A citation-based method for searching scientific literature

Debyani Chakravarty, David B Solit. Nat Rev Genet 2021
Times Cited: 21







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



Times Cited
  Times     Co-cited
Similarity


Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
23

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
23

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
Alex H Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P Duren, Jianjiong Gao, Julie McMurry,[...]. Nat Genet 2020
60
19


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
19

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
19

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
19

Molecular Landscape and Actionable Alterations in a Genomically Guided Cancer Clinical Trial: National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH).
Keith T Flaherty, Robert J Gray, Alice P Chen, Shuli Li, Lisa M McShane, David Patton, Stanley R Hamilton, P Mickey Williams, A John Iafrate, Jeffrey Sklar,[...]. J Clin Oncol 2020
73
14

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.
Stefan C Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester,[...]. Cell 2021
78
14

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki,[...]. Genome Med 2017
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
853
14

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
378
14

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
14

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Helen Davies, Dominik Glodzik, Sandro Morganella, Lucy R Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M Sieuwerts,[...]. Nat Med 2017
445
14

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
14

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
Marilyn M Li, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, Cindy L Vnencak-Jones, Daynna J Wolff, Anas Younes,[...]. J Mol Diagn 2017
753
14

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
14

Role of non-coding sequence variants in cancer.
Ekta Khurana, Yao Fu, Dimple Chakravarty, Francesca Demichelis, Mark A Rubin, Mark Gerstein. Nat Rev Genet 2016
272
9


Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X.
Yu Liu, Chunliang Li, Shuhong Shen, Xiaolong Chen, Karol Szlachta, Michael N Edmonson, Ying Shao, Xiaotu Ma, Judith Hyle, Shaela Wright,[...]. Nat Genet 2020
27
9

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Juul, Ziao Lin,[...]. Nature 2020
207
9

Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.
Helen Zhu, Liis Uusküla-Reimand, Keren Isaev, Lina Wadi, Azad Alizada, Shimin Shuai, Vincent Huang, Dike Aduluso-Nwaobasi, Marta Paczkowska, Diala Abd-Rabbo,[...]. Mol Cell 2020
26
9

Patterns of somatic structural variation in human cancer genomes.
Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber,[...]. Nature 2020
224
9

Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.
Christophe Le Tourneau, Jean-Pierre Delord, Anthony Gonçalves, Céline Gavoille, Coraline Dubot, Nicolas Isambert, Mario Campone, Olivier Trédan, Marie-Ange Massiani, Cécile Mauborgne,[...]. Lancet Oncol 2015
636
9

Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board.
W Brian Dalton, Patrick M Forde, Hyunseok Kang, Roisin M Connolly, Vered Stearns, Christopher D Gocke, James R Eshleman, Jennifer Axilbund, Dana Petry, Cindy Geoghegan,[...]. JCO Precis Oncol 2017
44
9

Impact of Precision Medicine in Diverse Cancers: A Meta-Analysis of Phase II Clinical Trials.
Maria Schwaederle, Melissa Zhao, J Jack Lee, Alexander M Eggermont, Richard L Schilsky, John Mendelsohn, Vladimir Lazar, Razelle Kurzrock. J Clin Oncol 2015
263
9

SvABA: genome-wide detection of structural variants and indels by local assembly.
Jeremiah A Wala, Pratiti Bandopadhayay, Noah F Greenwald, Ryan O'Rourke, Ted Sharpe, Chip Stewart, Steve Schumacher, Yilong Li, Joachim Weischenfeldt, Xiaotong Yao,[...]. Genome Res 2018
137
9

Genomic footprints of activated telomere maintenance mechanisms in cancer.
Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe,[...]. Nat Commun 2020
42
9

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
Pauline Robbe, Niko Popitsch, Samantha J L Knight, Pavlos Antoniou, Jennifer Becq, Miao He, Alexander Kanapin, Anastasia Samsonova, Dimitrios V Vavoulis, Mark T Ross,[...]. Genet Med 2018
77
9


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
933
9

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
660
9

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

A machine learning approach for somatic mutation discovery.
Derrick E Wood, James R White, Andrew Georgiadis, Beth Van Emburgh, Sonya Parpart-Li, Jason Mitchell, Valsamo Anagnostou, Noushin Niknafs, Rachel Karchin, Eniko Papp,[...]. Sci Transl Med 2018
43
9

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.
Philip J Stephens, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, King Wai Lau, David Beare, Lucy A Stebbings,[...]. Cell 2011
9


A Compendium of Mutational Signatures of Environmental Agents.
Jill E Kucab, Xueqing Zou, Sandro Morganella, Madeleine Joel, A Scott Nanda, Eszter Nagy, Celine Gomez, Andrea Degasperi, Rebecca Harris, Stephen P Jackson,[...]. Cell 2019
221
9

The life history of 21 breast cancers.
Serena Nik-Zainal, Peter Van Loo, David C Wedge, Ludmil B Alexandrov, Christopher D Greenman, King Wai Lau, Keiran Raine, David Jones, John Marshall, Manasa Ramakrishna,[...]. Cell 2012
878
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
901
9

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
657
9

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
235
9

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Brian J Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev. Genome Biol 2019
168
9

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
Zhongwu Lai, Aleksandra Markovets, Miika Ahdesmaki, Brad Chapman, Oliver Hofmann, Robert McEwen, Justin Johnson, Brian Dougherty, J Carl Barrett, Jonathan R Dry. Nucleic Acids Res 2016
371
9

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
9

Copy number signatures and mutational processes in ovarian carcinoma.
Geoff Macintyre, Teodora E Goranova, Dilrini De Silva, Darren Ennis, Anna M Piskorz, Matthew Eldridge, Daoud Sie, Liz-Anne Lewsley, Aishah Hanif, Cheryl Wilson,[...]. Nat Genet 2018
155
9

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
589
9

Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers.
Aparna R Parikh, Ignaty Leshchiner, Liudmila Elagina, Lipika Goyal, Chaya Levovitz, Giulia Siravegna, Dimitri Livitz, Kahn Rhrissorrakrai, Elizabeth E Martin, Emily E Van Seventer,[...]. Nat Med 2019
184
9

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen. Genome Med 2018
267
9

COSMIC: somatic cancer genetics at high-resolution.
Simon A Forbes, David Beare, Harry Boutselakis, Sally Bamford, Nidhi Bindal, John Tate, Charlotte G Cole, Sari Ward, Elisabeth Dawson, Laura Ponting,[...]. Nucleic Acids Res 2017
9

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
406
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.