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2007
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proceedings
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A large-scale evaluation of computational protein function prediction
Predrag Radivojac
,
Wyatt T Clark
,
Tal Ronnen Oron
,
Alexandra M Schnoes
,
Tobias Wittkop
,
Artem Sokolov
,
Kiley Graim
,
Christopher Funk
,
Karin Verspoor
,
Asa Ben-Hur
,
Gaurav Pandey
,
Jeffrey M Yunes
,
Ameet S Talwalkar
,
Susanna Repo
,
Michael L Souza
,
Damiano Piovesan
,
Rita Casadio
,
Zheng Wang
,
Jianlin Cheng
,
Hai Fang
,
Julian Gough
,
Patrik Koskinen
,
Petri Toronen
,
Jussi Nokso-Koivisto
,
Liisa Holm
,
Domenico Cozzetto
,
Daniel W A Buchan
,
Kevin Bryson
,
David T Jones
,
Bhakti Limaye
,
Harshal Inamdar
,
Avik Datta
,
Sunitha K Manjari
,
Rajendra Joshi
,
Meghana Chitale
,
Daisuke Kihara
,
Andreas M Lisewski
,
Serkan Erdin
,
Eric Venner
,
Olivier Lichtarge
,
Robert Rentzsch
,
Haixuan Yang
,
Alfonso E Romero
,
Prajwal Bhat
,
Alberto Paccanaro
,
Tobias Hamp
,
Rebecca Kaszner
,
Stefan Seemayer
,
Esmeralda Vicedo
,
Christian Schaefer
,
Dominik Achten
,
Florian Auer
,
Ariane Boehm
,
Tatjana Braun
,
Maximilian Hecht
,
Mark Heron
,
Peter Honigschmid
,
Thomas A Hopf
,
Stefanie Kaufmann
,
Michael Kiening
,
Denis Krompass
,
Cedric Landerer
,
Yannick Mahlich
,
Manfred Roos
,
Jari Bjorne
,
Tapio Salakoski
,
Andrew Wong
,
Hagit Shatkay
,
Fanny Gatzmann
,
Ingolf Sommer
,
Mark N Wass
,
Michael J E Sternberg
,
Nives Skunca
,
Fran Supek
,
Matko Bosnjak
,
Pance Panov
,
Saso Dzeroski
,
Tomislav Smuc
,
Yiannis A I Kourmpetis
,
Aalt D J van Dijk
,
Cajo J F ter Braak
,
Yuanpeng Zhou
,
Qingtian Gong
,
Xinran Dong
,
Weidong Tian
,
Marco Falda
,
Paolo Fontana
,
Enrico Lavezzo
,
Barbara Di Camillo
,
Stefano Toppo
,
Liang Lan
,
Nemanja Djuric
,
Yuhong Guo
,
Slobodan Vucetic
,
Amos Bairoch
,
Michal Linial
,
Patricia C Babbitt
,
Steven E Brenner
,
Christine Orengo
,
Burkhard Rost
,
Sean D Mooney
, and
Iddo Friedberg
.
Nat Meth
(
January 2013
)
Predrag Radivojac
,
Wyatt T Clark
,
Tal Ronnen Oron
,
Alexandra M Schnoes
,
Tobias Wittkop
,
Artem Sokolov
,
Kiley Graim
,
Christopher Funk
,
Karin Verspoor
,
Asa Ben-Hur
,
Gaurav Pandey
,
Jeffrey M Yunes
,
Ameet S Talwalkar
,
Susanna Repo
,
Michael L Souza
,
Damiano Piovesan
,
Rita Casadio
,
Zheng Wang
,
Jianlin Cheng
,
Hai Fang
,
Julian Gough
,
Patrik Koskinen
,
Petri Toronen
,
Jussi Nokso-Koivisto
,
Liisa Holm
,
Domenico Cozzetto
,
Daniel W A Buchan
,
Kevin Bryson
,
David T Jones
,
Bhakti Limaye
,
Harshal Inamdar
,
Avik Datta
,
Sunitha K Manjari
,
Rajendra Joshi
,
Meghana Chitale
,
Daisuke Kihara
,
Andreas M Lisewski
,
Serkan Erdin
,
Eric Venner
,
Olivier Lichtarge
,
Robert Rentzsch
,
Haixuan Yang
,
Alfonso E Romero
,
Prajwal Bhat
,
Alberto Paccanaro
,
Tobias Hamp
,
Rebecca Kaszner
,
Stefan Seemayer
,
Esmeralda Vicedo
,
Christian Schaefer
,
Dominik Achten
,
Florian Auer
,
Ariane Boehm
,
Tatjana Braun
,
Maximilian Hecht
,
Mark Heron
,
Peter Honigschmid
,
Thomas A Hopf
,
Stefanie Kaufmann
,
Michael Kiening
,
Denis Krompass
,
Cedric Landerer
,
Yannick Mahlich
,
Manfred Roos
,
Jari Bjorne
,
Tapio Salakoski
,
Andrew Wong
,
Hagit Shatkay
,
Fanny Gatzmann
,
Ingolf Sommer
,
Mark N Wass
,
Michael J E Sternberg
,
Nives Skunca
,
Fran Supek
,
Matko Bosnjak
,
Pance Panov
,
Saso Dzeroski
,
Tomislav Smuc
,
Yiannis A I Kourmpetis
,
Aalt D J van Dijk
,
Cajo J F ter Braak
,
Yuanpeng Zhou
,
Qingtian Gong
,
Xinran Dong
,
Weidong Tian
,
Marco Falda
,
Paolo Fontana
,
Enrico Lavezzo
,
Barbara Di Camillo
,
Stefano Toppo
,
Liang Lan
,
Nemanja Djuric
,
Yuhong Guo
,
Slobodan Vucetic
,
Amos Bairoch
,
Michal Linial
,
Patricia C Babbitt
,
Steven E Brenner
,
Christine Orengo
,
Burkhard Rost
,
Sean D Mooney
, and
Iddo Friedberg
.
Nat Meth
(
January 2013
)
3 months and 18 days ago
by
vch
1
nat-meth
nat-meth
URL
DOI
TeX
The gene normalization task in BioCreative III.
Zhiyong Lu
,
Hung-Yu Kao
,
Chih-Hsuan Wei
,
Minlie Huang
,
Jingchen Liu
,
Cheng-Ju Kuo
,
Chun-Nan Hsu
,
Richard Tzong-Han Tsai
,
Hong-Jie Dai
,
Naoaki Okazaki
,
Han-Cheol Cho
,
Martin Gerner
,
Illés Solt
,
Shashank Agarwal
,
Feifan Liu
,
Dina Vishnyakova
,
Patrick Ruch
,
Martin Romacker
,
Fabio Rinaldi
,
Sanmitra Bhattacharya
,
Padmini Srinivasan
,
Hongfang Liu
,
Manabu Torii
,
Sérgio Matos
,
David Campos
,
Karin Verspoor
,
Kevin M. Livingston
, and
W. John Wilbur
.
BMC Bioinformatics
12(S-8):S2
(
2011
)
Zhiyong Lu
,
Hung-Yu Kao
,
Chih-Hsuan Wei
,
Minlie Huang
,
Jingchen Liu
,
Cheng-Ju Kuo
,
Chun-Nan Hsu
,
Richard Tzong-Han Tsai
,
Hong-Jie Dai
,
Naoaki Okazaki
,
Han-Cheol Cho
,
Martin Gerner
,
Illés Solt
,
Shashank Agarwal
,
Feifan Liu
,
Dina Vishnyakova
,
Patrick Ruch
,
Martin Romacker
,
Fabio Rinaldi
,
Sanmitra Bhattacharya
,
Padmini Srinivasan
,
Hongfang Liu
,
Manabu Torii
,
Sérgio Matos
,
David Campos
,
Karin Verspoor
,
Kevin M. Livingston
, and
W. John Wilbur
.
BMC Bioinformatics
12(S-8):S2
(
2011
)
4 months and 20 days ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
Yoshinobu Kano
,
Jari Björne
,
Filip Ginter
,
Tapio Salakoski
,
Ekaterina Buyko
,
Udo Hahn
,
K. Bretonnel Cohen
,
Karin Verspoor
,
Christophe Roeder
,
Lawrence E. Hunter
,
Halil Kilicoglu
,
Sabine Bergler
,
Sofie Van Landeghem
,
Thomas Van Parys
,
Yves Van de Peer
,
Makoto Miwa
,
Sophia Ananiadou
,
Mariana L. Neves
,
Alberto D. Pascual-Montano
,
Arzucan Özgür
,
Dragomir R. Radev
,
Sebastian Riedel
,
Rune Sætre
,
Hong-Woo Chun
,
Jin-Dong Kim
,
Sampo Pyysalo
,
Tomoko Ohta
, and
Jun ichi Tsujii
.
BMC Bioinformatics
(
2011
)
Yoshinobu Kano
,
Jari Björne
,
Filip Ginter
,
Tapio Salakoski
,
Ekaterina Buyko
,
Udo Hahn
,
K. Bretonnel Cohen
,
Karin Verspoor
,
Christophe Roeder
,
Lawrence E. Hunter
,
Halil Kilicoglu
,
Sabine Bergler
,
Sofie Van Landeghem
,
Thomas Van Parys
,
Yves Van de Peer
,
Makoto Miwa
,
Sophia Ananiadou
,
Mariana L. Neves
,
Alberto D. Pascual-Montano
,
Arzucan Özgür
,
Dragomir R. Radev
,
Sebastian Riedel
,
Rune Sætre
,
Hong-Woo Chun
,
Jin-Dong Kim
,
Sampo Pyysalo
,
Tomoko Ohta
, and
Jun ichi Tsujii
.
BMC Bioinformatics
(
2011
)
4 months and 21 days ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Concept annotation in the CRAFT corpus.
Michael Bada
,
Miriam Eckert
,
Donald Evans
,
Kristin Garcia
,
Krista Shipley
,
Dmitry Sitnikov
,
William A. Baumgartner Jr.
,
K. Bretonnel Cohen
,
Karin Verspoor
,
Judith A. Blake
, and
Lawrence E. Hunter
.
BMC Bioinformatics
(
2012
)
Michael Bada
,
Miriam Eckert
,
Donald Evans
,
Kristin Garcia
,
Krista Shipley
,
Dmitry Sitnikov
,
William A. Baumgartner Jr.
,
K. Bretonnel Cohen
,
Karin Verspoor
,
Judith A. Blake
, and
Lawrence E. Hunter
.
BMC Bioinformatics
(
2012
)
4 months and 21 days ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.
Karin Verspoor
,
Kevin Bretonnel Cohen
,
Arrick Lanfranchi
,
Colin Warner
,
Helen L. Johnson
,
Christophe Roeder
,
Jinho D. Choi
,
Christopher Funk
,
Yuriy Malenkiy
,
Miriam Eckert
,
Nianwen Xue
,
William A. Baumgartner Jr.
,
Michael Bada
,
Martha Palmer
, and
Lawrence E. Hunter
.
BMC Bioinformatics
(
2012
)
Karin Verspoor
,
Kevin Bretonnel Cohen
,
Arrick Lanfranchi
,
Colin Warner
,
Helen L. Johnson
,
Christophe Roeder
,
Jinho D. Choi
,
Christopher Funk
,
Yuriy Malenkiy
,
Miriam Eckert
,
Nianwen Xue
,
William A. Baumgartner Jr.
,
Michael Bada
,
Martha Palmer
, and
Lawrence E. Hunter
.
BMC Bioinformatics
(
2012
)
4 months and 21 days ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Protein annotation as term categorization in the gene ontology using word proximity networks.
Karin Verspoor
,
Judith D. Cohn
,
Cliff Joslyn
,
Susan M. Mniszewski
,
Andreas Rechtsteiner
,
Luis Mateus Rocha
, and
Tiago Simas
.
BMC Bioinformatics
(
2005
)
Karin Verspoor
,
Judith D. Cohn
,
Cliff Joslyn
,
Susan M. Mniszewski
,
Andreas Rechtsteiner
,
Luis Mateus Rocha
, and
Tiago Simas
.
BMC Bioinformatics
(
2005
)
7 months ago
by
dblp
2
dblp
dblp
URL
DOI
TeX
Pattern Learning through Distant Supervision for Extraction of Protein-Residue Associations in the Biomedical Literature.
K. E. Ravikumar
,
Haibin Liu
,
Judith D. Cohn
,
Michael E. Wall
, and
Karin Verspoor
.
ICMLA 2,
page 59-65.
IEEE Computer Society,
(
2011
)
K. E. Ravikumar
,
Haibin Liu
,
Judith D. Cohn
,
Michael E. Wall
, and
Karin Verspoor
.
ICMLA 2,
page 59-65.
IEEE Computer Society,
(
2011
)
7 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks
Alaa Abi-Haidar
,
Jasleen Kaur
,
Ana Gabriela Maguitman
,
Predrag Radivojac
,
Andreas Rechtsteiner
,
Karin Verspoor
,
Zhiping Wang
, and
Luis Mateus Rocha
.
CoRR
(
2008
)
Alaa Abi-Haidar
,
Jasleen Kaur
,
Ana Gabriela Maguitman
,
Predrag Radivojac
,
Andreas Rechtsteiner
,
Karin Verspoor
,
Zhiping Wang
, and
Luis Mateus Rocha
.
CoRR
(
2008
)
7 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Simple Similarity-based Question Answering Strategies for Biomedical Text.
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
7 months ago
by
promisenoe
3
dblp
dblp
URL
DOI
TeX
Simple Similarity-based Question Answering Strategies for Biomedical Text.
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
7 months ago
by
dbenz_test
3
dblp
dblp
URL
DOI
TeX
Simple Similarity-based Question Answering Strategies for Biomedical Text.
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
David Martínez
,
Andrew MacKinlay
,
Diego Mollá Aliod
,
Lawrence Cavedon
, and
Karin Verspoor
.
CLEF Online Working Notes/Labs/Workshop,
(
2012
)
8 months ago
by
dblp
3
dblp
dblp
URL
DOI
TeX
High-Precision Biological Event Extraction: Effects of System and of Data.
K. Bretonnel Cohen
,
Karin Verspoor
,
Helen L. Johnson
,
Christophe Roeder
,
Philip V. Ogren
,
William A. Baumgartner Jr.
,
Elizabeth K. White
,
Hannah J. Tipney
, and
Lawrence Hunter
.
Computational Intelligence
27(4):681-701
(
2011
)
K. Bretonnel Cohen
,
Karin Verspoor
,
Helen L. Johnson
,
Christophe Roeder
,
Philip V. Ogren
,
William A. Baumgartner Jr.
,
Elizabeth K. White
,
Hannah J. Tipney
, and
Lawrence Hunter
.
Computational Intelligence
27(4):681-701
(
2011
)
a year and 4 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System.
Kevin M. Livingston
,
Helen L. Johnson
,
Karin Verspoor
, and
Lawrence Hunter
.
ICSC,
page 40-45.
IEEE,
(
2010
)
Kevin M. Livingston
,
Helen L. Johnson
,
Karin Verspoor
, and
Lawrence Hunter
.
ICSC,
page 40-45.
IEEE,
(
2010
)
2 years and a month ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.
Carsten Görg
,
Hannah J. Tipney
,
Karin Verspoor
,
William A. Baumgartner Jr.
,
K. Bretonnel Cohen
,
John Stasko
, and
Lawrence Hunter
.
KES 4,
volume 6279 of Lecture Notes in Computer Science,
page 420-429.
Springer,
(
2010
)
Carsten Görg
,
Hannah J. Tipney
,
Karin Verspoor
,
William A. Baumgartner Jr.
,
K. Bretonnel Cohen
,
John Stasko
, and
Lawrence Hunter
.
KES 4,
volume 6279 of Lecture Notes in Computer Science,
page 420-429.
Springer,
(
2010
)
2 years and 6 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
The structural and content aspects of abstracts versus bodies of full text journal articles are different.
K. Bretonnel Cohen
,
Helen L. Johnson
,
Karin Verspoor
,
Christophe Roeder
, and
Lawrence Hunter
.
BMC Bioinformatics
(
2010
)
K. Bretonnel Cohen
,
Helen L. Johnson
,
Karin Verspoor
,
Christophe Roeder
, and
Lawrence Hunter
.
BMC Bioinformatics
(
2010
)
2 years and 6 months ago
by
dblp
3
dblp
dblp
URL
DOI
TeX
Distributed Representations of Bio-Ontologies for Semantic Web Services
Cliff Joslyn
,
Damian Gessler
,
Stefan Schmidt
, and
Karin Verspoor
.
Joint BioLink and BioOntologies SIG of ISMB 2006,
(
2006
)
Cliff Joslyn
,
Damian Gessler
,
Stefan Schmidt
, and
Karin Verspoor
.
Joint BioLink and BioOntologies SIG of ISMB 2006,
(
2006
)
2 years and 8 months ago
by
algebradresden
1
2006
proceedings
publication
schmidt
2006
proceedings
publication
schmidt
URL
DOI
TeX
Visual Analytics & Ontologies for Discovering the Genetic Basis of Cancer
D. Gessler
,
C. Joslyn
,
N. Noy
,
M. Musen
,
K. Verspoor
,
R. Bueno
,
S.E. Schmidt
,
B. Koester
,
V. Velculescu
, and
T. Sjoblom
.
Los Alamos Unlimited Release Report
(
2007
)
D. Gessler
,
C. Joslyn
,
N. Noy
,
M. Musen
,
K. Verspoor
,
R. Bueno
,
S.E. Schmidt
,
B. Koester
,
V. Velculescu
, and
T. Sjoblom
.
Los Alamos Unlimited Release Report
(
2007
)
2 years and 8 months ago
by
algebradresden
1
2007
journal
koester
publication
schmidt
2007
journal
koester
publication
schmidt
URL
DOI
TeX
Integrating Semantic Data Sources for Disease-implicated Gene Discovery
D. Gessler
,
C. Joslyn
,
B. Koester
,
S.E. Schmidt
, and
K. Verspoor
.
5th Annual Rocky Mountains Bioinformatics Conference,
(
2007
)
D. Gessler
,
C. Joslyn
,
B. Koester
,
S.E. Schmidt
, and
K. Verspoor
.
5th Annual Rocky Mountains Bioinformatics Conference,
(
2007
)
2 years and 8 months ago
by
algebradresden
1
2007
koester
proceedings
publication
schmidt
2007
koester
proceedings
publication
schmidt
URL
DOI
TeX
Exploring Species-Based Strategies for Gene Normalization.
Karin Verspoor
,
Christophe Roeder
,
Helen L. Johnson
,
K. Bretonnel Cohen
,
William A. Baumgartner Jr.
, and
Lawrence Hunter
.
IEEE/ACM Trans. Comput. Biology Bioinform.
7(3):462-471
(
2010
)
Karin Verspoor
,
Christophe Roeder
,
Helen L. Johnson
,
K. Bretonnel Cohen
,
William A. Baumgartner Jr.
, and
Lawrence Hunter
.
IEEE/ACM Trans. Comput. Biology Bioinform.
7(3):462-471
(
2010
)
2 years and 9 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
A UIMA wrapper for the NCBO annotator.
Christophe Roeder
,
Clement Jonquet
,
Nigam H. Shah
,
William A. Baumgartner Jr.
,
Karin Verspoor
, and
Lawrence Hunter
.
Bioinformatics
26(14):1800-1801
(
2010
)
Christophe Roeder
,
Clement Jonquet
,
Nigam H. Shah
,
William A. Baumgartner Jr.
,
Karin Verspoor
, and
Lawrence Hunter
.
Bioinformatics
26(14):1800-1801
(
2010
)
2 years and 9 months ago
by
dblp
1
dblp
dblp
URL
DOI
TeX
BibSonomy is offered by the
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of the University of Kassel, the
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