A citation-based method for searching scientific literature

Hongjian Qi, Haicang Zhang, Yige Zhao, Chen Chen, John J Long, Wendy K Chung, Yongtao Guan, Yufeng Shen. Nat Commun 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
100

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
488
100

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
472
100

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.
Karthik A Jagadeesh, Aaron M Wenger, Mark J Berger, Harendra Guturu, Peter D Stenson, David N Cooper, Jonathan A Bernstein, Gill Bejerano. Nat Genet 2016
330
100

Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar.
Anaïs Mottaz, Fabrice P A David, Anne-Lise Veuthey, Yum L Yip. Bioinformatics 2010
83
100

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
100


DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Daniel Quang, Yifei Chen, Xiaohui Xie. Bioinformatics 2015
369
100

Predicting the functional consequences of cancer-associated amino acid substitutions.
Hashem A Shihab, Julian Gough, David N Cooper, Ian N M Day, Tom R Gaunt. Bioinformatics 2013
123
100


SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
100


Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.
Yves Dehouck, Aline Grosfils, Benjamin Folch, Dimitri Gilis, Philippe Bogaerts, Marianne Rooman. Bioinformatics 2009
221
50

Supervised non-negative matrix factorization methods for MALDI imaging applications.
Johannes Leuschner, Maximilian Schmidt, Pascal Fernsel, Delf Lachmund, Tobias Boskamp, Peter Maass. Bioinformatics 2019
6
50

Computational identification of deleterious synonymous variants in human genomes using a feature-based approach.
Fang Shi, Yao Yao, Yannan Bin, Chun-Hou Zheng, Junfeng Xia. BMC Med Genomics 2019
17
50

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
50

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
582
50

Semantic prioritization of novel causative genomic variants.
Imane Boudellioua, Rozaimi B Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf. PLoS Comput Biol 2017
19
50

Dual-network sparse graph regularized matrix factorization for predicting miRNA-disease associations.
Ming-Ming Gao, Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Chun-Hou Zheng. Mol Omics 2019
10
50

Metagenes and molecular pattern discovery using matrix factorization.
Jean-Philippe Brunet, Pablo Tamayo, Todd R Golub, Jill P Mesirov. Proc Natl Acad Sci U S A 2004
664
50

SNMFCA: supervised NMF-based image classification and annotation.
Liping Jing, Chao Zhang, Michael K Ng. IEEE Trans Image Process 2012
11
50



Fuse: multiple network alignment via data fusion.
Vladimir Gligorijević, Noël Malod-Dognin, Nataša Pržulj. Bioinformatics 2016
19
50

A systematic survey of loss-of-function variants in human protein-coding genes.
Daniel G MacArthur, Suganthi Balasubramanian, Adam Frankish, Ni Huang, James Morris, Klaudia Walter, Luke Jostins, Lukas Habegger, Joseph K Pickrell, Stephen B Montgomery,[...]. Science 2012
751
50

Improved exome prioritization of disease genes through cross-species phenotype comparison.
Peter N Robinson, Sebastian Köhler, Anika Oellrich, Kai Wang, Christopher J Mungall, Suzanna E Lewis, Nicole Washington, Sebastian Bauer, Dominik Seelow, Peter Krawitz,[...]. Genome Res 2014
179
50

Identifying novel constrained elements by exploiting biased substitution patterns.
Manuel Garber, Mitchell Guttman, Michele Clamp, Michael C Zody, Nir Friedman, Xiaohui Xie. Bioinformatics 2009
191
50

Discovering disease-disease associations by fusing systems-level molecular data.
Marinka Žitnik, Vuk Janjić, Chris Larminie, Blaž Zupan, Nataša Pržulj. Sci Rep 2013
53
50

Detection of nonneutral substitution rates on mammalian phylogenies.
Katherine S Pollard, Melissa J Hubisz, Kate R Rosenbloom, Adam Siepel. Genome Res 2010
50

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
131
50



Methods for biological data integration: perspectives and challenges.
Vladimir Gligorijević, Nataša Pržulj. J R Soc Interface 2015
70
50


A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.
Miao-Xin Li, Hong-Sheng Gui, Johnny S H Kwan, Su-Ying Bao, Pak C Sham. Nucleic Acids Res 2012
162
50

MutationTaster evaluates disease-causing potential of sequence alterations.
Jana Marie Schwarz, Christian Rödelsperger, Markus Schuelke, Dominik Seelow. Nat Methods 2010
50

Prediction and interpretation of deleterious coding variants in terms of protein structural stability.
François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman. Sci Rep 2018
26
50

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness.
Michiru Nishita, Seung-Yeol Park, Tadashi Nishio, Koki Kamizaki, ZhiChao Wang, Kota Tamada, Toru Takumi, Ryuju Hashimoto, Hiroki Otani, Gregory J Pazour,[...]. Sci Rep 2017
50


Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Adam Siepel, Gill Bejerano, Jakob S Pedersen, Angie S Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, Ladeana W Hillier, Stephen Richards,[...]. Genome Res 2005
50

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.
Ada Hamosh, Alan F Scott, Joanna S Amberger, Carol A Bocchini, Victor A McKusick. Nucleic Acids Res 2005
50

An integrative approach to predicting the functional effects of non-coding and coding sequence variation.
Hashem A Shihab, Mark F Rogers, Julian Gough, Matthew Mort, David N Cooper, Ian N M Day, Tom R Gaunt, Colin Campbell. Bioinformatics 2015
262
50

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
50

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
773
50

Identifying a high fraction of the human genome to be under selective constraint using GERP++.
Eugene V Davydov, David L Goode, Marina Sirota, Gregory M Cooper, Arend Sidow, Serafim Batzoglou. PLoS Comput Biol 2010
848
50

Data Fusion by Matrix Factorization.
Marinka Žitnik, Blaž Zupan. IEEE Trans Pattern Anal Mach Intell 2015
59
50

eXtasy: variant prioritization by genomic data fusion.
Alejandro Sifrim, Dusan Popovic, Leon-Charles Tranchevent, Amin Ardeshirdavani, Ryo Sakai, Peter Konings, Joris R Vermeesch, Jan Aerts, Bart De Moor, Yves Moreau. Nat Methods 2013
98
50

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
50

VarCards: an integrated genetic and clinical database for coding variants in the human genome.
Jinchen Li, Leisheng Shi, Kun Zhang, Yi Zhang, Shanshan Hu, Tingting Zhao, Huajing Teng, Xianfeng Li, Yi Jiang, Liying Ji,[...]. Nucleic Acids Res 2018
67
50

The role of the interactome in the maintenance of deleterious variability in human populations.
Luz Garcia-Alonso, Jorge Jiménez-Almazán, Jose Carbonell-Caballero, Alicia Vela-Boza, Javier Santoyo-López, Guillermo Antiñolo, Joaquin Dopazo. Mol Syst Biol 2014
22
50


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.