 | 2009 |
|---|
| 62 |       | Cecilia N. Arighi,
Hongfang Liu,
Darren A. Natale,
Winona C. Barker,
Harold J. Drabkin,
Judith A. Blake,
Barry Smith,
Cathy H. Wu:
TGF-beta signaling proteins and the Protein Ontology.
BMC Bioinformatics 10(S-5): (2009) |
| 61 | | Sarah Hunter,
Rolf Apweiler,
Teresa K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Peer Bork,
Ujjwal Das,
Louise Daugherty,
Lauranne Duquenne,
Robert D. Finn,
Julian Gough,
Daniel H. Haft,
Nicolas Hulo,
Daniel Kahn,
Elizabeth Kelly,
Aurélie Laugraud,
Ivica Letunic,
David Lonsdale,
Rodrigo Lopez,
Martin Madera,
John Maslen,
Craig McAnulla,
Jennifer McDowall,
Jaina Mistry,
Alex Mitchell,
Nicola J. Mulder,
Darren A. Natale,
Christine A. Orengo,
Antony F. Quinn,
Jeremy D. Selengut,
Christian J. A. Sigrist,
Manjula Thimma,
Paul D. Thomas,
Franck Valentin,
Derek Wilson,
Cathy H. Wu,
Corin Yeats:
InterPro: the integrative protein signature database.
Nucleic Acids Research 37(Database-Issue): 211-215 (2009) |
| 2008 |
|---|
| 60 | | Guixian Xu,
Lanlan Yin,
Manabu Torii,
Zhendong Niu,
Cathy H. Wu,
Zhang-Zhi Hu,
Hongfang Liu:
Document Classification for Mining Host Pathogen Protein-Protein Interactions.
BIBM 2008: 461-466 |
| 59 | | Zhang-Zhi Hu,
K. Bretonnel Cohen,
Lynette Hirschman,
Alfonso Valencia,
Hongfang Liu,
Michelle G. Giglio,
Cathy H. Wu:
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology.
BIBM 2008: 467-472 |
| 58 |  | Harold J. Drabkin,
Cecilia N. Arighi,
Cathy H. Wu,
Judith A. Blake:
Functional Annotation of Protein Isoforms and Modified Forms.
BIOCOMP 2008: 701-707 |
| 57 | | Katherine G. Herbert,
Junilda Spirollari,
Jason Tsong-Li Wang,
William H. Piel,
John D. Westbrook,
Winona C. Barker,
Zhang-Zhi Hu,
Cathy H. Wu:
Bioinformatic Databases.
Wiley Encyclopedia of Computer Science and Engineering 2008 |
| 56 | | C. Zhang,
Oswald Crasta,
S. Cammer,
Rebecca Will,
Ron Kenyon,
D. Sullivan,
Q. Yu,
W. Sun,
R. Jha,
D. Liu,
Tian Xue,
Y. Zhang,
M. Moore,
Peter B. McGarvey,
Hongzhan Huang,
Yongxing Chen,
J. Zhang,
Raja Mazumder,
Cathy H. Wu,
Bruno W. S. Sobral:
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
Nucleic Acids Research 36(Database-Issue): 884-891 (2008) |
| 2007 |
|---|
| 55 | | Hongfang Liu,
Manabu Torii,
Zhang-Zhi Hu,
Cathy H. Wu:
Mapping Gene/Protein Names in Free Text to Biomedical Databases.
ICDM Workshops 2007: 101-106 |
| 54 | | Manabu Torii,
Zhang-Zhi Hu,
Min Song,
Cathy H. Wu,
Hongfang Liu:
A comparison study on algorithms of detecting long forms for short forms in biomedical text.
BMC Bioinformatics 8(S-9): (2007) |
| 53 | | Darren A. Natale,
Cecilia N. Arighi,
Winona C. Barker,
Judith A. Blake,
Ti-Cheng Chang,
Zhang-Zhi Hu,
Hongfang Liu,
Barry Smith,
Cathy H. Wu:
Framework for a Protein Ontology.
BMC Bioinformatics 8(S-9): (2007) |
| 52 | | Baris E. Suzek,
Hongzhan Huang,
Peter B. McGarvey,
Raja Mazumder,
Cathy H. Wu:
UniRef: comprehensive and non-redundant UniProt reference clusters.
Bioinformatics 23(10): 1282-1288 (2007) |
| 51 | | Peng Qiu,
Z. Jane Wang,
K. J. Ray Liu,
Zhang-Zhi Hu,
Cathy H. Wu:
Dependence network modeling for biomarker identification.
Bioinformatics 23(2): 198-206 (2007) |
| 50 | | Nicola J. Mulder,
Rolf Apweiler,
Teresa K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Peer Bork,
Virginie Buillard,
Lorenzo Cerutti,
Richard R. Copley,
Emmanuel Courcelle,
Ujjwal Das,
Louise Daugherty,
Mark Dibley,
Robert D. Finn,
Wolfgang Fleischmann,
Julian Gough,
Daniel H. Haft,
Nicolas Hulo,
Sarah Hunter,
Daniel Kahn,
Alexander Kanapin,
Anish Kejariwal,
Alberto Labarga,
Petra S. Langendijk-Genevaux,
David Lonsdale,
Rodrigo Lopez,
Ivica Letunic,
Martin Madera,
John Maslen,
Craig McAnulla,
Jennifer McDowall,
Jaina Mistry,
Alex Mitchell,
Anastasia N. Nikolskaya,
Sandra E. Orchard,
Christine A. Orengo,
Robert Petryszak,
Jeremy D. Selengut,
Christian J. A. Sigrist,
Paul D. Thomas,
Franck Valentin,
Derek Wilson,
Cathy H. Wu,
Corin Yeats:
New developments in the InterPro database.
Nucleic Acids Research 35(Database-Issue): 224-228 (2007) |
| 2006 |
|---|
| 49 | | Natalia V. Petrova,
Cathy H. Wu:
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
BMC Bioinformatics 7: 312 (2006) |
| 48 | | Hongfang Liu,
Zhang-Zhi Hu,
Jian Zhang,
Cathy H. Wu:
BioThesaurus: a web-based thesaurus of protein and gene names.
Bioinformatics 22(1): 103-105 (2006) |
| 47 | | X. Yuan,
Zhang-Zhi Hu,
H. T. Wu,
Manabu Torii,
Meenakshi Narayanaswamy,
K. E. Ravikumar,
K. Vijay-Shanker,
Cathy H. Wu:
An online literature mining tool for protein phosphorylation.
Bioinformatics 22(13): 1668-1669 (2006) |
| 46 | | Bo Han,
Zoran Obradovic,
Zhang-Zhi Hu,
Cathy H. Wu,
Slobodan Vucetic:
Substring selection for biomedical document classification.
Bioinformatics 22(17): 2136-2142 (2006) |
| 45 | | Cathy H. Wu,
Rolf Apweiler,
Amos Bairoch,
Darren A. Natale,
Winona C. Barker,
Brigitte Boeckmann,
Serenella Ferro,
Elisabeth Gasteiger,
Hongzhan Huang,
Rodrigo Lopez,
Michele Magrane,
Maria Jesus Martin,
Raja Mazumder,
Claire O'Donovan,
Nicole Redaschi,
Baris E. Suzek:
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic Acids Research 34(Database-Issue): 187-191 (2006) |
| 2005 |
|---|
| 44 | | Hongfang Liu,
Zhang-Zhi Hu,
Cathy H. Wu:
Dynamically Generating a Protein Entity Dictionary Using Online Resources.
ACL 2005 |
| 43 | | Hongfang Liu,
Zhang-Zhi Hu,
Cathy H. Wu:
DynGO: a tool for visualizing and mining of Gene Ontology and its associations.
BMC Bioinformatics 6: 201 (2005) |
| 42 | | Raja Mazumder,
Darren A. Natale,
Sudhir Murthy,
Rathi Thiagarajan,
Cathy H. Wu:
Computational identification of strain-, species- and genus-specific proteins.
BMC Bioinformatics 6: 279 (2005) |
| 41 | | Zhang-Zhi Hu,
Meenakshi Narayanaswamy,
K. E. Ravikumar,
K. Vijay-Shanker,
Cathy H. Wu:
Literature mining and database annotation of protein phosphorylation using a rule-based system.
Bioinformatics 21(11): 2759-2765 (2005) |
| 40 | | Amos Bairoch,
Rolf Apweiler,
Cathy H. Wu,
Winona C. Barker,
Brigitte Boeckmann,
Serenella Ferro,
Elisabeth Gasteiger,
Hongzhan Huang,
Rodrigo Lopez,
Michele Magrane,
Maria Jesus Martin,
Darren A. Natale,
Claire O'Donovan,
Nicole Redaschi,
Lai-Su L. Yeh:
The Universal Protein Resource (UniProt).
Nucleic Acids Research 33(Database-Issue): 154-159 (2005) |
| 39 | | Nicola J. Mulder,
Rolf Apweiler,
Teresa K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Paul Bradley,
Peer Bork,
Phillip Bucher,
Lorenzo Cerutti,
Richard R. Copley,
Emmanuel Courcelle,
Ujjwal Das,
Richard Durbin,
Wolfgang Fleischmann,
Julian Gough,
Daniel H. Haft,
Nicola Harte,
Nicolas Hulo,
Daniel Kahn,
Alexander Kanapin,
Maria Krestyaninova,
David Lonsdale,
Rodrigo Lopez,
Ivica Letunic,
Martin Madera,
John Maslen,
Jennifer McDowall,
Alex Mitchell,
Anastasia N. Nikolskaya,
Sandra E. Orchard,
Marco Pagni,
Chris P. Ponting,
Emmanuel Quevillon,
Jeremy D. Selengut,
Christian J. A. Sigrist,
Ville Silventoinen,
David J. Studholme,
Robert Vaughan,
Cathy H. Wu:
InterPro, progress and status in 2005.
Nucleic Acids Research 33(Database-Issue): 201-205 (2005) |
| 2004 |
|---|
| 38 | | Cathy H. Wu,
Hongzhan Huang,
Anastasia N. Nikolskaya,
Zhang-Zhi Hu,
Winona C. Barker:
The iProClass integrated database for protein functional analysis.
Computational Biology and Chemistry 28(1): 87-96 (2004) |
| 37 | | Zhang-Zhi Hu,
Inderjeet Mani,
Vincent Hermoso,
Hongfang Liu,
Cathy H. Wu:
iProLINK: an integrated protein resource for literature mining.
Computational Biology and Chemistry 28(5-6): 409-416 (2004) |
| 36 | | Hongzhan Huang,
Zhang-Zhi Hu,
Baris E. Suzek,
Cathy H. Wu:
The PIR integrated protein databases and data retrieval system.
Data Science Journal 3: 163-174 (2004) |
| 35 | | Cathy H. Wu,
Anastasia N. Nikolskaya,
Hongzhan Huang,
Lai-Su L. Yeh,
Darren A. Natale,
C. R. Vinayaka,
Zhang-Zhi Hu,
Raja Mazumder,
Sandeep Kumar,
Panagiotis Kourtesis,
Robert S. Ledley,
Baris E. Suzek,
Leslie Arminski,
Yongxing Chen,
Jian Zhang,
Jorge Louie Cardenas,
Sehee Chung,
Jorge Castro-Alvear,
Georgi Dinkov,
Winona C. Barker:
PIRSF: family classification system at the Protein Information Resource.
Nucleic Acids Research 32(Database-Issue): 112-114 (2004) |
| 34 | | Rolf Apweiler,
Amos Bairoch,
Cathy H. Wu,
Winona C. Barker,
Brigitte Boeckmann,
Serenella Ferro,
Elisabeth Gasteiger,
Hongzhan Huang,
Rodrigo Lopez,
Michele Magrane,
Maria Jesus Martin,
Darren A. Natale,
Claire O'Donovan,
Nicole Redaschi,
Lai-Su L. Yeh:
UniProt: the Universal Protein knowledgebase.
Nucleic Acids Research 32(Database-Issue): 115-119 (2004) |
| 33 | | Katherine G. Herbert,
Narain H. Gehani,
William H. Piel,
Jason Tsong-Li Wang,
Cathy H. Wu:
BIO-AJAX: An Extensible Framework for Biological Data Cleaning.
SIGMOD Record 33(2): 51-57 (2004) |
| 2003 |
|---|
| 32 | | Jason Tsong-Li Wang,
Cathy H. Wu,
Paul P. Wang:
Computational Biology and Genome Informatics
World Scientific 2003 |
| 31 | | Lynette Hirschman,
Carol Friedman,
Robin McEntire,
Cathy H. Wu:
Linking Biomedical Language, Information and Knowledge - Session Introduction.
Pacific Symposium on Biocomputing 2003: 388-390 |
| 30 | | Cathy H. Wu:
The Protein Information Resource for Functional Genomics and Proteomics.
Computational Biology and Genome Informatics 2003: 117-137 |
| 29 | | Cathy H. Wu,
Hongzhan Huang,
Lai-Su L. Yeh,
Winona C. Barker:
Protein family classification and functional annotation.
Computational Biology and Chemistry 27(1): 37-47 (2003) |
| 28 | | Cathy H. Wu,
Lai-Su L. Yeh,
Hongzhan Huang,
Leslie Arminski,
Jorge Castro-Alvear,
Yongxing Chen,
Zhang-Zhi Hu,
Panagiotis Kourtesis,
Robert S. Ledley,
Baris E. Suzek,
C. R. Vinayaka,
Jian Zhang,
Winona C. Barker:
The Protein Information Resource.
Nucleic Acids Research 31(1): 345-347 (2003) |
| 27 | | Hongzhan Huang,
Winona C. Barker,
Yongxing Chen,
Cathy H. Wu:
iProClass: an integrated database of protein family, function and structure information.
Nucleic Acids Research 31(1): 390-392 (2003) |
| 2002 |
|---|
| 26 | | Lynette Hirschman,
Jong C. Park,
Jun-ichi Tsujii,
Cathy H. Wu,
Limsoon Wong:
Literature Data Mining for Biology - Session Introduction.
Pacific Symposium on Biocomputing 2002: 323-325 |
| 25 | | Lynette Hirschman,
Jong C. Park,
Jun-ichi Tsujii,
Limsoon Wong,
Cathy H. Wu:
Accomplishments and challenges in literature data mining for biology.
Bioinformatics 18(12): 1553-1561 (2002) |
| 24 | | Cathy H. Wu,
Hongzhan Huang,
Leslie Arminski,
Jorge Castro-Alvear,
Yongxing Chen,
Zhang-Zhi Hu,
Robert S. Ledley,
Kali C. Lewis,
Hans-Werner Mewes,
Bruce C. Orcutt,
Baris E. Suzek,
Akira Tsugita,
C. R. Vinayaka,
Lai-Su L. Yeh,
Jian Zhang,
Winona C. Barker:
The Protein Information Resource: an integrated public resource of functional annotation of proteins.
Nucleic Acids Research 30(1): 35-37 (2002) |
| 2001 |
|---|
| 23 | | Jason Tsong-Li Wang,
Qicheng Ma,
Dennis Shasha,
Cathy H. Wu:
New techniques for extracting features from protein sequences.
IBM Systems Journal 40(2): 426-441 (2001) |
| 22 | | Qicheng Ma,
Jason Tsong-Li Wang,
Dennis Shasha,
Cathy H. Wu:
DNA sequence classification via an expectation maximization algorithm and neural networks: a case study.
IEEE Transactions on Systems, Man, and Cybernetics, Part C 31(4): 468-475 (2001) |
| 21 | | Winona C. Barker,
John S. Garavelli,
Zhenglin Hou,
Hongzhan Huang,
Robert S. Ledley,
Peter B. McGarvey,
Hans-Werner Mewes,
Bruce C. Orcutt,
Friedhelm Pfeiffer,
Akira Tsugita,
C. R. Vinayaka,
Chunlin Xiao,
Lai-Su L. Yeh,
Cathy H. Wu:
Protein Information Resource: a community resource for expert annotation of protein data.
Nucleic Acids Research 29(1): 29-32 (2001) |
| 20 | | Cathy H. Wu,
Chunlin Xiao,
Zhenglin Hou,
Hongzhan Huang,
Winona C. Barker:
iProClass: an integrated, comprehensive and annotated protein classification database.
Nucleic Acids Research 29(1): 52-54 (2001) |
| 2000 |
|---|
| 19 | | Jason Tsong-Li Wang,
Qicheng Ma,
Dennis Shasha,
Cathy H. Wu:
Application of neural networks to biological data mining: a case study in protein sequence classification.
KDD 2000: 305-309 |
| 18 | | Peter B. McGarvey,
Hongzhan Huang,
Winona C. Barker,
Bruce C. Orcutt,
John S. Garavelli,
Geetha Y. Srinivasarao,
Lai-Su L. Yeh,
Chunlin Xiao,
Cathy H. Wu:
PIR: a new resource for bioinformatics.
Bioinformatics 16(3): 290-291 (2000) |
| 17 | | Hongzhan Huang,
Chunlin Xiao,
Cathy H. Wu:
ProClass protein family database.
Nucleic Acids Research 28(1): 273-276 (2000) |
| 16 | | Winona C. Barker,
John S. Garavelli,
Hongzhan Huang,
Peter B. McGarvey,
Bruce C. Orcutt,
Geetha Y. Srinivasarao,
Chunlin Xiao,
Lai-Su L. Yeh,
Robert S. Ledley,
Joseph F. Janda,
Friedhelm Pfeiffer,
Hans-Werner Mewes,
Akira Tsugita,
Cathy H. Wu:
The Protein Information Resource (PIR).
Nucleic Acids Research 28(1): 41-44 (2000) |
| 1999 |
|---|
| 15 | | Cathy H. Wu,
Hongzhan Huang,
Jerry McLarty:
Gene Family Identification Network Design for Protein Sequence Analysis.
International Journal on Artificial Intelligence Tools 8(4): 419-432 (1999) |
| 14 | | Cathy H. Wu,
Sailaja Shivakumar,
Hongzhan Huang:
ProClass Protein Family Database.
Nucleic Acids Research 27(1): 272-274 (1999) |
| 13 | | Winona C. Barker,
John S. Garavelli,
Peter B. McGarvey,
Christopher R. Marzec,
Bruce C. Orcutt,
Geetha Y. Srinivasarao,
Lai-Su L. Yeh,
Robert S. Ledley,
Hans-Werner Mewes,
Friedhelm Pfeiffer,
Akira Tsugita,
Cathy H. Wu:
The PIR-International Protein Sequence Database.
Nucleic Acids Research 27(1): 39-43 (1999) |
| 1998 |
|---|
| 12 | | Cathy H. Wu,
Sailaja Shivakumar,
Chittari V. Shivakumar,
Sheng-Chih Chen:
GeneFIND web server for protein family identification and information retrieval.
Bioinformatics 14(2): 223-224 (1998) |
| 1997 |
|---|
| 11 | | Cathy H. Wu,
Hsi-Lien Chen,
Sheng-Chih Chen:
Counter-Propagation Neural Networks for Molecular Sequence Classification: Supervised LVQ and Dynamic Node Allocation.
Appl. Intell. 7(1): 27-38 (1997) |
| 10 | | Cathy H. Wu:
Artificial Neural Networks for Molecular Sequence Analysis.
Computers & Chemistry 21(4): 237-255 (1997) |
| 1996 |
|---|
| 9 | | Cathy H. Wu,
S. Zhao,
H.-L. Chen,
C. J. Lo,
Jerry McLarty:
Motif identification neural design for rapid and sensitive protein family search.
Computer Applications in the Biosciences 12(2): 109-118 (1996) |
| 8 | | Cathy H. Wu,
S. Zhao,
H.-L. Chen:
A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies.
Journal of Computational Biology 3(4): 547-562 (1996) |
| 1995 |
|---|
| 7 | | Cathy H. Wu,
Michael W. Berry,
Sailaja Shivakumar:
Neural Networks for Full-Scale Protein Sequence Classification: Sequence Encoding with Singular Value Decomposition.
Machine Learning 21(1-2): 177-193 (1995) |
| 1993 |
|---|
| 6 | | Cathy H. Wu,
Michael W. Berry,
Yuk-Shing Fung,
Jerry McLarty:
Neural Networks for Molecular Sequence Classification.
ISMB 1993: 429-437 |
| 5 | | Cathy H. Wu:
Classification Neural Networks for Rapid Sequence Annotation and Automated Database Organization.
Computers & Chemistry 17(2): 219-227 (1993) |
| 1992 |
|---|
| 4 | | Cathy H. Wu,
George M. Whitson,
Chun-Tse Hsiao,
Cheng-Fu Huang:
Classification Artificial Neural Systems for Genome Research.
SC 1992: 797-803 |
| 1991 |
|---|
| 3 | | Cathy H. Wu,
Tzx-Chung Chang:
Protein Classification Using a Neural Network Database System.
Conference on Analysis of Neural Network Applications 1991: 29-41 |
| 1990 |
|---|
| 2 | | Cathy H. Wu,
George M. Whitson:
Artificial Neural System for Gene Classification Using a Domain Database.
ACM Conference on Computer Science 1990: 288-292 |
| 1 | | George M. Whitson,
Cathy H. Wu,
Pam Taylor:
Using an Artificial Neural System to Determine the Knowledge Base of an Expert System.
SIGSMALL/PC Symposium 1990: 268-270 |
