A citation-based method for searching scientific literature

Andrew V Uzilov, Wei Ding, Marc Y Fink, Yevgeniy Antipin, Andrew S Brohl, Claire Davis, Chun Yee Lau, Chetanya Pandya, Hardik Shah, Yumi Kasai, James Powell, Mark Micchelli, Rafael Castellanos, Zhongyang Zhang, Michael Linderman, Yayoi Kinoshita, Micol Zweig, Katie Raustad, Kakit Cheung, Diane Castillo, Melissa Wooten, Imane Bourzgui, Leah C Newman, Gintaras Deikus, Bino Mathew, Jun Zhu, Benjamin S Glicksberg, Aye S Moe, Jun Liao, Lisa Edelmann, Joel T Dudley, Robert G Maki, Andrew Kasarskis, Randall F Holcombe, Milind Mahajan, Ke Hao, Boris Reva, Janina Longtine, Daniela Starcevic, Robert Sebra, Michael J Donovan, Shuyu Li, Eric E Schadt, Rong Chen. Genome Med 2016
Times Cited: 55







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



Times Cited
  Times     Co-cited
Similarity


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

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
14

Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth.
Rajen J Mody, Yi-Mi Wu, Robert J Lonigro, Xuhong Cao, Sameek Roychowdhury, Pankaj Vats, Kevin M Frank, John R Prensner, Irfan Asangani, Nallasivam Palanisamy,[...]. JAMA 2015
239
12

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.
Himisha Beltran, Kenneth Eng, Juan Miguel Mosquera, Alexandros Sigaras, Alessandro Romanel, Hanna Rennert, Myriam Kossai, Chantal Pauli, Bishoy Faltas, Jacqueline Fontugne,[...]. JAMA Oncol 2015
195
12

Personalized oncology through integrative high-throughput sequencing: a pilot study.
Sameek Roychowdhury, Matthew K Iyer, Dan R Robinson, Robert J Lonigro, Yi-Mi Wu, Xuhong Cao, Shanker Kalyana-Sundaram, Lee Sam, O Alejandro Balbin, Michael J Quist,[...]. Sci Transl Med 2011
430
12

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
12

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
10

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
10

Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials.
Funda Meric-Bernstam, Lauren Brusco, Kenna Shaw, Chacha Horombe, Scott Kopetz, Michael A Davies, Mark Routbort, Sarina A Piha-Paul, Filip Janku, Naoto Ueno,[...]. J Clin Oncol 2015
281
10

Limits to Personalized Cancer Medicine.
Ian F Tannock, John A Hickman. N Engl J Med 2016
213
10

A new initiative on precision medicine.
Francis S Collins, Harold Varmus. N Engl J Med 2015
10

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

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
669
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

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
9

High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial.
Christophe Massard, Stefan Michiels, Charles Ferté, Marie-Cécile Le Deley, Ludovic Lacroix, Antoine Hollebecque, Loic Verlingue, Ecaterina Ileana, Silvia Rosellini, Samy Ammari,[...]. Cancer Discov 2017
327
9

Multicenter Feasibility Study of Tumor Molecular Profiling to Inform Therapeutic Decisions in Advanced Pediatric Solid Tumors: The Individualized Cancer Therapy (iCat) Study.
Marian H Harris, Steven G DuBois, Julia L Glade Bender, AeRang Kim, Brian D Crompton, Erin Parker, Ian P Dumont, Andrew L Hong, Dongjing Guo, Alanna Church,[...]. JAMA Oncol 2016
121
7

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors.
D Williams Parsons, Angshumoy Roy, Yaping Yang, Tao Wang, Sarah Scollon, Katie Bergstrom, Robin A Kerstein, Stephanie Gutierrez, Andrea K Petersen, Abhishek Bavle,[...]. JAMA Oncol 2016
246
7


Integrated genomic characterization of endometrial carcinoma.
Cyriac Kandoth, Nikolaus Schultz, Andrew D Cherniack, Rehan Akbani, Yuexin Liu, Hui Shen, A Gordon Robertson, Itai Pashtan, Ronglai Shen, Christopher C Benz,[...]. Nature 2013
7


dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
7

COSMIC: exploring the world's knowledge of somatic mutations in human cancer.
Simon A Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, Sally Bamford, Charlotte Cole, Sari Ward,[...]. Nucleic Acids Res 2015
7

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
7


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
7

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
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

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
249
7

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
609
7


First-line crizotinib versus chemotherapy in ALK-positive lung cancer.
Benjamin J Solomon, Tony Mok, Dong-Wan Kim, Yi-Long Wu, Kazuhiko Nakagawa, Tarek Mekhail, Enriqueta Felip, Federico Cappuzzo, Jolanda Paolini, Tiziana Usari,[...]. N Engl J Med 2014
7

Integrative clinical genomics of metastatic cancer.
Dan R Robinson, Yi-Mi Wu, Robert J Lonigro, Pankaj Vats, Erin Cobain, Jessica Everett, Xuhong Cao, Erica Rabban, Chandan Kumar-Sinha, Victoria Raymond,[...]. Nature 2017
403
7

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial.
Tracy L Stockley, Amit M Oza, Hal K Berman, Natasha B Leighl, Jennifer J Knox, Frances A Shepherd, Eric X Chen, Monika K Krzyzanowska, Neesha Dhani, Anthony M Joshua,[...]. Genome Med 2016
138
7

Germline Mutations in Predisposition Genes in Pediatric Cancer.
Jinghui Zhang, Michael F Walsh, Gang Wu, Michael N Edmonson, Tanja A Gruber, John Easton, Dale Hedges, Xiaotu Ma, Xin Zhou, Donald A Yergeau,[...]. N Engl J Med 2015
573
5

Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors.
Daniel H Hovelson, Andrew S McDaniel, Andi K Cani, Bryan Johnson, Kate Rhodes, Paul D Williams, Santhoshi Bandla, Geoffrey Bien, Paul Choppa, Fiona Hyland,[...]. Neoplasia 2015
153
5

High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.
Nikhil Wagle, Michael F Berger, Matthew J Davis, Brendan Blumenstiel, Matthew Defelice, Panisa Pochanard, Matthew Ducar, Paul Van Hummelen, Laura E Macconaill, William C Hahn,[...]. Cancer Discov 2012
397
5


The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
5

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
5

Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens.
Colin C Pritchard, Stephen J Salipante, Karen Koehler, Christina Smith, Sheena Scroggins, Brent Wood, David Wu, Ming K Lee, Suzanne Dintzis, Andrew Adey,[...]. J Mol Diagn 2014
195
5



On the Road to Precision Cancer Medicine: Analysis of Genomic Biomarker Actionability in 439 Patients.
Maria Schwaederle, Gregory A Daniels, David E Piccioni, Paul T Fanta, Richard B Schwab, Kelly A Shimabukuro, Barbara A Parker, Razelle Kurzrock. Mol Cancer Ther 2015
60
5

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
5

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
5

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
5

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
5

Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.
Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V Uzilov, Rong Chen. BMC Bioinformatics 2016
10
30

Analytical validation of whole exome and whole genome sequencing for clinical applications.
Michael D Linderman, Tracy Brandt, Lisa Edelmann, Omar Jabado, Yumi Kasai, Ruth Kornreich, Milind Mahajan, Hardik Shah, Andrew Kasarskis, Eric E Schadt. BMC Med Genomics 2014
68
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.