A citation-based method for searching scientific literature

Matthew T Chang, Tripti Shrestha Bhattarai, Alison M Schram, Craig M Bielski, Mark T A Donoghue, Philip Jonsson, Debyani Chakravarty, Sarah Phillips, Cyriac Kandoth, Alexander Penson, Alexander Gorelick, Tambudzai Shamu, Swati Patel, Christopher Harris, JianJiong Gao, Selcuk Onur Sumer, Ritika Kundra, Pedram Razavi, Bob T Li, Dalicia N Reales, Nicholas D Socci, Gowtham Jayakumaran, Ahmet Zehir, Ryma Benayed, Maria E Arcila, Sarat Chandarlapaty, Marc Ladanyi, Nikolaus Schultz, José Baselga, Michael F Berger, Neal Rosen, David B Solit, David M Hyman, Barry S Taylor. Cancer Discov 2018
Times Cited: 139







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



Times Cited
  Times     Co-cited
Similarity


Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity.
Matthew T Chang, Saurabh Asthana, Sizhi Paul Gao, Byron H Lee, Jocelyn S Chapman, Cyriac Kandoth, JianJiong Gao, Nicholas D Socci, David B Solit, Adam B Olshen,[...]. Nat Biotechnol 2016
425
38

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
819
37

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
35

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.
Donavan T Cheng, Talia N Mitchell, Ahmet Zehir, Ronak H Shah, Ryma Benayed, Aijazuddin Syed, Raghu Chandramohan, Zhen Yu Liu, Helen H Won, Sasinya N Scott,[...]. J Mol Diagn 2015
32

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
23

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
23

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
23


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
20

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
16


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
14

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
915
14

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets.
Jianjiong Gao, Matthew T Chang, Hannah C Johnsen, Sizhi Paul Gao, Brooke E Sylvester, Selcuk Onur Sumer, Hongxin Zhang, David B Solit, Barry S Taylor, Nikolaus Schultz,[...]. Genome Med 2017
113
12

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
12

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
760
11

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
11

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
993
11

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
11

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
740
11

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, Arpad M Danos, Benjamin J Ainscough, Cody A Ramirez, Damian T Rieke, Lynzey Kujan,[...]. Nat Genet 2017
259
11


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
529
10

Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer.
Craig M Bielski, Mark T A Donoghue, Mayur Gadiya, Aphrothiti J Hanrahan, Helen H Won, Matthew T Chang, Philip Jonsson, Alexander V Penson, Alexander Gorelick, Christopher Harris,[...]. Cancer Cell 2018
46
21

Genome-wide somatic variant calling using localized colored de Bruijn graphs.
Giuseppe Narzisi, André Corvelo, Kanika Arora, Ewa A Bergmann, Minita Shah, Rajeeva Musunuri, Anne-Katrin Emde, Nicolas Robine, Vladimir Vacic, Michael C Zody. Commun Biol 2018
50
20

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features.
Rémi Buisson, Adam Langenbucher, Danae Bowen, Eugene E Kwan, Cyril H Benes, Lee Zou, Michael S Lawrence. Science 2019
108
10

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
10

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
10

HER kinase inhibition in patients with HER2- and HER3-mutant cancers.
David M Hyman, Sarina A Piha-Paul, Helen Won, Jordi Rodon, Cristina Saura, Geoffrey I Shapiro, Dejan Juric, David I Quinn, Victor Moreno, Bernard Doger,[...]. Nature 2018
349
9

The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers.
Britta Weigelt, Rui Bi, Rahul Kumar, Pedro Blecua, Diana L Mandelker, Felipe C Geyer, Fresia Pareja, Paul A James, Fergus J Couch, Diana M Eccles,[...]. J Natl Cancer Inst 2018
59
15

The Genomic Landscape of Mucinous Breast Cancer.
Fresia Pareja, Ju Youn Lee, David N Brown, Salvatore Piscuoglio, Rodrigo Gularte-Mérida, Pier Selenica, Arnaud Da Cruz Paula, Sasi Arunachalam, Rahul Kumar, Felipe C Geyer,[...]. J Natl Cancer Inst 2019
41
21

Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer.
Fabrice André, Eva Ciruelos, Gabor Rubovszky, Mario Campone, Sibylle Loibl, Hope S Rugo, Hiroji Iwata, Pierfranco Conte, Ingrid A Mayer, Bella Kaufman,[...]. N Engl J Med 2019
781
9

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Giuseppe Narzisi, Jason A O'Rawe, Ivan Iossifov, Han Fang, Yoon-Ha Lee, Zihua Wang, Yiyang Wu, Gholson J Lyon, Michael Wigler, Michael C Schatz. Nat Methods 2014
133
9

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
8


Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.
Diana Mandelker, Liying Zhang, Yelena Kemel, Zsofia K Stadler, Vijai Joseph, Ahmet Zehir, Nisha Pradhan, Angela Arnold, Michael F Walsh, Yirong Li,[...]. JAMA 2017
219
8

Implementing Genome-Driven Oncology.
David M Hyman, Barry S Taylor, José Baselga. Cell 2017
253
8

The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers.
Pedram Razavi, Matthew T Chang, Guotai Xu, Chaitanya Bandlamudi, Dara S Ross, Neil Vasan, Yanyan Cai, Craig M Bielski, Mark T A Donoghue, Philip Jonsson,[...]. Cancer Cell 2018
317
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
468
8

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
8

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
8

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations.
David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero,[...]. Genome Med 2018
204
8


Genomic profiling of primary and recurrent adult granulosa cell tumors of the ovary.
Arnaud Da Cruz Paula, Edaise M da Silva, Sheila E Segura, Fresia Pareja, Rui Bi, Pier Selenica, Sarah H Kim, Lorenzo Ferrando, Mahsa Vahdatinia, Robert A Soslow,[...]. Mod Pathol 2020
19
42

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Eliezer M Van Allen, Nikhil Wagle, Petar Stojanov, Danielle L Perrin, Kristian Cibulskis, Sara Marlow, Judit Jane-Valbuena, Dennis C Friedrich, Gregory Kryukov, Scott L Carter,[...]. Nat Med 2014
370
7

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency.
Dung T Le, Jennifer N Uram, Hao Wang, Bjarne R Bartlett, Holly Kemberling, Aleksandra D Eyring, Andrew D Skora, Brandon S Luber, Nilofer S Azad, Dan Laheru,[...]. N Engl J Med 2015
7

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
Garrett M Frampton, Alex Fichtenholtz, Geoff A Otto, Kai Wang, Sean R Downing, Jie He, Michael Schnall-Levin, Jared White, Eric M Sanford, Peter An,[...]. Nat Biotechnol 2013
7

AKT Inhibition in Solid Tumors With AKT1 Mutations.
David M Hyman, Lillian M Smyth, Mark T A Donoghue, Shannon N Westin, Philippe L Bedard, Emma J Dean, Hideaki Bando, Anthony B El-Khoueiry, José A Pérez-Fidalgo, Alain Mita,[...]. J Clin Oncol 2017
167
7

Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data.
Sumit Middha, Liying Zhang, Khedoudja Nafa, Gowtham Jayakumaran, Donna Wong, Hyunjae R Kim, Justyna Sadowska, Michael F Berger, Deborah F Delair, Jinru Shia,[...]. JCO Precis Oncol 2017
157
7

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D McLellan, Michael C Wendl, Li Ding. Bioinformatics 2014
323
7


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.