A citation-based method for searching scientific literature

Xin Hu, Qianghu Wang, Ming Tang, Floris Barthel, Samirkumar Amin, Kosuke Yoshihara, Frederick M Lang, Emmanuel Martinez-Ledesma, Soo Hyun Lee, Siyuan Zheng, Roel G W Verhaak. Nucleic Acids Res 2018
Times Cited: 115







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



Times Cited
  Times     Co-cited
Similarity


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
35

The emerging complexity of gene fusions in cancer.
Fredrik Mertens, Bertil Johansson, Thoas Fioretos, Felix Mitelman. Nat Rev Cancer 2015
383
20

The landscape and therapeutic relevance of cancer-associated transcript fusions.
K Yoshihara, Q Wang, W Torres-Garcia, S Zheng, R Vegesna, H Kim, R G W Verhaak. Oncogene 2015
306
19

The landscape of kinase fusions in cancer.
Nicolas Stransky, Ethan Cerami, Stefanie Schalm, Joseph L Kim, Christoph Lengauer. Nat Commun 2014
589
14

PRADA: pipeline for RNA sequencing data analysis.
Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F Berger, John N Weinstein, Gad Getz, Roel G W Verhaak. Bioinformatics 2014
106
13

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
13

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
14

The impact of translocations and gene fusions on cancer causation.
Felix Mitelman, Bertil Johansson, Fredrik Mertens. Nat Rev Cancer 2007
908
12

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.
Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee,[...]. Nucleic Acids Res 2017
55
20

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
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer.
Manabu Soda, Young Lim Choi, Munehiro Enomoto, Shuji Takada, Yoshihiro Yamashita, Shunpei Ishikawa, Shin-ichiro Fujiwara, Hideki Watanabe, Kentaro Kurashina, Hisashi Hatanaka,[...]. Nature 2007
9

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Daehwan Kim, Steven L Salzberg. Genome Biol 2011
530
9

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
9

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
9

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, S Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson,[...]. Sci Signal 2013
9

OncoKB: A Precision Oncology Knowledge Base.
Debyani Chakravarty, Jianjiong Gao, Sarah M Phillips, Ritika Kundra, Hongxin Zhang, Jiaojiao Wang, Julia E Rudolph, Rona Yaeger, Tara Soumerai, Moriah H Nissan,[...]. JCO Precis Oncol 2017
9

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
9

Oncogenic Signaling Pathways in The Cancer Genome Atlas.
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K Chatila, Augustin Luna, Konnor C La, Sofia Dimitriadoy, David L Liu, Havish S Kantheti, Sadegh Saghafinia,[...]. Cell 2018
9

FusionGDB: fusion gene annotation DataBase.
Pora Kim, Xiaobo Zhou. Nucleic Acids Res 2019
39
23

Recurrent chimeric fusion RNAs in non-cancer tissues and cells.
Mihaela Babiceanu, Fujun Qin, Zhongqiu Xie, Yuemeng Jia, Kevin Lopez, Nick Janus, Loryn Facemire, Shailesh Kumar, Yuwei Pang, Yanjun Qi,[...]. Nucleic Acids Res 2016
105
8

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
8


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
8

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.
Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan,[...]. Genome Biol 2013
131
8

Comprehensive Characterization of Cancer Driver Genes and Mutations.
Matthew H Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C Wendl, Jaegil Kim, Brendan Reardon,[...]. Cell 2018
901
8

COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
8

ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern. Nucleic Acids Res 2017
32
21

Identification of targetable FGFR gene fusions in diverse cancers.
Yi-Mi Wu, Fengyun Su, Shanker Kalyana-Sundaram, Nickolay Khazanov, Bushra Ateeq, Xuhong Cao, Robert J Lonigro, Pankaj Vats, Rui Wang, Su-Fang Lin,[...]. Cancer Discov 2013
492
7

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Matthew K Iyer, Arul M Chinnaiyan, Christopher A Maher. Bioinformatics 2011
197
7

JAFFA: High sensitivity transcriptome-focused fusion gene detection.
Nadia M Davidson, Ian J Majewski, Alicia Oshlack. Genome Med 2015
89
7

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
7

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
7

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.
Scott A Tomlins, Daniel R Rhodes, Sven Perner, Saravana M Dhanasekaran, Rohit Mehra, Xiao-Wei Sun, Sooryanarayana Varambally, Xuhong Cao, Joelle Tchinda, Rainer Kuefer,[...]. Science 2005
7


INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Jin Zhang, Nicole M White, Heather K Schmidt, Robert S Fulton, Chad Tomlinson, Wesley C Warren, Richard K Wilson, Christopher A Maher. Genome Res 2016
73
9

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.
Gabriele Picco, Elisabeth D Chen, Luz Garcia Alonso, Fiona M Behan, Emanuel Gonçalves, Graham Bignell, Angela Matchan, Beiyuan Fu, Ruby Banerjee, Elizabeth Anderson,[...]. Nat Commun 2019
55
12

Pan-cancer patterns of somatic copy number alteration.
Travis I Zack, Stephen E Schumacher, Scott L Carter, Andre D Cherniack, Gordon Saksena, Barbara Tabak, Michael S Lawrence, Cheng-Zhong Zhsng, Jeremiah Wala, Craig H Mermel,[...]. Nat Genet 2013
6

Absolute quantification of somatic DNA alterations in human cancer.
Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir,[...]. Nat Biotechnol 2012
6

Transforming fusions of FGFR and TACC genes in human glioblastoma.
Devendra Singh, Joseph Minhow Chan, Pietro Zoppoli, Francesco Niola, Ryan Sullivan, Angelica Castano, Eric Minwei Liu, Jonathan Reichel, Paola Porrati, Serena Pellegatta,[...]. Science 2012
524
6

A comprehensive transcriptional portrait of human cancer cell lines.
Christiaan Klijn, Steffen Durinck, Eric W Stawiski, Peter M Haverty, Zhaoshi Jiang, Hanbin Liu, Jeremiah Degenhardt, Oleg Mayba, Florian Gnad, Jinfeng Liu,[...]. Nat Biotechnol 2015
395
6

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
Matteo Benelli, Chiara Pescucci, Giuseppina Marseglia, Marco Severgnini, Francesca Torricelli, Alberto Magi. Bioinformatics 2012
100
6

The landscape of somatic copy-number alteration across human cancers.
Rameen Beroukhim, Craig H Mermel, Dale Porter, Guo Wei, Soumya Raychaudhuri, Jerry Donovan, Jordi Barretina, Jesse S Boehm, Jennifer Dobson, Mitsuyoshi Urashima,[...]. Nature 2010
6

ChimerDB 4.0: an updated and expanded database of fusion genes.
Ye Eun Jang, Insu Jang, Sunkyu Kim, Subin Cho, Daehan Kim, Keonwoo Kim, Jaewon Kim, Jimin Hwang, Sangok Kim, Jaesang Kim,[...]. Nucleic Acids Res 2020
19
31

Recurrent read-through fusion transcripts in breast cancer.
Katherine E Varley, Jason Gertz, Brian S Roberts, Nicholas S Davis, Kevin M Bowling, Marie K Kirby, Amy S Nesmith, Patsy G Oliver, William E Grizzle, Andres Forero,[...]. Breast Cancer Res Treat 2014
110
5

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth, Chip Stewart, Julian Hess, Singer Ma, Kami E Chiotti, Michael McLellan,[...]. Cell Syst 2018
342
5



Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.
Craig P Giacomini, Steven Sun, Sushama Varma, A Hunter Shain, Marilyn M Giacomini, Jay Balagtas, Robert T Sweeney, Everett Lai, Catherine A Del Vecchio, Andrew D Forster,[...]. PLoS Genet 2013
83
6

Recurrent R-spondin fusions in colon cancer.
Somasekar Seshagiri, Eric W Stawiski, Steffen Durinck, Zora Modrusan, Elaine E Storm, Caitlin B Conboy, Subhra Chaudhuri, Yinghui Guan, Vasantharajan Janakiraman, Bijay S Jaiswal,[...]. Nature 2012
684
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.