A citation-based method for searching scientific literature

Laure Frésard, Craig Smail, Nicole M Ferraro, Nicole A Teran, Xin Li, Kevin S Smith, Devon Bonner, Kristin D Kernohan, Shruti Marwaha, Zachary Zappala, Brunilda Balliu, Joe R Davis, Boxiang Liu, Cameron J Prybol, Jennefer N Kohler, Diane B Zastrow, Chloe M Reuter, Dianna G Fisk, Megan E Grove, Jean M Davidson, Taila Hartley, Ruchi Joshi, Benjamin J Strober, Sowmithri Utiramerur, Lars Lind, Erik Ingelsson, Alexis Battle, Gill Bejerano, Jonathan A Bernstein, Euan A Ashley, Kym M Boycott, Jason D Merker, Matthew T Wheeler, Stephen B Montgomery. Nat Med 2019
Times Cited: 108







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



Times Cited
  Times     Co-cited
Similarity


Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.
Beryl B Cummings, Jamie L Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A Reghan Foley, Veronique Bolduc, Leigh B Waddell, Sarah A Sandaradura, Gina L O'Grady,[...]. Sci Transl Med 2017
339
56

Genetic diagnosis of Mendelian disorders via RNA sequencing.
Laura S Kremer, Daniel M Bader, Christian Mertes, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B Haack, Elisabeth Graf, Thomas Schwarzmayr, Caterina Terrile,[...]. Nat Commun 2017
253
53

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
36

Diagnostic utility of transcriptome sequencing for rare Mendelian diseases.
Hane Lee, Alden Y Huang, Lee-Kai Wang, Amanda J Yoon, Genecee Renteria, Ascia Eskin, Rebecca H Signer, Naghmeh Dorrani, Shirley Nieves-Rodriguez, Jijun Wan,[...]. Genet Med 2020
63
53

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.
Hernan D Gonorazky, Sergey Naumenko, Arun K Ramani, Viswateja Nelakuditi, Pouria Mashouri, Peiqui Wang, Dennis Kao, Krish Ohri, Senthuri Viththiyapaskaran, Mark A Tarnopolsky,[...]. Am J Hum Genet 2019
99
33

Predicting Splicing from Primary Sequence with Deep Learning.
Kishore Jaganathan, Sofia Kyriazopoulou Panagiotopoulou, Jeremy F McRae, Siavash Fazel Darbandi, David Knowles, Yang I Li, Jack A Kosmicki, Juan Arbelaez, Wenwu Cui, Grace B Schwartz,[...]. Cell 2019
519
24

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
23

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
20

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases.
Michelle M Clark, Zornitza Stark, Lauge Farnaes, Tiong Y Tan, Susan M White, David Dimmock, Stephen F Kingsmore. NPJ Genom Med 2018
234
16

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
15

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.
Hernan D Gonorazky, Sergey Naumenko, Arun K Ramani, Viswateja Nelakuditi, Pouria Mashouri, Peiqui Wang, Dennis Kao, Krish Ohri, Senthuri Viththiyapaskaran, Mark A Tarnopolsky,[...]. Am J Hum Genet 2019
26
57

OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data.
Felix Brechtmann, Christian Mertes, Agnė Matusevičiūtė, Vicente A Yépez, Žiga Avsec, Maximilian Herzog, Daniel M Bader, Holger Prokisch, Julien Gagneur. Am J Hum Genet 2018
39
38

Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq.
Joseph K Aicher, Paul Jewell, Jorge Vaquero-Garcia, Yoseph Barash, Elizabeth J Bhoj. Genet Med 2020
21
71

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.
Yaping Yang, Donna M Muzny, Jeffrey G Reid, Matthew N Bainbridge, Alecia Willis, Patricia A Ward, Alicia Braxton, Joke Beuten, Fan Xia, Zhiyv Niu,[...]. N Engl J Med 2013
14


Transcriptomic signatures across human tissues identify functional rare genetic variation.
Nicole M Ferraro, Benjamin J Strober, Jonah Einson, Nathan S Abell, Francois Aguet, Alvaro N Barbeira, Margot Brandt, Maja Bucan, Stephane E Castel, Joe R Davis,[...]. Science 2020
46
30

Detection of aberrant splicing events in RNA-seq data using FRASER.
Christian Mertes, Ines F Scheller, Vicente A Yépez, Muhammed H Çelik, Yingjiqiong Liang, Laura S Kremer, Mirjana Gusic, Holger Prokisch, Julien Gagneur. Nat Commun 2021
25
56

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing.
David R Murdock, Hongzheng Dai, Lindsay C Burrage, Jill A Rosenfeld, Shamika Ketkar, Michaela F Müller, Vicente A Yépez, Julien Gagneur, Pengfei Liu, Shan Chen,[...]. J Clin Invest 2021
33
42

Molecular findings among patients referred for clinical whole-exome sequencing.
Yaping Yang, Donna M Muzny, Fan Xia, Zhiyv Niu, Richard Person, Yan Ding, Patricia Ward, Alicia Braxton, Min Wang, Christian Buhay,[...]. JAMA 2014
876
13

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test.
Anath C Lionel, Gregory Costain, Nasim Monfared, Susan Walker, Miriam S Reuter, S Mohsen Hosseini, Bhooma Thiruvahindrapuram, Daniele Merico, Rebekah Jobling, Thomas Nalpathamkalam,[...]. Genet Med 2018
240
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

Annotation-free quantification of RNA splicing using LeafCutter.
Yang I Li, David A Knowles, Jack Humphrey, Alvaro N Barbeira, Scott P Dickinson, Hae Kyung Im, Jonathan K Pritchard. Nat Genet 2018
224
12

Whole exome sequencing of suspected mitochondrial patients in clinical practice.
Saskia B Wortmann, David A Koolen, Jan A Smeitink, Lambert van den Heuvel, Richard J Rodenburg. J Inherit Metab Dis 2015
133
11

Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease.
Kimberly Splinter, David R Adams, Carlos A Bacino, Hugo J Bellen, Jonathan A Bernstein, Alys M Cheatle-Jarvela, Christine M Eng, Cecilia Esteves, William A Gahl, Rizwan Hamid,[...]. N Engl J Med 2018
149
11

The impact of rare variation on gene expression across tissues.
Xin Li, Yungil Kim, Emily K Tsang, Joe R Davis, Farhan N Damani, Colby Chiang, Gaelen T Hess, Zachary Zappala, Benjamin J Strober, Alexandra J Scott,[...]. Nature 2017
132
11

RNA mis-splicing in disease.
Marina M Scotti, Maurice S Swanson. Nat Rev Genet 2016
564
11

Genetic regulatory variation in populations informs transcriptome analysis in rare disease.
Pejman Mohammadi, Stephane E Castel, Beryl B Cummings, Jonah Einson, Christina Sousa, Paul Hoffman, Sandra Donkervoort, Zhuoxun Jiang, Payam Mohassel, A Reghan Foley,[...]. Science 2019
43
25

Clinical exome sequencing for genetic identification of rare Mendelian disorders.
Hane Lee, Joshua L Deignan, Naghmeh Dorrani, Samuel P Strom, Sibel Kantarci, Fabiola Quintero-Rivera, Kingshuk Das, Traci Toy, Bret Harry, Michael Yourshaw,[...]. JAMA 2014
617
10

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
10

Reanalysis of Clinical Exome Sequencing Data.
Pengfei Liu, Linyan Meng, Elizabeth A Normand, Fan Xia, Xiaofei Song, Andrew Ghazi, Jill Rosenfeld, Pilar L Magoulas, Alicia Braxton, Patricia Ward,[...]. N Engl J Med 2019
104
10

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases.
Garrett Jenkinson, Yang I Li, Shubham Basu, Margot A Cousin, Gavin R Oliver, Eric W Klee. Bioinformatics 2020
13
76

GeneMatcher: a matching tool for connecting investigators with an interest in the same gene.
Nara Sobreira, François Schiettecatte, David Valle, Ada Hamosh. Hum Mutat 2015
749
9

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders.
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord,[...]. Genet Med 2018
160
9

Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance.
Htoo A Wai, Jenny Lord, Matthew Lyon, Adam Gunning, Hugh Kelly, Penelope Cibin, Eleanor G Seaby, Kerry Spiers-Fitzgerald, Jed Lye, Sian Ellard,[...]. Genet Med 2020
52
17

Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.
Jennifer E Posey, Tamar Harel, Pengfei Liu, Jill A Rosenfeld, Regis A James, Zeynep H Coban Akdemir, Magdalena Walkiewicz, Weimin Bi, Rui Xiao, Yan Ding,[...]. N Engl J Med 2017
391
8

Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing.
Ahmed Alfares, Taghrid Aloraini, Lamia Al Subaie, Abdulelah Alissa, Ahmed Al Qudsi, Ahmed Alahmad, Fuad Al Mutairi, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid,[...]. Genet Med 2018
73
10

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

Long-Read Sequencing Emerging in Medical Genetics.
Tuomo Mantere, Simone Kersten, Alexander Hoischen. Front Genet 2019
138
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

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
8

New perspective in diagnostics of mitochondrial disorders: two years' experience with whole-exome sequencing at a national paediatric centre.
Ewa Pronicka, Dorota Piekutowska-Abramczuk, Elżbieta Ciara, Joanna Trubicka, Dariusz Rokicki, Agnieszka Karkucińska-Więckowska, Magdalena Pajdowska, Elżbieta Jurkiewicz, Paulina Halat, Joanna Kosińska,[...]. J Transl Med 2016
133
8

Detection of aberrant gene expression events in RNA sequencing data.
Vicente A Yépez, Christian Mertes, Michaela F Müller, Daniela Klaproth-Andrade, Leonhard Wachutka, Laure Frésard, Mirjana Gusic, Ines F Scheller, Patricia F Goldberg, Holger Prokisch,[...]. Nat Protoc 2021
21
38

In silico prediction of splice-altering single nucleotide variants in the human genome.
Xueqiu Jian, Eric Boerwinkle, Xiaoming Liu. Nucleic Acids Res 2014
254
7

Pathogenic variants that alter protein code often disrupt splicing.
Rachel Soemedi, Kamil J Cygan, Christy L Rhine, Jing Wang, Charlston Bulacan, John Yang, Pinar Bayrak-Toydemir, Jamie McDonald, William G Fairbrother. Nat Genet 2017
102
7

The Expanding Landscape of Alternative Splicing Variation in Human Populations.
Eddie Park, Zhicheng Pan, Zijun Zhang, Lan Lin, Yi Xing. Am J Hum Genet 2018
161
7

Deep intronic mutations and human disease.
Rita Vaz-Drago, Noélia Custódio, Maria Carmo-Fonseca. Hum Genet 2017
189
7

Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy.
D C Wallace, G Singh, M T Lott, J A Hodge, T G Schurr, A M Lezza, L J Elsas, E K Nikoskelainen. Science 1988
7

Clinical application of whole-exome sequencing across clinical indications.
Kyle Retterer, Jane Juusola, Megan T Cho, Patrik Vitazka, Francisca Millan, Federica Gibellini, Annette Vertino-Bell, Nizar Smaoui, Julie Neidich, Kristin G Monaghan,[...]. Genet Med 2016
542
7

Translating RNA sequencing into clinical diagnostics: opportunities and challenges.
Sara A Byron, Kendall R Van Keuren-Jensen, David M Engelthaler, John D Carpten, David W Craig. Nat Rev Genet 2016
325
7

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers.
Aaron M Wenger, Harendra Guturu, Jonathan A Bernstein, Gill Bejerano. Genet Med 2017
167
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.