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