Volume 25; Issue 12

Main
Bioinformatics
Volume 25; Issue 12

Bioinformatics

Volume 25; Issue 12

1

WebGBrowse--a web server for GBrowse

Podicheti, R., Gollapudi, R., Dong, Q.

Journal:

Year:

2009

Language:

english

File:

PDF, 207 KB

english, 2009

2

Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis

Hall, B. M., Ma, C.-X., Liang, P., Singh, K. K.

Journal:

Year:

2009

Language:

english

File:

PDF, 110 KB

english, 2009

3

Cross species analysis of microarray expression data

Lu, Y., Huggins, P., Bar-Joseph, Z.

Journal:

Year:

2009

Language:

english

File:

PDF, 490 KB

english, 2009

4

KELLER: estimating time-varying interactions between genes

Song, L., Kolar, M., Xing, E. P.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.20 MB

english, 2009

5

Computing galled networks from real data

Huson, D. H., Rupp, R., Berry, V., Gambette, P., Paul, C.

Journal:

Year:

2009

Language:

english

File:

PDF, 881 KB

english, 2009

6

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation

Wallach, I., Lilien, R. H.

Journal:

Year:

2009

Language:

english

File:

PDF, 486 KB

english, 2009

7

Cloud computing

Bateman, A., Wood, M.

Journal:

Year:

2009

Language:

english

File:

PDF, 43 KB

english, 2009

8

Modeling stochasticity and robustness in gene regulatory networks

Garg, A., Mohanram, K., Di Cara, A., De Micheli, G., Xenarios, I.

Journal:

Year:

2009

Language:

english

File:

PDF, 976 KB

english, 2009

9

Predicting and understanding the stability of G-quadruplexes

Stegle, O., Payet, L., Mergny, J.-L., MacKay, D. J. C., Huppert, J. L.

Journal:

Year:

2009

Language:

english

File:

PDF, 660 KB

english, 2009

10

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

Tuncbag, N., Gursoy, A., Keskin, O.

Journal:

Year:

2009

Language:

english

File:

PDF, 194 KB

english, 2009

11

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations

Du, P., Feng, G., Flatow, J., Song, J., Holko, M., Kibbe, W. A., Lin, S. M.

Journal:

Year:

2009

Language:

english

File:

PDF, 353 KB

english, 2009

12

Alignment of the UMLS semantic network with BioTop: methodology and assessment

Schulz, S., Beisswanger, E., van den Hoek, L., Bodenreider, O., van Mulligen, E. M.

Journal:

Year:

2009

Language:

english

File:

PDF, 145 KB

english, 2009

13

A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients

Journal:

Year:

2009

Language:

english

File:

PDF, 71 KB

english, 2009

14

Efficient exact motif discovery

Marschall, T., Rahmann, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 241 KB

english, 2009

15

Global alignment of protein-protein interaction networks by graph matching methods

Zaslavskiy, M., Bach, F., Vert, J.-P.

Journal:

Year:

2009

Language:

english

File:

PDF, 485 KB

english, 2009

16

Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space

Geiger, D., Meek, C., Wexler, Y.

Journal:

Year:

2009

Language:

english

File:

PDF, 479 KB

english, 2009

17

Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate

O'Connor, T. D., Mundy, N. I.

Journal:

Year:

2009

Language:

english

File:

PDF, 195 KB

english, 2009

18

A local multiple alignment method for detection of non-coding RNA sequences

Tabei, Y., Asai, K.

Journal:

Year:

2009

Language:

english

File:

PDF, 172 KB

english, 2009

19

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

Lubliner, S., Segal, E.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.01 MB

english, 2009

20

ELISA-BASE: an integrated bioinformatics tool for analyzing and tracking ELISA microarray data

White, A. M., Collett, J. R., Seurynck-Servoss, S. L., Daly, D. S., Zangar, R. C.

Journal:

Year:

2009

Language:

english

File:

PDF, 103 KB

english, 2009

21

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data

Yin, J., Jordan, M. I., Song, Y. S.

Journal:

Year:

2009

Language:

english

File:

PDF, 275 KB

english, 2009

22

Fewer permutations, more accurate P-values

Knijnenburg, T. A., Wessels, L. F. A., Reinders, M. J. T., Shmulevich, I.

Journal:

Year:

2009

Language:

english

File:

PDF, 540 KB

english, 2009

23

Proteome coverage prediction with infinite Markov models

Claassen, M., Aebersold, R., Buhmann, J. M.

Journal:

Year:

2009

Language:

english

File:

PDF, 314 KB

english, 2009

24

MapView: visualization of short reads alignment on a desktop computer

Bao, H., Guo, H., Wang, J., Zhou, R., Lu, X., Shi, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 62 KB

english, 2009

25

Predicting functionality of protein-DNA interactions by integrating diverse evidence

Ucar, D., Beyer, A., Parthasarathy, S., Workman, C. T.

Journal:

Year:

2009

Language:

english

File:

PDF, 385 KB

english, 2009

26

CROC: finding chromosomal clusters in eukaryotic genomes

Pignatelli, M., Serras, F., Moya, A., Guigo, R., Corominas, M.

Journal:

Year:

2009

Language:

english

File:

PDF, 64 KB

english, 2009

27

Probabilistic retrieval and visualization of biologically relevant microarray experiments

Caldas, J., Gehlenborg, N., Faisal, A., Brazma, A., Kaski, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 898 KB

english, 2009

28

PICKY: a novel SVD-based NMR spectra peak picking method

Alipanahi, B., Gao, X., Karakoc, E., Donaldson, L., Li, M.

Journal:

Year:

2009

Language:

english

File:

PDF, 804 KB

english, 2009

29

BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases

Stres, B., Tiedje, J. M., Murovec, B.

Journal:

Year:

2009

Language:

english

File:

PDF, 136 KB

english, 2009

30

Predictions of RNA secondary structure by combining homologous sequence information

Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.

Journal:

Year:

2009

Language:

english

File:

PDF, 720 KB

english, 2009

31

A general computational method for robustness analysis with applications to synthetic gene networks

Rizk, A., Batt, G., Fages, F., Soliman, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 6.09 MB

english, 2009

32

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

Xie, L., Xie, L., Bourne, P. E.

Journal:

Year:

2009

Language:

english

File:

PDF, 489 KB

english, 2009

33

Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules

Meng, J., Gao, S.-J., Huang, Y.

Journal:

Year:

2009

Language:

english

File:

PDF, 439 KB

english, 2009

34

A stochastic model for the evolution of metabolic networks with neighbor dependence

Mithani, A., Preston, G. M., Hein, J.

Journal:

Year:

2009

Language:

english

File:

PDF, 228 KB

english, 2009

35

Viruses selectively mutate their CD8+ T-cell epitopes--a large-scale immunomic analysis

Vider-Shalit, T., Sarid, R., Maman, K., Tsaban, L., Levi, R., Louzoun, Y.

Journal:

Year:

2009

Language:

english

File:

PDF, 400 KB

english, 2009

36

Family classification without domain chaining

Joseph, J. M., Durand, D.

Journal:

Year:

2009

Language:

english

File:

PDF, 872 KB

english, 2009

37

Model-based clustering of array CGH data

Shah, S. P., Cheung, K-J., Johnson, N. A., Alain, G., Gascoyne, R. D., Horsman, D. E., Ng, R. T., Murphy, K. P.

Journal:

Year:

2009

Language:

english

File:

PDF, 788 KB

english, 2009

38

Editorial

Gusfield, D., Tramontano, A.

Journal:

Year:

2009

Language:

english

File:

PDF, 31 KB

english, 2009

39

IsoRankN: spectral methods for global alignment of multiple protein networks

Liao, C.-S., Lu, K., Baym, M., Singh, R., Berger, B.

Journal:

Year:

2009

Language:

english

File:

PDF, 267 KB

english, 2009

40

Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network

Guo, Z., Li, Y., Gong, X., Yao, C., Ma, W., Wang, D., Li, Y., Zhu, J., Zhang, M., Yang, D., Wang, J.

Journal:

Year:

2009

File:

PDF, 34 KB

2009

41

Inference of locus-specific ancestry in closely related populations

Pasaniuc, B., Sankararaman, S., Kimmel, G., Halperin, E.

Journal:

Year:

2009

Language:

english

File:

PDF, 380 KB

english, 2009

42

Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum

Huang, Y., Wuchty, S., Ferdig, M. T., Przytycka, T. M.

Journal:

Year:

2009

Language:

english

File:

PDF, 240 KB

english, 2009

43

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., Kanehisa, M.

Journal:

Year:

2009

Language:

english

File:

PDF, 450 KB

english, 2009

44

Protein function annotation from sequence: prediction of residues interacting with RNA

Spriggs, R. V., Murakami, Y., Nakamura, H., Jones, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 101 KB

english, 2009

45

Grouped graphical Granger modeling for gene expression regulatory networks discovery

Lozano, A. C., Abe, N., Liu, Y., Rosset, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 633 KB

english, 2009

46

A partition function algorithm for interacting nucleic acid strands

Chitsaz, H., Salari, R., Sahinalp, S. C., Backofen, R.

Journal:

Year:

2009

Language:

english

File:

PDF, 420 KB

english, 2009

47

Pokefind: a novel topological filter for use with protein structure prediction

Khatib, F., Rohl, C. A., Karplus, K.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.01 MB

english, 2009

48

Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum

Jurgelenaite, R., Dijkstra, T. M. H., Kocken, C. H. M., Heskes, T.

Journal:

Year:

2009

Language:

english

File:

PDF, 593 KB

english, 2009

49

A multivariate regression approach to association analysis of a quantitative trait network

Kim, S., Sohn, K.-A., Xing, E. P.

Journal:

Year:

2009

Language:

english

File:

PDF, 662 KB

english, 2009

50

Application and evaluation of automated semantic annotation of gene expression experiments

French, L., Lane, S., Law, T., Xu, L., Pavlidis, P.

Journal:

Year:

2009

Language:

english

File:

PDF, 133 KB

english, 2009

51

BIPA: a database for protein-nucleic acid interaction in 3D structures

Lee, S., Blundell, T. L

Journal:

Year:

2009

Language:

english

File:

PDF, 295 KB

english, 2009

52

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

Marsella, L., Sirocco, F., Trovato, A., Seno, F., Tosatto, S. C.E.

Journal:

Year:

2009

Language:

english

File:

PDF, 455 KB

english, 2009

53

Author Index

Journal:

Year:

2009

Language:

english

File:

PDF, 33 KB

english, 2009

54

Domain-oriented edge-based alignment of protein interaction networks

Guo, X., Hartemink, A. J.

Journal:

Year:

2009

Language:

english

File:

PDF, 552 KB

english, 2009

55

ProtVirDB: a database of protozoan virulent proteins

Ramana, J., Gupta, D.

Journal:

Year:

2009

Language:

english

File:

PDF, 80 KB

english, 2009

56

A framework to refine particle clusters produced by EMAN

Fan, L., Zhang, F., Wang, G., Liu, Z.

Journal:

Year:

2009

Language:

english

File:

PDF, 153 KB

english, 2009

57

A Classifier-based approach to identify genetic similarities between diseases

Schaub, M. A., Kaplow, I. M., Sirota, M., Do, C. B., Butte, A. J., Batzoglou, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 272 KB

english, 2009

58

Network-based prediction of metabolic enzymes' subcellular localization

Mintz-Oron, S., Aharoni, A., Ruppin, E., Shlomi, T.

Journal:

Year:

2009

Language:

english

File:

PDF, 460 KB

english, 2009

59

Constrained mixture estimation for analysis and robust classification of clinical time series

Costa, I. G., Schonhuth, A., Hafemeister, C., Schliep, A.

Journal:

Year:

2009

Language:

english

File:

PDF, 478 KB

english, 2009

60

ModLink+: improving fold recognition by using protein-protein interactions

Fornes, O., Aragues, R., Espadaler, J., Marti-Renom, M. A., Sali, A., Oliva, B.

Journal:

Year:

2009

Language:

english

File:

PDF, 610 KB

english, 2009

61

Clustered alignments of gene-expression time series data

Smith, A. A., Vollrath, A., Bradfield, C. A., Craven, M.

Journal:

Year:

2009

Language:

english

File:

PDF, 555 KB

english, 2009

62

Toward a gold standard for promoter prediction evaluation

Abeel, T., Van de Peer, Y., Saeys, Y.

Journal:

Year:

2009

Language:

english

File:

PDF, 315 KB

english, 2009

63

Ontology quality assurance through analysis of term transformations

Verspoor, K., Dvorkin, D., Cohen, K. B., Hunter, L.

Journal:

Year:

2009

Language:

english

File:

PDF, 164 KB

english, 2009

64

Assessing phylogenetic motif models for predicting transcription factor binding sites

Hawkins, J., Grant, C., Noble, W. S., Bailey, T. L.

Journal:

Year:

2009

Language:

english

File:

PDF, 275 KB

english, 2009

65

Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models

Bhaskar, A., Song, Y. S.

Journal:

Year:

2009

Language:

english

File:

PDF, 249 KB

english, 2009

66

ISMB/ECCB 2009 Stockholm

Sagot, M.-F., McKay, B.J. M., Myers, G.

Journal:

Year:

2009

Language:

english

File:

PDF, 89 KB

english, 2009