A citation-based method for searching scientific literature

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, Elicia Estrella, Hemakumar M Reddy, Fengmei Zhao, Ben Weisburd, Konrad J Karczewski, Anne H O'Donnell-Luria, Daniel Birnbaum, Anna Sarkozy, Ying Hu, Hernan Gonorazky, Kristl Claeys, Himanshu Joshi, Adam Bournazos, Emily C Oates, Roula Ghaoui, Mark R Davis, Nigel G Laing, Ana Topf, Peter B Kang, Alan H Beggs, Kathryn N North, Volker Straub, James J Dowling, Francesco Muntoni, Nigel F Clarke, Sandra T Cooper, Carsten G Bönnemann, Daniel G MacArthur. Sci Transl Med 2017
Times Cited: 275







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



Times Cited
  Times     Co-cited
Similarity


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
203
41

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
40

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
74
36

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
321
23

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
20

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.
Laure Frésard, Craig Smail, Nicole M Ferraro, Nicole A Teran, Xin Li, Kevin S Smith, Devon Bonner, Kristin D Kernohan, Shruti Marwaha, Zachary Zappala,[...]. Nat Med 2019
77
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
18

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
15


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
34
38

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
25
48

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
12

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
192
10

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
572
10


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
10


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
814
9

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
88
10

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
174
9

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
9

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
9

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
9

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
13
69

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
9


The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.
Peter D Stenson, Matthew Mort, Edward V Ball, Katy Evans, Matthew Hayden, Sally Heywood, Michelle Hussain, Andrew D Phillips, David N Cooper. Hum Genet 2017
623
8

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
919
8

Use of Whole-Exome Sequencing for Diagnosis of Limb-Girdle Muscular Dystrophy: Outcomes and Lessons Learned.
Roula Ghaoui, Sandra T Cooper, Monkol Lek, Kristi Jones, Alastair Corbett, Stephen W Reddel, Merrilee Needham, Christina Liang, Leigh B Waddell, Garth Nicholson,[...]. JAMA Neurol 2015
107
8


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
131
8

RNA mis-splicing in disease.
Marina M Scotti, Maurice S Swanson. Nat Rev Genet 2016
467
8

ClinGen--the Clinical Genome Resource.
Heidi L Rehm, Jonathan S Berg, Lisa D Brooks, Carlos D Bustamante, James P Evans, Melissa J Landrum, David H Ledbetter, Donna R Maglott, Christa Lese Martin, Robert L Nussbaum,[...]. N Engl J Med 2015
508
8

RNAseq analysis for the diagnosis of muscular dystrophy.
Hernan Gonorazky, Minggao Liang, Beryl Cummings, Monkol Lek, Johann Micallef, Cynthia Hawkins, Raveen Basran, Ronald Cohn, Michael D Wilson, Daniel MacArthur,[...]. Ann Clin Transl Neurol 2015
48
16

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing.
Jun Cheng, Thi Yen Duong Nguyen, Kamil J Cygan, Muhammed Hasan Çelik, William G Fairbrother, Žiga Avsec, Julien Gagneur. Genome Biol 2019
39
20

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
16
50

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
166
8

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
13
61

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
625
7

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
104
7

Integrative omics for health and disease.
Konrad J Karczewski, Michael P Snyder. Nat Rev Genet 2018
272
7

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
330
7

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
7

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants.
Aziz Belkadi, Alexandre Bolze, Yuval Itan, Aurélie Cobat, Quentin B Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, Laurent Abel. Proc Natl Acad Sci U S A 2015
259
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7

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
59
11

Human Splicing Finder: an online bioinformatics tool to predict splicing signals.
François-Olivier Desmet, Dalil Hamroun, Marine Lalande, Gwenaëlle Collod-Béroud, Mireille Claustres, Christophe Béroud. Nucleic Acids Res 2009
7

Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy.
Kristin D Kernohan, Laure Frésard, Zachary Zappala, Taila Hartley, Kevin S Smith, Justin Wagner, Hongbin Xu, Arran McBride, Pierre R Bourque, Care Rare Canada Consortium,[...]. Hum Mutat 2017
18
38

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
10
70

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
279
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.