2005 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 2
OCTOBER-DECEMBER 2005 (Vol. 2, No. 4) pp. 380-384
1545-5963/05/$31.00 © 2005 IEEE

Published by the IEEE Computer Society
2005 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 2
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This index covers all technical items—papers, correspondence, reviews, etc.—that appeared in this periodical during 2005, and items from previous years that were commented upon or corrected in 2005. Departments and other items may also be covered if they have been judged to have archival value.
The Author Index contains the primary entry for each item, listed under the first author's name. The primary entry includes the coauthors' names, the title of the paper or other item, and its location, specified by the publication abbreviation, year, month, and inclusive pagination. The Subject Index contains entries describing the item under all appropriate subject headings, plus the first author's name, the publication abbreviation, month, and year, and inclusive pages. Subject cross-references are included to assist in finding items of interest. Note that the item title is found only under the primary entry in the Author Index.

AUTHOR INDEX

A

Alber, M.S., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Allali, J., and M.-F. Sagot. A new distance for high level RNA secondary structure comparison; T-CBB Jan-Mar 053-14

Au Wai-Ho, see Wai-Ho Au, T-CBB Apr-Jun 0583-101

B

Bafna, V., see Zhang, S., T-CBB Oct-Dec 05366-379

Bailey, T.C., see Turner, H.L., T-CBB Oct-Dec 05316-329

Benini, L., see Yoon, S., T-CBB Oct-Dec 05339-354

Bertrand, D., and O. Gascuel. Topological rearrangements and local search method for tandem duplication trees; T-CBB Jan-Mar 0515-28

Biyani, P., Xiaolin Wu, and A. Sinha. Joint classification and pairing of human chromosomes; T-CBB Apr-Jun 05102-109

Boden, M., see Hawkins, J., T-CBB Jul-Sep 05243-253

Boscolo, R., C. Sabatti, J.C. Liao, and V.P. Roychowdhury. A generalized framework for network component analysis; T-CBB Oct-Dec 05289-301

Breitling, R., see Rogers, S., T-CBB Apr-Jun 05143-156

Brown, D.G. Optimizing multiple seeds for protein homology search; T-CBB Jan-Mar 0529-38

C

Cai, J., see Zhang, J., T-CBB Jul-Sep 05217-230

Campbell, C., see Rogers, S., T-CBB Apr-Jun 05143-156

Chan, K.C.C., see Wai-Ho Au, T-CBB Apr-Jun 0583-101

Chaturvedi, R., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Chen, R., see Zhang, J., T-CBB Jul-Sep 05217-230

Chen, X., J. Zheng, Z. Fu, P. Nan, Y. Zhong, S. Lonardi, and T. Jiang. Assignment of orthologous genes via genome rearrangement; T-CBB Oct-Dec 05302-315

Chong Tan Eng, see Li Shen, T-CBB Apr-Jun 05166-175

Cickovski, T.M., C. Huang, R. Chaturvedi, T. Glimm, H.G.E. Hentschel, M.S. Alber, J.A. Glazier, S.A. Newman, and J.A. Izaguirre. A framework for three-dimensional simulation of morphogenesis; T-CBB Oct-Dec 05273-288

Ciliax, B.J., see Ying Liu, T-CBB Jan-Mar 0562-76

Civera, J., see Ying Liu, T-CBB Jan-Mar 0562-76

Corrales, F.J., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Costa, I.G., see Schliep, A., T-CBB Jul-Sep 05179-193

Crochemore, M., see Pisanti, N., T-CBB Jan-Mar 0540-50

D

Dasigi, V., see Ying Liu, T-CBB Jan-Mar 0562-76

De Micheli, G., see Yoon, S., T-CBB Oct-Dec 05339-354

Demir, C., S.H. Gultekin, and B. Yener. Learning the topological properties of brain tumors; T-CBB Jul-Sep 05262-270

Dingledine, R., see Ying Liu, T-CBB Jan-Mar 0562-76

E

Eng Chong Tan, see Li Shen, T-CBB Apr-Jun 05166-175

Eskin, E., see Zhang, S., T-CBB Oct-Dec 05366-379

F

Fu, Z., see Chen, X., T-CBB Oct-Dec 05302-315

Furlanello, C., M. Serafini, S. Merler, and G. Jurman. Semisupervised learning for molecular profiling; T-CBB Apr-Jun 05110-118

G

Gao, F., see Kundaje, A., T-CBB Jul-Sep 05194-202

Gao, W., see Zhang, J., T-CBB Jul-Sep 05217-230

Gascuel, O., see Bertrand, D., T-CBB Jan-Mar 0515-28

Girolami, M., see Rogers, S., T-CBB Apr-Jun 05143-156

Glazier, J.A., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Glimm, T., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Grossi, R., see Pisanti, N., T-CBB Jan-Mar 0540-50

Gultekin, S.H., see Demir, C., T-CBB Jul-Sep 05262-270

Guruceaga, E., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Gustafsson, M., M. Hornquist, and A. Lombardi. Constructing and analyzing a large-scale gene-to-gene regulatory network --lasso-constrained inference and biological validation; T-CBB Jul-Sep 05254-261

H

Haas, B., see Zhang, S., T-CBB Oct-Dec 05366-379

Hawkins, J., and M. Boden. The applicability of recurrent neural networks for biological sequence analysis; T-CBB Jul-Sep 05243-253

He, S., see Zhang, J., T-CBB Jul-Sep 05217-230

Hemingway, C.A., see Turner, H.L., T-CBB Oct-Dec 05316-329

Hentschel, H.G.E., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Ho Loi Sy, see Rajapakse, J.C., T-CBB Apr-Jun 05131-142

Hornquist, M., see Gustafsson, M., T-CBB Jul-Sep 05254-261

Huang, C., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

I

Izaguirre, J.A., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

J

Jiang, T., see Chen, X., T-CBB Oct-Dec 05302-315

Jinbo Xu. Fold recognition by predicted alignment accuracy; T-CBB Apr-Jun 05157-165

Jonassen, I., see Junhyong Kim, T-CBB Jan-Mar 051-2

Junhyong Kim, and I. Jonassen. Guest editorial: WABI Special Section Part II [special section intro. on the Fourth International Workshop on Algorithms in Bioinformatics, 2004]; T-CBB Jan-Mar 051-2

Jurman, G., see Furlanello, C., T-CBB Apr-Jun 05110-118

K

Kao, C.-P., see Tseng, V.S., T-CBB Oct-Dec 05355-365

Kaski, S., J. Nikkila, J. Sinkkonen, L. Lahti, J.E.A. Knuuttila, and C. Roos. Associative clustering for exploring dependencies between functional genomics data sets; T-CBB Jul-Sep 05203-216

Keedwell, E., and A. Narayanan. Discovering gene networks with a neural-genetic hybrid; T-CBB Jul-Sep 05231-242

Kim Junhyong, see Junhyong Kim, T-CBB Jan-Mar 051-2

Knuuttila, J.E.A., see Kaski, S., T-CBB Jul-Sep 05203-216

Krzanowski, W.J., see Turner, H.L., T-CBB Oct-Dec 05316-329

Kucherov, G., L. Noe, and M. Roytberg. Multiseed lossless filtration; T-CBB Jan-Mar 0551-61

Kundaje, A., M. Middendorf, F. Gao, C. Wiggins, and C. Leslie. Combining sequence and time series expression data to learn transcriptional modules; T-CBB Jul-Sep 05194-202

L

Lahti, L., see Kaski, S., T-CBB Jul-Sep 05203-216

Leslie, C., see Kundaje, A., T-CBB Jul-Sep 05194-202

Liao, J.C., see Boscolo, R., T-CBB Oct-Dec 05289-301

Ling, C.X., W.S. Noble, and Qiang Yang. Guest editor's introduction to the special issue: Machine learning for bioinformatics, Part 1; T-CBB Apr-Jun 0581-82

Ling, C.X., W.S. Noble, and Qiang Yang. Guest editor's introduction to the special section: Machine learning for bioinformatics, Part 2 [special section intro.]; T-CBB Jul-Sep 05177-178

Li Shen, and Eng Chong Tan. Dimension reduction-based penalized logistic regression for cancer classification using microarray data; T-CBB Apr-Jun 05166-175

Liu Ying, see Ying Liu, T-CBB Jan-Mar 0562-76

Loi Sy Ho, see Rajapakse, J.C., T-CBB Apr-Jun 05131-142

Lombardi, A., see Gustafsson, M., T-CBB Jul-Sep 05254-261

Lonardi, S., see Chen, X., T-CBB Oct-Dec 05302-315

M

Mamitsuka, H. Essential latent knowledge for protein-protein interactions: analysis by an unsupervised learning approach; T-CBB Apr-Jun 05119-130

Martinez-Cruz, L.A., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Mato, J.M., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Merler, S., see Furlanello, C., T-CBB Apr-Jun 05110-118

Middendorf, M., see Kundaje, A., T-CBB Jul-Sep 05194-202

N

Nan, P., see Chen, X., T-CBB Oct-Dec 05302-315

Narayanan, A., see Keedwell, E., T-CBB Jul-Sep 05231-242

Nardini, C., see Yoon, S., T-CBB Oct-Dec 05339-354

Navathe, S.B., see Ying Liu, T-CBB Jan-Mar 0562-76

Newman, S.A., see Cickovski, T.M., T-CBB Oct-Dec 05273-288

Nikkila, J., see Kaski, S., T-CBB Jul-Sep 05203-216

Noble, W.S., see Ling, C.X., T-CBB Apr-Jun 0581-82

Noble, W.S., see Ling, C.X., T-CBB Jul-Sep 05177-178

Noe, L., see Kucherov, G., T-CBB Jan-Mar 0551-61

P

Pisanti, N., M. Crochemore, R. Grossi, and M.-F. Sagot. Bases of motifs for generating repeated patterns with wild cards; T-CBB Jan-Mar 0540-50

Podhorski, A., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Q

Qiang Yang, see Ling, C.X., T-CBB Apr-Jun 0581-82

Qiang Yang, see Ling, C.X., T-CBB Jul-Sep 05177-178

R

Rajapakse, J.C., and Loi Sy Ho. Markov encoding for detecting signals in genomic sequences; T-CBB Apr-Jun 05131-142

Ram, A., see Ying Liu, T-CBB Jan-Mar 0562-76

Rogers, S., M. Girolami, C. Campbell, and R. Breitling. The latent process decomposition of cDNA microarray data sets; T-CBB Apr-Jun 05143-156

Roos, C., see Kaski, S., T-CBB Jul-Sep 05203-216

Roychowdhury, V.P., see Boscolo, R., T-CBB Oct-Dec 05289-301

Roytberg, M., see Kucherov, G., T-CBB Jan-Mar 0551-61

Rubio, A., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

S

Sabatti, C., see Boscolo, R., T-CBB Oct-Dec 05289-301

Sagot, M.-F., see Allali, J., T-CBB Jan-Mar 053-14

Sagot, M.-F., see Pisanti, N., T-CBB Jan-Mar 0540-50

Schliep, A., I.G. Costa, C. Steinhoff, and A. Schonhuth. Analyzing gene expression time-courses; T-CBB Jul-Sep 05179-193

Schonhuth, A., see Schliep, A., T-CBB Jul-Sep 05179-193

Segura, V., see Sevilla, J.L., T-CBB Oct-Dec 05330-338

Serafini, M., see Furlanello, C., T-CBB Apr-Jun 05110-118

Sevilla, J.L., V. Segura, A. Podhorski, E. Guruceaga, J.M. Mato, L.A. Martinez-Cruz, F.J. Corrales, and A. Rubio. Correlation between gene expression and GO semantic similarity; T-CBB Oct-Dec 05330-338

Shen Li, see Li Shen, T-CBB Apr-Jun 05166-175

Sinha, A., see Biyani, P., T-CBB Apr-Jun 05102-109

Sinkkonen, J., see Kaski, S., T-CBB Jul-Sep 05203-216

Steinhoff, C., see Schliep, A., T-CBB Jul-Sep 05179-193

Sy Ho Loi, see Rajapakse, J.C., T-CBB Apr-Jun 05131-142

T

Tan Eng Chong, see Li Shen, T-CBB Apr-Jun 05166-175

Tseng, V.S., and C.-P. Kao. Efficiently mining gene expression data via a novel parameterless clustering method; T-CBB Oct-Dec 05355-365

Turner, H.L., T.C. Bailey, W.J. Krzanowski, and C.A. Hemingway. Biclustering models for structured microarray data; T-CBB Oct-Dec 05316-329

W

Wai-Ho Au, K.C.C. Chan, A.K.C. Wong, and Yang Wang. Attribute clustering for grouping, selection, and classification of gene expression data; T-CBB Apr-Jun 0583-101

Wang Yang, see Wai-Ho Au, T-CBB Apr-Jun 0583-101

Wiggins, C., see Kundaje, A., T-CBB Jul-Sep 05194-202

Wong, A.K.C., see Wai-Ho Au, T-CBB Apr-Jun 0583-101

Wu Xiaolin, see Biyani, P., T-CBB Apr-Jun 05102-109

X

Xiaolin Wu, see Biyani, P., T-CBB Apr-Jun 05102-109

Xu Jinbo, see Jinbo Xu, T-CBB Apr-Jun 05157-165

Y

Yang Qiang, see Ling, C.X., T-CBB Apr-Jun 0581-82

Yang Qiang, see Ling, C.X., T-CBB Jul-Sep 05177-178

Yang Wang, see Wai-Ho Au, T-CBB Apr-Jun 0583-101

Yener, B., see Demir, C., T-CBB Jul-Sep 05262-270

Ying Liu, S.B. Navathe, J. Civera, V. Dasigi, A. Ram, B.J. Ciliax, and R. Dingledine. Text mining biomedical literature for discovering gene-to-gene relationships: A comparative study of algorithms; T-CBB Jan-Mar 0562-76

Yoon, S., C. Nardini, L. Benini, and G. De Micheli. Discovering coherent biclusters from gene expression data using zero suppressed binary decision diagrams; T-CBB Oct-Dec 05339-354

Z

Zeng, R., see Zhang, J., T-CBB Jul-Sep 05217-230

Zhang, J., W. Gao, J. Cai, S. He, R. Zeng, and R. Chen. Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra; T-CBB Jul-Sep 05217-230

Zhang, S., B. Haas, E. Eskin, and V. Bafna. Searching genomes for noncoding RNA using FastR; T-CBB Oct-Dec 05366-379

Zheng, J., see Chen, X., T-CBB Oct-Dec 05302-315

Zhong, Y., see Chen, X., T-CBB Oct-Dec 05302-315

SUBJECT INDEX

A
Arrays

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

Artificial intelligence;
see Learning (artificial intelligence)
B
Bayes procedures

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

Biocomputing

bases of motifs for generating repeated patterns with wild cards. Pisanti, N., + , T-CBB Jan-Mar 0540-50

multiseed lossless filtration. Kucherov, G., + , T-CBB Jan-Mar 0551-61

optimizing multiple seeds for protein homology search. Brown, D.G., T-CBB Jan-Mar 0529-38

topological rearrangements and local search method for tandem duplication trees. Bertrand, D., + , T-CBB Jan-Mar 0515-28

Biological cells

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

Biological organs;
see Brain
Biological system modeling

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

Biological tissues

framework for three-dimensional simulation of morphogenesis. Cickovski, T.M., + , T-CBB Oct-Dec 05273-288

Biological tissues;
see Tumors
Biology

applicability of recurrent neural networks for biological sequence analysis. Hawkins, J., + , T-CBB Jul-Sep 05243-253

associative clustering for exploring dependencies between functional genomics data sets. Kaski, S., + , T-CBB Jul-Sep 05203-216

generalized framework for network component analysis. Boscolo, R., + , T-CBB Oct-Dec 05289-301

lasso-constrained inference and biological validation. Gustafsson, M., + , T-CBB Jul-Sep 05254-261

machine learning for bioinformatics, Part 1 (special issue). T-CBB Apr-Jun 0581-175

machine learning for bioinformatics, Part 1 (special issue intro.). Ling, C. X., + , T-CBB Apr-Jun 0581-82

machine learning for bioinformatics, Part 2 (special section). T-CBB Jul-Sep 05177-253

machine learning for bioinformatics, Part 2 (special section intro.). Ling, C.X., + , T-CBB Jul-Sep 05177-178

predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra. Zhang, J., + , T-CBB Jul-Sep 05217-230

Biology;
see Genetics
Biomedical computing

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

detecting sigs., genomic seqs., Markov encoding. Rajapakse, J.C., + , T-CBB Apr-Jun 05131-142

grouping, selection, class. of gene expression data, attribute clustering. Wai-Ho Au, + , T-CBB Apr-Jun 0583-101

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

mol. profiling, semisupervised learning. Furlanello, C., + , T-CBB Apr-Jun 05110-118

predicted alignment accuracy, fold recogn. Jinbo Xu, T-CBB Apr-Jun 05157-165

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

Biomedical engineering

bases of motifs for generating repeated patterns with wild cards. Pisanti, N., + , T-CBB Jan-Mar 0540-50

biclustering models for structured microarray data. Turner, H.L., + , T-CBB Oct-Dec 05316-329

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

text mining biomedical literature for discovering gene-to-gene relationships, comparative study of algorithms. Ying Liu, + , T-CBB Jan-Mar 0562-76

Biophysics;
see Cellular biophysics; Molecular biophysics
Brain

learning the topological properties of brain tumors. Demir, C., + , T-CBB Jul-Sep 05262-270

C
Cellular automata

framework for three-dimensional simulation of morphogenesis. Cickovski, T.M., + , T-CBB Oct-Dec 05273-288

Cellular biophysics

assignment of orthologous genes via genome rearrangement. Chen, X., + , T-CBB Oct-Dec 05302-315

Cluster approximation

associative clustering for exploring dependencies between functional genomics data sets. Kaski, S., + , T-CBB Jul-Sep 05203-216

biclustering models for structured microarray data. Turner, H.L., + , T-CBB Oct-Dec 05316-329

coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. Yoon, S., + , T-CBB Oct-Dec 05339-354

combining sequence and time series expression data to learn transcriptional modules. Kundaje, A., + , T-CBB Jul-Sep 05194-202

mining gene expression data via a novel parameterless clustering method. Tseng, V.S., + , T-CBB Oct-Dec 05355-365

text mining biomedical literature for discovering gene-to-gene relationships, comparative study of algorithms. Ying Liu, + , T-CBB Jan-Mar 0562-76

Complexity theory

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

Correlation theory

correlation between gene expression and GO semantic similarity. Sevilla, J.L., + , T-CBB Oct-Dec 05330-338

D
Data analysis

generalized framework for network component analysis. Boscolo, R., + , T-CBB Oct-Dec 05289-301

Database management systems;
see Distributed databases; Relational databases
Data handling;
see Data analysis
Data mining

mining gene expression data via a novel parameterless clustering method. Tseng, V.S., + , T-CBB Oct-Dec 05355-365

text mining biomedical literature for discovering gene-to-gene relationships, comparative study of algorithms. Ying Liu, + , T-CBB Jan-Mar 0562-76

Data models

coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. Yoon, S., + , T-CBB Oct-Dec 05339-354

correlation between gene expression and GO semantic similarity. Sevilla, J.L., + , T-CBB Oct-Dec 05330-338

Data structures;
see Data models; Tree data structures
Display instrumentation;
see Three-dimensional displays
Distributed databases

combining sequence and time series expression data to learn transcriptional modules. Kundaje, A., + , T-CBB Jul-Sep 05194-202

Distributed processing;
see Distributed databases
DNA

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

E
Encoding

detecting sigs., genomic seqs., Markov encoding. Rajapakse, J.C., + , T-CBB Apr-Jun 05131-142

Engineering;
see Biomedical engineering
Entropy

mol. profiling, semisupervised learning. Furlanello, C., + , T-CBB Apr-Jun 05110-118

Estimation theory;
see Maximum likelihood estimation
Evolutionary computation;
see Cellular automata; Genetic algorithms
F
Filtration

multiseed lossless filtration. Kucherov, G., + , T-CBB Jan-Mar 0551-61

Finite automata;
see Cellular automata
G
Genetic algorithms

discovering gene networks with a neural-genetic hybrid. Keedwell, E., + , T-CBB Jul-Sep 05231-242

Genetic engineering

assignment of orthologous genes via genome rearrangement. Chen, X., + , T-CBB Oct-Dec 05302-315

coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. Yoon, S., + , T-CBB Oct-Dec 05339-354

correlation between gene expression and GO semantic similarity. Sevilla, J.L., + , T-CBB Oct-Dec 05330-338

mining gene expression data via a novel parameterless clustering method. Tseng, V.S., + , T-CBB Oct-Dec 05355-365

searching genomes for noncoding RNA using FastR. Zhang, S., + , T-CBB Oct-Dec 05366-379

topological rearrangements and local search method for tandem duplication trees. Bertrand, D., + , T-CBB Jan-Mar 0515-28

Genetics

analyzing gene expression time-courses. Schliep, A., + , T-CBB Jul-Sep 05179-193

assignment of orthologous genes via genome rearrangement. Chen, X., + , T-CBB Oct-Dec 05302-315

associative clustering for exploring dependencies between functional genomics data sets. Kaski, S., + , T-CBB Jul-Sep 05203-216

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. Yoon, S., + , T-CBB Oct-Dec 05339-354

combining sequence and time series expression data to learn transcriptional modules. Kundaje, A., + , T-CBB Jul-Sep 05194-202

correlation between gene expression and GO semantic similarity. Sevilla, J.L., + , T-CBB Oct-Dec 05330-338

detecting sigs., genomic seqs., Markov encoding. Rajapakse, J.C., + , T-CBB Apr-Jun 05131-142

discovering gene networks with a neural-genetic hybrid. Keedwell, E., + , T-CBB Jul-Sep 05231-242

generalized framework for network component analysis. Boscolo, R., + , T-CBB Oct-Dec 05289-301

grouping, selection, class. of gene expression data, attribute clustering. Wai-Ho Au, + , T-CBB Apr-Jun 0583-101

lasso-constrained inference and biological validation. Gustafsson, M., + , T-CBB Jul-Sep 05254-261

mining gene expression data via a novel parameterless clustering method. Tseng, V.S., + , T-CBB Oct-Dec 05355-365

mol. profiling, semisupervised learning. Furlanello, C., + , T-CBB Apr-Jun 05110-118

predicted alignment accuracy, fold recogn. Jinbo Xu, T-CBB Apr-Jun 05157-165

searching genomes for noncoding RNA using FastR. Zhang, S., + , T-CBB Oct-Dec 05366-379

H
Hidden Markov models

analyzing gene expression time-courses. Schliep, A., + , T-CBB Jul-Sep 05179-193

Humanities;
see Literature
I
IEEE

list of reviewers, 2004. T-CBB Jan-Mar 0577-78

Information systems;
see Medical information systems
Information theory;
see Correlation theory; Encoding; Entropy
K
Knowledge acquisition;
see Data mining
L
Learning (artificial intelligence)

analyzing gene expression time-courses. Schliep, A., + , T-CBB Jul-Sep 05179-193

Learning (artificial intelligence);
see Unsupervised learning
Learning systems

applicability of recurrent neural networks for biological sequence analysis. Hawkins, J., + , T-CBB Jul-Sep 05243-253

associative clustering for exploring dependencies between functional genomics data sets. Kaski, S., + , T-CBB Jul-Sep 05203-216

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

learning the topological properties of brain tumors. Demir, C., + , T-CBB Jul-Sep 05262-270

machine learning for bioinformatics, Part 1 (special issue). T-CBB Apr-Jun 0581-175

machine learning for bioinformatics, Part 1 (special issue intro.). Ling, C. X., + , T-CBB Apr-Jun 0581-82

machine learning for bioinformatics, Part 2 (special section). T-CBB Jul-Sep 05177-253

machine learning for bioinformatics, Part 2 (special section intro.). Ling, C.X., + , T-CBB Jul-Sep 05177-178

mol. profiling, semisupervised learning. Furlanello, C., + , T-CBB Apr-Jun 05110-118

Least squares methods

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

Literature

text mining biomedical literature for discovering gene-to-gene relationships, comparative study of algorithms. Ying Liu, + , T-CBB Jan-Mar 0562-76

Logistics

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

M
Macromolecules

new distance for high level RNA secondary structure comparison. Allali, J., + , T-CBB Jan-Mar 053-14

searching genomes for noncoding RNA using FastR. Zhang, S., + , T-CBB Oct-Dec 05366-379

Macromolecules;
see DNA
Markov processes

detecting sigs., genomic seqs., Markov encoding. Rajapakse, J.C., + , T-CBB Apr-Jun 05131-142

Markov processes;
see Hidden Markov models
Mass spectroscopy

predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra. Zhang, J., + , T-CBB Jul-Sep 05217-230

Mathematics;
see Probability; Statistics
Maximum likelihood estimation

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

Medical administrative data processing;
see Medical information systems
Medical diagnosis

cancer class., microarray data, dimens. reduction-based penalized logistic regression. Li Shen, + , T-CBB Apr-Jun 05166-175

Medical information processing

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Jan-Mar 051-38

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Jan-Mar 051-2

Medical information systems

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Jan-Mar 051-38

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Jan-Mar 051-2

learning the topological properties of brain tumors. Demir, C., + , T-CBB Jul-Sep 05262-270

optimizing multiple seeds for protein homology search. Brown, D.G., T-CBB Jan-Mar 0529-38

Meetings

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Jan-Mar 051-38

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Jan-Mar 051-2

Metals;
see Zinc
Microorganisms

searching genomes for noncoding RNA using FastR. Zhang, S., + , T-CBB Oct-Dec 05366-379

Molecular biophysics

analyzing gene expression time-courses. Schliep, A., + , T-CBB Jul-Sep 05179-193

Molecules;
see Macromolecules; Molecular biophysics
N
Natural sciences;
see Biology
Neural nets

applicability of recurrent neural networks for biological sequence analysis. Hawkins, J., + , T-CBB Jul-Sep 05243-253

discovering gene networks with a neural-genetic hybrid. Keedwell, E., + , T-CBB Jul-Sep 05231-242

Neural networks

detecting sigs., genomic seqs., Markov encoding. Rajapakse, J.C., + , T-CBB Apr-Jun 05131-142

O
Optimization;
see Genetic algorithms
Optimization methods

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

Organic compounds

lasso-constrained inference and biological validation. Gustafsson, M., + , T-CBB Jul-Sep 05254-261

Organic compounds;
see DNA; Proteins
P
Parameter estimation;
see Maximum likelihood estimation
Prediction methods

predicted alignment accuracy, fold recogn. Jinbo Xu, T-CBB Apr-Jun 05157-165

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

Probability

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

human chromosomes, joint class. and pairing. Biyani, P., + , T-CBB Apr-Jun 05102-109

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

Proteins

predicted alignment accuracy, fold recogn. Jinbo Xu, T-CBB Apr-Jun 05157-165

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

R
Randomized algorithms;
see Genetic algorithms
Relational databases

grouping, selection, class. of gene expression data, attribute clustering. Wai-Ho Au, + , T-CBB Apr-Jun 0583-101

S
Sequences

applicability of recurrent neural networks for biological sequence analysis. Hawkins, J., + , T-CBB Jul-Sep 05243-253

bases of motifs for generating repeated patterns with wild cards. Pisanti, N., + , T-CBB Jan-Mar 0540-50

multiseed lossless filtration. Kucherov, G., + , T-CBB Jan-Mar 0551-61

predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra. Zhang, J., + , T-CBB Jul-Sep 05217-230

Simulation

framework for three-dimensional simulation of morphogenesis. Cickovski, T.M., + , T-CBB Oct-Dec 05273-288

Special issues and sections

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Jan-Mar 051-38

2004 Fourth International Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Jan-Mar 051-2

Spectroscopy

predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra. Zhang, J., + , T-CBB Jul-Sep 05217-230

Spectroscopy;
see Mass spectroscopy
Statistical analysis;
see Maximum likelihood estimation
Statistics

cDNA microarray data sets, latent proc. decomp. Rogers, S., + , T-CBB Apr-Jun 05143-156

grouping, selection, class. of gene expression data, attribute clustering. Wai-Ho Au, + , T-CBB Apr-Jun 0583-101

Statistics;
see Time series
Stochastic processes;
see Markov processes
T
Thermodynamic properties;
see Entropy
Three-dimensional displays

framework for three-dimensional simulation of morphogenesis. Cickovski, T.M., + , T-CBB Oct-Dec 05273-288

generalized framework for network component analysis. Boscolo, R., + , T-CBB Oct-Dec 05289-301

Time series

combining sequence and time series expression data to learn transcriptional modules. Kundaje, A., + , T-CBB Jul-Sep 05194-202

lasso-constrained inference and biological validation. Gustafsson, M., + , T-CBB Jul-Sep 05254-261

Tree data structures

new distance for high level RNA secondary structure comparison. Allali, J., + , T-CBB Jan-Mar 053-14

Trees (graphs)

high level RNA secondary struct. comp., dist. Allali, J., + , T-CBB Jan-Mar 053-14

Tumors

learning the topological properties of brain tumors. Demir, C., + , T-CBB Jul-Sep 05262-270

U
Unsupervised learning

coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. Yoon, S., + , T-CBB Oct-Dec 05339-354

protein-protein interacts., essential latent knowledge. Mamitsuka, H., T-CBB Apr-Jun 05119-130

X
XML

framework for three-dimensional simulation of morphogenesis. Cickovski, T.M., + , T-CBB Oct-Dec 05273-288

Z
Zinc

topological rearrangements and local search method for tandem duplication trees. Bertrand, D., + , T-CBB Jan-Mar 0515-28

 
 
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