Volume 20; Issue 18

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Bioinformatics
Volume 20; Issue 18

Bioinformatics

Volume 20; Issue 18

1

CLANS: a Java application for visualizing protein families based on pairwise similarity

Frickey, T., Lupas, A.

Journal:

Year:

2004

Language:

english

File:

PDF, 155 KB

english, 2004

2

Analysis of array CGH data: from signal ratio to gain and loss of DNA regions

Hupe, P., Stransky, N., Thiery, J.-P., Radvanyi, F., Barillot, E.

Journal:

Year:

2004

Language:

english

File:

PDF, 375 KB

english, 2004

3

Preferred in vivo ubiquitination sites

Catic, A., Collins, C., Church, G. M., Ploegh, H. L.

Journal:

Year:

2004

Language:

english

File:

PDF, 192 KB

english, 2004

4

Discovery of meaningful associations in genomic data using partial correlation coefficients

de la Fuente, A., Bing, N., Hoeschele, I., Mendes, P.

Journal:

Year:

2004

Language:

english

File:

PDF, 168 KB

english, 2004

5

Advances to Bayesian network inference for generating causal networks from observational biological data

Yu, J., Smith, V. A., Wang, P. P., Hartemink, A. J., Jarvis, E. D.

Journal:

Year:

2004

Language:

english

File:

PDF, 470 KB

english, 2004

6

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Boyle, E. I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J. M., Sherlock, G.

Journal:

Year:

2004

Language:

english

File:

PDF, 90 KB

english, 2004

7

Modeling interactome: scale-free or geometric?

Przulj, N., Corneil, D. G., Jurisica, I.

Journal:

Year:

2004

Language:

english

File:

PDF, 213 KB

english, 2004

8

DNMAD: web-based diagnosis and normalization for microarray data

Vaquerizas, J. M., Dopazo, J., Diaz-Uriarte, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 42 KB

english, 2004

9

Accurate detection of aneuploidies in array CGH and gene expression microarray data

Myers, C. L., Dunham, M. J., Kung, S. Y., Troyanskaya, O. G.

Journal:

Year:

2004

Language:

english

File:

PDF, 217 KB

english, 2004

10

NMRb: a web-site repository for raw NMR datasets

Pons, J. L., Malliavin, T. E., Tramesel, D., Delsuc, M. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 42 KB

english, 2004

11

SelSim: a program to simulate population genetic data with natural selection and recombination

Spencer, C. C. A., Coop, G.

Journal:

Year:

2004

Language:

english

File:

PDF, 108 KB

english, 2004

12

Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum

Anderle, M., Roy, S., Lin, H., Becker, C., Joho, K.

Journal:

Year:

2004

Language:

english

File:

PDF, 1012 KB

english, 2004

13

Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform

Lee, S., Cho, M.-K., Jung, J.-W., Kim, J.-H., Lee, W.

Journal:

Year:

2004

Language:

english

File:

PDF, 928 KB

english, 2004

14

Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data

Knowlton, N., Dozmorov, I. M., Centola, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 64 KB

english, 2004

15

Conserved network motifs allow protein-protein interaction prediction

Albert, I., Albert, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 186 KB

english, 2004

16

A probabilistic measure for alignment-free sequence comparison

Pham, T. D., Zuegg, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 83 KB

english, 2004

17

The Baumgartner-Wei -Schindler test for the detection of differentially expressed genes in replicated microarray experiments

Neuhauser, M., Senske, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 520 KB

english, 2004

18

Gene selection using a two-level hierarchical Bayesian model

Bae, K., Mallick, B. K.

Journal:

Year:

2004

Language:

english

File:

PDF, 171 KB

english, 2004

19

GenePicker: replicate analysis of Affymetrix gene expression microarrays

Finocchiaro, G., Parise, P., Minardi, S. P., Alcalay, M., Muller, H.

Journal:

Year:

2004

Language:

english

File:

PDF, 348 KB

english, 2004

20

ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms

Rosenfeld, J. A., Sarkar, I. N., Planet, P. J., Figurski, D. H., DeSalle, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 138 KB

english, 2004

21

GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data

Wu, C.-C., Huang, H.-C., Juan, H.-F., Chen, S.-T.

Journal:

Year:

2004

Language:

english

File:

PDF, 45 KB

english, 2004

22

The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses

Linder, R., Dew, D., Sudhoff, H., Theegarten, D., Remberger, K., Poppl, S. J., Wagner, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 294 KB

english, 2004

23

Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser

McDonald, D. M., Chen, H., Su, H., Marshall, B. B.

Journal:

Year:

2004

Language:

english

File:

PDF, 106 KB

english, 2004

24

Predicting GPCR-G-protein coupling using hidden Markov models

Sreekumar, K. R., Huang, Y., Pausch, M. H., Gulukota, K.

Journal:

Year:

2004

Language:

english

File:

PDF, 123 KB

english, 2004

25

Importing MAGE-ML format microarray data into BioConductor

Durinck, S., Allemeersch, J., Carey, V. J., Moreau, Y., De Moor, B.

Journal:

Year:

2004

Language:

english

File:

PDF, 37 KB

english, 2004

26

Comparative analysis of methods for representing and searching for transcription factor binding sites

Osada, R., Zaslavsky, E., Singh, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 115 KB

english, 2004

27

BagBoosting for tumor classification with gene expression data

Journal:

Year:

2004

Language:

english

File:

PDF, 436 KB

english, 2004

28

SARGE: a tool for creation of putative genetic networks

Shaw, O. J., Harwood, C., Steggles, L. J., Wipat, A.

Journal:

Year:

2004

Language:

english

File:

PDF, 179 KB

english, 2004

29

VisRD--visual recombination detection

Forslund, K., Huson, D. H., Moulton, V.

Journal:

Year:

2004

Language:

english

File:

PDF, 47 KB

english, 2004

30

Highly specific prediction of phosphorylation sites in proteins

Koenig, M., Grabe, N.

Journal:

Year:

2004

Language:

english

File:

PDF, 333 KB

english, 2004

31

Accuracy improvement for identifying translation initiation sites in microbial genomes

Zhu, H.-Q., Hu, G.-Q., Ouyang, Z.-Q., Wang, J., She, Z.-S.

Journal:

Year:

2004

Language:

english

File:

PDF, 131 KB

english, 2004

32

CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome

Hitte, C., Derrien, T., Andre, C., Ostrander, E. A., Galibert, F.

Journal:

Year:

2004

Language:

english

File:

PDF, 148 KB

english, 2004

33

ViTO: tool for refinement of protein sequence-structure alignments

Catherinot, V., Labesse, G.

Journal:

Year:

2004

Language:

english

File:

PDF, 185 KB

english, 2004

34

A metric model of amino acid substitution

Xu, W., Miranke, D. P.

Journal:

Year:

2004

Language:

english

File:

PDF, 22 KB

english, 2004

35

CSB.DB: a comprehensive systems-biology database

Steinhauser, D., Usadel, B., Luedemann, A., Thimm, O., Kopka, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 242 KB

english, 2004

36

EC_oligos: automated and whole-genome primer design for exons within one or between two genomes

Liu, S., Tinker, N. A., Molnar, S. J., Mather, D. E.

Journal:

Year:

2004

Language:

english

File:

PDF, 42 KB

english, 2004

37

Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling

Yuryev, A., Huang, J., Scott, K. E., Kuebler, J., Donaldson, M., Phillips, M. S., Pohl, M., Boyce-Jacino, M. T.

Journal:

Year:

2004

Language:

english

File:

PDF, 389 KB

english, 2004

38

DAGchainer: a tool for mining segmental genome duplications and synteny

Haas, B. J., Delcher, A. L., Wortman, J. R., Salzberg, S. L.

Journal:

Year:

2004

Language:

english

File:

PDF, 190 KB

english, 2004

39

PLPMDB: Pyridoxal-5'-phosphate dependent enzymes mutants database

Journal:

Year:

2004

Language:

english

File:

PDF, 37 KB

english, 2004

40

PCOAT: positional correlation analysis using multiple methods

Qi, Y., Grishin, N. V.

Journal:

Year:

2004

Language:

english

File:

PDF, 108 KB

english, 2004

41

Ontologies for Behavior

Journal:

Year:

2004

Language:

english

File:

PDF, 47 KB

english, 2004

42

Effects of pooling mRNA in microarray class comparisons

Shih, J. H., Michalowska, A. M., Dobbin, K., Ye, Y., Qiu, T. H., Green, J. E.

Journal:

Year:

2004

Language:

english

File:

PDF, 96 KB

english, 2004

43

DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria

Wang, Y., Leung, F. C. C.

Journal:

Year:

2004

Language:

english

File:

PDF, 243 KB

english, 2004

44

Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting

Samuelsson, J., Dalevi, D., Levander, F., Rognvaldsson, T.

Journal:

Year:

2004

Language:

english

File:

PDF, 179 KB

english, 2004

45

Limited agreement among three global gene expression methods highlights the requirement for non-global validation

Haverty, P. M., Hsiao, L.-L., Gullans, S. R., Hansen, U., Weng, Z.

Journal:

Year:

2004

Language:

english

File:

PDF, 425 KB

english, 2004

46

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach

Siew, J. P. Y., Khan, A. M., Tan, P. T. J., Koh, J. L. Y., Seah, S. H., Koo, C. Y., Chai, S. C., Armugam, A., Brusic, V., Jeyaseelan, K.

Journal:

Year:

2004

Language:

english

File:

PDF, 356 KB

english, 2004

47

DIVAA: analysis of amino acid diversity in multiple aligned protein sequences

Rodi, D. J., Mandava, S., Makowski, L.

Journal:

Year:

2004

Language:

english

File:

PDF, 341 KB

english, 2004

48

Interactive gene-order comparison for multiple small genomes

Kaluszka, A., Gibas, C.

Journal:

Year:

2004

Language:

english

File:

PDF, 300 KB

english, 2004

49

Training HMM structure with genetic algorithm for biological sequence analysis

Won, K.-J., Prugel-Bennett, A., Krogh, A.

Journal:

Year:

2004

Language:

english

File:

PDF, 126 KB

english, 2004

50

Discovering patterns to extract protein-protein interactions from full texts

Huang, M., Zhu, X., Hao, Y., Payan, D. G., Qu, K., Li, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 535 KB

english, 2004

51

MedlineR: an open source library in R for Medline literature data mining

Lin, S. M., McConnell, P., Johnson, K. F., Shoemaker, J.

Journal:

Year:

2004

Language:

english

File:

PDF, 70 KB

english, 2004

52

limmaGUI: A graphical user interface for linear modeling of microarray data

Wettenhall, J. M., Smyth, G. K.

Journal:

Year:

2004

Language:

english

File:

PDF, 63 KB

english, 2004

53

Reducing storage requirements for biological sequence comparison

Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., Yorke, J. A.

Journal:

Year:

2004

Language:

english

File:

PDF, 266 KB

english, 2004

54

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome

Accardo, M. C., Giordano, E., Riccardo, S., Digilio, F. A., Iazzetti, G., Calogero, R. A., Furia, M.

Journal:

Year:

2004

Language:

english

File:

PDF, 133 KB

english, 2004

55

A graph-theoretic approach to testing associations between disparate sources of functional genomics data

Balasubramanian, R., LaFramboise, T., Scholtens, D., Gentleman, R.

Journal:

Year:

2004

Language:

english

File:

PDF, 124 KB

english, 2004