A citation-based method for searching scientific literature

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, Eric D Chow, Efstathios Kanterakis, Hong Gao, Amirali Kia, Serafim Batzoglou, Stephan J Sanders, Kyle Kai-How Farh. Cell 2019
Times Cited: 408







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



Times Cited
  Times     Co-cited
Similarity


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
39

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
35


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
17

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
16

Improved splice site detection in Genie.
M G Reese, F H Eeckman, D Kulp, D Haussler. J Comput Biol 1997
15

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
12

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
302
11


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
11

In silico prediction of splice-altering single nucleotide variants in the human genome.
Xueqiu Jian, Eric Boerwinkle, Xiaoming Liu. Nucleic Acids Res 2014
230
11

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
11

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
11


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
226
10

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
678
10

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
10

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
10

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
10

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
97
9

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
8

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
35
22


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
51
13

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi,[...]. Am J Hum Genet 2016
631
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

CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.
Philipp Rentzsch, Max Schubach, Jay Shendure, Martin Kircher. Genome Med 2021
49
14

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
7

Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion.
Ahmad N Abou Tayoun, Tina Pesaran, Marina T DiStefano, Andrea Oza, Heidi L Rehm, Leslie G Biesecker, Steven M Harrison. Hum Mutat 2018
191
7

ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease.
Riccardo Sangermano, Mubeen Khan, Stéphanie S Cornelis, Valerie Richelle, Silvia Albert, Alejandro Garanto, Duaa Elmelik, Raheel Qamar, Dorien Lugtenberg, L Ingeborgh van den Born,[...]. Genome Res 2018
76
7

Deep-intronic ABCA4 variants explain missing heritability in Stargardt disease and allow correction of splice defects by antisense oligonucleotides.
Riccardo Sangermano, Alejandro Garanto, Mubeen Khan, Esmee H Runhart, Miriam Bauwens, Nathalie M Bax, L Ingeborgh van den Born, Muhammad Imran Khan, Stéphanie S Cornelis, Joke B G M Verheij,[...]. Genet Med 2019
81
7

OMIM.org: leveraging knowledge across phenotype-gene relationships.
Joanna S Amberger, Carol A Bocchini, Alan F Scott, Ada Hamosh. Nucleic Acids Res 2019
205
6

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
86
6


DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
Helen V Firth, Shola M Richards, A Paul Bevan, Stephen Clayton, Manuel Corpas, Diana Rajan, Steven Van Vooren, Yves Moreau, Roger M Pettett, Nigel P Carter. Am J Hum Genet 2009
6

ClinVar: public archive of interpretations of clinically relevant variants.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover,[...]. Nucleic Acids Res 2016
6

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
6

GeneSplicer: a new computational method for splice site prediction.
M Pertea, X Lin, S L Salzberg. Nucleic Acids Res 2001
341
6


Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort.
Raphaël Leman, Pascaline Gaildrat, Gérald Le Gac, Chandran Ka, Yann Fichou, Marie-Pierre Audrezet, Virginie Caux-Moncoutier, Sandrine M Caputo, Nadia Boutry-Kryza, Mélanie Léone,[...]. Nucleic Acids Res 2018
40
15

ESEfinder: A web resource to identify exonic splicing enhancers.
Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q Zhang, Adrian R Krainer. Nucleic Acids Res 2003
6

Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants.
Claude Houdayer, Virginie Caux-Moncoutier, Sophie Krieger, Michel Barrois, Françoise Bonnet, Violaine Bourdon, Myriam Bronner, Monique Buisson, Florence Coulet, Pascaline Gaildrat,[...]. Hum Mutat 2012
160
6

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
6

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework.
Sarah E Brnich, Ahmad N Abou Tayoun, Fergus J Couch, Garry R Cutting, Marc S Greenblatt, Christopher D Heinen, Dona M Kanavy, Xi Luo, Shannon M McNulty, Lea M Starita,[...]. Genome Med 2019
113
6

Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease.
Jinkuk Kim, Chunguang Hu, Christelle Moufawad El Achkar, Lauren E Black, Julie Douville, Austin Larson, Mary K Pendergast, Sara F Goldkind, Eunjung A Lee, Ashley Kuniholm,[...]. N Engl J Med 2019
211
6

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
22
22

Learning the sequence determinants of alternative splicing from millions of random sequences.
Alexander B Rosenberg, Rupali P Patwardhan, Jay Shendure, Georg Seelig. Cell 2015
114
5

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.
Keren J Carss, Gavin Arno, Marie Erwood, Jonathan Stephens, Alba Sanchis-Juan, Sarah Hull, Karyn Megy, Detelina Grozeva, Eleanor Dewhurst, Samantha Malka,[...]. Am J Hum Genet 2017
212
5


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