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Issue No.04 - October-December (2004 vol.1)
pp: 191-192
Published by the IEEE Computer Society
This index covers all technical items—papers, correspondence, reviews, etc.—that appeared in this periodical during 2004, and items from previous years that were commented upon or corrected in 2004. 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

B

Bafna, V., and V. Bansal.The number of recombination events in a sample history: conflict graph and lower bounds; T-CBB April-Jun 04 78-90

Banni, H., H. Hyyro, A. Shinohara, M. Takeda, K. Nakai, and S. Miyano. An O(N2) algorithm for discovering optimal Boolean pattern pairs; T-CBB Oct.-Dec 04 159-170

Bansal, V., see Bafna, V., T-CBB April-Jun 04 78-90

C

Cameron, M., H.E. Williams, and A. Cannane. Improved gapped alignment in BLAST; T-CBB July-Sep 04 116-129

Cannane, A., see Cameron, M., T-CBB July-Sep 04 116-129

Csuros, M. Maximum-scoring segment sets; T-CBB Oct.-Dec 04 139-150

D

Dezulian, T., see Huson, D.H., T-CBB Oct.-Dec 04 151-158

Dress, A.W.M., and D.H. Huson.Constructing splits graphs; T-CBB July-Sep 04 109-115

E

Evans, S.N., and T. Warnow. Unidentifiable divergence times in rates-across-sites models; T-CBB July-Sep 04 130-134

G

Giegerich, R., see Hochsmann, M., T-CBB Jan.-Mar 04 53-62

Gramm, J. A polynomial-time algorithm for the matching of crossing contact-map patterns; T-CBB Oct.-Dec 04 171-180

Gusfield, D. Introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics; T-CBB Jan.-Mar 04 2-3

H

Hochsmann, M., B. Voss, and R. Giegerich.Pure multiple RNA secondary structure alignments: a progressive profile approach; T-CBB Jan.-Mar 04 53-62

Hofacker, I.L., see Witwer, C., T-CBB April-Jun 04 66-77

Huson, D.H., see Dress, A.W.M., T-CBB July-Sep 04 109-115

Huson, D.H., T. Dezulian, T. Klopper, and M.A. Steel. Phylogenetic super-networks from partial trees; T-CBB Oct.-Dec 04 151-158

Hyyro, H., see Banni, H., T-CBB Oct.-Dec 04 159-170

J

Janardan, R., see Ye, J., T-CBB Oct.-Dec 04 181-190

Jonassen, I., see Junhyong Kim, T-CBB Oct.-Dec 04 137-138

Junhyong Kim, and I. Jonassen. Guest editorial: WABI special section part I [special section intro.]; T-CBB Oct.-Dec 04 137-138

K

Kim Junhyong, see Junhyong Kim, T-CBB Oct.-Dec 04 137-138

Klopper, T., see Huson, D.H., T-CBB Oct.-Dec 04 151-158

L

Li, T., see Ye, J., T-CBB Oct.-Dec 04 181-190

Linder, C.R., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

Liu, L.-T., see Raphael, B., T-CBB April-Jun 04 91-94

M

Madeira, S.C., and A.L. Oliveira. Biclustering algorithms for biological data analysis: a survey; T-CBB Jan.-Mar 04 24-45

Miyano, S., see Banni, H., T-CBB Oct.-Dec 04 159-170

Moret, B.M.E., L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme. Phylogenetic networks: modeling, reconstructibility, and accuracy; T-CBB Jan.-Mar 04 13-23

N

Nakai, K., see Banni, H., T-CBB Oct.-Dec 04 159-170

Nakhleh, L., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

O

Oliveira, A.L., see Madeira, S.C., T-CBB Jan.-Mar 04 24-45

P

Padolina, A., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

Preparata, F.P. Sequencing-by-hybridization revisited: the analog-spectrum proposal; T-CBB Jan.-Mar 04 46-52

R

Raphael, B., L.-T. Liu, and G. Varghese. A uniform projection method for motif discovery in DNA sequences; T-CBB April-Jun 04 91-94

S

Scheid, S., and R. Spang. A stochastic downhill search algorithm for estimating the local false discovery rate; T-CBB July-Sep 04 98-108

Shinohara, A., see Banni, H., T-CBB Oct.-Dec 04 159-170

Spang, R., see Scheid, S., T-CBB July-Sep 04 98-108

Stadler, P.F., see Witwer, C., T-CBB April-Jun 04 66-77

Steel, M.A., see Huson, D.H., T-CBB Oct.-Dec 04 151-158

Sun, J., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

T

Takeda, M., see Banni, H., T-CBB Oct.-Dec 04 159-170

Tholse, A., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

Timme, R., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

V

Varghese, G., see Raphael, B., T-CBB April-Jun 04 91-94

Voss, B., see Hochsmann, M., T-CBB Jan.-Mar 04 53-62

W

Warnow, T., see Moret, B.M.E., T-CBB Jan.-Mar 04 13-23

Warnow, T., see Evans, S.N., T-CBB July-Sep 04 130-134

Williams, H.E., see Cameron, M., T-CBB July-Sep 04 116-129

Witwer, C., I.L. Hofacker, and P.F. Stadler.Prediction of consensus RNA secondary structures including pseudoknots; T-CBB April-Jun 04 66-77

X

Xiong, T., see Ye, J., T-CBB Oct.-Dec 04 181-190

Y

Ye, J., T. Li, T. Xiong, and R. Janardan. Using uncorrelated discriminant analysis for tissue classification with gene expression data; T-CBB Oct.-Dec 04 181-190

SUBJECT INDEX

A
Algebra;
see Polynomials
Algorithm theory

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

O(N2) algorithm for discovering optimal Boolean pattern pairs. Banni, H., + , T-CBB Oct.-Dec 04 159-170

B
Biochemistry

polynomial-time algorithm for the matching of crossing contact-map patterns. Gramm, J., T-CBB Oct.-Dec 04 171-180

Biocomputing

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Gusfield, D., T-CBB Jan.-Mar 04 2-3

maximum-scoring segment sets. Csuros, M., T-CBB Oct.-Dec 04 139-150

O(N2) algorithm for discovering optimal Boolean pattern pairs. Banni, H., + , T-CBB Oct.-Dec 04 159-170

phylogenetic super-networks from partial trees. Huson, D.H., + , T-CBB Oct.-Dec 04 151-158

polynomial-time algorithm for the matching of crossing contact-map patterns. Gramm, J., T-CBB Oct.-Dec 04 171-180

uncorrelated discriminant analysis for tissue classification with gene expression data. Ye, J., + , T-CBB Oct.-Dec 04 181-190

Biological system modeling

phylogenetic nets., modeling, reconstructibility, accuracy. Moret, B.M.E., + , T-CBB Jan.-Mar 04 13-23

recomb. events, sample hist., no. Bafna, V., + , T-CBB April-Jun 04 78-90

sequencing-by-hybridization, analog-spectrum proposal. Preparata, F.P., T-CBB Jan.-Mar 04 46-52

Biological tissues

uncorrelated discriminant analysis for tissue classification with gene expression data. Ye, J., + , T-CBB Oct.-Dec 04 181-190

Biology

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Gusfield, D., T-CBB Jan.-Mar 04 2-3

Biology;
see Biochemistry; Genetics
Biology computing

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Gusfield, D., T-CBB Jan.-Mar 04 2-3

maximum-scoring segment sets. Csuros, M., T-CBB Oct.-Dec 04 139-150

phylogenetic super-networks from partial trees. Huson, D.H., + , T-CBB Oct.-Dec 04 151-158

Biomedical computing

consensus RNA secondary structs. incl. pseudoknots, predict. Witwer, C., + , T-CBB April-Jun 04 66-77

data anal., survey, biclustering algms. Madeira, S.C., + , T-CBB Jan.-Mar 04 24-45

motif discovery, DNA seqs., uniform projection method. Raphael, B., + , T-CBB April-Jun 04 91-94

pure multiple RNA secondary struct. alignments. Hochsmann, M., + , T-CBB Jan.-Mar 04 53-62

recomb. events, sample hist., no. Bafna, V., + , T-CBB April-Jun 04 78-90

Boolean algebra;
see Boolean functions
Boolean functions

O(N2) algorithm for discovering optimal Boolean pattern pairs. Banni, H., + , T-CBB Oct.-Dec 04 159-170

C
Chemistry;
see Biochemistry
Classification

uncorrelated discriminant analysis for tissue classification with gene expression data. Ye, J., + , T-CBB Oct.-Dec 04 181-190

Computation theory

Introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Gusfield, D., T-CBB Jan.-Mar 04 2-3

maximum-scoring segment sets. Csuros, M., T-CBB Oct.-Dec 04 139-150

Computation theory;
see Algorithm theory
Computer graphics

constructing splits graphs. Dress, A.W.M., + , T-CBB July-Sep 04 109-115

D
Directed graphs

phylogenetic nets., modeling, reconstructibility, accuracy. Moret, B.M.E., + , T-CBB Jan.-Mar 04 13-23

Display instrumentation;
see Three-dimensional displays
DNA

motif discovery, DNA seqs., uniform projection method. Raphael, B., + , T-CBB April-Jun 04 91-94

sequencing-by-hybridization, analog-spectrum proposal. Preparata, F.P., T-CBB Jan.-Mar 04 46-52

Dynamic programming

improved gapped alignment in BLAST. Cameron, M., + , T-CBB July-Sep 04 116-129

E
Energy states;
see Molecular orientation
Error analysis

stochastic downhill search algorithm for estimating the local false discovery rate. Scheid, S., + , T-CBB July-Sep 04 98-108

Estimation theory;
see Maximum likelihood estimation
F
Formal logic;
see Boolean functions
Functions;
see Boolean functions
G
Gamma distribution

unidentifiable divergence times in rates-across-sites models. Evans, S.N., + , T-CBB July-Sep 04 130-134

Genetics

iol. data anal., survey, biclustering algms. Madeira, S.C., + , T-CBB Jan.-Mar 04 24-45

constructing splits graphs. Dress, A.W.M., + , T-CBB July-Sep 04 109-115

phylogenetic super-networks from partial trees. Huson, D.H., + , T-CBB Oct.-Dec 04 151-158

recomb. events, sample hist., no. Bafna, V., + , T-CBB April-Jun 04 78-90

stochastic downhill search algorithm for estimating the local false discovery rate. Scheid, S., + , T-CBB July-Sep 04 98-108

uncorrelated discriminant analysis for tissue classification with gene expression data. Ye, J., + , T-CBB Oct.-Dec 04 181-190

unidentifiable divergence times in rates-across-sites models. Evans, S.N., + , T-CBB July-Sep 04 130-134

Graph theory;
see Directed graphs
I
Information analysis

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Gusfield, D., T-CBB Jan.-Mar 04 2-3

maximum-scoring segment sets. Csuros, M., T-CBB Oct.-Dec 04 139-150

Information analysis;
see Classification
Information science;
see Information analysis
Information systems;
see Medical information systems
L
Liquid structure;
see Molecular orientation
M
Macromolecules;
see DNA
Mathematical programming;
see Dynamic programming
Mathematics;
see Statistics
Maximum likelihood estimation

unidentifiable divergence times in rates-across-sites models. Evans, S.N., + , T-CBB July-Sep 04 130-134

Medical administrative data processing;
see Medical information systems
Medical information systems

improved gapped alignment in BLAST. Cameron, M., + , T-CBB July-Sep 04 116-129

Meetings

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

Modeling

unidentifiable divergence times in rates-across-sites models. Evans, S.N., + , T-CBB July-Sep 04 130-134

Molecular orientation

improved gapped alignment in BLAST. Cameron, M., + , T-CBB July-Sep 04 116-129

Molecules;
see Molecular orientation
N
Natural sciences;
see Biology
Natural sciences computing;
see Biology computing
Numerical analysis;
see Error analysis
O
Organic compounds;
see DNA
P
Parameter estimation;
see Maximum likelihood estimation
Polynomials

polynomial-time algorithm for the matching of crossing contact-map patterns. Gramm, J., T-CBB Oct.-Dec 04 171-180

Probability;
see Gamma distribution
S
Search problems

improved gapped alignment in BLAST. Cameron, M., + , T-CBB July-Sep 04 116-129

stochastic downhill search algorithm for estimating the local false discovery rate. Scheid, S., + , T-CBB July-Sep 04 98-108

Solid structure;
see Molecular orientation
Special issues and sections

2004 Workshop on Algorithms in Bioinformatics, WABI (special section). T-CBB Oct.-Dec 04 137-180

2004 Workshop on Algorithms in Bioinformatics, WABI (special section intro.). Junhyong Kim, + , T-CBB Oct.-Dec 04 137-138

Statistical analysis;
see Maximum likelihood estimation
Statistics

unidentifiable divergence times in rates-across-sites models. Evans, S.N., + , T-CBB July-Sep 04 130-134

Stochastic processes

stochastic downhill search algorithm for estimating the local false discovery rate. Scheid, S., + , T-CBB July-Sep 04 98-108

T
Three-dimensional displays

polynomial-time algorithm for the matching of crossing contact-map patterns. Gramm, J., T-CBB Oct.-Dec 04 171-180

Trees (graphs)

pure multiple RNA secondary struct. alignments. Hochsmann, M., + , T-CBB Jan.-Mar 04 53-62

recomb. events, sample hist., no. Bafna, V., + , T-CBB April-Jun 04 78-90

Trees (mathematical)

phylogenetic super-networks from partial trees. Huson, D.H., + , T-CBB Oct.-Dec 04 151-158

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