-
1
-
-
0029365976
-
Locating protein coding regions in human DNA using a decision tree algorithm
-
Salzberg S. Locating protein coding regions in human DNA using a decision tree algorithm. J Comput Biol 1995, 2:473-485.
-
(1995)
J Comput Biol
, vol.2
, pp. 473-485
-
-
Salzberg, S.1
-
2
-
-
75149125730
-
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
-
Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV. Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics 2010, 11(suppl 1):S65.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Gupta, R.1
Wikramasinghe, P.2
Bhattacharyya, A.3
Perez, F.A.4
Pal, S.5
Davuluri, R.V.6
-
3
-
-
84873126382
-
Ensemble learning algorithms for classification of mtDNA into haplogroups
-
Epub ahead of print;March 4
-
Wong C, Li Y, Lee C, Huang CH. Ensemble learning algorithms for classification of mtDNA into haplogroups. Brief Bioinform (Epub ahead of print;March 4, 2010).
-
(2010)
Brief Bioinform
-
-
Wong, C.1
Li, Y.2
Lee, C.3
Huang, C.H.4
-
4
-
-
0033692876
-
Tissue classification with gene expression profiles
-
Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z. Tissue classification with gene expression profiles. J Comput Biol 2000, 7:559-583.
-
(2000)
J Comput Biol
, vol.7
, pp. 559-583
-
-
Ben-Dor, A.1
Bruhn, L.2
Friedman, N.3
Nachman, I.4
Schummer, M.5
Yakhini, Z.6
-
6
-
-
6944251719
-
Predicting gene function in Saccharomyces cerevisiae
-
Clare A, King RD. Predicting gene function in Saccharomyces cerevisiae. Bioinformatics 2003, 19(suppl 2):ii42-49.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Clare, A.1
King, R.D.2
-
7
-
-
0038681269
-
Statistical models for discerning protein structures containing the DNAbinding helix-turn-helix motif
-
McLaughlin WA, Berman HM. Statistical models for discerning protein structures containing the DNAbinding helix-turn-helix motif. J Mol Biol 2003, 330:43-55.
-
(2003)
J Mol Biol
, vol.330
, pp. 43-55
-
-
McLaughlin, W.A.1
Berman, H.M.2
-
8
-
-
37849032668
-
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools
-
Shen YQ, Burger G. 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools. BMC Bioinformatics 2007, 8:420.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 420
-
-
Shen, Y.Q.1
Burger, G.2
-
9
-
-
77149177676
-
Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics
-
Jung J, Ryu T, Hwang Y, Lee E, Lee D. Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol 2010, 17:97-105.
-
(2010)
J Comput Biol
, vol.17
, pp. 97-105
-
-
Jung, J.1
Ryu, T.2
Hwang, Y.3
Lee, E.4
Lee, D.5
-
10
-
-
13244265581
-
Information assessment on predicting protein-protein interactions
-
Lin N, Wu B, Jansen R, GersteinM, Zhao H. Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004, 5:154.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 154
-
-
Lin, N.1
Wu, B.2
Jansen, R.3
Gerstein, M.4
Zhao, H.5
-
12
-
-
0029036696
-
Analysis of a 2(9) full factorial chemical library
-
Young SS, Hawkins DM. Analysis of a 2(9) full factorial chemical library. J Med Chem 1995, 38:2784-2788.
-
(1995)
J Med Chem
, vol.38
, pp. 2784-2788
-
-
Young, S.S.1
Hawkins, D.M.2
-
13
-
-
0141890760
-
Predictive toxicology: benchmarking molecular descriptors and statistical methods
-
Feng J, Lurati L, Ouyang H, Robinson T, Wang Y, Yuan S, Young SS. Predictive toxicology: benchmarking molecular descriptors and statistical methods. J Chem Inf Comput Sci 2003, 43:1463-1470.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 1463-1470
-
-
Feng, J.1
Lurati, L.2
Ouyang, H.3
Robinson, T.4
Wang, Y.5
Yuan, S.6
Young, S.S.7
-
14
-
-
0004255908
-
-
New York:McGraw Hill Higher Education
-
Mitchell TM. Machine Learning. New York:McGraw Hill Higher Education; 1997.
-
(1997)
Machine Learning
-
-
Mitchell, T.M.1
-
15
-
-
33644752875
-
Decision trees for classification: a review and some new results
-
Pal SK, Pla A, eds. Singapore: World Scientific Publishing Company
-
Kothari R, Dong M. Decision trees for classification: a review and some new results. In: Pal SK, Pla A, eds. Pattern Recognition from Classical to Modern Approaches. Singapore: World Scientific Publishing Company; 2002 169-186.
-
(2002)
Pattern Recognition from Classical to Modern Approaches
, pp. 169-186
-
-
Kothari, R.1
Dong, M.2
-
16
-
-
70649114623
-
Navigating random forests and related advances in algorithmic modeling
-
Siroky DS. Navigating random forests and related advances in algorithmic modeling. Stat Surv 2009, 3:147-163.
-
(2009)
Stat Surv
, vol.3
, pp. 147-163
-
-
Siroky, D.S.1
-
17
-
-
33644855553
-
Decision tree methods in pharmaceutical research
-
Blower PE, Cross KP. Decision tree methods in pharmaceutical research. Curr TopMed Chem 2006, 6:31-39.
-
(2006)
Curr TopMed Chem
, vol.6
, pp. 31-39
-
-
Blower, P.E.1
Cross, K.P.2
-
19
-
-
33744584654
-
Induction of decision trees
-
Quinlan JR. Induction of decision trees. Mach Learn 1986, 1:81-106.
-
(1986)
Mach Learn
, vol.1
, pp. 81-106
-
-
Quinlan, J.R.1
-
21
-
-
0003802343
-
-
New York: Chapman and Hall; San Mateo, CA: Morgan Kaufmann Publishers
-
Breiman L, Friedman F, Stone C, Olshen R. Classification and Regression Trees. New York: Chapman and Hall; San Mateo, CA: Morgan Kaufmann Publishers; 1984, 368.
-
(1984)
Classification and Regression Trees
, pp. 368
-
-
Breiman, L.1
Friedman, F.2
Stone, C.3
Olshen, R.4
-
22
-
-
0042942219
-
Families of splitting criteria for classification trees
-
Shih Y-S. Families of splitting criteria for classification trees. Stat Comput 1999, 9:309-315.
-
(1999)
Stat Comput
, vol.9
, pp. 309-315
-
-
Shih, Y.-S.1
-
23
-
-
0042409675
-
Selecting the best categorical split for classification trees
-
Shih Y-S. Selecting the best categorical split for classification trees. Stat Probab Lett 2001, 54:341-345.
-
(2001)
Stat Probab Lett
, vol.54
, pp. 341-345
-
-
Shih, Y.-S.1
-
24
-
-
65849418129
-
A tree-based method for modeling a multivariate ordinal response
-
Zhang H, Ye Y. A tree-based method for modeling a multivariate ordinal response. Stat Interface 2008, 1:169-178.
-
(2008)
Stat Interface
, vol.1
, pp. 169-178
-
-
Zhang, H.1
Ye, Y.2
-
25
-
-
33747841010
-
Pathway analysis using random forests classification and regression
-
Pang H, Lin A, Holford M, Enerson BE, Lu B, Lawton MP, Floyd E, Zhao H. Pathway analysis using random forests classification and regression. Bioinformatics 2006, 22:2028-2036.
-
(2006)
Bioinformatics
, vol.22
, pp. 2028-2036
-
-
Pang, H.1
Lin, A.2
Holford, M.3
Enerson, B.E.4
Lu, B.5
Lawton, M.P.6
Floyd, E.7
Zhao, H.8
-
26
-
-
33846643930
-
Exploiting interactions among polymorphisms contributing to complex disease traitswith boosted generative modeling
-
Wang LY, Comaniciu D, Fasulo D. Exploiting interactions among polymorphisms contributing to complex disease traitswith boosted generative modeling. J Comput Biol 2006, 13:1673-1684.
-
(2006)
J Comput Biol
, vol.13
, pp. 1673-1684
-
-
Wang, L.Y.1
Comaniciu, D.2
Fasulo, D.3
-
27
-
-
33846937260
-
Repetitive sequence environment distinguishes housekeeping genes
-
Eller CD, RegelsonM, Merriman B, Nelson S, Horvath S, Marahrens Y. Repetitive sequence environment distinguishes housekeeping genes. Gene 2007, 390:153-165.
-
(2007)
Gene
, vol.390
, pp. 153-165
-
-
Eller, C.D.1
Regelson, M.2
Merriman, B.3
Nelson, S.4
Horvath, S.5
Marahrens, Y.6
-
28
-
-
34547596338
-
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
-
Jiang P, Wu H, WangW, MaW, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 2007, 35:W339-344.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Jiang, P.1
Wu, H.2
Wang, W.3
Ma, W.4
Sun, X.5
Lu, Z.6
-
29
-
-
0035478854
-
Random Forests
-
Breiman L. Random Forests. Mach Learn 2001, 45:5-32.
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
31
-
-
37649007447
-
A forest-based approach to identifying gene and gene-gene interactions
-
Chen X, Liu CT, Zhang M, Zhang H. A forest-based approach to identifying gene and gene-gene interactions. Proc Natl Acad Sci USA 2007, 104:19199-19203.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19199-19203
-
-
Chen, X.1
Liu, C.T.2
Zhang, M.3
Zhang, H.4
-
32
-
-
0037388166
-
Cell and tumor classification using gene expression data: construction of forests
-
Zhang H, Yu C-Y, Singer B. Cell and tumor classification using gene expression data: construction of forests. Proc Natl Acad Sci USA 2003, 100:4168-4172.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4168-4172
-
-
Zhang, H.1
Yu, C.-Y.2
Singer, B.3
-
34
-
-
33847096395
-
Bias in random forest variable importance measures: illustrations, sources and a solution
-
Strobl C, Boulesteix AL, Zeileis A, Hothorn T. Bias in random forest variable importance measures: illustrations, sources and a solution. BMC Bioinformatics 2007, 8:25.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 25
-
-
Strobl, C.1
Boulesteix, A.L.2
Zeileis, A.3
Hothorn, T.4
-
35
-
-
77951970995
-
aximal conditional chisquare importance in random forests
-
Wang M, Chen X, Zhang H. Maximal conditional chisquare importance in random forests. Bioinformatics 2010, 26:831-837.
-
(2010)
Bioinformatics
, vol.26
, pp. 831-837
-
-
Wang, M.1
Chen, X.2
Zhang, H.3
-
36
-
-
48549095457
-
Conditional variable importance for random forests
-
Strobl C, Boulesteix AL, Kneib T, Augustin T, Zeileis A. Conditional variable importance for random forests. BMC Bioinformatics 2008, 9:307.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 307
-
-
Strobl, C.1
Boulesteix, A.L.2
Kneib, T.3
Augustin, T.4
Zeileis, A.5
-
37
-
-
67650770061
-
Predictor correlation impacts machine learning algorithms: implications for genomic studies
-
Nicodemus KK, Malley JD. Predictor correlation impacts machine learning algorithms: implications for genomic studies. Bioinformatics 2009, 25:1884-1890.
-
(2009)
Bioinformatics
, vol.25
, pp. 1884-1890
-
-
Nicodemus, K.K.1
Malley, J.D.2
-
38
-
-
64549095229
-
Performance of random forest when SNPs are in linkage disequilibrium
-
Meng YA, Yu Y, Cupples LA, Farrer LA, Lunetta KL. Performance of random forest when SNPs are in linkage disequilibrium. BMC Bioinformatics 2009, 10:78.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 78
-
-
Meng, Y.A.1
Yu, Y.2
Cupples, L.A.3
Farrer, L.A.4
Lunetta, K.L.5
-
39
-
-
84863447426
-
Search for the smallest random forest
-
Zhang H, Wang M. Search for the smallest random forest. Stat Interface 2009, 2:381.
-
(2009)
Stat Interface
, vol.2
, pp. 381
-
-
Zhang, H.1
Wang, M.2
-
40
-
-
0037137519
-
A gene-expression signature as a predictor of survival in breast cancer
-
van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009.
-
(2002)
N Engl J Med
, vol.347
, pp. 1999-2009
-
-
van de Vijver, M.J.1
He, Y.D.2
van't Veer, L.J.3
Dai, H.4
Hart, A.A.5
Voskuil, D.W.6
Schreiber, G.J.7
Peterse, J.L.8
Roberts, C.9
Marton, M.J.10
-
41
-
-
0035735265
-
Computational identification of promoters and first exons in the human genome
-
Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29:412-417.
-
(2001)
Nat Genet
, vol.29
, pp. 412-417
-
-
Davuluri, R.V.1
Grosse, I.2
Zhang, M.Q.3
-
42
-
-
37249025294
-
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
-
Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 2007, 17:1865-1879.
-
(2007)
Genome Res
, vol.17
, pp. 1865-1879
-
-
Stark, A.1
Kheradpour, P.2
Parts, L.3
Brennecke, J.4
Hodges, E.5
Hannon, G.J.6
Kellis, M.7
-
43
-
-
41049110433
-
Functional discrimination of membrane proteins using machine learning techniques
-
Gromiha MM, Yabuki Y. Functional discrimination of membrane proteins using machine learning techniques. BMC Bioinformatics 2008, 9:135.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 135
-
-
Gromiha, M.M.1
Yabuki, Y.2
-
44
-
-
44449122934
-
Investigation of transmembrane proteins using a computational approach
-
Yang JY, YangMQ, Dunker AK, Deng Y, Huang X. Investigation of transmembrane proteins using a computational approach. BMC Genomics 2008, 9(suppl 1): S7.
-
(2008)
BMC Genomics
, vol.9
, Issue.SUPPL. 1
-
-
Yang, J.Y.1
Yang, M.Q.2
Dunker, A.K.3
Deng, Y.4
Huang, X.5
-
45
-
-
33646018046
-
Evaluation of different biological data and computational classification methods for use in protein interaction prediction
-
Qi Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006, 63:490-500.
-
(2006)
Proteins
, vol.63
, pp. 490-500
-
-
Qi, Y.1
Bar-Joseph, Z.2
Klein-Seetharaman, J.3
-
46
-
-
2942541277
-
Predicting cocomplexed protein pairs using genomic and proteomic data integration
-
Zhang LV, Wong SL, KingOD, Roth FP. Predicting cocomplexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 2004, 5:38.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 38
-
-
Zhang, L.V.1
Wong, S.L.2
King, O.D.3
Roth, F.P.4
-
47
-
-
28944450149
-
Prediction of protein-protein interactions using random decision forest framework
-
Chen XW, Liu M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 2005, 21:4394-4400.
-
(2005)
Bioinformatics
, vol.21
, pp. 4394-4400
-
-
Chen, X.W.1
Liu, M.2
-
48
-
-
77950200613
-
Prediction of the clinical phenotype of Fabry disease based on protein sequential and structural information
-
Saito S, Ohno K, Sese J, Sugawara K, Sakuraba H. Prediction of the clinical phenotype of Fabry disease based on protein sequential and structural information. J Hum Genet 2010.
-
(2010)
J Hum Genet
-
-
Saito, S.1
Ohno, K.2
Sese, J.3
Sugawara, K.4
Sakuraba, H.5
-
49
-
-
77949750180
-
Gene expression profiles identify inflammatory signatures in dendritic cells
-
Torri A, Beretta O, Ranghetti A, Granucci F, Ricciardi-Castagnoli P, FotiM. Gene expression profiles identify inflammatory signatures in dendritic cells. PLoS One 2010, 5:e9404.
-
(2010)
PLoS One
, vol.5
-
-
Torri, A.1
Beretta, O.2
Ranghetti, A.3
Granucci, F.4
Ricciardi-Castagnoli, P.5
Foti, M.6
-
50
-
-
33846011470
-
A five-gene signature and clinical outcome in nonsmall-cell lung cancer
-
Chen HY, Yu SL, Chen CH, Chang GC, Chen CY, Yuan A, Cheng CL, Wang CH, Terng HJ, Kao SF, et al. A five-gene signature and clinical outcome in nonsmall-cell lung cancer. N Engl J Med 2007, 356:11-20.
-
(2007)
N Engl J Med
, vol.356
, pp. 11-20
-
-
Chen, H.Y.1
Yu, S.L.2
Chen, C.H.3
Chang, G.C.4
Chen, C.Y.5
Yuan, A.6
Cheng, C.L.7
Wang, C.H.8
Terng, H.J.9
Kao, S.F.10
-
51
-
-
75149183709
-
Virtual screening of bioassay data
-
Schierz AC. Virtual screening of bioassay data. J Cheminform 2009, 1:21.
-
(2009)
J Cheminform
, vol.1
, pp. 21
-
-
Schierz, A.C.1
-
52
-
-
77951955992
-
Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments
-
Kirchner M, Timm W, Fong P, Wangemann P, Steen H. Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments. Bioinformatics 2010, 26:791-797.
-
(2010)
Bioinformatics
, vol.26
, pp. 791-797
-
-
Kirchner, M.1
Timm, W.2
Fong, P.3
Wangemann, P.4
Steen, H.5
-
53
-
-
77349123492
-
Computer aided diagnosis system for the Alzheimer's disease based on partial least squares and random forest SPECT image classification
-
Ramirez J, Gorriz JM, Segovia F, Chaves R, Salas-Gonzalez D, López M, Alvarez I, Padilla P. Computer aided diagnosis system for the Alzheimer's disease based on partial least squares and random forest SPECT image classification. Neurosci Lett 2010, 472:99-103.
-
(2010)
Neurosci Lett
, vol.472
, pp. 99-103
-
-
Ramirez, J.1
Gorriz, J.M.2
Segovia, F.3
Chaves, R.4
Salas-Gonzalez, D.5
López, M.6
Alvarez, I.7
Padilla, P.8
-
54
-
-
0037270514
-
Towards reconstruction of gene networks from expression data by supervised learning
-
Soinov LA, Krestyaninova MA, Brazma A. Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol 2003, 4:R6.
-
(2003)
Genome Biol
, vol.4
-
-
Soinov, L.A.1
Krestyaninova, M.A.2
Brazma, A.3
-
55
-
-
25444453244
-
Screening large-scale association study data: exploiting interactions using random forests
-
Lunetta KL, Hayward LB, Segal J, Van Eerdewegh P. Screening large-scale association study data: exploiting interactions using random forests. BMC Genet 2004, 5:32.
-
(2004)
BMC Genet
, vol.5
, pp. 32
-
-
Lunetta, K.L.1
Hayward, L.B.2
Segal, J.3
Van Eerdewegh, P.4
-
56
-
-
77949388276
-
The behaviour of random forest permutation-based variable importance measures under predictor correlation
-
Nicodemus KK, Malley JD, Strobl C, Ziegler A. The behaviour of random forest permutation-based variable importance measures under predictor correlation. BMC Bioinformatics 2010, 11:110.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 110
-
-
Nicodemus, K.K.1
Malley, J.D.2
Strobl, C.3
Ziegler, A.4
-
57
-
-
82355167935
-
Detecting genes and gene-gene interactions for age-related macular degeneration with a forest-based approach
-
Wang M, Zhang M, Chen X, Zhang H. Detecting genes and gene-gene interactions for age-related macular degeneration with a forest-based approach. Stat Biopharm Res 2009, 1:424-430.
-
(2009)
Stat Biopharm Res
, vol.1
, pp. 424-430
-
-
Wang, M.1
Zhang, M.2
Chen, X.3
Zhang, H.4
-
58
-
-
20244380171
-
Complement factor H polymorphism in age-related macular degeneration
-
Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005, 308:385-389.
-
(2005)
Science
, vol.308
, pp. 385-389
-
-
Klein, R.J.1
Zeiss, C.2
Chew, E.Y.3
Tsai, J.Y.4
Sackler, R.S.5
Haynes, C.6
Henning, A.K.7
SanGiovanni, J.P.8
Mane, S.M.9
Mayne, S.T.10
|