A citation-based method for searching scientific literature

Remo Calabrese, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. Hum Mutat 2009
Times Cited: 387







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



Times Cited
  Times     Co-cited
Similarity


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
58


Predicting the functional effect of amino acid substitutions and indels.
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan. PLoS One 2012
43

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
976
36


Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Hashem A Shihab, Julian Gough, David N Cooper, Peter D Stenson, Gary L A Barker, Keith J Edwards, Ian N M Day, Tom R Gaunt. Hum Mutat 2013
716
30

SIFT web server: predicting effects of amino acid substitutions on proteins.
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
30


SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
26

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
26

Automated inference of molecular mechanisms of disease from amino acid substitutions.
Biao Li, Vidhya G Krishnan, Matthew E Mort, Fuxiao Xin, Kishore K Kamati, David N Cooper, Sean D Mooney, Predrag Radivojac. Bioinformatics 2009
540
25

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
24

Better prediction of functional effects for sequence variants.
Maximilian Hecht, Yana Bromberg, Burkhard Rost. BMC Genomics 2015
264
23

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.
Vikas Pejaver, Jorge Urresti, Jose Lugo-Martinez, Kymberleigh A Pagel, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N Cooper, Jonathan Sebat, Lilia M Iakoucheva,[...]. Nat Commun 2020
112
23


Human non-synonymous SNPs: server and survey.
Vasily Ramensky, Peer Bork, Shamil Sunyaev. Nucleic Acids Res 2002
19

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
19

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
18

Predicting deleterious amino acid substitutions.
P C Ng, S Henikoff. Genome Res 2001
18

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
17


SNAP: predict effect of non-synonymous polymorphisms on function.
Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
553
17

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
16


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
16

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
15

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.
Hanka Venselaar, Tim A H Te Beek, Remko K P Kuipers, Maarten L Hekkelman, Gert Vriend. BMC Bioinformatics 2010
533
15

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.
Emidio Capriotti, Remo Calabrese, Piero Fariselli, Pier Luigi Martelli, Russ B Altman, Rita Casadio. BMC Genomics 2013
158
15

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update.
Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí. Nucleic Acids Res 2017
90
16

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky. PLoS Comput Biol 2014
396
14

SIFT missense predictions for genomes.
Robert Vaser, Swarnaseetha Adusumalli, Sim Ngak Leng, Mile Sikic, Pauline C Ng. Nat Protoc 2016
612
14

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
784
13

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies.
Chengliang Dong, Peng Wei, Xueqiu Jian, Richard Gibbs, Eric Boerwinkle, Kai Wang, Xiaoming Liu. Hum Mol Genet 2015
609
12

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2010
12

PMUT: a web-based tool for the annotation of pathological mutations on proteins.
Carles Ferrer-Costa, Josep Lluis Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, Modesto Orozco. Bioinformatics 2005
384
12

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
Emidio Capriotti, Piero Fariselli. Nucleic Acids Res 2017
62
19

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
12

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
407
12

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
12

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

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


TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
11

Collective judgment predicts disease-associated single nucleotide variants.
Emidio Capriotti, Russ B Altman, Yana Bromberg. BMC Genomics 2013
146
10


PON-P2: prediction method for fast and reliable identification of harmful variants.
Abhishek Niroula, Siddhaling Urolagin, Mauno Vihinen. PLoS One 2015
129
10

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Daniel Quang, Yifei Chen, Xiaohui Xie. Bioinformatics 2015
488
10

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity.
Dominik G Grimm, Chloé-Agathe Azencott, Fabian Aicheler, Udo Gieraths, Daniel G MacArthur, Kaitlin E Samocha, David N Cooper, Peter D Stenson, Mark J Daly, Jordan W Smoller,[...]. Hum Mutat 2015
177
10

PANTHER: a library of protein families and subfamilies indexed by function.
Paul D Thomas, Michael J Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, Robin Daverman, Karen Diemer, Anushya Muruganujan, Apurva Narechania. Genome Res 2003
10

SNAP predicts effect of mutations on protein function.
Yana Bromberg, Guy Yachdav, Burkhard Rost. Bioinformatics 2008
165
10


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.