowski, Lijun Yao,[...]. Cell Rep 2018
253
7


VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
7

Detecting and characterizing circular RNAs.
William R Jeck, Norman E Sharpless. Nat Biotechnol 2014
7

Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs.
Qiupeng Zheng, Chunyang Bao, Weijie Guo, Shuyi Li, Jie Chen, Bing Chen, Yanting Luo, Dongbin Lyu, Yan Li, Guohai Shi,[...]. Nat Commun 2016
7

Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
7

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.
Silvia Liu, Wei-Hsiang Tsai, Ying Ding, Rui Chen, Zhou Fang, Zhiguang Huo, SungHwan Kim, Tianzhou Ma, Ting-Yu Chang, Nolan Michael Priedigkeit,[...]. Nucleic Acids Res 2016
103
7

circBase: a database for circular RNAs.
Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA 2014
997
7

The emerging complexity of gene fusions in cancer.
Fredrik Mertens, Bertil Johansson, Thoas Fioretos, Felix Mitelman. Nat Rev Cancer 2015
383
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6

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
6

A comprehensive overview and evaluation of circular RNA detection tools.
Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou. PLoS Comput Biol 2017
224
6

Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.
Jakub O Westholm, Pedro Miura, Sara Olson, Sol Shenker, Brian Joseph, Piero Sanfilippo, Susan E Celniker, Brenton R Graveley, Eric C Lai. Cell Rep 2014
604
6

Comparison of circular RNA prediction tools.
Thomas B Hansen, Morten T Venø, Christian K Damgaard, Jørgen Kjems. Nucleic Acids Res 2016
243
6

Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
Henrik Edgren, Astrid Murumagi, Sara Kangaspeska, Daniel Nicorici, Vesa Hongisto, Kristine Kleivi, Inga H Rye, Sandra Nyberg, Maija Wolf, Anne-Lise Borresen-Dale,[...]. Genome Biol 2011
213
6

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
Huanying Ge, Kejun Liu, Todd Juan, Fang Fang, Matthew Newman, Wolfgang Hoeck. Bioinformatics 2011
175
6

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures.
H L Sanger, G Klotz, D Riesner, H J Gross, A K Kleinschmidt. Proc Natl Acad Sci U S A 1976
6


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
6

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, Ge Gao. Nucleic Acids Res 2007
6

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Liang Sun, Haitao Luo, Dechao Bu, Guoguang Zhao, Kuntao Yu, Changhai Zhang, Yuanning Liu, Runsheng Chen, Yi Zhao. Nucleic Acids Res 2013
926
6


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.