A citation-based method for searching scientific literature

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
Times Cited: 73







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



Times Cited
  Times     Co-cited
Similarity


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
27

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
26

The emerging complexity of gene fusions in cancer.
Fredrik Mertens, Bertil Johansson, Thoas Fioretos, Felix Mitelman. Nat Rev Cancer 2015
383
23

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
23

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
993
23

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
21

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
21


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 impact of translocations and gene fusions on cancer causation.
Felix Mitelman, Bertil Johansson, Fredrik Mertens. Nat Rev Cancer 2007
908
19

Transcriptome sequencing to detect gene fusions in cancer.
Christopher A Maher, Chandan Kumar-Sinha, Xuhong Cao, Shanker Kalyana-Sundaram, Bo Han, Xiaojun Jing, Lee Sam, Terrence Barrette, Nallasivam Palanisamy, Arul M Chinnaiyan. Nature 2009
596
19


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
17

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
17

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
17

Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions.
Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L Vizmanos, Francisco J Novo. Bioinformatics 2013
69
17

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
16

JAFFA: High sensitivity transcriptome-focused fusion gene detection.
Nadia M Davidson, Ian J Majewski, Alicia Oshlack. Genome Med 2015
89
16

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Daehwan Kim, Steven L Salzberg. Genome Biol 2011
530
16

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
16

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
15

INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Jin Zhang, Elaine R Mardis, Christopher A Maher. Bioinformatics 2017
62
17

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
13

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
13

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
13

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Matthew K Iyer, Arul M Chinnaiyan, Christopher A Maher. Bioinformatics 2011
197
13

Derivation of HLA types from shotgun sequence datasets.
René L Warren, Gina Choe, Douglas J Freeman, Mauro Castellarin, Sarah Munro, Richard Moore, Robert A Holt. Genome Med 2012
115
13

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
13

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

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, S Cenk Sahinalp. Bioinformatics 2011
32
28

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
12


Complex landscapes of somatic rearrangement in human breast cancer genomes.
Philip J Stephens, David J McBride, Meng-Lay Lin, Ignacio Varela, Erin D Pleasance, Jared T Simpson, Lucy A Stebbings, Catherine Leroy, Sarah Edkins, Laura J Mudie,[...]. Nature 2009
626
10

The landscape of kinase fusions in cancer.
Nicolas Stransky, Ethan Cerami, Stefanie Schalm, Joseph L Kim, Christoph Lengauer. Nat Commun 2014
589
10

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang, Devin P Locke,[...]. Nat Methods 2009
937
10

Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts.
Shunqiang Li, Dong Shen, Jieya Shao, Robert Crowder, Wenbin Liu, Aleix Prat, Xiaping He, Shuying Liu, Jeremy Hoog, Charles Lu,[...]. Cell Rep 2013
421
10


pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens.
Jasreet Hundal, Beatriz M Carreno, Allegra A Petti, Gerald P Linette, Obi L Griffith, Elaine R Mardis, Malachi Griffith. Genome Med 2016
216
10

DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M Stütz, Vladimir Benes, Jan O Korbel. Bioinformatics 2012
10

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
10


TumorFusions: an integrative resource for cancer-associated transcript fusions.
Xin Hu, Qianghu Wang, Ming Tang, Floris Barthel, Samirkumar Amin, Kosuke Yoshihara, Frederick M Lang, Emmanuel Martinez-Ledesma, Soo Hyun Lee, Siyuan Zheng,[...]. Nucleic Acids Res 2018
115
10

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
9

State-of-the-art fusion-finder algorithms sensitivity and specificity.
Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele A Calogero. Biomed Res Int 2013
65
10

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.
Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao, Zhongming Zhao. Brief Bioinform 2013
78
9

Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer.
Dan R Robinson, Shanker Kalyana-Sundaram, Yi-Mi Wu, Sunita Shankar, Xuhong Cao, Bushra Ateeq, Irfan A Asangani, Matthew Iyer, Christopher A Maher, Catherine S Grasso,[...]. Nat Med 2011
250
9

Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma.
Cristina Tognon, Stevan R Knezevich, David Huntsman, Calvin D Roskelley, Natalya Melnyk, Joan A Mathers, Laurence Becker, Fatima Carneiro, Nicol MacPherson, Doug Horsman,[...]. Cancer Cell 2002
602
9

SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer.
David S Rickman, Dorothee Pflueger, Benjamin Moss, Vanessa E VanDoren, Chen X Chen, Alexandre de la Taille, Rainer Kuefer, Ashutosh K Tewari, Sunita R Setlur, Francesca Demichelis,[...]. Cancer Res 2009
148
9

Chimeric transcript discovery by paired-end transcriptome sequencing.
Christopher A Maher, Nallasivam Palanisamy, John C Brenner, Xuhong Cao, Shanker Kalyana-Sundaram, Shujun Luo, Irina Khrebtukova, Terrence R Barrette, Catherine Grasso, Jindan Yu,[...]. Proc Natl Acad Sci U S A 2009
246
9

SomaticSniper: identification of somatic point mutations in whole genome sequencing data.
David E Larson, Christopher C Harris, Ken Chen, Daniel C Koboldt, Travis E Abbott, David J Dooling, Timothy J Ley, Elaine R Mardis, Richard K Wilson, Li Ding. Bioinformatics 2012
372
9


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.