Volume 20; Issue 16

Main
Bioinformatics
Volume 20; Issue 16

Bioinformatics

Volume 20; Issue 16

1

Analyzing time series gene expression data

Journal:

Year:

2004

Language:

english

File:

PDF, 230 KB

english, 2004

2

GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers

D'Addabbo, P., Lenzi, L., Facchin, F., Casadei, R., Canaider, S., Vitale, L., Frabetti, F., Carinci, P., Zannotti, M., Strippoli, P.

Journal:

Year:

2004

Language:

english

File:

PDF, 41 KB

english, 2004

3

Incremental generation of summarized clustering hierarchy for protein family analysis

Chen, C.-Y., Oyang, Y.-J., Juan, H.-F.

Journal:

Year:

2004

Language:

english

File:

PDF, 144 KB

english, 2004

4

FigSearch: a figure legend indexing and classification system

Liu, F., Jenssen, T.-K., Nygaard, V., Sack, J., Hovig, E.

Journal:

Year:

2004

Language:

english

File:

PDF, 50 KB

english, 2004

5

A collaborative database of inbred mouse strain characteristics

Grubb, S. C., Churchill, G. A., Bogue, M. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 40 KB

english, 2004

6

An efficient algorithm for optimizing whole genome alignment with noise

Wong, P. W. H., Lam, T. W., Lu, N., Ting, H. F., Yiu, S. M.

Journal:

Year:

2004

Language:

english

File:

PDF, 275 KB

english, 2004

7

MathSBML: a package for manipulating SBML-based biological models

Shapiro, B. E., Hucka, M., Finney, A., Doyle, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 47 KB

english, 2004

8

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura

Grad, Y. H., Roth, F. P., Halfon, M. S., Church, G. M.

Journal:

Year:

2004

Language:

english

File:

PDF, 649 KB

english, 2004

9

Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor

Tessier, D., Bardiaux, B., Larre, C., Popineau, Y.

Journal:

Year:

2004

Language:

english

File:

PDF, 49 KB

english, 2004

10

LUCY2: an interactive DNA sequence quality trimming and vector removal tool

Li, S., Chou, H.-H.

Journal:

Year:

2004

Language:

english

File:

PDF, 284 KB

english, 2004

11

Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies

Lee, W. H., Vega, V. B.

Journal:

Year:

2004

Language:

english

File:

PDF, 41 KB

english, 2004

12

Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach

Alexandridis, R., Lin, S., Irwin, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 112 KB

english, 2004

13

DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants

Kyoda, K., Baba, K., Onami, S., Kitano, H.

Journal:

Year:

2004

Language:

english

File:

PDF, 342 KB

english, 2004

14

SCA db: spinocerebellar ataxia candidate gene database

Liu, Y.-F., Yang, U.-C.

Journal:

Year:

2004

Language:

english

File:

PDF, 470 KB

english, 2004

15

Mining gene expression data based on template theory

Journal:

Year:

2004

Language:

english

File:

PDF, 354 KB

english, 2004

16

Rainbow: a toolbox for phylogenetic supertree construction and analysis

Chen, D., Eulenstein, O., Fernandez-Baca, D.

Journal:

Year:

2004

Language:

english

File:

PDF, 270 KB

english, 2004

17

Which is better for cDNA-microarray-based classification: ratios or direct intensities

Attoor, S., Dougherty, E. R., Chen, Y., Bittner, M. L., Trent, J. M.

Journal:

Year:

2004

Language:

english

File:

PDF, 474 KB

english, 2004

18

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

Majoros, W. H., Pertea, M., Salzberg, S. L.

Journal:

Year:

2004

Language:

english

File:

PDF, 40 KB

english, 2004

19

A statistical framework for genomic data fusion

Lanckriet, G. R. G., De Bie, T., Cristianini, N., Jordan, M. I., Noble, W. S.

Journal:

Year:

2004

Language:

english

File:

PDF, 117 KB

english, 2004

20

ClutrFree: cluster tree visualization and interpretation

Bidaut, G., Ochs, M. F.

Journal:

Year:

2004

Language:

english

File:

PDF, 237 KB

english, 2004

21

CoPS: Comprehensive Peptide Signature Database

Prakash, T., Khandelwal, M., Dasgupta, D., Dash, D., Brahmachari, S. K.

Journal:

Year:

2004

Language:

english

File:

PDF, 133 KB

english, 2004

22

SWAPSC: sliding window analysis procedure to detect selective constraints

Journal:

Year:

2004

Language:

english

File:

PDF, 166 KB

english, 2004

23

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions

Liu, D., Weinberg, C. R., Peddada, S. D.

Journal:

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

24

The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data

Mansourian, R., Mutch, D. M., Antille, N., Aubert, J., Fogel, P., Le Goff, J.-M., Moulin, J., Petrov, A., Rytz, A., Voegel, J. J., Roberts, M.-A.

Journal:

Year:

2004

Language:

english

File:

PDF, 225 KB

english, 2004

25

A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments

Broet, P., Lewin, A., Richardson, S., Dalmasso, C., Magdelenat, H.

Journal:

Year:

2004

Language:

english

File:

PDF, 224 KB

english, 2004

26

Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway

van Bakel, H., Huynen, M., Wijmenga, C.

Journal:

Year:

2004

Language:

english

File:

PDF, 588 KB

english, 2004

27

A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Zhang, S.-D., Gant, T. W.

Journal:

Year:

2004

Language:

english

File:

PDF, 110 KB

english, 2004

28

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets

Lazzarato, F., Franceschinis, G., Botta, M., Cordero, F., Calogero, R. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 46 KB

english, 2004

29

STAR: an algorithm to Search for Tandem Approximate Repeats

Delgrange, O., Rivals, E.

Journal:

Year:

2004

Language:

english

File:

PDF, 347 KB

english, 2004

30

Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry

Goldberg, R. N., Tewari, Y. B., Bhat, T. N.

Journal:

Year:

2004

Language:

english

File:

PDF, 288 KB

english, 2004

31

ICBS: a database of interactions between protein chains mediated by -sheet formation

Dou, Y., Baisnee, P.-F., Pollastri, G., Pecout, Y., Nowick, J., Baldi, P.

Journal:

Year:

2004

Language:

english

File:

PDF, 425 KB

english, 2004

32

Qxpak: a versatile mixed model application for genetical genomics and QTL analyses

Perez-Enciso, M., Misztal, I.

Journal:

Year:

2004

Language:

english

File:

PDF, 191 KB

english, 2004

33

PaVESy: Pathway Visualization and Editing System

Ludemann, A., Weicht, D., Selbig, J., Kopka, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 174 KB

english, 2004

34

Distribution of information in biomedical abstracts and full-text publications

Schuemie, M. J., Weeber, M., Schijvenaars, B. J. A., van Mulligen, E. M., van der Eijk, C. C., Jelier, R., Mons, B., Kors, J. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 97 KB

english, 2004

35

TargetDB: a target registration database for structural genomics projects

Chen, L., Oughtred, R., Berman, H. M., Westbrook, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 134 KB

english, 2004

36

Exhaustive whole-genome tandem repeats search

Krishnan, A., Tang, F.

Journal:

Year:

2004

Language:

english

File:

PDF, 294 KB

english, 2004

37

Gene-Ontology-based clustering of gene expression data

Adryan, B., Schuh, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 39 KB

english, 2004

38

Genome wide identification and classification of alternative splicing based on EST data

Gupta, S., Zink, D., Korn, B., Vingron, M., Haas, S. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 195 KB

english, 2004

39

Mining gene expression data for positive and negative co-regulated gene clusters

Ji, L., Tan, K.-L.

Journal:

Year:

2004

Language:

english

File:

PDF, 94 KB

english, 2004

40

Predicting allergenic proteins using wavelet transform

Li, K.-B., Issac, P., Krishnan, A.

Journal:

Year:

2004

Language:

english

File:

PDF, 74 KB

english, 2004

41

Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins

Kinjo, A. R., Nishikawa, K.

Journal:

Year:

2004

Language:

english

File:

PDF, 76 KB

english, 2004

42

Correcting log ratios for signal saturation in cDNA microarrays

Dodd, L. E., Korn, E. L., McShane, L. M., Chandramouli, G.V.R., Chuang, E. Y.

Journal:

Year:

2004

Language:

english

File:

PDF, 279 KB

english, 2004

43

Faster cyclic loess: normalizing RNA arrays via linear models

Ballman, K. V., Grill, D. E., Oberg, A. L., Therneau, T. M.

Journal:

Year:

2004

Language:

english

File:

PDF, 626 KB

english, 2004

44

Regulatory motif finding by logic regression

Keles, S., van der Laan, M. J., Vulpe, C.

Journal:

Year:

2004

Language:

english

File:

PDF, 196 KB

english, 2004

45

Command line tool for calculating theoretical MS spectra for given sequences

Boehm, A. M., Grosse-Coosmann, F., Sickmann, A.

Journal:

Year:

2004

Language:

english

File:

PDF, 179 KB

english, 2004

46

A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles

Luo, F., Khan, L., Bastani, F., Yen, I-L., Zhou, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 411 KB

english, 2004

47

Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays

Seo, J., Bakay, M., Chen, Y.-W., Hilmer, S., Shneiderman, B., Hoffman, E. P

Journal:

Year:

2004

Language:

english

File:

PDF, 464 KB

english, 2004

48

GDPC: connecting researchers with multiple integrated data sources

Casstevens, T. M., Buckler, E. S.

Journal:

Year:

2004

Language:

english

File:

PDF, 113 KB

english, 2004

49

BacTregulators: a database of transcriptional regulators in bacteria and archaea

Martinez-Bueno, M., Molina-Henares, A. J., Pareja, E., Ramos, J. L., Tobes, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 113 KB

english, 2004

50

The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions

Barth, S., Fischer, M., Schmid, R. D., Pleiss, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 45 KB

english, 2004

51

A mixture model for estimating the local false discovery rate in DNA microarray analysis

Liao, J.G., Lin, Y., Selvanayagam, Z. E., Shih, W. J.

Journal:

Year:

2004

Language:

english

File:

PDF, 132 KB

english, 2004

52

Dblox: a genome-wide test for ancient segmental duplication

Friedman, R., Ekollu, V., Rose, J. R., Hughes, A. L.

Journal:

Year:

2004

Language:

english

File:

PDF, 37 KB

english, 2004

53

A System for Automated Bacterial (genome) Integrated Annotation--SABIA

Almeida, L. G. P., Paixao, R., Souza, R. C., da Costa, G. C., Barrientos, F. J. A., dos Santos, M. T., de Almeida, D. F., Vasconcelos, A. T. R.

Journal:

Year:

2004

Language:

english

File:

PDF, 38 KB

english, 2004

54

A neural network method for prediction of -turn types in proteins using evolutionary information

Kaur, H., Raghava, G. P. S.

Journal:

Year:

2004

Language:

english

File:

PDF, 110 KB

english, 2004

55

GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms

Smid, M., Dorssers, L. C. J.

Journal:

Year:

2004

Language:

english

File:

PDF, 588 KB

english, 2004

56

Efficient combination of multiple word models for improved sequence comparison

Huang, X., Ye, L., Chou, H.-H., Yang, I-H., Chao, K.-M.

Journal:

Year:

2004

Language:

english

File:

PDF, 65 KB

english, 2004

57

THEA: ontology-driven analysis of microarray data

Pasquier, C., Girardot, F., Jevardat de Fombelle, K., Christen, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 218 KB

english, 2004

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