A citation-based method for searching scientific literature

Zachary S Bohannan, Antonina Mitrofanova. Comput Struct Biotechnol J 2019
Times Cited: 14







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



Times Cited
  Times     Co-cited
Similarity


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
21

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
21

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
21

Variant Review with the Integrative Genomics Viewer.
James T Robinson, Helga Thorvaldsdóttir, Aaron M Wenger, Ahmet Zehir, Jill P Mesirov. Cancer Res 2017
350
21

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
21

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
21

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples.
Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Lana M Sheta, Shahil P Pema, Alina D Schmidt, Megan Richters, Kelsy C Cotto,[...]. Genet Med 2019
30
14


Talazoparib in Patients with Advanced Breast Cancer and a Germline BRCA Mutation.
Jennifer K Litton, Hope S Rugo, Johannes Ettl, Sara A Hurvitz, Anthony Gonçalves, Kyung-Hun Lee, Louis Fehrenbacher, Rinat Yerushalmi, Lida A Mina, Miguel Martin,[...]. N Engl J Med 2018
734
14

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding,[...]. J Mol Diagn 2018
173
14

Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova. J Mol Diagn 2017
283
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
669
14

Pathogenic Germline Variants in 10,389 Adult Cancers.
Kuan-Lin Huang, R Jay Mashl, Yige Wu, Deborah I Ritter, Jiayin Wang, Clara Oh, Marta Paczkowska, Sheila Reynolds, Matthew A Wyczalkowski, Ninad Oak,[...]. Cell 2018
311
14

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours.
Louise Harewood, Kamal Kishore, Matthew D Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V Peter Collins, Peter Fraser. Genome Biol 2017
76
14


From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Geraldine A Van der Auwera, Mauricio O Carneiro, Christopher Hartl, Ryan Poplin, Guillermo Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault,[...]. Curr Protoc Bioinformatics 2013
14

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
14

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.
Farhana R Pinu, David J Beale, Amy M Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J Schirra, David Wishart. Metabolites 2019
182
14

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
14

RNA-Seq differential expression analysis: An extended review and a software tool.
Juliana Costa-Silva, Douglas Domingues, Fabricio Martins Lopes. PLoS One 2017
190
14

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz. Contemp Oncol (Pozn) 2015
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


Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
14

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
14

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
14

Association of Inherited Pathogenic Variants in Checkpoint Kinase 2 (CHEK2) With Susceptibility to Testicular Germ Cell Tumors.
Saud H AlDubayan, Louise C Pyle, Marija Gamulin, Tomislav Kulis, Nathanael D Moore, Amaro Taylor-Weiner, Anis A Hamid, Brendan Reardon, Bradley Wubbenhorst, Rama Godse,[...]. JAMA Oncol 2019
26
14

A universal SNP and small-indel variant caller using deep neural networks.
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar,[...]. Nat Biotechnol 2018
232
14


Evolution and functional impact of rare coding variation from deep sequencing of human exomes.
Jacob A Tennessen, Abigail W Bigham, Timothy D O'Connor, Wenqing Fu, Eimear E Kenny, Simon Gravel, Sean McGee, Ron Do, Xiaoming Liu, Goo Jun,[...]. Science 2012
14

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
14

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
14

Prevalence and detection of low-allele-fraction variants in clinical cancer samples.
Hyun-Tae Shin, Yoon-La Choi, Jae Won Yun, Nayoung K D Kim, Sook-Young Kim, Hyo Jeong Jeon, Jae-Yong Nam, Chung Lee, Daeun Ryu, Sang Cheol Kim,[...]. Nat Commun 2017
92
14

Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine.
Keyan Salari, Konrad J Karczewski, Louanne Hudgins, Kelly E Ormond. PLoS One 2013
64
7


Implementing genomic medicine in the clinic: the future is here.
Teri A Manolio, Rex L Chisholm, Brad Ozenberger, Dan M Roden, Marc S Williams, Richard Wilson, David Bick, Erwin P Bottinger, Murray H Brilliant, Charis Eng,[...]. Genet Med 2013
343
7

Multiple hypothesis testing in genomics.
Jelle J Goeman, Aldo Solari. Stat Med 2014
128
7


Medical student preparedness for an era of personalized medicine: findings from one US medical school.
Caroline Eden, Kipp W Johnson, Omri Gottesman, Erwin P Bottinger, Noura S Abul-Husn. Per Med 2016
19
7

Statistical Methods in Integrative Genomics.
Sylvia Richardson, George C Tseng, Wei Sun. Annu Rev Stat Appl 2016
40
7

Criteria for the use of omics-based predictors in clinical trials.
Lisa M McShane, Margaret M Cavenagh, Tracy G Lively, David A Eberhard, William L Bigbee, P Mickey Williams, Jill P Mesirov, Mei-Yin C Polley, Kelly Y Kim, James V Tricoli,[...]. Nature 2013
144
7

Patients' understanding of and responses to multiplex genetic susceptibility test results.
Kimberly A Kaphingst, Colleen M McBride, Christopher Wade, Sharon Hensley Alford, Robert Reid, Eric Larson, Andreas D Baxevanis, Lawrence C Brody. Genet Med 2012
89
7

Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, Cedric Notredame. Nat Biotechnol 2017
403
7

Communication and data-intensive science in the beginning of the 21st century.
Jack Faris, Evelyne Kolker, Alex Szalay, Leon Bradlow, Ewa Deelman, Wu Feng, Judy Qiu, Donna Russell, Elizabeth Stewart, Eugene Kolker. OMICS 2011
4
25


Common pitfalls in statistical analysis: The perils of multiple testing.
Priya Ranganathan, C S Pramesh, Marc Buyse. Perspect Clin Res 2016
49
7


Consumer Perceptions of Interactions With Primary Care Providers After Direct-to-Consumer Personal Genomic Testing.
Cathelijne H van der Wouden, Deanna Alexis Carere, Anke H Maitland-van der Zee, Mack T Ruffin, J Scott Roberts, Robert C Green. Ann Intern Med 2016
69
7


Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.
Ariane L Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel. BMC Bioinformatics 2017
24
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.