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Supplement 1 for Table 4 . 79 highly cited biomedical text mining papers
No Title Author Country Source of LiteratureYear of
publication
Time
s
Annual
Average
Times
Cited
1 Systematic and integrative
analysis of large gene lists
using DAVID
bioinformatics resources
Huang, Da Wei; Sherman,
Brad T.; Lempicki, Richard A.
USA NATURE PROTOCOLS 2009 3177 529.50
2 The Gene Ontology
Annotation (GOA)
Database: sharing
knowledge in Uniprot with
Gene Ontology
Camon, E; Magrane, M;
Barrell, D,ect
UK NUCLEIC ACIDS
RESEARCH
2004 366 33.27
3 RegulonDB (version 6.0):
gene regulation model of
Escherichia coli K-12
Gama-Castro, Socorro;
Jimenez-Jacinto, Veronica;
Peralta-Gil, Martin,ect
Morelos NUCLEIC ACIDS
RESEARCH
2008 274 39.14
beyond transcription, active
(experimental) annotated
promoters and Textpresso
navigation
4 Cluster analysis for gene
expression data: A survey
Jiang, DX; Tang, C; Zhang,
AD
USA IEEE TRANSACTIONS
ON KNOWLEDGE AND
DATA ENGINEERING
2004 269 24.45
5 Literature mining for the
biologist: from information
retrieval to biological
discovery
Jensen, LJ; Saric, J; Bork, P Germany NATURE REVIEWS
GENETICS
2006 237 26.33
6 Computational cluster
validation in post-genomic
data analysis
Handl, J; Knowles, J; Kell, DB UK BIOINFORMATICS 2005 236 23.60
7 Clustering by compression Cilibrasi, R; Vitanyi, PMB Netherlands IEEE TRANSACTIONS
ON INFORMATION
THEORY
2005 228 22.80
8 The Mouse Genome
Database (MGD): mouse
biology and model systems
Bult, Carol J.; Eppig, Janan T.;
Kadin, James A. ,ect
USA. NUCLEIC ACIDS
RESEARCH
2008 222 31.71
9 Textpresso: An ontology-
based information retrieval
and extraction system for
biological literature
Muller, HM; Kenny, EE;
Sternberg, PW
USA. PLOS BIOLOGY 2004 201 18.27
10 A survey of current work in
biomedical text mining
Cohen, AM; Hersh, WR USA. BRIEFINGS IN
BIOINFORMATICS
2005 177 17.70
11
Textpresso: An ontology-based information retrieval and extraction system for biological literature
Muller, HM; Kenny, EE; Sternberg, PW USA PLOS BIOLOGY 2004
171 19
12
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments
Al-Shahrour, Fatima; Minguez, Pablo; Tarraga, Joaquin; Montaner, David; Alloza, Eva; Vaquerizas, Juan M.; Conde, Lucia; Blaschke, Christian; Vera, Javier; Dopazo, Joaquin Spain
NUCLEIC ACIDS RESEARCH 2006
168 24
13 Overview of BioCreAtIvE: Hirschman, L; Yeh, A; USA,Spain BMC BIOINFORMATICS 2005 151 16.8
critical assessment of information extraction for biology Blaschke, C; Valencia, A
14A text-mining analysis of the human phenome
van Driel, MA; Bruggeman, J; Vriend, G; Brunner, HG; Leunissen, JA Netherlands
EUROPEAN JOURNAL OF HUMAN GENETICS 2006
150 18.8
15
A systematic review of modafinil: Potential clinical uses and mechanisms of action Ballon, JS; Feifel, D USA
JOURNAL OF CLINICAL PSYCHIATRY 2006
144 18
16BRENDA, the enzyme information system in 2011
Scheer, Maurice; Grote, Andreas; Chang, Antje; Schomburg, Ida; Munaretto, Cornelia; Rother, Michael; Soehngen, Carola; Stelzer, Michael; Thiele, Juliane; Schomburg, Dietmar Germany
NUCLEIC ACIDS RESEARCH 2011
135 45
17
FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
Al-Shahrour, Fatima; Minguez, Pablo; Tarraga, Joaquin; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquin Spain
NUCLEIC ACIDS RESEARCH 2007
132 18.9
18 GeneWays: a system for Rzhetsky, A; Iossifov, I; USA,Japan JOURNAL OF 2004 123 12.3
extracting, analyzing, visualizing, and integrating molecular pathway data
Koike, T; Krauthammer, M; Kra, P; Morris, M; Yu, H; Duboue, PA; Weng, WB; Wilbur, WJ; Hatzivassiloglou, V; Friedman, C
BIOMEDICAL INFORMATICS
19
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text Settles, B USA BIOINFORMATICS 2005
117 14.6
20
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
Ramani, AK; Bunescu, RC; Mooney, RJ; Marcotte, EM USA GENOME BIOLOGY 2005
116 12.9
21
Discovering disease-genes by topological features in human protein-protein interaction network Xu, Jianzhen; Li, Yongjin Peoples R China BIOINFORMATICS 2006
115 16.4
22
Multilabel neural networks with applications to functional genomics and text categorization
Zhang, Min-Ling; Zhou, Zhi-Hua Peoples R China
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2006
113 16.1
23 Integration of text- and data-mining using ontologies
Tiffin, N; Kelso, JF; Powell, AR; Pan, H; Bajic, VB; Hide,
South Africa,Singapore
NUCLEIC ACIDS RESEARCH
2005 109 15.6
successfully selects disease gene candidates WA
24
Molecular characterization of pediatric gastrointestinal stromal tumors
Agaram, Narasimhan P.; Laquaglia, Michael P.; Ustun, Berrin; Guo, Tianhua; Wong, Grace C.; Socci, Nicholas D.; Maki, Robert G.; DeMatteo, Ronald P.; Besmer, Peter; Antonescu, Cristina R. USA
CLINICAL CANCER RESEARCH 2008
108 18
25The Human Serum Metabolome
Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul; Hollander, Zsuzsanna; Pedersen, Theresa L.; Smith, Steven R.; Bamforth, Fiona; Greiner, Russ; McManus, Bruce; Newman, John W.; Goodfriend, Theodore; Wishart, David S. Canada,USA PLOS ONE 2011
105 35
26
Discovery of drug mode of action and drug repositioning from transcriptional responses
Iorio, Francesco; Bosotti, Roberta; Scacheri, Emanuela; Belcastro, Vincenzo; Mithbaokar, Pratibha; Ferriero, Rosa; Murino, Loredana; Tagliaferri, Roberto; Brunetti-Pierri, Nicola; Isacchi, Antonella; di Bernardo, Diego Italy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2010
102 25.5
27
Text mining and its potential applications in systems biology
Ananiadou, Sophia; Kell, Douglas B.; Tsujii, Jun-ichi UK,JAPAN
TRENDS IN BIOTECHNOLOGY 2006 102
14.6
28Machine learning in bioinformatics
Larranaga, Pedro; Calvo, Borja; Santana, Roberto; Bielza, Concha; Galdiano, Josu; Inza, Inaki; Lozano, Jose A.; Armananzas, Ruben; Santafe, Guzman; Perez, Aritz; Robles, Victor Spain,USA
BRIEFINGS IN BIOINFORMATICS 2006
97 13.9
29 Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila
Bergman, CM; Carlson, JW; Celniker, SE
UK,USA BIOINFORMATICS 2005 93 10.3
melanogaster
30
Text mining and ontologies in biomedicine: Making sense of raw text
Spasic, I; Ananiadou, S; McNaught, J; Kumar, A UK
BRIEFINGS IN BIOINFORMATICS 2005
88 9.78
31
Experiencing SAX: a novel symbolic representation of time series
Lin, Jessica; Keogh, Eamonn; Wei, Li; Lonardi, Stefano USA
DATA MINING AND KNOWLEDGE DISCOVERY 2007
87 14.5
32
Alternative splicing in cancer: Noise, functional, or systematic?
Skotheim, Rolf I.; Nees, Matthias Finland,Norway
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY 2007
86 14.3
33Hedgehog signaling pathway and gastric cancer Katoh, Y; Katoh, M Japan
CANCER BIOLOGY & THERAPY 2005
85 10.6
34The human cerebrospinal fluid metabolome
Wishart, David S.; Lewis, Michael J.; Morrissey, Joshua A.; Flegel, Mitchel D.; Jeroncic, Kevin; Xiong, Yeping; Cheng, Dean; Eisner, Roman; Gautam, Bijaya; Tzur, Dan; Sawhney, Summit; Bamforth, Fiona; Greiner, Russ; Li, Liang Canada
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 2008
81 16.2
35 Babelomics: an integrative platform for the analysis of transcriptomics, proteomics
Medina, Ignacio; Carbonell, Jose; Pulido, Luis; Madeira, Sara C.; Goetz, Stefan;
Spain,Portugal NUCLEIC ACIDS RESEARCH
2010 80 20
and genomic data with advanced functional profiling
Conesa, Ana; Tarraga, Joaquin; Pascual-Montano, Alberto; Nogales-Cadenas, Ruben; Santoyo, Javier; Garcia, Francisco; Marba, Martina; Montaner, David; Dopazo, Joaquin
36
Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network
Li, S.; Zhang, Z. Q.; Wu, L. J.; Zhang, X. G.; Li, Y. D.; Wang, Y. Y. Peoples R China IET SYSTEMS BIOLOGY 2007
79 11.3
37
A human functional protein interaction network and its application to cancer data analysis
Wu, Guanming; Feng, Xin; Stein, Lincoln Canada,USA GENOME BIOLOGY 2010
73 18.3
38Frontiers of biomedical text mining: current progress
Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B. France,USA
BRIEFINGS IN BIOINFORMATICS 2007
73 12.2
39
Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells Kell, DB UK FEBS JOURNAL 2006
73 9.13
40 Corpus annotation for mining biomedical events
Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi
Japan,UK BMC BIOINFORMATICS 2008 73 12.2
from literature
41
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
Persico, M; Ceol, A; Gavrila, C; Hoffmann, R; Florio, A; Cesareni, G Italy,USA BMC BIOINFORMATICS 2005
73 8.11
42
Linking genes to literature: text mining, information extraction, and retrieval applications for biology
Krallinger, Martin; Valencia, Alfonso; Hirschman, Lynette Spain GENOME BIOLOGY 2008
73 12.2
43
Identification and characterization of human HES2, HES3, and HES5 genes in silico Katoh, M; Katoh, M Japan
INTERNATIONAL JOURNAL OF ONCOLOGY 2004
73 12.2
44
Text-mining and information-retrieval services for molecular biology Krallinger, M; Valencia, A Spain GENOME BIOLOGY 2005
72 8
45
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Cheng, Dean; Knox, Craig; Young, Nelson; Stothard, Paul; Damaraju, Sambasivarao; Wishart, David S. Canada
NUCLEIC ACIDS RESEARCH 2008
70 11.7
46
Systematic association of genes to phenotypes by genome and literature mining
Korbel, JO; Doerks, T; Jensen, LJ; Perez-Iratxeta, C; Kaczanowski, S; Hooper, SD; Andrade, MA; Bork, P
Germany,Canada, Poland PLOS BIOLOGY 2005
70 7.78
47
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
Krallinger, Martin; Morgan, Alexander; Smith, Larry; Leitner, Florian; Tanabe, Lorraine; Wilbur, John; Hirschman, Lynette; Valencia, Alfonso USA,Spain GENOME BIOLOGY 2008
68 11.3
48
The mouse genome database (MGD): new features facilitating a model system
Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.; Kadin, James A.; Richardson, Joel E. USA
NUCLEIC ACIDS RESEARCH 2007
68 9.71
49
Recognizing names in biomedical texts: a machine learning approach
Zhou, GD; Zhang, J; Su, J; Shen, D; Tan, CL Singapore BIOINFORMATICS 2004
67 6.7
50HAGR: the human ageing genomic resources
de Magalhaes, JP; Costa, J; Toussaint, O USA
NUCLEIC ACIDS RESEARCH 2005
67 7.44
51
Text processing through web services: calling Whatizit
Rebholz-Schuhmann, Dietrich; Arregui, Miguel; Gaudan, Sylvain; Kirsch, Harald; Jimeno, Antonio UK BIOINFORMATICS 2008
66 11
52 An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
Camon, EB; Barrell, DG; Dimmer, EC; Lee, V; Magrane, M; Maslen, J; Binns,
UK BMC BIOINFORMATICS 2005 63 7
D; Apweiler, R
53
Knowledge discovery in traditional Chinese medicine: State of the art and perspectives
Feng, Yi; Wu, Zhaohui; Zhou, Xuezhong; Zhou, Zhongmei; Fan, Weiyu Peoples R China
ARTIFICIAL INTELLIGENCE IN MEDICINE 2006
62 8.86
54The edaphic factor in the origin of plant species Rajakaruna, N USA
INTERNATIONAL GEOLOGY REVIEW 2004
61 6.78
55Target discovery from data mining approaches
Yang, Yongliang; Adelstein, S. James; Kassis, Amin I. USA
DRUG DISCOVERY TODAY 2009
60 12
56
Expression and genomic profiling of colorectal cancer
Cardoso, J.; Boer, J.; Morreau, H.; Fodde, R. Netherlands
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER 2007
59 8.43
57WNT antagonist, SFRP1, is Hedgehog signaling target Katoh, Y; Katoh, M Japan
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 2006
58 7.25
58
The Mouse Genome Database genotypes::phenotypes
Blake, Judith A.; Bult, Carol J.; Eppig, Janan T.; Kadin, James A.; Richardson, Joel E. USA
NUCLEIC ACIDS RESEARCH 2009
57 11.4
59BioCreAtIvE task IA: gene mention finding evaluation
Yeh, A; Morgan, A; Colosimo, M; Hirschman, L USA BMC BIOINFORMATICS 2005
56 6.22
60The application of systems biology to drug discovery
Cho, Carolyn R.; Labow, Mark; Reinhardt, Mischa; van Oostrum, Jan; Peitsch, Manuel C. USA
CURRENT OPINION IN CHEMICAL BIOLOGY 2006
55 6.88
61 Evidence-Based Annotation Zhou, Yingyao; USA PLOS ONE 2008 54 9
of the Malaria Parasite's Genome Using Comparative Expression Profiling
Ramachandran, Vandana; Kumar, Kota Arun; Westenberger, Scott; Refour, Phillippe; Zhou, Bin; Li, Fengwu; Young, Jason A.; Chen, Kaisheng; Plouffe, David; Henson, Kerstin; Nussenzweig, Victor; Carlton, Jane; Vinetz, Joseph M.; Duraisingh, Manoj T.; Winzeler, Elizabeth A.
62
Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer
Kulasingam, Vathany; Pavlou, Maria P.; Diamandis, Eleftherios P. Canada
NATURE REVIEWS CANCER 2010
53 13.3
63Evaluation of BioCreAtIvE assessment of task 2
Blaschke, C; Leon, EA; Krallinger, M; Valencia, A Spain BMC BIOINFORMATICS 2005
52 5.78
64
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
Al-Shahrour, Fatima; Carbonell, Jose; Minguez, Pablo; Goetz, Stefan; Conesa, Ana; Tarrraga, Joaquin; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquin Spain
NUCLEIC ACIDS RESEARCH 2008
50 8.33
65 Networks Inferred from Alexopoulos, Leonidas G.; USA MOLECULAR & 2010 50 12.5
Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes
Saez-Rodriguez, Julio; Cosgrove, Benjamin D.; Lauffenburger, Douglas A.; Sorger, Peter K.
CELLULAR PROTEOMICS
66
Text mining approaches in molecular biology and biomedicine
Krallinger, M; Erhardt, RAA; Valencia, A Spain
DRUG DISCOVERY TODAY 2005
50 5.56
67
Techniques: Bioprospecting historical herbal texts by hunting for new leads in old tomes
Buenz, EJ; Schnepple, DJ; Bauer, BA; Elkin, PL; Riddle, JM; Motley, TJ USA
TRENDS IN PHARMACOLOGICAL SCIENCES 2004
47 4.7
68
Cancer systems biology: exploring cancer-associated genes on cellular networks
Wang, E.; Lenferink, A.; Connor-McCourt, M. O. Canada
CELLULAR AND MOLECULAR LIFE SCIENCES 2007
47 7.83
69
The next generation of literature analysis: Integration of genomic analysis into text mining
Scherf, M; Epple, A; Werner, T Germany
BRIEFINGS IN BIOINFORMATICS 2005
46 5.75
70
PROMISCUOUS: a database for network-based drug-repositioning
von Eichborn, Joachim; Murgueitio, Manuela S.; Dunkel, Mathias; Koerner, Soeren; Bourne, Philip E.; Preissner, Robert Germany,USA
NUCLEIC ACIDS RESEARCH 2011
46 15.3
71
Gene regulatory networks in lactation: identification of global principles using bioinformatics
Lemay, Danielle G.; Neville, Margaret C.; Rudolph, Michael C.; Pollard, Katherine S.; German, J. Bruce USA
BMC SYSTEMS BIOLOGY 2007
46 7.67
72
Event extraction for systems biology by text mining the literature
Ananiadou, Sophia; Pyysalo, Sampo; Tsujii, Jun'ichi; Kell, Douglas B. Japan
TRENDS IN BIOTECHNOLOGY 2010
45 11.3
73
Computational methods for Traditional Chinese Medicine: A survey
Lukman, Suryani; He, Yulan; Hui, Siu-Cheung UK
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2007
45 7.5
74
2-Alkyl-4-hydroxymethylfuran-3-carboxylic acids, antibiotic production inducers discovered by Streptomyces coelicolor genome mining
Corre, Christophe; Song, Lijiang; O'Rourke, Sean; Chater, Keith F.; Challis, Gregory L. UK
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2008
44 8.8
75
Dynamic interaction networks in a hierarchically organized tissue
Kirouac, Daniel C.; Ito, Caryn; Csaszar, Elizabeth; Roch, Aline; Yu, Mei; Sykes, Edward A.; Bader, Gary D.; Zandstra, Peter W. Canada
MOLECULAR SYSTEMS BIOLOGY 2010
43 10.8
76
LINNAEUS: A species name identification system for biomedical literature
Gerner, Martin; Nenadic, Goran; Bergman, Casey M. UK BMC BIOINFORMATICS 2010
43 10.8
77 A Pathway-Based View of Li, Yong; Agarwal, Pankaj USA PLOS ONE 2009 42 10.5
Human Diseases and Disease Relationships
78
Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models
Saez-Rodriguez, Julio; Alexopoulos, Leonidas G.; Zhang, MingSheng; Morris, Melody K.; Lauffenburger, Douglas A.; Sorger, Peter K. USA CANCER RESEARCH 2011
42 21
79
Urine proteomics for profiling of human disease using high accuracy mass spectrometry
Kentsis, Alex; Monigatti, Flavio; Dorff, Kevin; Campagne, Fabien; Bachur, Richard; Steen, Hanno USA
PROTEOMICS CLINICAL APPLICATIONS 2009
42 10.5