A citation-based method for searching scientific literature

Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
Times Cited: 543







List of co-cited articles
666 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
39


I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
926
26

SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
23


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
363
19

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
19

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
18

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
16

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
16

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
14

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
142
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
692
14

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
13

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
13


Human non-synonymous SNPs: server and survey.
Vasily Ramensky, Peer Bork, Shamil Sunyaev. Nucleic Acids Res 2002
13


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
690
13

Functional annotations improve the predictive score of human disease-related mutations in proteins.
Remo Calabrese, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. Hum Mutat 2009
378
13

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
592
13

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
505
12

Collective judgment predicts disease-associated single nucleotide variants.
Emidio Capriotti, Russ B Altman, Yana Bromberg. BMC Genomics 2013
136
12

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
12

Better prediction of functional effects for sequence variants.
Maximilian Hecht, Yana Bromberg, Burkhard Rost. BMC Genomics 2015
244
11


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
11

SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features.
Christopher M Yates, Ioannis Filippis, Lawrence A Kelley, Michael J E Sternberg. J Mol Biol 2014
121
11

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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
10

mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
448
10

Predicting deleterious amino acid substitutions.
P C Ng, S Henikoff. Genome Res 2001
10


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
356
10

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
694
10

AUGUSTUS: a web server for gene finding in eukaryotes.
Mario Stanke, Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern. Nucleic Acids Res 2004
687
10

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
10


Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
10

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
9

COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
9


Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
9

InterProScan 5: genome-scale protein function classification.
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka,[...]. Bioinformatics 2014
9

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
9


CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
372
8

SDM--a server for predicting effects of mutations on protein stability and malfunction.
Catherine L Worth, Robert Preissner, Tom L Blundell. Nucleic Acids Res 2011
296
8

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


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.