Volume 12; Issue 6

Journal of Computational Biology

Volume 12; Issue 6

1

Finding Motifs with Insufficient Number of Strong Binding Sites

Leung, Henry C.M., Chin, Francis Y.L., Yiu, S.M., Rosenfeld, Roni, Tsang, W.W.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 153 KB

english, 2005

2

Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement

Sankoff, David, Trinh, Phil

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 141 KB

english, 2005

3

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

Sharan, Roded, Ideker, Trey, Kelley, Brian, Shamir, Ron, Karp, Richard M.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 260 KB

english, 2005

4

A Random Graph Approach to NMR Sequential Assignment

Bailey-Kellogg, Chris, Chainraj, Sheetal, Pandurangan, Gopal

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 196 KB

english, 2005

5

A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme

Lilien, Ryan H., Stevens, Brian W., Anderson, Amy C., Donald, Bruce R.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 305 KB

english, 2005

6

Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs

Huan, Jun, Bandyopadhyay, Deepak, Wang, Wei, Snoeyink, Jack, Prins, Jan, Tropsha, Alexander

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 332 KB

english, 2005

7

Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming

Li, Jing, Jiang, Tao

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 261 KB

english, 2005

8

Learning Multiple Evolutionary Pathways from Cross-Sectional Data

Beerenwinkel, Niko, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Selbig, Joachim, Lengauer, Thomas

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 146 KB

english, 2005

9

Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings

Erdmann, Michael A.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 1.06 MB

english, 2005

10

Reconstructing Reticulate Evolution in Species—Theory and Practice

Nakhleh, Luay, Warnow, Tandy, Linder, C. Randal, John, Katherine St.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 175 KB

english, 2005

11

Using Motion Planning to Study RNA Folding Kinetics

Tang, Xinyu, Kirkpatrick, Bonnie, Thomas, Shawna, Song, Guang, Amato, Nancy M.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 259 KB

english, 2005

12

Correction

Journal:

Journal of Computational Biology

Year:

2005

File:

PDF, 9 KB

2005

13

A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs

Li, Haifeng, Jiang, Tao

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 123 KB

english, 2005

14

Finding Short DNA Motifs Using Permuted Markov Models

Zhao, Xiaoyue, Huang, Haiyan, Speed, Terence P.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 201 KB

english, 2005

15

Preface: Special RECOMB 2004 Issue

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 18 KB

english, 2005

16

Checking Homogeneity of Motifs' Distribution in Heterogenous Sequences

Ledent, Sabrina, Robin, Stéphane

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 240 KB

english, 2005

17

A Discriminative Model for Identifying Spatial cis-Regulatory Modules

Segal, Eran, Sharan, Roded

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 507 KB

english, 2005

18

Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling

Chatterji, Sourav, Pachter, Lior

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 97 KB

english, 2005

19

Designing Multiple Simultaneous Seeds for DNA Similarity Search

Sun, Yanni, Buhler, Jeremy

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 133 KB

english, 2005

20

Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays

Wu, Zhijin, Irizarry, Rafael A.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 3.38 MB

english, 2005

21

Identifying Conserved Gene Clusters in the Presence of Homology Families

He, Xin, Goldwasser, Michael H.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 158 KB

english, 2005

22

Finding Anchors for Genomic Sequence Comparison

Lippert, Ross A., Zhao, Xiaoyue, Florea, Liliana, Mobarry, Clark, Istrail, Sorin

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 152 KB

english, 2005

23

Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils

Menke, Matthew, King, Jonathan, Berger, Bonnie, Cowen, Lenore

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 122 KB

english, 2005

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