A citation-based method for searching scientific literature

Olivier Bodenreider. Nucleic Acids Res 2004
Times Cited: 1286







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



Times Cited
  Times     Co-cited
Similarity


MIMIC-III, a freely accessible critical care database.
Alistair E W Johnson, Tom J Pollard, Lu Shen, Li-Wei H Lehman, Mengling Feng, Mohammad Ghassemi, Benjamin Moody, Peter Szolovits, Leo Anthony Celi, Roger G Mark. Sci Data 2016
18

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.
Guergana K Savova, James J Masanz, Philip V Ogren, Jiaping Zheng, Sunghwan Sohn, Karin C Kipper-Schuler, Christopher G Chute. J Am Med Inform Assoc 2010
761
17

BioBERT: a pre-trained biomedical language representation model for biomedical text mining.
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang. Bioinformatics 2020
430
13


DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
9

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text.
Özlem Uzuner, Brett R South, Shuying Shen, Scott L DuVall. J Am Med Inform Assoc 2011
375
8

An overview of MetaMap: historical perspective and recent advances.
Alan R Aronson, François-Michel Lang. J Am Med Inform Assoc 2010
548
7

PREDICT: a method for inferring novel drug indications with application to personalized medicine.
Assaf Gottlieb, Gideon Y Stein, Eytan Ruppin, Roded Sharan. Mol Syst Biol 2011
367
7

Comparative Toxicogenomics Database (CTD): update 2021.
Allan Peter Davis, Cynthia J Grondin, Robin J Johnson, Daniela Sciaky, Jolene Wiegers, Thomas C Wiegers, Carolyn J Mattingly. Nucleic Acids Res 2021
145
7

node2vec: Scalable Feature Learning for Networks.
Aditya Grover, Jure Leskovec. KDD 2016
379
6

NCBI disease corpus: a resource for disease name recognition and concept normalization.
Rezarta Islamaj Doğan, Robert Leaman, Zhiyong Lu. J Biomed Inform 2014
133
6

SNOMED-CT: The advanced terminology and coding system for eHealth.
Kevin Donnelly. Stud Health Technol Inform 2006
158
6

Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.
Weiyi Sun, Anna Rumshisky, Ozlem Uzuner. J Am Med Inform Assoc 2013
142
6

The SIDER database of drugs and side effects.
Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork. Nucleic Acids Res 2016
380
5


Medical Subject Headings (MeSH).
C E Lipscomb. Bull Med Libr Assoc 2000
308
5

The human disease network.
Kwang-Il Goh, Michael E Cusick, David Valle, Barton Childs, Marc Vidal, Albert-László Barabási. Proc Natl Acad Sci U S A 2007
5

Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.
Kory Kreimeyer, Matthew Foster, Abhishek Pandey, Nina Arya, Gwendolyn Halford, Sandra F Jones, Richard Forshee, Mark Walderhaug, Taxiarchis Botsis. J Biomed Inform 2017
153
5


MetaMap Lite: an evaluation of a new Java implementation of MetaMap.
Dina Demner-Fushman, Willie J Rogers, Alan R Aronson. J Am Med Inform Assoc 2017
57
8

Enhancing clinical concept extraction with contextual embeddings.
Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts. J Am Med Inform Assoc 2019
59
8

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.
George Hripcsak, Jon D Duke, Nigam H Shah, Christian G Reich, Vojtech Huser, Martijn J Schuemie, Marc A Suchard, Rae Woong Park, Ian Chi Kei Wong, Peter R Rijnbeek,[...]. Stud Health Technol Inform 2015
437
5

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm.
Huimin Luo, Jianxin Wang, Min Li, Junwei Luo, Xiaoqing Peng, Fang-Xiang Wu, Yi Pan. Bioinformatics 2016
121
5

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
5

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
4

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.
Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. J Am Med Inform Assoc 2018
110
4

Extracting information from the text of electronic medical records to improve case detection: a systematic review.
Elizabeth Ford, John A Carroll, Helen E Smith, Donia Scott, Jackie A Cassell. J Am Med Inform Assoc 2016
138
4

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry,[...]. Nucleic Acids Res 2019
293
4

Clinical Natural Language Processing in languages other than English: opportunities and challenges.
Aurélie Névéol, Hercules Dalianis, Sumithra Velupillai, Guergana Savova, Pierre Zweigenbaum. J Biomed Semantics 2018
38
10

The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions.
María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, Thierry Declerck. J Biomed Inform 2013
108
4

Cadec: A corpus of adverse drug event annotations.
Sarvnaz Karimi, Alejandro Metke-Jimenez, Madonna Kemp, Chen Wang. J Biomed Inform 2015
36
11


A comparison of word embeddings for the biomedical natural language processing.
Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul Kingsbury, Hongfang Liu. J Biomed Inform 2018
87
4


Drug repositioning through integration of prior knowledge and projections of drugs and diseases.
Ping Xuan, Yangkun Cao, Tiangang Zhang, Xiao Wang, Shuxiang Pan, Tonghui Shen. Bioinformatics 2019
33
12

Drug repositioning by integrating target information through a heterogeneous network model.
Wenhui Wang, Sen Yang, Xiang Zhang, Jing Li. Bioinformatics 2014
129
4

Identification of Drug-Disease Associations Using Information of Molecular Structures and Clinical Symptoms via Deep Convolutional Neural Network.
Zhanchao Li, Qixing Huang, Xingyu Chen, Yang Wang, Jinlong Li, Yun Xie, Zong Dai, Xiaoyong Zou. Front Chem 2020
10
40

Predicting drug-disease associations by using similarity constrained matrix factorization.
Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu. BMC Bioinformatics 2018
73
5


Predicting drug-disease associations through layer attention graph convolutional network.
Zhouxin Yu, Feng Huang, Xiaohan Zhao, Wenjie Xiao, Wen Zhang. Brief Bioinform 2021
33
12

Semantic similarity in biomedical ontologies.
Catia Pesquita, Daniel Faria, André O Falcão, Phillip Lord, Francisco M Couto. PLoS Comput Biol 2009
354
4

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall,[...]. Nat Biotechnol 2007
4

A new method to measure the semantic similarity of GO terms.
James Z Wang, Zhidian Du, Rapeeporn Payattakool, Philip S Yu, Chin-Fu Chen. Bioinformatics 2007
558
4

Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.
Seyedmostafa Sheikhalishahi, Riccardo Miotto, Joel T Dudley, Alberto Lavelli, Fabio Rinaldi, Venet Osmani. JMIR Med Inform 2019
89
4

Data-driven prediction of drug effects and interactions.
Nicholas P Tatonetti, Patrick P Ye, Roxana Daneshjou, Russ B Altman. Sci Transl Med 2012
338
4

Similarity-based machine learning methods for predicting drug-target interactions: a brief review.
Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, Shanfeng Zhu. Brief Bioinform 2014
159
3

Combining drug and gene similarity measures for drug-target elucidation.
Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan. J Comput Biol 2011
92
3

What can natural language processing do for clinical decision support?
Dina Demner-Fushman, Wendy W Chapman, Clement J McDonald. J Biomed Inform 2009
229
3

The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2020
483
3

Disease networks. Uncovering disease-disease relationships through the incomplete interactome.
Jörg Menche, Amitabh Sharma, Maksim Kitsak, Susan Dina Ghiassian, Marc Vidal, Joseph Loscalzo, Albert-László Barabási. Science 2015
643
3


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.