A citation-based method for searching scientific literature

Brian J Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev. Genome Biol 2019
Times Cited: 175







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



Times Cited
  Times     Co-cited
Similarity


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
27

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
240
19

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
18


Accurate and efficient detection of gene fusions from RNA sequencing data.
Sebastian Uhrig, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H Toprak, Olaf Neumann, Albrecht Stenzinger, Claudia Scholl,[...]. Genome Res 2021
60
26

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
14

The impact of translocations and gene fusions on cancer causation.
Felix Mitelman, Bertil Johansson, Fredrik Mertens. Nat Rev Cancer 2007
898
14

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

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
12

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
12

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
680
11

The emerging complexity of gene fusions in cancer.
Fredrik Mertens, Bertil Johansson, Thoas Fioretos, Felix Mitelman. Nat Rev Cancer 2015
375
11

JAFFA: High sensitivity transcriptome-focused fusion gene detection.
Nadia M Davidson, Ian J Majewski, Alicia Oshlack. Genome Med 2015
87
11

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
128
10

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
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
10

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
10

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
9

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Daehwan Kim, Steven L Salzberg. Genome Biol 2011
522
9

Diagnosis of fusion genes using targeted RNA sequencing.
Erin E Heyer, Ira W Deveson, Danson Wooi, Christina I Selinger, Ruth J Lyons, Vanessa M Hayes, Sandra A O'Toole, Mandy L Ballinger, Devinder Gill, David M Thomas,[...]. Nat Commun 2019
69
13

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
9

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
71
12

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
99
9

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
383
9

The repertoire of mutational signatures in human cancer.
Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R Covington, Dmitry A Gordenin, Erik N Bergstrom,[...]. Nature 2020
942
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

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
8

Strelka2: fast and accurate calling of germline and somatic variants.
Sangtae Kim, Konrad Scheffler, Aaron L Halpern, Mitchell A Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Yeonbin Kim, Doruk Beyter, Peter Krusche,[...]. Nat Methods 2018
420
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

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
90
8

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
8

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Matthew K Iyer, Arul M Chinnaiyan, Christopher A Maher. Bioinformatics 2011
197
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
101
8

The landscape of genomic alterations across childhood cancers.
Susanne N Gröbner, Barbara C Worst, Joachim Weischenfeldt, Ivo Buchhalter, Kortine Kleinheinz, Vasilisa A Rudneva, Pascal D Johann, Gnana Prakash Balasubramanian, Maia Segura-Wang, Sebastian Brabetz,[...]. Nature 2018
612
7

Immunogenic neoantigens derived from gene fusions stimulate T cell responses.
Wei Yang, Ken-Wing Lee, Raghvendra M Srivastava, Fengshen Kuo, Chirag Krishna, Diego Chowell, Vladimir Makarov, Douglas Hoen, Martin G Dalin, Leonard Wexler,[...]. Nat Med 2019
156
7

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
7

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
7

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
977
7

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
593
7

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
960
7

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
7

Genomic basis for RNA alterations in cancer.
Claudia Calabrese, Natalie R Davidson, Deniz Demircioğlu, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette,[...]. Nature 2020
158
7


Sclerosing Polycystic "Adenosis" of Salivary Glands: A Neoplasm Characterized by PI3K Pathway Alterations More Correctly Named Sclerosing Polycystic Adenoma.
Justin A Bishop, Jeffrey Gagan, Daniel Baumhoer, Anne L McLean-Holden, Bahram R Oliai, Marta Couce, Lester D R Thompson. Head Neck Pathol 2020
29
20

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.
Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B Alexandrov, Michael N Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C Rusch, John Easton,[...]. Nature 2018
382
6

Opportunities and challenges in long-read sequencing data analysis.
Shanika L Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E Ritchie, Quentin Gouil. Genome Biol 2020
303
6

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
109
6

The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
6

OptiType: precision HLA typing from next-generation sequencing data.
András Szolek, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, Oliver Kohlbacher. Bioinformatics 2014
335
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.