A citation-based method for searching scientific literature

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, Adam Kiezun, Peter S Hammerman, Aaron McKenna, Yotam Drier, Lihua Zou, Alex H Ramos, Trevor J Pugh, Nicolas Stransky, Elena Helman, Jaegil Kim, Carrie Sougnez, Lauren Ambrogio, Elizabeth Nickerson, Erica Shefler, Maria L Cortés, Daniel Auclair, Gordon Saksena, Douglas Voet, Michael Noble, Daniel DiCara, Pei Lin, Lee Lichtenstein, David I Heiman, Timothy Fennell, Marcin Imielinski, Bryan Hernandez, Eran Hodis, Sylvan Baca, Austin M Dulak, Jens Lohr, Dan-Avi Landau, Catherine J Wu, Jorge Melendez-Zajgla, Alfredo Hidalgo-Miranda, Amnon Koren, Steven A McCarroll, Jaume Mora, Brian Crompton, Robert Onofrio, Melissa Parkin, Wendy Winckler, Kristin Ardlie, Stacey B Gabriel, Charles W M Roberts, Jaclyn A Biegel, Kimberly Stegmaier, Adam J Bass, Levi A Garraway, Matthew Meyerson, Todd R Golub, Dmitry A Gordenin, Shamil Sunyaev, Eric S Lander, Gad Getz. Nature 2013
Times Cited: 3487







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



Times Cited
  Times     Co-cited
Similarity


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
21

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
18

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
17

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

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
13

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
12

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
12


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
11

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


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
9

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.
Naiyer A Rizvi, Matthew D Hellmann, Alexandra Snyder, Pia Kvistborg, Vladimir Makarov, Jonathan J Havel, William Lee, Jianda Yuan, Phillip Wong, Teresa S Ho,[...]. Science 2015
8

Neoantigens in cancer immunotherapy.
Ton N Schumacher, Robert D Schreiber. Science 2015
8

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
560
8

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S Taylor, Charles Swanton. Genome Biol 2016
610
8

The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers.
Zbyslaw Sondka, Sally Bamford, Charlotte G Cole, Sari A Ward, Ian Dunham, Simon A Forbes. Nat Rev Cancer 2018
522
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
8

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
Katherine A Hoadley, Christina Yau, Toshinori Hinoue, Denise M Wolf, Alexander J Lazar, Esther Drill, Ronglai Shen, Alison M Taylor, Andrew D Cherniack, Vésteinn Thorsson,[...]. Cell 2018
964
7

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
7

Molecular and genetic properties of tumors associated with local immune cytolytic activity.
Michael S Rooney, Sachet A Shukla, Catherine J Wu, Gad Getz, Nir Hacohen. Cell 2015
7

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
7

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
7

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
7

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

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
7

Maftools: efficient and comprehensive analysis of somatic variants in cancer.
Anand Mayakonda, De-Chen Lin, Yassen Assenov, Christoph Plass, H Phillip Koeffler. Genome Res 2018
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
193
6


OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
David Tamborero, Abel Gonzalez-Perez, Nuria Lopez-Bigas. Bioinformatics 2013
273
6

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.
Loris Mularoni, Radhakrishnan Sabarinathan, Jordi Deu-Pons, Abel Gonzalez-Perez, Núria López-Bigas. Genome Biol 2016
143
6

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
268
6

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
6

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

Genetic basis for clinical response to CTLA-4 blockade in melanoma.
Alexandra Snyder, Vladimir Makarov, Taha Merghoub, Jianda Yuan, Jesse M Zaretsky, Alexis Desrichard, Logan A Walsh, Michael A Postow, Phillip Wong, Teresa S Ho,[...]. N Engl J Med 2014
6

Somatic mutant clones colonize the human esophagus with age.
Iñigo Martincorena, Joanna C Fowler, Agnieszka Wabik, Andrew R J Lawson, Federico Abascal, Michael W J Hall, Alex Cagan, Kasumi Murai, Krishnaa Mahbubani, Michael R Stratton,[...]. Science 2018
477
6

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
6

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
6

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

The cancer genome.
Michael R Stratton, Peter J Campbell, P Andrew Futreal. Nature 2009
6

Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.
Iñigo Martincorena, Amit Roshan, Moritz Gerstung, Peter Ellis, Peter Van Loo, Stuart McLaren, David C Wedge, Anthony Fullam, Ludmil B Alexandrov, Jose M Tubio,[...]. Science 2015
932
6

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
6

An immunogenic personal neoantigen vaccine for patients with melanoma.
Patrick A Ott, Zhuting Hu, Derin B Keskin, Sachet A Shukla, Jing Sun, David J Bozym, Wandi Zhang, Adrienne Luoma, Anita Giobbie-Hurder, Lauren Peter,[...]. Nature 2017
6

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.
Pornpimol Charoentong, Francesca Finotello, Mihaela Angelova, Clemens Mayer, Mirjana Efremova, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski. Cell Rep 2017
6

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
6


Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.
Ahmet Zehir, Ryma Benayed, Ronak H Shah, Aijazuddin Syed, Sumit Middha, Hyunjae R Kim, Preethi Srinivasan, Jianjiong Gao, Debyani Chakravarty, Sean M Devlin,[...]. Nat Med 2017
5

Somatic mutation in cancer and normal cells.
Iñigo Martincorena, Peter J Campbell. Science 2015
597
5

A census of human cancer genes.
P Andrew Futreal, Lachlan Coin, Mhairi Marshall, Thomas Down, Timothy Hubbard, Richard Wooster, Nazneen Rahman, Michael R Stratton. Nat Rev Cancer 2004
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.