A citation-based method for searching scientific literature

Kuan-Lin Huang, R Jay Mashl, Yige Wu, Deborah I Ritter, Jiayin Wang, Clara Oh, Marta Paczkowska, Sheila Reynolds, Matthew A Wyczalkowski, Ninad Oak, Adam D Scott, Michal Krassowski, Andrew D Cherniack, Kathleen E Houlahan, Reyka Jayasinghe, Liang-Bo Wang, Daniel Cui Zhou, Di Liu, Song Cao, Young Won Kim, Amanda Koire, Joshua F McMichael, Vishwanathan Hucthagowder, Tae-Beom Kim, Abigail Hahn, Chen Wang, Michael D McLellan, Fahd Al-Mulla, Kimberly J Johnson, Olivier Lichtarge, Paul C Boutros, Benjamin Raphael, Alexander J Lazar, Wei Zhang, Michael C Wendl, Ramaswamy Govindan, Sanjay Jain, David Wheeler, Shashikant Kulkarni, John F Dipersio, Jüri Reimand, Funda Meric-Bernstam, Ken Chen, Ilya Shmulevich, Sharon E Plon, Feng Chen, Li Ding. Cell 2018
Times Cited: 311







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



Times Cited
  Times     Co-cited
Similarity



Patterns and functional implications of rare germline variants across 12 cancer types.
Charles Lu, Mingchao Xie, Michael C Wendl, Jiayin Wang, Michael D McLellan, Mark D M Leiserson, Kuan-Lin Huang, Matthew A Wyczalkowski, Reyka Jayasinghe, Tapahsama Banerjee,[...]. Nat Commun 2015
151
16

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
16

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
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
13

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
13


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
11

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
9

Risks of Breast, Ovarian, and Contralateral Breast Cancer for BRCA1 and BRCA2 Mutation Carriers.
Karoline B Kuchenbaecker, John L Hopper, Daniel R Barnes, Kelly-Anne Phillips, Thea M Mooij, Marie-José Roos-Blom, Sarah Jervis, Flora E van Leeuwen, Roger L Milne, Nadine Andrieu,[...]. JAMA 2017
994
9

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
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
538
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

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
9

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
8

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
8

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
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
415
8

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
8

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

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
8

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
8

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth, Chip Stewart, Julian Hess, Singer Ma, Kami E Chiotti, Michael McLellan,[...]. Cell Syst 2018
276
8

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
8

Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer.
Colin C Pritchard, Joaquin Mateo, Michael F Walsh, Navonil De Sarkar, Wassim Abida, Himisha Beltran, Andrea Garofalo, Roman Gulati, Suzanne Carreira, Rosalind Eeles,[...]. N Engl J Med 2016
772
7

CADD: predicting the deleteriousness of variants throughout the human genome.
Philipp Rentzsch, Daniela Witten, Gregory M Cooper, Jay Shendure, Martin Kircher. Nucleic Acids Res 2019
7

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
792
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
6

Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.
Hannah Carter, Rachel Marty, Matan Hofree, Andrew M Gross, James Jensen, Kathleen M Fisch, Xingyu Wu, Christopher DeBoever, Eric L Van Nostrand, Yan Song,[...]. Cancer Discov 2017
76
7

A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1.
Y Miki, J Swensen, D Shattuck-Eidens, P A Futreal, K Harshman, S Tavtigian, Q Liu, C Cochran, L M Bennett, W Ding. Science 1994
6

A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
6

Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer.
Fergus J Couch, Steven N Hart, Priyanka Sharma, Amanda Ewart Toland, Xianshu Wang, Penelope Miron, Janet E Olson, Andrew K Godwin, V Shane Pankratz, Curtis Olswold,[...]. J Clin Oncol 2015
389
6

CharGer: clinical Characterization of Germline variants.
Adam D Scott, Kuan-Lin Huang, Amila Weerasinghe, R Jay Mashl, Qingsong Gao, Fernanda Martins Rodrigues, Matthew A Wyczalkowski, Li Ding. Bioinformatics 2019
17
35

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
6

ClinVar: public archive of relationships among sequence variation and human phenotype.
Melissa J Landrum, Jennifer M Lee, George R Riley, Wonhee Jang, Wendy S Rubinstein, Deanna M Church, Donna R Maglott. Nucleic Acids Res 2014
6

ClinVar: improving access to variant interpretations and supporting evidence.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang,[...]. Nucleic Acids Res 2018
6

Olaparib for Metastatic Castration-Resistant Prostate Cancer.
Johann de Bono, Joaquin Mateo, Karim Fizazi, Fred Saad, Neal Shore, Shahneen Sandhu, Kim N Chi, Oliver Sartor, Neeraj Agarwal, David Olmos,[...]. N Engl J Med 2020
517
6

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.
Theo A Knijnenburg, Linghua Wang, Michael T Zimmermann, Nyasha Chambwe, Galen F Gao, Andrew D Cherniack, Huihui Fan, Hui Shen, Gregory P Way, Casey S Greene,[...]. Cell Rep 2018
366
6

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
6

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
6

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
6

The evolutionary history of 2,658 cancers.
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu,[...]. Nature 2020
273
5

A study of over 35,000 women with breast cancer tested with a 25-gene panel of hereditary cancer genes.
Saundra S Buys, John F Sandbach, Amanda Gammon, Gayle Patel, John Kidd, Krystal L Brown, Lavania Sharma, Jennifer Saam, Johnathan Lancaster, Mary B Daly. Cancer 2017
201
5

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
5

Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA.
Kasmintan A Schrader, Donavan T Cheng, Vijai Joseph, Meera Prasad, Michael Walsh, Ahmet Zehir, Ai Ni, Tinu Thomas, Ryma Benayed, Asad Ashraf,[...]. JAMA Oncol 2016
184
5

Prevalence of Germline Variants in Prostate Cancer and Implications for Current Genetic Testing Guidelines.
Piper Nicolosi, Elisa Ledet, Shan Yang, Scott Michalski, Brandy Freschi, Erin O'Leary, Edward D Esplin, Robert L Nussbaum, Oliver Sartor. JAMA Oncol 2019
114
5

Accurate classification of BRCA1 variants with saturation genome editing.
Gregory M Findlay, Riza M Daza, Beth Martin, Melissa D Zhang, Anh P Leith, Molly Gasperini, Joseph D Janizek, Xingfan Huang, Lea M Starita, Jay Shendure. Nature 2018
273
5

Meta-analysis of BRCA1 and BRCA2 penetrance.
Sining Chen, Giovanni Parmigiani. J Clin Oncol 2007
5

Environmental and heritable factors in the causation of cancer--analyses of cohorts of twins from Sweden, Denmark, and Finland.
P Lichtenstein, N V Holm, P K Verkasalo, A Iliadou, J Kaprio, M Koskenvuo, E Pukkala, A Skytthe, K Hemminki. N Engl J Med 2000
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.