A citation-based method for searching scientific literature

Simon Kebede Merid, Daria Goranskaya, Andrey Alexeyenko. BMC Bioinformatics 2014
Times Cited: 41







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



Times Cited
  Times     Co-cited
Similarity


Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
41

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
31

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
21

MuSiC: identifying mutational significance in cancer genomes.
Nathan D Dees, Qunyuan Zhang, Cyriac Kandoth, Michael C Wendl, William Schierding, Daniel C Koboldt, Thomas B Mooney, Matthew B Callaway, David Dooling, Elaine R Mardis,[...]. Genome Res 2012
355
21

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.
Mark D M Leiserson, Fabio Vandin, Hsin-Ta Wu, Jason R Dobson, Jonathan V Eldridge, Jacob L Thomas, Alexandra Papoutsaki, Younhun Kim, Beifang Niu, Michael McLellan,[...]. Nat Genet 2015
395
21


Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.
Benjamin J Raphael, Jason R Dobson, Layla Oesper, Fabio Vandin. Genome Med 2014
100
17

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.
Andrey Alexeyenko, Woojoo Lee, Maria Pernemalm, Justin Guegan, Philippe Dessen, Vladimir Lazar, Janne Lehtiö, Yudi Pawitan. BMC Bioinformatics 2012
64
17

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
14

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
14

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
14

Comprehensive identification of mutational cancer driver genes across 12 tumor types.
David Tamborero, Abel Gonzalez-Perez, Christian Perez-Llamas, Jordi Deu-Pons, Cyriac Kandoth, Jüri Reimand, Michael S Lawrence, Gad Getz, Gary D Bader, Li Ding,[...]. Sci Rep 2013
308
14

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
David Tamborero, Abel Gonzalez-Perez, Nuria Lopez-Bigas. Bioinformatics 2013
202
14

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Ara Cho, Jung Eun Shim, Eiru Kim, Fran Supek, Ben Lehner, Insuk Lee. Genome Biol 2016
59
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
539
14

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.
Hannah Carter, Sining Chen, Leyla Isik, Svitlana Tyekucheva, Victor E Velculescu, Kenneth W Kinzler, Bert Vogelstein, Rachel Karchin. Cancer Res 2009
274
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
12


The KEGG databases at GenomeNet.
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Akihiro Nakaya. Nucleic Acids Res 2002
721
12

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
12


Mutational landscape and significance across 12 major cancer types.
Cyriac Kandoth, Michael D McLellan, Fabio Vandin, Kai Ye, Beifang Niu, Charles Lu, Mingchao Xie, Qunyuan Zhang, Joshua F McMichael, Matthew A Wyczalkowski,[...]. Nature 2013
12

Network-based stratification of tumor mutations.
Matan Hofree, John P Shen, Hannah Carter, Andrew Gross, Trey Ideker. Nat Methods 2013
387
12

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah. Genome Biol 2012
115
12

The cancer genome.
Michael R Stratton, Peter J Campbell, P Andrew Futreal. Nature 2009
12


Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
12

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
140
12

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin, Sungjoon Kim, Christopher J Wilson, Joseph Lehár, Gregory V Kryukov, Dmitriy Sonkin,[...]. Nature 2012
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


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


Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
9

Mutual exclusivity analysis identifies oncogenic network modules.
Giovanni Ciriello, Ethan Cerami, Chris Sander, Nikolaus Schultz. Genome Res 2012
364
9

Algorithms for detecting significantly mutated pathways in cancer.
Fabio Vandin, Eli Upfal, Benjamin J Raphael. J Comput Biol 2011
213
9

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
9


CORUM: the comprehensive resource of mammalian protein complexes.
Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen,[...]. Nucleic Acids Res 2008
226
9

De novo discovery of mutated driver pathways in cancer.
Fabio Vandin, Eli Upfal, Benjamin J Raphael. Genome Res 2012
227
9

Supervised risk predictor of breast cancer based on intrinsic subtypes.
Joel S Parker, Michael Mullins, Maggie C U Cheang, Samuel Leung, David Voduc, Tammi Vickery, Sherri Davies, Christiane Fauron, Xiaping He, Zhiyuan Hu,[...]. J Clin Oncol 2009
9

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Charles J Vaske, Stephen C Benz, J Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M Stuart. Bioinformatics 2010
419
9

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.
Denis Bertrand, Kern Rei Chng, Faranak Ghazi Sherbaf, Anja Kiesel, Burton K H Chia, Yee Yen Sia, Sharon K Huang, Dave S B Hoon, Edison T Liu, Axel Hillmer,[...]. Nucleic Acids Res 2015
49
9

Driver and passenger mutations in cancer.
Julia R Pon, Marco A Marra. Annu Rev Pathol 2015
117
9

Functional impact bias reveals cancer drivers.
Abel Gonzalez-Perez, Nuria Lopez-Bigas. Nucleic Acids Res 2012
192
9

The genomic landscapes of human breast and colorectal cancers.
Laura D Wood, D Williams Parsons, Siân Jones, Jimmy Lin, Tobias Sjöblom, Rebecca J Leary, Dong Shen, Simina M Boca, Thomas Barber, Janine Ptak,[...]. Science 2007
9

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
9

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

The consensus coding sequences of human breast and colorectal cancers.
Tobias Sjöblom, Siân Jones, Laura D Wood, D Williams Parsons, Jimmy Lin, Thomas D Barber, Diana Mandelker, Rebecca J Leary, Janine Ptak, Natalie Silliman,[...]. Science 2006
9

Patterns of somatic mutation in human cancer genomes.
Christopher Greenman, Philip Stephens, Raffaella Smith, Gillian L Dalgliesh, Christopher Hunter, Graham Bignell, Helen Davies, Jon Teague, Adam Butler, Claire Stevens,[...]. Nature 2007
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.