A citation-based method for searching scientific literature

Zbyslaw Sondka, Sally Bamford, Charlotte G Cole, Sari A Ward, Ian Dunham, Simon A Forbes. Nat Rev Cancer 2018
Times Cited: 446







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



Times Cited
  Times     Co-cited
Similarity


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
16

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
15

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
15

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
14

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
14

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
798
14

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
13

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
12

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
12

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
811
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12


Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
11

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
865
10


Universal Patterns of Selection in Cancer and Somatic Tissues.
Iñigo Martincorena, Keiran M Raine, Moritz Gerstung, Kevin J Dawson, Kerstin Haase, Peter Van Loo, Helen Davies, Michael R Stratton, Peter J Campbell. Cell 2017
493
10

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
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
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

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
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
9

A method and server for predicting damaging missense mutations.
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
9


The cancer genome.
Michael R Stratton, Peter J Campbell, P Andrew Futreal. Nature 2009
9

A compendium of mutational cancer driver genes.
Francisco Martínez-Jiménez, Ferran Muiños, Inés Sentís, Jordi Deu-Pons, Iker Reyes-Salazar, Claudia Arnedo-Pac, Loris Mularoni, Oriol Pich, Jose Bonet, Hanna Kranas,[...]. Nat Rev Cancer 2020
185
8

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
8

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
8

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
8

International network of cancer genome projects.
Thomas J Hudson, Warwick Anderson, Axel Artez, Anna D Barker, Cindy Bell, Rosa R Bernabé, M K Bhan, Fabien Calvo, Iiro Eerola, Daniela S Gerhard,[...]. Nature 2010
8

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
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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
7

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.
Dimitra Repana, Joel Nulsen, Lisa Dressler, Michele Bortolomeazzi, Santhilata Kuppili Venkata, Aikaterini Tourna, Anna Yakovleva, Tommaso Palmieri, Francesca D Ciccarelli. Genome Biol 2019
229
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


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
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

Evaluating the evaluation of cancer driver genes.
Collin J Tokheim, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Rachel Karchin. Proc Natl Acad Sci U S A 2016
179
7

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
7

Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome.
Teresa Davoli, Andrew Wei Xu, Kristen E Mengwasser, Laura M Sack, John C Yoon, Peter J Park, Stephen J Elledge. Cell 2013
454
6

IntOGen-mutations identifies cancer drivers across tumor types.
Abel Gonzalez-Perez, Christian Perez-Llamas, Jordi Deu-Pons, David Tamborero, Michael P Schroeder, Alba Jene-Sanz, Alberto Santos, Nuria Lopez-Bigas. Nat Methods 2013
354
6

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
6

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
6

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
6

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
294
6

SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
6

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
6

Discovery and saturation analysis of cancer genes across 21 tumour types.
Michael S Lawrence, Petar Stojanov, Craig H Mermel, James T Robinson, Levi A Garraway, Todd R Golub, Matthew Meyerson, Stacey B Gabriel, Eric S Lander, Gad Getz. Nature 2014
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.