-
1
-
-
0030831182
-
Genetic and physical maps of Saccharomyces cerevisiae
-
Cherry JM, Ball C, Weng S, et al. Genetic and physical maps of Saccharomyces cerevisiae. Nature 1997;387(6632):67-73.
-
(1997)
Nature
, vol.387
, Issue.6632
, pp. 67-73
-
-
Cherry, J.M.1
Ball, C.2
Weng, S.3
-
3
-
-
0037336350
-
Integration from proteins to organs: the Physiome Project
-
Hunter PJ, Borg TK. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol 2003;4(3): 237-43.
-
(2003)
Nat Rev Mol Cell Biol
, vol.4
, Issue.3
, pp. 237-243
-
-
Hunter, P.J.1
Borg, T.K.2
-
4
-
-
43049143055
-
Mapping and sequencing of structural variation from eight human genomes
-
Kidd JM, Cooper GM, Donahue WF, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008;453(7191):56-64.
-
(2008)
Nature
, vol.453
, Issue.7191
, pp. 56-64
-
-
Kidd, J.M.1
Cooper, G.M.2
Donahue, W.F.3
-
5
-
-
77956114532
-
Is a gene-centric human proteome project the best way for proteomics to serve biology?
-
Rabilloud T, Hochstrasser D, Simpson RJ. Is a gene-centric human proteome project the best way for proteomics to serve biology? Proteomics 2010;10(17):3067-72.
-
(2010)
Proteomics
, vol.10
, Issue.17
, pp. 3067-3072
-
-
Rabilloud, T.1
Hochstrasser, D.2
Simpson, R.J.3
-
6
-
-
58149199579
-
FlyBase: enhancing Drosophila gene ontology annotations
-
Tweedie S, Ashburner M, Falls K, et al. FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res 2009;37:D555-9.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Tweedie, S.1
Ashburner, M.2
Falls, K.3
-
7
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H, Tombor B, Albert R, et al. The large-scale organization of metabolic networks. Nature 2000;407(6804): 651-4.
-
(2000)
Nature
, vol.407
, Issue.6804
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
-
8
-
-
46449127838
-
Self-correcting networks: function, robustness, and motif distributions in biological signal processing
-
Kaluza P, Vingron M, Mikhailov AS. Self-correcting networks: function, robustness, and motif distributions in biological signal processing. Chaos 2008;18(2):026113.
-
(2008)
Chaos
, vol.18
, Issue.2
, pp. 026113
-
-
Kaluza, P.1
Vingron, M.2
Mikhailov, A.S.3
-
9
-
-
54249137797
-
Feedback loops shape cellular signals in space and time
-
Brandman O, Meyer T. Feedback loops shape cellular signals in space and time. Science 2008;322(5900):390-5.
-
(2008)
Science
, vol.322
, Issue.5900
, pp. 390-395
-
-
Brandman, O.1
Meyer, T.2
-
10
-
-
0036500993
-
Systems biology: a brief overview
-
Kitano H. Systems biology: a brief overview. Science 2002; 295(5560):1662-4.
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1662-1664
-
-
Kitano, H.1
-
11
-
-
0034625005
-
Cell signaling pathways as control modules: complexity for simplicity?
-
Lauffenburger DA. Cell signaling pathways as control modules: complexity for simplicity? ProcNatlAcad SciUSA 2000; 97(10):5031-3.
-
(2000)
ProcNatlAcad SciUSA
, vol.97
, Issue.10
, pp. 5031-5033
-
-
Lauffenburger, D.A.1
-
12
-
-
77955104946
-
Comparison study of microarray meta-analysis methods
-
Campain A, Yang Y. Comparison study of microarray meta-analysis methods. BMC Bioinformatics 2010;11(1):408.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 408
-
-
Campain, A.1
Yang, Y.2
-
13
-
-
33747017793
-
Bayesian models for pooling microarray studies with multiple sources of replications
-
Conlon EM, Song JJ, Liu JS. Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics 2006;7:247.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 247
-
-
Conlon, E.M.1
Song, J.J.2
Liu, J.S.3
-
14
-
-
77955725963
-
Data integration in genetics and genomics: methods and challenges
-
Hamid JS, Hu P, Roslin NM, et al. Data integration in genetics and genomics: methods and challenges. Hum Genomics Proteomics 2009;2009:869093.
-
(2009)
Hum Genomics Proteomics
, vol.2009
, pp. 869093
-
-
Hamid, J.S.1
Hu, P.2
Roslin, N.M.3
-
15
-
-
84865093692
-
Facing the challenges of data integration in biosciences
-
EL_13_3_13
-
Li A. Facing the challenges of data integration in biosciences. Engineer Lett 2006;13(3):EL_13_3_13.
-
(2006)
Engineer Lett
, vol.13
, Issue.3
-
-
Li, A.1
-
16
-
-
3042694117
-
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
-
Rhodes DR, Yu JJ, Shanker K, et al. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 2004;101(25): 9309-14.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.25
, pp. 9309-9314
-
-
Rhodes, D.R.1
Yu, J.J.2
Shanker, K.3
-
17
-
-
43649083387
-
Structural robustness of metabolic networks with respect to multiple knockouts
-
Behre J, Wilhelm T, von Kamp A, et al. Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol 2008;252(3):433-41.
-
(2008)
J Theor Biol
, vol.252
, Issue.3
, pp. 433-441
-
-
Behre, J.1
Wilhelm, T.2
von Kamp, A.3
-
18
-
-
0032520557
-
Ordered and disordered dynamics in random networks
-
Glass L, Hill C. Ordered and disordered dynamics in random networks. Europhys Lett 1998;41(6):599-604.
-
(1998)
Europhys Lett
, vol.41
, Issue.6
, pp. 599-604
-
-
Glass, L.1
Hill, C.2
-
19
-
-
79951735333
-
Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation
-
Quo CF, Moffitt RA, Merrill AH, Jr, et al. Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation. J Comput Biol 2011;18(2): 169-82.
-
(2011)
J Comput Biol
, vol.18
, Issue.2
, pp. 169-182
-
-
Quo, C.F.1
Moffitt, R.A.2
Merrill Jr., A.H.3
-
20
-
-
0014649230
-
Biochemical systems analysis 1. Some mathematical properties of rate law for component enzymatic reactions
-
Savageau MA. Biochemical systems analysis. 1. Some mathematical properties of rate law for component enzymatic reactions. J Theor Biol 1969;25(3):365-9.
-
(1969)
J Theor Biol
, vol.25
, Issue.3
, pp. 365-369
-
-
Savageau, M.A.1
-
22
-
-
0034712843
-
Robust perfect adaptation in bacterial chemotaxis through integral feedback control
-
Yi TM, Huang Y, Simon MI, et al. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 2000;97(9): 4649-53.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.9
, pp. 4649-4653
-
-
Yi, T.M.1
Huang, Y.2
Simon, M.I.3
-
23
-
-
77952477753
-
Pairwise selection assembly for sequence-independent construction of long-length DNA
-
Blake WJ, Chapman BA, Zindal A, et al. Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Res 2010;38(8): 2594-602.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.8
, pp. 2594-2602
-
-
Blake, W.J.1
Chapman, B.A.2
Zindal, A.3
-
24
-
-
66149172363
-
Diversity-based, model-guided construction of synthetic gene networks with predicted functions
-
Ellis T, Wang X, Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotech 2009;27(5):465-71.
-
(2009)
Nat Biotech
, vol.27
, Issue.5
, pp. 465-471
-
-
Ellis, T.1
Wang, X.2
Collins, J.J.3
-
25
-
-
73949123429
-
Considerations for the design and construction of a synthetic platform cell for biotechnological applications
-
Foley PL, Shuler ML. Considerations for the design and construction of a synthetic platform cell for biotechnological applications. Biotechnol Bioengineer 2010;105(1):26-36.
-
(2010)
Biotechnol Bioengineer
, vol.105
, Issue.1
, pp. 26-36
-
-
Foley, P.L.1
Shuler, M.L.2
-
27
-
-
78650276265
-
Introduction of customized inserts for streamlined assembly and optimization of biobrick synthetic genetic circuits
-
Norville JE, Derda R, Gupta S, et al. Introduction of customized inserts for streamlined assembly and optimization of biobrick synthetic genetic circuits. J Biol Engineer 2010;4(1): 1-11.
-
(2010)
J Biol Engineer
, vol.4
, Issue.1
, pp. 1-11
-
-
Norville, J.E.1
Derda, R.2
Gupta, S.3
-
28
-
-
68949161807
-
Programming cells by multiplex genome engineering and accelerated evolution
-
Wang HH, Isaacs FJ, Carr PA, et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009;460(7257):894-8.
-
(2009)
Nature
, vol.460
, Issue.7257
, pp. 894-898
-
-
Wang, H.H.1
Isaacs, F.J.2
Carr, P.A.3
-
29
-
-
0028806048
-
Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray
-
Schena M, Shalon D, Davis RW, et al. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 1995;270(5235):467-70.
-
(1995)
Science
, vol.270
, Issue.5235
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
-
30
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li B, Ruotti V, Stewart RM, et al. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 2010;26(4):493-500.
-
(2010)
Bioinformatics
, vol.26
, Issue.4
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
-
31
-
-
77952956167
-
Decoding signalling networks by mass spectrometry-based proteomics
-
Choudhary C, Mann M. Decoding signalling networks by mass spectrometry-based proteomics. Nat RevMol Cell Biol 2010;11(6):427-39.
-
(2010)
Nat RevMol Cell Biol
, vol.11
, Issue.6
, pp. 427-439
-
-
Choudhary, C.1
Mann, M.2
-
32
-
-
50649120833
-
Metabolic gene regulation in a dynamically changing environment
-
Bennett MR, Pang WL, Ostroff NA, et al. Metabolic gene regulation in a dynamically changing environment. Nature 2008;454(7208):1119-22.
-
(2008)
Nature
, vol.454
, Issue.7208
, pp. 1119-1122
-
-
Bennett, M.R.1
Pang, W.L.2
Ostroff, N.A.3
-
33
-
-
84908086129
-
Models for financial sustainability of biological databases and resources
-
bap017
-
Chandras C, Weaver T, Zouberakis M, et al. Models for financial sustainability of biological databases and resources. Database 2009;2009:bap017.
-
(2009)
Database
, vol.2009
-
-
Chandras, C.1
Weaver, T.2
Zouberakis, M.3
-
34
-
-
0038002409
-
Identification and correction of spurious spatial correlations in microarray data
-
46, 48
-
Qian JA, Kluger Y, Yu HY, et al. Identification and correction of spurious spatial correlations in microarray data. BioTechniques 2003;35(1):42-44. 46, 48.
-
(2003)
BioTechniques
, vol.35
, Issue.1
, pp. 42-44
-
-
Qian, J.A.1
Kluger, Y.2
Yu, H.Y.3
-
35
-
-
1342294092
-
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
-
Yang YH, Dudoit S, Luu P, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002;30(4):e15.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.4
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
-
36
-
-
3242732932
-
Possible sources of dye-related signal correlation bias in two-color DNA microarray assays
-
Cox WG, Beaudet MP, Agnew JY, et al. Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal Biochem 2004;331(2):243-54.
-
(2004)
Anal Biochem
, vol.331
, Issue.2
, pp. 243-254
-
-
Cox, W.G.1
Beaudet, M.P.2
Agnew, J.Y.3
-
37
-
-
0036574916
-
Statistical issues with microarrays: processing and analysis
-
Nadon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends in Genetics 2002;18(5): 265-71.
-
(2002)
Trends in Genetics
, vol.18
, Issue.5
, pp. 265-271
-
-
Nadon, R.1
Shoemaker, J.2
-
38
-
-
34249720475
-
chip artifact CORRECTion (caCORRECT): A bioinformatics system for quality assurance of genomics and proteomics array data
-
Stokes TH, Moffitt RA, Phan JH, et al. chip artifact CORRECTion (caCORRECT): A bioinformatics system for quality assurance of genomics and proteomics array data. Ann Biomed Engineer 2007;35(6):1068-80.
-
(2007)
Ann Biomed Engineer
, vol.35
, Issue.6
, pp. 1068-1080
-
-
Stokes, T.H.1
Moffitt, R.A.2
Phan, J.H.3
-
39
-
-
67650908913
-
Managing and analyzing next-generation sequence data
-
Richter BG, Sexton DP. Managing and analyzing next-generation sequence data. PLoS Comput Biol 2009; 5(6):e1000369.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.6
-
-
Richter, B.G.1
Sexton, D.P.2
-
40
-
-
39649084637
-
Bioinformatics challenges of new sequencing technology
-
Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008;24(3):142-9.
-
(2008)
Trends Genet
, vol.24
, Issue.3
, pp. 142-149
-
-
Pop, M.1
Salzberg, S.L.2
-
41
-
-
77952745346
-
BING: biomedical informatics pipeline for next generation sequencing
-
Kriseman J, Busick C, Szelinger S, et al. BING: biomedical informatics pipeline for next generation sequencing. J Biom Inform 2010;43(3):428-34.
-
(2010)
J Biom Inform
, vol.43
, Issue.3
, pp. 428-434
-
-
Kriseman, J.1
Busick, C.2
Szelinger, S.3
-
42
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 2010;11(5): 473-83.
-
(2010)
Brief Bioinform
, vol.11
, Issue.5
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
43
-
-
77949512406
-
Tablet-next generation sequence assembly visualization
-
Milne I, Bayer M, Cardle L, et al. Tablet-next generation sequence assembly visualization. Bioinformatics 2010;26(3): 401-2.
-
(2010)
Bioinformatics
, vol.26
, Issue.3
, pp. 401-402
-
-
Milne, I.1
Bayer, M.2
Cardle, L.3
-
44
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-Seq
-
Jiang H, Wong WH. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 2009;25(8): 1026-32.
-
(2009)
Bioinformatics
, vol.25
, Issue.8
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
45
-
-
77955443472
-
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
-
Au KF, Jiang H, Lin L, et al. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 2010;38(14):4570-8.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.14
, pp. 4570-4578
-
-
Au, K.F.1
Jiang, H.2
Lin, L.3
-
46
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent WJ. BLAT-The BLAST-like alignment tool. Genome Res 2002;12(4):656-64.
-
(2002)
Genome Res
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
47
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25(9): 1105-11.
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
48
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson G, Schein J, Chiu R, et al. De novo assembly and analysis of RNA-seq data. Nat Methods 2010;7(11): U909-62.
-
(2010)
Nat Methods
, vol.7
, Issue.11
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
-
49
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011;29(7):644-52.
-
(2011)
Nat Biotechnol
, vol.29
, Issue.7
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
-
50
-
-
68949206409
-
Applying mass spectrometrybased proteomics to genetics, genomics and network biology
-
Gstaiger M, Aebersold R. Applying mass spectrometrybased proteomics to genetics, genomics and network biology. Nat Rev Genet 2009;10(9):617-27.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.9
, pp. 617-627
-
-
Gstaiger, M.1
Aebersold, R.2
-
51
-
-
61349147183
-
MALDI Imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers
-
Deininger SO, Ebert MP, Futterer A, et al. MALDI Imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers. J Proteome Res 2008;7(12):5230-6.
-
(2008)
J Proteome Res
, vol.7
, Issue.12
, pp. 5230-5236
-
-
Deininger, S.O.1
Ebert, M.P.2
Futterer, A.3
-
52
-
-
79959459290
-
Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering
-
Alexandrov T, Kobarg JH. Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering. Bioinformatics 2011;27(13):I230-8.
-
(2011)
Bioinformatics
, vol.27
, Issue.13
-
-
Alexandrov, T.1
Kobarg, J.H.2
-
53
-
-
70349974835
-
MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78 kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections
-
Djidja MC, Claude E, Snel MF, et al. MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78 kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. J ProteomeRes 2009;8(10):4876-84.
-
(2009)
J ProteomeRes
, vol.8
, Issue.10
, pp. 4876-4884
-
-
Djidja, M.C.1
Claude, E.2
Snel, M.F.3
-
54
-
-
77954406077
-
Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry
-
Liu Y, Chen Y, Momin A, et al. Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry. Mol Cancer 2010;9:186.
-
(2010)
Mol Cancer
, vol.9
, pp. 186
-
-
Liu, Y.1
Chen, Y.2
Momin, A.3
-
55
-
-
77950661168
-
Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry
-
Rauser S, Marquardt C, Balluff B, et al. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J Proteome Res 2010;9(4):1854-63.
-
(2010)
J Proteome Res
, vol.9
, Issue.4
, pp. 1854-1863
-
-
Rauser, S.1
Marquardt, C.2
Balluff, B.3
-
56
-
-
78650761774
-
Nanostructure-initiator mass spectrometry metabolite analysis and imaging
-
Greving MP, Patti GJ, Siuzdak G. Nanostructure-initiator mass spectrometry metabolite analysis and imaging. Anal Chem 2011;83(1):2-7.
-
(2011)
Anal Chem
, vol.83
, Issue.1
, pp. 2-7
-
-
Greving, M.P.1
Patti, G.J.2
Siuzdak, G.3
-
57
-
-
53049095378
-
Mass spectrometry image correlation: quantifying colocalization
-
McDonnell LA, van Remoortere A, van Zeijl RJM, et al. Mass spectrometry image correlation: quantifying colocalization. J Proteome Res 2008;7(8):3619-27.
-
(2008)
J Proteome Res
, vol.7
, Issue.8
, pp. 3619-3627
-
-
McDonnell, L.A.1
van Remoortere, A.2
van Zeijl, R.J.M.3
-
58
-
-
33846015488
-
Matrix-free methods for laser desorption/ionization mass spectrometry
-
Peterson DS. Matrix-free methods for laser desorption/ionization mass spectrometry. Mass Spectrometry Rev 2007;26(1): 19-34.
-
(2007)
Mass Spectrometry Rev
, vol.26
, Issue.1
, pp. 19-34
-
-
Peterson, D.S.1
-
59
-
-
77949688458
-
Reverse engineering of bacterial chemotaxis pathway via frequency domain analysis
-
Luo J, Wang J, Ma TM, et al. Reverse engineering of bacterial chemotaxis pathway via frequency domain analysis. PLoS One 2010;5(3):e9182.
-
(2010)
PLoS One
, vol.5
, Issue.3
-
-
Luo, J.1
Wang, J.2
Ma, T.M.3
-
60
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME) -toward standards for microarray data
-
Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME) -toward standards for microarray data. Nat Genet 2001; 29(4):365-71.
-
(2001)
Nat Genet
, vol.29
, Issue.4
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
-
61
-
-
45749118607
-
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
-
Taylor CF, Field D, Sansone S-A, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotech 2008; 26(8):889-96.
-
(2008)
Nat Biotech
, vol.26
, Issue.8
, pp. 889-896
-
-
Taylor, C.F.1
Field, D.2
Sansone, S.-A.3
-
62
-
-
4444309760
-
Potential of metabolomics as a functional genomics tool
-
Bino RJ, Hall RD, Fiehn O, et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci 2004;9(9): 418-25.
-
(2004)
Trends Plant Sci
, vol.9
, Issue.9
, pp. 418-425
-
-
Bino, R.J.1
Hall, R.D.2
Fiehn, O.3
-
63
-
-
77957204152
-
Minimum information about a neuroscience investigation (MINI): electrophysiology
-
hdl:10101/ npre.12008.11720
-
Gibson F, Overton PG, Smulders TV, et al. Minimum information about a neuroscience investigation (MINI): electrophysiology. Nat Precedings 2008. hdl:10101/ npre.12008.11720.10101.
-
(2008)
Nat Precedings
, pp. 10101
-
-
Gibson, F.1
Overton, P.G.2
Smulders, T.V.3
-
64
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novere N, Finney A, Hucka M, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotech 2005;23(12):1509-15.
-
(2005)
Nat Biotech
, vol.23
, Issue.12
, pp. 1509-1515
-
-
Le Novere, N.1
Finney, A.2
Hucka, M.3
-
65
-
-
79955570036
-
Minimum information about a simulation experiment (MIASE)
-
Waltemath D, Adams R, Beard DA, et al. Minimum information about a simulation experiment (MIASE). PLoS Comput Biol 2011;7(4):e1001122.
-
(2011)
PLoS Comput Biol
, vol.7
, Issue.4
-
-
Waltemath, D.1
Adams, R.2
Beard, D.A.3
-
66
-
-
12344319205
-
Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies
-
Stoeckert CJ, Quackenbush J, Brazma A, et al. Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies. DDT:Targets 2004;3(4):159-64.
-
(2004)
DDT:Targets
, vol.3
, Issue.4
, pp. 159-164
-
-
Stoeckert, C.J.1
Quackenbush, J.2
Brazma, A.3
-
67
-
-
0038745251
-
Systems Biology Markup Language (SBML) Level 2: structures and facilities for model definitions
-
Hucka M, Finney AM, Hoops S, et al. Systems Biology Markup Language (SBML) Level 2: structures and facilities for model definitions. Nat Precedings 2007. http://hdl.nature. com/10101/npre.2007.58.1.
-
(2007)
Nat Precedings
-
-
Hucka, M.1
Finney, A.M.2
Hoops, S.3
-
68
-
-
40349100409
-
MIRIAM resources: tools to generate and resolve robust cross-references in Systems Biology
-
Laibe C, Le Novere N. MIRIAM resources: tools to generate and resolve robust cross-references in Systems Biology. BMCSys Biol 2007;1:58.
-
(2007)
BMCSys Biol
, vol.1
, pp. 58
-
-
Laibe, C.1
Le Novere, N.2
-
69
-
-
77950369345
-
Data clustering: 50 years beyond K-means
-
Jain AK. Data clustering: 50 years beyond K-means. Pattern Recognit Lett 2010;31(8):651-66.
-
(2010)
Pattern Recognit Lett
, vol.31
, Issue.8
, pp. 651-666
-
-
Jain, A.K.1
-
70
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen MB, Spellman PT, Brown PO, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad SciUSA 1998;95(25):14863-8.
-
(1998)
Proc Natl Acad SciUSA
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
-
71
-
-
47249160807
-
Genetic weighted k-means algorithm for clustering large-scale gene expression data
-
Wu FX. Genetic weighted k-means algorithm for clustering large-scale gene expression data. BMC Bioinformatics 2008; 9(Suppl 6):S12.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL 6
-
-
Wu, F.X.1
-
72
-
-
40449141013
-
What is principal component analysis?
-
Ringnér M. What is principal component analysis? Nat Biotechnol 2008;26(3):303-4.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.3
, pp. 303-304
-
-
Ringnér, M.1
-
73
-
-
33646137384
-
A systematic comparison and evaluation of biclustering methods for gene expression data
-
Preli A, Bleuler S, Zimmermann P, et al. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 2006;22(9):1122-9.
-
(2006)
Bioinformatics
, vol.22
, Issue.9
, pp. 1122-1129
-
-
Preli, A.1
Bleuler, S.2
Zimmermann, P.3
-
74
-
-
77957674888
-
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
-
Freyhult E, Landfors M, Ö nskog J, et al. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. BMC Bioinformatics 2010;11(1):503.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 503
-
-
Freyhult, E.1
Landfors, M.2
Ö nskog, J.3
-
75
-
-
35748932917
-
A review of feature selection techniques in bioinformatics
-
Saeys Y, Inza I, Larranaga P. A review of feature selection techniques in bioinformatics. Bioinformatics 2007;23(19): 2507-17.
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2507-2517
-
-
Saeys, Y.1
Inza, I.2
Larranaga, P.3
-
76
-
-
0037245343
-
Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification
-
Simon R, Radmacher M, Dobbin K, et al. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003;95(1): 14-8.
-
(2003)
J Natl Cancer Inst
, vol.95
, Issue.1
, pp. 14-18
-
-
Simon, R.1
Radmacher, M.2
Dobbin, K.3
-
77
-
-
65549115157
-
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment
-
Phan JH, Moffitt RA, Stokes TH, et al. Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. Trends Biotechnol 2009; 27(6):350-8.
-
(2009)
Trends Biotechnol
, vol.27
, Issue.6
, pp. 350-358
-
-
Phan, J.H.1
Moffitt, R.A.2
Stokes, T.H.3
-
78
-
-
77955131271
-
A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data
-
Luo J, Schumacher M, Scherer A, et al. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. PharmacogenomicsJ 2010;10(4):278-91.
-
(2010)
PharmacogenomicsJ
, vol.10
, Issue.4
, pp. 278-291
-
-
Luo, J.1
Schumacher, M.2
Scherer, A.3
-
79
-
-
76649101119
-
Optimal classifier selection and negative bias in error rate estimation: an empirical study on high-dimensional prediction
-
Boulesteix AL, Strobl C. Optimal classifier selection and negative bias in error rate estimation: an empirical study on high-dimensional prediction. BMC Med Res Methodology 2009;9(1):85.
-
(2009)
BMC Med Res Methodology
, vol.9
, Issue.1
, pp. 85
-
-
Boulesteix, A.L.1
Strobl, C.2
-
80
-
-
77957988489
-
Class prediction for high-dimensional classimbalanced data
-
Lusa L. Class prediction for high-dimensional classimbalanced data. BMC Bioinformatics 2010;11(1):523.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 523
-
-
Lusa, L.1
-
81
-
-
77949535610
-
Over-optimism in bioinformatics research
-
Boulesteix AL. Over-optimism in bioinformatics research. Bioinformatics 2010;26(3):437.
-
(2010)
Bioinformatics
, vol.26
, Issue.3
, pp. 437
-
-
Boulesteix, A.L.1
-
82
-
-
77955127780
-
Consistency of predictive signature genes and classifiers generated using different microarray platforms
-
Fan X, Lobenhofer E, Chen M, et al. Consistency of predictive signature genes and classifiers generated using different microarray platforms. Pharmacogenomics J 2010; 10(4):247-57.
-
(2010)
Pharmacogenomics J
, vol.10
, Issue.4
, pp. 247-257
-
-
Fan, X.1
Lobenhofer, E.2
Chen, M.3
-
83
-
-
77955160229
-
k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction
-
Parry R, Jones W, Stokes T, et al. k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction. Pharmacogenomics J 2010;10(4): 292-309.
-
(2010)
Pharmacogenomics J
, vol.10
, Issue.4
, pp. 292-309
-
-
Parry, R.1
Jones, W.2
Stokes, T.3
-
84
-
-
78650735473
-
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
-
Shi L, Campbell G, Jones WD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotech 2010;28(8):827.
-
(2010)
Nat Biotech
, vol.28
, Issue.8
, pp. 827
-
-
Shi, L.1
Campbell, G.2
Jones, W.D.3
-
85
-
-
45849113320
-
On the epistemological crisis in genomics
-
Dougherty ER. On the epistemological crisis in genomics. Curr Genomics 2008;9(2):69-79.
-
(2008)
Curr Genomics
, vol.9
, Issue.2
, pp. 69-79
-
-
Dougherty, E.R.1
-
86
-
-
33748204139
-
Microarray analysis and tumor classification
-
Quackenbush J. Microarray analysis and tumor classification. NEngJMed 2006;355(9):960.
-
(2006)
NEngJMed
, vol.355
, Issue.9
, pp. 960
-
-
Quackenbush, J.1
-
87
-
-
73949136029
-
The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade
-
Weigelt B, Baehner FL, Reis JS. The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade. J Pathol 2010;220(2):263-80.
-
(2010)
J Pathol
, vol.220
, Issue.2
, pp. 263-280
-
-
Weigelt, B.1
Baehner, F.L.2
Reis, J.S.3
-
88
-
-
13444249852
-
Prediction of cancer outcome with microarrays: a multiple random validation strategy
-
Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005;365:488-92.
-
(2005)
Lancet
, vol.365
, pp. 488-492
-
-
Michiels, S.1
Koscielny, S.2
Hill, C.3
-
89
-
-
0037076322
-
Selection bias in gene extraction on the basis of microarray gene-expression data
-
Ambroise C, McLachlan GJ. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad SciUSA 2002;99(10):6562-6.
-
(2002)
Proc Natl Acad SciUSA
, vol.99
, Issue.10
, pp. 6562-6566
-
-
Ambroise, C.1
McLachlan, G.J.2
-
90
-
-
33644860703
-
Bias in error estimation when using cross-validation for model selection
-
Varma S, Simon R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 2006;7:91.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 91
-
-
Varma, S.1
Simon, R.2
-
91
-
-
1342330535
-
Is cross-validation valid for small-sample microarray classification?
-
Braga-Neto UM, Dougherty ER. Is cross-validation valid for small-sample microarray classification? Bioinformatics 2004;20(3):374-80.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 374-380
-
-
Braga-Neto, U.M.1
Dougherty, E.R.2
-
92
-
-
18744413287
-
Estimating misclassification error with small samples via bootstrap cross-validation
-
Fu WJJ, Carroll RJ, Wang SJ. Estimating misclassification error with small samples via bootstrap cross-validation. Bioinformatics 2005;21(9):1979-86.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1979-1986
-
-
Fu, W.J.J.1
Carroll, R.J.2
Wang, S.J.3
-
93
-
-
50349090268
-
Crossvalidation and bootstrapping are unreliable in small sample classification
-
Isaksson A, Wallman M, Goransson H, et al. Crossvalidation and bootstrapping are unreliable in small sample classification. PatternRecognition Lett 2008;29(14):1960-5.
-
(2008)
PatternRecognition Lett
, vol.29
, Issue.14
, pp. 1960-1965
-
-
Isaksson, A.1
Wallman, M.2
Goransson, H.3
-
94
-
-
74549174585
-
DNA microarrays are predictive of cancer prognosis: a re-evaluation
-
Fan X, Shi L, Fang H, et al. DNA microarrays are predictive of cancer prognosis: a re-evaluation. Clin Cancer Res 2010; 16(2):629.
-
(2010)
Clin Cancer Res
, vol.16
, Issue.2
, pp. 629
-
-
Fan, X.1
Shi, L.2
Fang, H.3
-
95
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, et al. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003;302(5643):249-55.
-
(2003)
Science
, vol.302
, Issue.5643
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
-
96
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I, Basso K, et al. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006;7(Suppl 1):S7.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL 1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
-
97
-
-
0033655775
-
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
-
Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Sym Biocomput 2000;418-29.
-
(2000)
Pac Sym Biocomput
, pp. 418-429
-
-
Butte, A.J.1
Kohane, I.S.2
-
98
-
-
34250658998
-
Bayesian methods in bioinformatics and computational systems biology
-
Wilkinson DJ. Bayesian methods in bioinformatics and computational systems biology. Brief Bioinform 2007;8(2):109-16.
-
(2007)
Brief Bioinform
, vol.8
, Issue.2
, pp. 109-116
-
-
Wilkinson, D.J.1
-
99
-
-
17244382596
-
Logistic regression and Bayesian networks to study outcomes using large datasets
-
Lee S, Abbott P, Johantgen M. Logistic regression and Bayesian networks to study outcomes using large datasets. Nurs Res 2005;54(2):133-8.
-
(2005)
Nurs Res
, vol.54
, Issue.2
, pp. 133-138
-
-
Lee, S.1
Abbott, P.2
Johantgen, M.3
-
100
-
-
16844366938
-
Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia
-
Sebastiani P, Ramoni MF, Nolan V, et al. Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia. Nat Genet 2005;37(4):435-40.
-
(2005)
Nat Genet
, vol.37
, Issue.4
, pp. 435-440
-
-
Sebastiani, P.1
Ramoni, M.F.2
Nolan, V.3
-
101
-
-
79960888804
-
Inferring causal genomic alterations in breast cancer using gene expression data
-
Tran LM, Zhang B, Zhang Z, et al. Inferring causal genomic alterations in breast cancer using gene expression data. BMC Sys Biol 2011;5:121.
-
(2011)
BMC Sys Biol
, vol.5
, pp. 121
-
-
Tran, L.M.1
Zhang, B.2
Zhang, Z.3
-
102
-
-
75149195336
-
The transcriptional network for mesenchymal transformation of brain tumours
-
Carro MS, Lim WK, Alvarez MJ, et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature 2010;463(7279):U318-68.
-
(2010)
Nature
, vol.463
, Issue.7279
-
-
Carro, M.S.1
Lim, W.K.2
Alvarez, M.J.3
-
103
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith JJ, Hayete B, Thaden JT, et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. Plos Biol 2007; 5(1):54-66.
-
(2007)
Plos Biol
, vol.5
, Issue.1
, pp. 54-66
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
-
104
-
-
45149106353
-
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
-
Zhu J, Zhang B, Smith EN, et al. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 2008;40(7):854-61.
-
(2008)
Nat Genet
, vol.40
, Issue.7
, pp. 854-861
-
-
Zhu, J.1
Zhang, B.2
Smith, E.N.3
-
106
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach D, Prill RJ, Schaffter T, et al. Revealing strengths and weaknesses of methods for gene network inference. ProcNatl Acad SciUSA 2010;107(14):6286-91.
-
(2010)
ProcNatl Acad SciUSA
, vol.107
, Issue.14
, pp. 6286-6291
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
-
107
-
-
79955371637
-
Insights gained from the reverse engineering of gene networks in keloid fibroblasts
-
Ooi BNS, Phan TT. Insights gained from the reverse engineering of gene networks in keloid fibroblasts. Theor BiolMedModel 2011;8:13.
-
(2011)
Theor BiolMedModel
, vol.8
, pp. 13
-
-
Ooi, B.N.S.1
Phan, T.T.2
-
108
-
-
12344259602
-
Advances to Bayesian network inference for generating causal networks from observational biological data
-
Yu J, Smith VA, Wang PP, et al. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 2004;20(18): 3594-603.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
-
109
-
-
0014489272
-
Metabolic stability and epigenesis in randomly constructed genetic nets
-
Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 1969;22(3): 437-67.
-
(1969)
J Theor Biol
, vol.22
, Issue.3
, pp. 437-467
-
-
Kauffman, S.A.1
-
110
-
-
0036184629
-
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty ER, Kim S, et al. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002;18(2):261-74.
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
-
114
-
-
0028844979
-
A mathematical framework for describing and analyzing gene regulatory networks
-
Mestl T, Plahte E, Omholt SW. A mathematical framework for describing and analyzing gene regulatory networks. JTheor Biol 1995;176(2):291-300.
-
(1995)
J Theor Biol
, vol.176
, Issue.2
, pp. 291-300
-
-
Mestl, T.1
Plahte, E.2
Omholt, S.W.3
-
115
-
-
0014658880
-
Biochemical systems analysis. 2. Steady-state solutions for an N-pool system using a power-law approximation
-
Savageau MA. Biochemical systems analysis. 2. Steady-state solutions for an N-pool system using a power-law approximation. J Theor Biol 1969;25(3):370-9.
-
(1969)
J Theor Biol
, vol.25
, Issue.3
, pp. 370-379
-
-
Savageau, M.A.1
-
116
-
-
33845373861
-
Studies concerning affinity (translated)
-
Waage P, Gulberg CM. Studies concerning affinity (translated). J Chem Education 1986;63(12):1044-7.
-
(1986)
J Chem Education
, vol.63
, Issue.12
, pp. 1044-1047
-
-
Waage, P.1
Gulberg, C.M.2
-
117
-
-
0028108519
-
Metabolic flux balancing - basic concepts, scientific and practical use
-
Varma A, Palsson BO. Metabolic flux balancing - basic concepts, scientific and practical use. Nat Biotech 1994; 12(10):994-8.
-
(1994)
Nat Biotech
, vol.12
, Issue.10
, pp. 994-998
-
-
Varma, A.1
Palsson, B.O.2
-
118
-
-
0026802334
-
Metabolic control analysis - a survey of its theoretical and experimental development
-
Fell DA. Metabolic control analysis - a survey of its theoretical and experimental development. Biochem J 1992;286: 313-30.
-
(1992)
Biochem J
, vol.286
, pp. 313-330
-
-
Fell, D.A.1
-
119
-
-
13444283465
-
Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae
-
Alvarez-Vasquez F, Sims KJ, Cowart LA, et al. Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 2005;433(7024):425-30.
-
(2005)
Nature
, vol.433
, Issue.7024
, pp. 425-430
-
-
Alvarez-Vasquez, F.1
Sims, K.J.2
Cowart, L.A.3
-
120
-
-
79551688548
-
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism
-
Gupta S, Maurya MR, Merrill AH, Jr, et al. Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. BMC Sys Biol 2011;5:26.
-
(2011)
BMC Sys Biol
, vol.5
, pp. 26
-
-
Gupta, S.1
Maurya, M.R.2
Merrill Jr., A.H.3
-
121
-
-
4544346660
-
Robustness of cellular functions
-
Stelling J, Sauer U, Szallasi Z, et al. Robustness of cellular functions. Cell 2004;118(6):675-85.
-
(2004)
Cell
, vol.118
, Issue.6
, pp. 675-685
-
-
Stelling, J.1
Sauer, U.2
Szallasi, Z.3
-
124
-
-
53549128661
-
The immune system and its ecology
-
Tauber AI. The immune system and its ecology. Philos Sci 2008;75(2):224-45.
-
(2008)
Philos Sci
, vol.75
, Issue.2
, pp. 224-245
-
-
Tauber, A.I.1
-
125
-
-
69249203708
-
The brainstem respiratory network: an overview of a half century of research
-
Bianchi AL, Gestreau C. The brainstem respiratory network: an overview of a half century of research. Resp PhysiolNeurobiol 2009;168(1-2):4-12.
-
(2009)
Resp PhysiolNeurobiol
, vol.168
, Issue.1-2
, pp. 4-12
-
-
Bianchi, A.L.1
Gestreau, C.2
-
126
-
-
67650435037
-
The systems analysis approach to mechanosensory coding
-
French AS. The systems analysis approach to mechanosensory coding. Biol Cyber 2009;100(6):417-26.
-
(2009)
Biol Cyber
, vol.100
, Issue.6
, pp. 417-426
-
-
French, A.S.1
-
127
-
-
77950897710
-
Application of the principles of systems biology and Wiener's cybernetics for analysis of regulation of energy fluxes in muscle cells in vivo
-
Guzun R, Saks V. Application of the principles of systems biology and Wiener's cybernetics for analysis of regulation of energy fluxes in muscle cells in vivo. Int JMol Sci 2010; 11(3):982-1019.
-
(2010)
Int JMol Sci
, vol.11
, Issue.3
, pp. 982-1019
-
-
Guzun, R.1
Saks, V.2
-
128
-
-
0033552946
-
Robustness in bacterial chemotaxis
-
Alon U, Surette MG, Barkai N, et al. Robustness in bacterial chemotaxis. Nature 1999;397(6715):168-71.
-
(1999)
Nature
, vol.397
, Issue.6715
, pp. 168-171
-
-
Alon, U.1
Surette, M.G.2
Barkai, N.3
-
129
-
-
0030797355
-
Robustness in simple biochemical networks
-
Barkai N, Leibler S. Robustness in simple biochemical networks. Nature 1997;387(6636):913-7.
-
(1997)
Nature
, vol.387
, Issue.6636
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
130
-
-
77954024185
-
A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli
-
Shimizu TS, Tu Y, Berg HC. A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Sys Biol 2010;6:382.
-
(2010)
Mol Sys Biol
, vol.6
, pp. 382
-
-
Shimizu, T.S.1
Tu, Y.2
Berg, H.C.3
-
131
-
-
77953808473
-
Next-generation genomics: an integrative approach
-
Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet 2010;11(7): 476-86.
-
(2010)
Nat Rev Genet
, vol.11
, Issue.7
, pp. 476-486
-
-
Hawkins, R.D.1
Hon, G.C.2
Ren, B.3
-
132
-
-
80053599055
-
An integrative genomics approach to biomarker discovery in breast cancer
-
Hicks C, Asfour R, Pannuti A, et al. An integrative genomics approach to biomarker discovery in breast cancer. Cancer Inform 2011;10:185-204.
-
(2011)
Cancer Inform
, vol.10
, pp. 185-204
-
-
Hicks, C.1
Asfour, R.2
Pannuti, A.3
-
133
-
-
57749180003
-
Integrative biology - a strategy for systems biomedicine
-
Liu ET. Integrative biology - a strategy for systems biomedicine. Nat Rev Genet 2009;10(1):64-8.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.1
, pp. 64-68
-
-
Liu, E.T.1
-
134
-
-
79953318394
-
Integrative genomics identifies molecular alterations that challenge the linear model of melanoma progression
-
Rose AE, Poliseno L, Wang J, et al. Integrative genomics identifies molecular alterations that challenge the linear model of melanoma progression. Cancer Res 2011;71(7): 2561-71.
-
(2011)
Cancer Res
, vol.71
, Issue.7
, pp. 2561-2571
-
-
Rose, A.E.1
Poliseno, L.2
Wang, J.3
-
135
-
-
79952122331
-
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing
-
Sun Z, Asmann YW, Kalari KR, et al. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoSOne 2011;6(2):e17490.
-
(2011)
PLoSOne
, vol.6
, Issue.2
-
-
Sun, Z.1
Asmann, Y.W.2
Kalari, K.R.3
-
136
-
-
78651409984
-
Integrative genomics identifies LMO1 as a neuroblastoma oncogene
-
Wang K, Diskin SJ, Zhang H, et al. Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Nature 2011;469(7329):216-20.
-
(2011)
Nature
, vol.469
, Issue.7329
, pp. 216-220
-
-
Wang, K.1
Diskin, S.J.2
Zhang, H.3
-
137
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
Bell D, Berchuck A, Birrer M, et al. Integrated genomic analyses of ovarian carcinoma. Nature 2011;474(7353):609-15.
-
(2011)
Nature
, vol.474
, Issue.7353
, pp. 609-615
-
-
Bell, D.1
Berchuck, A.2
Birrer, M.3
-
138
-
-
77957154710
-
Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM)
-
Carter H, Samayoa J, Hruban RH, et al. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biol Ther 2010;10(6):582-7.
-
(2010)
Cancer Biol Ther
, vol.10
, Issue.6
, pp. 582-587
-
-
Carter, H.1
Samayoa, J.2
Hruban, R.H.3
-
139
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
Chin L, Meyerson M, Aldape K, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008;455(7216):1061-8.
-
(2008)
Nature
, vol.455
, Issue.7216
, pp. 1061-1068
-
-
Chin, L.1
Meyerson, M.2
Aldape, K.3
-
140
-
-
79952389826
-
Algorithms for detecting significantly mutated pathways in cancer
-
Vandin F, Upfal E, Raphael BJ. Algorithms for detecting significantly mutated pathways in cancer. J Comp Bio 2011; 18(3):507-22.
-
(2011)
J Comp Bio
, vol.18
, Issue.3
, pp. 507-522
-
-
Vandin, F.1
Upfal, E.2
Raphael, B.J.3
-
141
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
Vaske CJ, Benz SC, Sanborn JZ, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010;26(12):i237-45.
-
(2010)
Bioinformatics
, vol.26
, Issue.12
-
-
Vaske, C.J.1
Benz, S.C.2
Sanborn, J.Z.3
-
142
-
-
0028891136
-
A model of excitation and adaptation in bacterial chemotaxis
-
Hauri DC, Ross J. A model of excitation and adaptation in bacterial chemotaxis. BiophysJ 1995;68(2):708-22.
-
(1995)
BiophysJ
, vol.68
, Issue.2
, pp. 708-722
-
-
Hauri, D.C.1
Ross, J.2
-
143
-
-
0000889294
-
Reduction of speech spectra by analysis-by-synthesis techniques
-
Bell CG, Stevens KN, House AS, et al. Reduction of speech spectra by analysis-by-synthesis techniques. J Acoustical Soc Am 1961;33(12):1725-8.
-
(1961)
J Acoustical Soc Am
, vol.33
, Issue.12
, pp. 1725-1728
-
-
Bell, C.G.1
Stevens, K.N.2
House, A.S.3
-
144
-
-
0038175144
-
GoMiner: a resource for biological interpretation of genomic and proteomic data
-
Zeeberg BR, Feng WM, Wang G, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003;4(4):R28.
-
(2003)
Genome Biol
, vol.4
, Issue.4
-
-
Zeeberg, B.R.1
Feng, W.M.2
Wang, G.3
-
145
-
-
68449088806
-
Synthetic protein scaffolds provide modular control over metabolic flux
-
Dueber JE, Wu GC, Malmirchegini GR, et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotech 2009;27(8):753-9.
-
(2009)
Nat Biotech
, vol.27
, Issue.8
, pp. 753-759
-
-
Dueber, J.E.1
Wu, G.C.2
Malmirchegini, G.R.3
-
146
-
-
72249110882
-
Control of DNA strand displacement kinetics using toehold exchange
-
Zhang DY, Winfree E. Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 2009; 131(47):17303-14.
-
(2009)
J Am Chem Soc
, vol.131
, Issue.47
, pp. 17303-17314
-
-
Zhang, D.Y.1
Winfree, E.2
-
147
-
-
79952111742
-
Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen pectobacterium atrosepticum
-
Fenyo D, (ed). New York: Humana Press
-
Lin K, Husmeier D, Dondelinger F, et al. Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen pectobacterium atrosepticum. In: Fenyo D, (ed). Computational Biology, Vol. 673. New York: Humana Press, 2010, 253-81.
-
(2010)
Computational Biology
, vol.673
, pp. 253-281
-
-
Lin, K.1
Husmeier, D.2
Dondelinger, F.3
-
148
-
-
79956204640
-
Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks
-
Menolascina F, di Bernardo M, di Bernardo D. Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks. Automatica 2011;47(6):1265-70.
-
(2011)
Automatica
, vol.47
, Issue.6
, pp. 1265-1270
-
-
Menolascina, F.1
di Bernardo, M.2
di Bernardo, D.3
-
149
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotech 2009;27(10):946-50.
-
(2009)
Nat Biotech
, vol.27
, Issue.10
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
150
-
-
77952492425
-
Tuning and controlling gene expression noise in synthetic gene networks
-
Murphy KF, Adams RM, Wang X, et al. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 2010;38(8):2712-26.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.8
, pp. 2712-2726
-
-
Murphy, K.F.1
Adams, R.M.2
Wang, X.3
-
151
-
-
67549145283
-
A synthetic genetic edge detection program
-
Tabor JJ, Salis HM, Simpson ZB, et al. A synthetic genetic edge detection program. Cell 2009;137(7):1272-81.
-
(2009)
Cell
, vol.137
, Issue.7
, pp. 1272-1281
-
-
Tabor, J.J.1
Salis, H.M.2
Simpson, Z.B.3
-
152
-
-
77950435582
-
A synthetic low-frequency mammalian oscillator
-
Tigges M, Denervaud N, Greber D, et al. A synthetic low-frequency mammalian oscillator. Nucleic Acids Res 2010;38(8):2702-11.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.8
, pp. 2702-2711
-
-
Tigges, M.1
Denervaud, N.2
Greber, D.3
-
153
-
-
78651397316
-
Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'
-
Tamsir A, Tabor JJ, Voigt CA. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 2011;469(7329):212-5.
-
(2011)
Nature
, vol.469
, Issue.7329
, pp. 212-215
-
-
Tamsir, A.1
Tabor, J.J.2
Voigt, C.A.3
-
154
-
-
77953584054
-
Creation of a bacterial cell controlled by a chemically synthesized genome
-
Gibson DG, Glass JI, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010;329(5987):52-6.
-
(2010)
Science
, vol.329
, Issue.5987
, pp. 52-56
-
-
Gibson, D.G.1
Glass, J.I.2
Lartigue, C.3
-
155
-
-
77955033157
-
SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs
-
Weeding E, Houle J, Kaznessis YN. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform 2010;11(4):394-402.
-
(2010)
Brief Bioinform
, vol.11
, Issue.4
, pp. 394-402
-
-
Weeding, E.1
Houle, J.2
Kaznessis, Y.N.3
-
156
-
-
79955710914
-
Eugene - A domain specific language for specifying and constraining synthetic biological parts, devices, and systems
-
Bilitchenko L, Liu A, Cheung S, et al. Eugene - A domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 2011;6(4): e18882.
-
(2011)
PLoS One
, vol.6
, Issue.4
-
-
Bilitchenko, L.1
Liu, A.2
Cheung, S.3
-
157
-
-
71849095864
-
TinkerCell: modular CAD tool for synthetic biology
-
doi:10.1186/1754-1611-1183-1119
-
Chandran D, Bergmann FT, Sauro HM. TinkerCell: modular CAD tool for synthetic biology. J Biol Engineer 2009;3(19). doi:10.1186/1754-1611-1183-1119.
-
(2009)
J Biol Engineer
, vol.3
, Issue.19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
158
-
-
77955155615
-
Noise and robustness in prokaryotic regulatory networks
-
Silva-Rocha R, de Lorenzo V. Noise and robustness in prokaryotic regulatory networks. Ann Rev Microbiol 2010; 64:257-75.
-
(2010)
Ann Rev Microbiol
, vol.64
, pp. 257-275
-
-
Silva-Rocha, R.1
de Lorenzo, V.2
-
159
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N, Linial M, Nachman I, et al. Using Bayesian networks to analyze expression data. J Comput Biol 2000; 7(3-4):601-20.
-
(2000)
J Comput Biol
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
-
161
-
-
63049094001
-
Phenotype forecasting with SNPs data through gene-based Bayesian networks
-
Malovini A, Nuzzo A, Ferrazzi F, et al. Phenotype forecasting with SNPs data through gene-based Bayesian networks. BMC Bioinformatics 2009;10:S7.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Malovini, A.1
Nuzzo, A.2
Ferrazzi, F.3
-
162
-
-
0036112213
-
Applications of generalized pair hidden Markov models to alignment and gene finding problems
-
Pachter L, Alexandersson M, Cawley S. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J Comput Biol 2002;9(2):389-99.
-
(2002)
J Comput Biol
, vol.9
, Issue.2
, pp. 389-399
-
-
Pachter, L.1
Alexandersson, M.2
Cawley, S.3
-
163
-
-
33845373861
-
Studies concerning affinity (translated)
-
Guldberg CM, Waage P. Studies concerning affinity (translated). J Chem Education 1986;63(12):1044-7.
-
(1986)
J Chem Education
, vol.63
, Issue.12
, pp. 1044-1047
-
-
Guldberg, C.M.1
Waage, P.2
-
164
-
-
0028108519
-
Metabolic flux balancing - basic concepts, scientific and practical use
-
Varma A, Palsson BO. Metabolic flux balancing - basic concepts, scientific and practical use. Bio-Technology 1994; 12(10):994-8.
-
(1994)
Bio-Technology
, vol.12
, Issue.10
, pp. 994-998
-
-
Varma, A.1
Palsson, B.O.2
-
165
-
-
77952522193
-
A synthetic circuit for selectively arresting daughter cells to create aging populations
-
Afonso B, Silver PA, Ajo-Franklin CM. A synthetic circuit for selectively arresting daughter cells to create aging populations. Nucleic Acids Res 2010;38(8):2727-35.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.8
, pp. 2727-2735
-
-
Afonso, B.1
Silver, P.A.2
Ajo-Franklin, C.M.3
|