-
1
-
-
70449375094
-
Learning gene regulatory networks from gene expression measurements using nonparametric molecular kinetics
-
Äijö T, Lähdesmäki H.Learning gene regulatory networks from gene expression measurements using nonparametric molecular kinetics.Bioinformatics.2009;25:2937-44.
-
(2009)
Bioinformatics.
, vol.25
, pp. 2937-2944
-
-
Äijö, T.1
Lähdesmäki, H.2
-
2
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T, Miyano S, Kuhara S.Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.Pac Symp Biocomput.1999:17-28.
-
(1999)
Pac Symp Biocomput.
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
3
-
-
77957141016
-
Inferring the conservative causal core of gene regulatory networks
-
Altay G, Emmert-Streib F.Inferring the conservative causal core of gene regulatory networks.BMC Syst Biol.2010;4:132.
-
(2010)
BMC Syst Biol.
, vol.4
, pp. 132
-
-
Altay, G.1
Emmert-Streib, F.2
-
4
-
-
84865294429
-
Genome-wide scale-free network inference for Candida albicans
-
Altwasser R, Linde J, Buyko E, Hahn U, Guthke R.Genome-wide scale-free network inference for Candida albicans.Front Microbiol.2012;3:51.
-
(2012)
Front Microbiol.
, vol.3
, pp. 51
-
-
Altwasser, R.1
Linde, J.2
Buyko, E.3
Hahn, U.4
Guthke, R.5
-
5
-
-
79952983516
-
Mathematical modeling of gene expression: A guide for the perplexed biologist
-
Ay A, Arnosti DN.Mathematical modeling of gene expression: a guide for the perplexed biologist.Crit Rev Biochem Mol Biol.2011;46:137-51.
-
(2011)
Crit Rev Biochem Mol Biol.
, vol.46
, pp. 137-151
-
-
Ay, A.1
Arnosti, D.N.2
-
6
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey TL, Bodén M, Buske FA, Frith M, Grant CE, Clementi L, et al.MEME SUITE: tools for motif discovery and searching.Nucleic Acids Res.2009; 37(Suppl 2):W202-8.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
Bodén, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
-
7
-
-
34548388925
-
Inference of gene networks from temporal gene expression profiles
-
Bansal M, di Bernardo D.Inference of gene networks from temporal gene expression profiles.IET Syst Biol.2007;1:306-12.
-
(2007)
IET Syst Biol.
, vol.1
, pp. 306-312
-
-
Bansal, M.1
di Bernardo, D.2
-
8
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M, Della Gatta G, di Bernardo D.Inference of gene regulatory networks and compound mode of action from time course gene expression profiles.Bioinformatics.2006;22:815-22.
-
(2006)
Bioinformatics.
, vol.22
, pp. 815-822
-
-
Bansal, M.1
Della Gatta, G.2
di Bernardo, D.3
-
10
-
-
84924338899
-
A community computational challenge to predict the activity of pairs of compounds
-
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, et al; NCI-DREAM Community.A community computational challenge to predict the activity of pairs of compounds.Nat Biotechnol.2014;32:1213-22.
-
(2014)
Nat Biotechnol.
, vol.32
, pp. 1213-1222
-
-
Bansal, M.1
Yang, J.2
Karan, C.3
Menden, M.P.4
Costello, J.C.5
Tang, H.6
-
11
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási AL, Albert R.Emergence of scaling in random networks.Science.1999;286(5439):509-12.
-
(1999)
Science.
, vol.286
, Issue.5439
, pp. 509-512
-
-
Barabási, A.L.1
Albert, R.2
-
12
-
-
0742305866
-
Network biology: Understanding the cell’s functional organization
-
Barabási AL, Oltvai ZN.Network biology: understanding the cell’s functional organization.Nat Rev Genet.2004;5:101-13.
-
(2004)
Nat Rev Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
13
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A.Reverse engineering of regulatory networks in human B cells.Nat Genet.2005;37:382-90.
-
(2005)
Nat Genet.
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
14
-
-
34547844156
-
Manual curation is not sufficient for annotation of genomic databases
-
Baumgartner WA Jr, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L.Manual curation is not sufficient for annotation of genomic databases.Bioinformatics.2007;23:i41-8.
-
(2007)
Bioinformatics.
, vol.23
, pp. i41-i48
-
-
Baumgartner Jr, W.A.1
Cohen, K.B.2
Fox, L.M.3
Acquaah-Mensah, G.4
Hunter, L.5
-
15
-
-
15944361900
-
Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data
-
Bernhard A, Hartemink AJ.Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.Pac Symp Biocomput.2005;2005:459-70.
-
(2005)
Pac Symp Biocomput.
, vol.2005
, pp. 459-470
-
-
Bernhard, A.1
Hartemink, A.J.2
-
16
-
-
84877734926
-
Improving breast cancer survival analysis through competition-based multidimensional modeling
-
Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, et al.Improving breast cancer survival analysis through competition-based multidimensional modeling.PLoS Comput Biol.2013;9(5):e1003047.
-
(2013)
PLoS Comput Biol.
, vol.9
, Issue.5
, pp. e1003047
-
-
Bilal, E.1
Dutkowski, J.2
Guinney, J.3
Jang, I.S.4
Logsdon, B.A.5
Pandey, G.6
-
17
-
-
84891796512
-
The Candida Genome Database: The new homology information page highlights protein similarity and phylogeny
-
Binkley J, Arnaud MB, Inglis DO, Skrzypek MS, Shah P, Wymore F, et al.The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny.Nucleic Acids Res.2014;42(Database issue):D711-6.
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.Database issue
, pp. D711-D716
-
-
Binkley, J.1
Arnaud, M.B.2
Inglis, D.O.3
Skrzypek, M.S.4
Shah, P.5
Wymore, F.6
-
18
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B.Trimmomatic: a flexible trimmer for Illumina sequence data.Bioinformatics.2014;30:2114-21.
-
(2014)
Bioinformatics.
, vol.30
, pp. 2114-2121
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
19
-
-
33747813561
-
The Inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, et al.The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.Genome Biol.2006;7(5):R36.
-
(2006)
Genome Biol.
, vol.7
, Issue.5
, pp. R36
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
Facciotti, M.4
Hood, L.5
Baliga, N.S.6
-
21
-
-
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 Symp Biocomput.2000:418-29.
-
(2000)
Pac Symp Biocomput.
, pp. 418-429
-
-
Butte, A.J.1
Kohane, I.S.2
-
22
-
-
84899733023
-
RECOMB/ISCB systems biology, regulatory genomics, and DREAM
-
Califano A, Kellis M, Stolovitzky G.RECOMB/ISCB systems biology, regulatory genomics, and DREAM.2013 special issue.J Comput Biol.2014;21:371-2.
-
(2014)
2013 special issue.J Comput Biol.
, vol.21
, pp. 371-372
-
-
Califano, A.1
Kellis, M.2
Stolovitzky, G.3
-
23
-
-
84901679193
-
Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals upregulation of nutrient acquisition and cell cycle genes
-
Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LCC, Valdameri G, et al.Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals upregulation of nutrient acquisition and cell cycle genes.BMC Genomics.2014;15:378.
-
(2014)
BMC Genomics.
, vol.15
, pp. 378
-
-
Camilios-Neto, D.1
Bonato, P.2
Wassem, R.3
Tadra-Sfeir, M.Z.4
Brusamarello-Santos, L.C.C.5
Valdameri, G.6
-
24
-
-
63049128934
-
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches
-
Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, et al.A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.Cell.2009;137:172-81.
-
(2009)
Cell.
, vol.137
, pp. 172-181
-
-
Cantone, I.1
Marucci, L.2
Iorio, F.3
Ricci, M.A.4
Belcastro, V.5
Bansal, M.6
-
25
-
-
84901748068
-
Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions
-
Choi YJ, Aliota MT, Mayhew GF, Erickson SM, Christensen BM.Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions.PloS Negl Trop Dis.2014;8(5):e2905.
-
(2014)
PloS Negl Trop Dis.
, vol.8
, Issue.5
, pp. e2905
-
-
Choi, Y.J.1
Aliota, M.T.2
Mayhew, G.F.3
Erickson, S.M.4
Christensen, B.M.5
-
26
-
-
77749251837
-
Success in the DREAM3 signaling response challenge using simple weightedaverage imputation: Lessons for community-wide experiments in systems biology
-
Clarke ND, Bourque G.Success in the DREAM3 signaling response challenge using simple weightedaverage imputation: lessons for community-wide experiments in systems biology.PLoS One.2010;5(1): e8417.
-
(2010)
PLoS One.
, vol.5
, Issue.1
, pp. e8417
-
-
Clarke, N.D.1
Bourque, G.2
-
27
-
-
54149084585
-
Multiple sclerosis
-
Compston A, Coles A.Multiple sclerosis.Lancet.2008;372(9648):1502-17.
-
(2008)
Lancet.
, vol.372
, Issue.9648
, pp. 1502-1517
-
-
Compston, A.1
Coles, A.2
-
28
-
-
84906549588
-
A community effort to assess and improve drug sensitivity prediction algorithms
-
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, et al.; NCI DREAM Community.A community effort to assess and improve drug sensitivity prediction algorithms.Nat Biotechnol.2014;32:1202-12.
-
(2014)
Nat Biotechnol.
, vol.32
, pp. 1202-1212
-
-
Costello, J.C.1
Heiser, L.M.2
Georgii, E.3
Gönen, M.4
Menden, M.P.5
Wang, N.J.6
-
29
-
-
84893443187
-
An extensive evaluation of read trimming effects on Illumina NGS data analysis
-
Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM.An extensive evaluation of read trimming effects on Illumina NGS data analysis.PLoS One.2013;8(12): e85024.
-
(2013)
PLoS One.
, vol.8
, Issue.12
, pp. e85024
-
-
Del Fabbro, C.1
Scalabrin, S.2
Morgante, M.3
Giorgi, F.M.4
-
30
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong H.Modeling and simulation of genetic regulatory systems: a literature review.J Comput Biol.2002;9:67-103.
-
(2002)
J Comput Biol.
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
31
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
D’haeseleer P, Liang S, Somogyi R.Genetic network inference: from co-expression clustering to reverse engineering.Bioinformatics.2000;16:707-26.
-
(2000)
Bioinformatics.
, vol.16
, pp. 707-726
-
-
D’haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
32
-
-
21444452397
-
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
-
di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, et al.Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks.Nat Biotechnol.2005;23:377-83.
-
(2005)
Nat Biotechnol.
, vol.23
, pp. 377-383
-
-
di Bernardo, D.1
Thompson, M.J.2
Gardner, T.S.3
Chobot, S.E.4
Eastwood, E.L.5
Wojtovich, A.P.6
-
33
-
-
77958516401
-
A Boolean approach to linear prediction for signaling network modeling
-
Eduati F, Corradin A, Di Camillo B, Toffolo G.A Boolean approach to linear prediction for signaling network modeling.PLoS One.2010;5(9):e12789.
-
(2010)
PLoS One.
, vol.5
, Issue.9
, pp. e12789
-
-
Eduati, F.1
Corradin, A.2
Di Camillo, B.3
Toffolo, G.4
-
35
-
-
84928888210
-
Gene regulatory networks and their applications: Understanding biological and medical problems in terms of networks
-
Emmert-Streib F, Dehmer M, Haibe-Kains B.Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks.Front Cell Dev Biol.2014;2:38.
-
(2014)
Front Cell Dev Biol.
, vol.2
, pp. 38
-
-
Emmert-Streib, F.1
Dehmer, M.2
Haibe-Kains, B.3
-
36
-
-
84888861753
-
Systematic evaluation of spliced alignment programs for RNAseq data
-
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, et al.; RGASP Consortium.Systematic evaluation of spliced alignment programs for RNAseq data.Nat Methods.2013;10:1185-91.
-
(2013)
Nat Methods.
, vol.10
, pp. 1185-1191
-
-
Engström, P.G.1
Steijger, T.2
Sipos, B.3
Grant, G.R.4
Kahles, A.5
Rätsch, G.6
-
37
-
-
33846521053
-
Reconstructing dynamic regulatory maps
-
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z.Reconstructing dynamic regulatory maps.Mol Syst Biol.2007;3:74.
-
(2007)
Mol Syst Biol.
, vol.3
, pp. 74
-
-
Ernst, J.1
Vainas, O.2
Harbison, C.T.3
Simon, I.4
Bar-Joseph, Z.5
-
38
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, et al.Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.PLoS Biol.2007;5(1):e8.
-
(2007)
PLoS Biol.
, vol.5
, Issue.1
, pp. e8
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
-
39
-
-
84891789990
-
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection
-
Fernández-Suárez XM, Rigden DJ, Galperin MY.The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.Nucleic Acids Res.2014;42(Database issue):D1-6.
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.Database issue
, pp. D1-D6
-
-
Fernández-Suárez, X.M.1
Rigden, D.J.2
Galperin, M.Y.3
-
40
-
-
84919415762
-
Reducing bias in RNA sequencing data: A novel approach to compute counts
-
Finotello F, Lavezzo E, Bianco L, Barzon L, Mazzon P, Fontana P, et al.Reducing bias in RNA sequencing data: a novel approach to compute counts.BMC Bioinformatics.2014;15(S-1):7.
-
(2014)
BMC Bioinformatics.
, vol.15
, Issue.S-1
, pp. 7
-
-
Finotello, F.1
Lavezzo, E.2
Bianco, L.3
Barzon, L.4
Mazzon, P.5
Fontana, P.6
-
41
-
-
84872528061
-
An effective framework for reconstructing gene regulatory networks from genetical genomics data
-
Flassig RJ, Heise S, Sundmacher K, Klamt S.An effective framework for reconstructing gene regulatory networks from genetical genomics data.Bioinformatics.2013;29:246-54.
-
(2013)
Bioinformatics.
, vol.29
, pp. 246-254
-
-
Flassig, R.J.1
Heise, S.2
Sundmacher, K.3
Klamt, S.4
-
42
-
-
84920836564
-
PLC and PI3K/Akt/mTOR signalling in disease and cancer
-
Follo MY, Manzoli L, Poli A, McCubrey JA, Cocco L.PLC and PI3K/Akt/mTOR signalling in disease and cancer.Adv Biol Regul.2015;57:10-6.
-
(2015)
Adv Biol Regul.
, vol.57
, pp. 10-16
-
-
Follo, M.Y.1
Manzoli, L.2
Poli, A.3
McCubrey, J.A.4
Cocco, L.5
-
44
-
-
38549140094
-
RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, et al.RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.Nucleic Acids Res.2008;36(Database issue):D120-4.
-
(2008)
Nucleic Acids Res.
, vol.36
, Issue.Database issue
, pp. D120-D124
-
-
Gama-Castro, S.1
Jiménez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Peñaloza-Spinola, M.I.5
Contreras-Moreira, B.6
-
45
-
-
14844286390
-
Reverse-engineering transcription control networks
-
Gardner TS, Faith JJ.Reverse-engineering transcription control networks.Phys Life Rev.2005;2:65-88.
-
(2005)
Phys Life Rev.
, vol.2
, pp. 65-88
-
-
Gardner, T.S.1
Faith, J.J.2
-
46
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ.Inferring genetic networks and identifying compound mode of action via expression profiling.Science.2003;301(5629):102-5.
-
(2003)
Science.
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
47
-
-
25444486700
-
Rheumatoid arthritis, a complex multifactorial disease: On the way toward individualized medicine
-
Glocker MO, Guthke R, Kekow J, Thiesen HJ.Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine.Med Res Rev.2006;26:63-87.
-
(2006)
Med Res Rev.
, vol.26
, pp. 63-87
-
-
Glocker, M.O.1
Guthke, R.2
Kekow, J.3
Thiesen, H.J.4
-
48
-
-
84856228299
-
More than just a metabolic regulator - Elucidation and validation of new targets of PdhR in Escherichia coli
-
Göhler AK, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, et al.More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli.BMC Syst Biol.2011;5: 197.
-
(2011)
BMC Syst Biol.
, vol.5
, pp. 197
-
-
Göhler, A.K.1
Kökpinar, Ö.2
Schmidt-Heck, W.3
Geffers, R.4
Guthke, R.5
Rinas, U.6
-
49
-
-
85005877161
-
Data integration in the era of omics: Current and future challenges
-
Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, et al.Data integration in the era of omics: current and future challenges.BMC Syst Biol.2014;8 (Suppl 2):I1.
-
(2014)
BMC Syst Biol.
, vol.8
, pp. I1
-
-
Gomez-Cabrero, D.1
Abugessaisa, I.2
Maier, D.3
Teschendorff, A.4
Merkenschlager, M.5
Gisel, A.6
-
50
-
-
78149421254
-
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models
-
Greenfield A, Madar A, Ostrer H, Bonneau R.DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models.PLoS One.2010;5(10):e13397.
-
(2010)
PLoS One.
, vol.5
, Issue.10
, pp. e13397
-
-
Greenfield, A.1
Madar, A.2
Ostrer, H.3
Bonneau, R.4
-
51
-
-
84876207916
-
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
-
Greenfield A, Hafemeister C, Bonneau R.Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks.Bioinformatics.2013;29:1060-7.
-
(2013)
Bioinformatics.
, vol.29
, pp. 1060-1067
-
-
Greenfield, A.1
Hafemeister, C.2
Bonneau, R.3
-
52
-
-
33747342709
-
Sensing by bacterial regulatory systems in host and non-host environments
-
Groisman EA, Mouslim C.Sensing by bacterial regulatory systems in host and non-host environments.Nat Rev Microbiol.2006;4:705-9.
-
(2006)
Nat Rev Microbiol.
, vol.4
, pp. 705-709
-
-
Groisman, E.A.1
Mouslim, C.2
-
53
-
-
77649327878
-
Multiple imputations applied to the DREAM3 phosphoproteomics challenge: A winning strategy
-
Guex N, Migliavacca E, Xenarios I.Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.PLoS One.2010;5(1): e8012.
-
(2010)
PLoS One.
, vol.5
, Issue.1
, pp. e8012
-
-
Guex, N.1
Migliavacca, E.2
Xenarios, I.3
-
54
-
-
79953871120
-
A computational framework for gene regulatory network inference that combines multiple methods and datasets
-
Gupta R, Stincone A, Antczak P, Durant S, Bicknell R, Bikfalvi A, et al.A computational framework for gene regulatory network inference that combines multiple methods and datasets.BMC Syst Biol.2011;5: 52.
-
(2011)
BMC Syst Biol.
, vol.5
, pp. 52
-
-
Gupta, R.1
Stincone, A.2
Antczak, P.3
Durant, S.4
Bicknell, R.5
Bikfalvi, A.6
-
55
-
-
77949535261
-
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge
-
Gustafsson M, Hörnquist M.Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge.PLoS One.2010;5(2):e9134.
-
(2010)
PLoS One.
, vol.5
, Issue.2
, pp. e9134
-
-
Gustafsson, M.1
Hörnquist, M.2
-
56
-
-
27644508196
-
Constructing and analyzing a large-scale gene-to-gene regulatory network--lasso-constrained inference and biological validation
-
Gustafsson M, Hörnquist M, Lombardi A.Constructing and analyzing a large-scale gene-to-gene regulatory network--lasso-constrained inference and biological validation.IEEE/ACM Trans Comput Biol Bioinform.2005;2:254-61.
-
(2005)
IEEE/ACM Trans Comput Biol Bioinform.
, vol.2
, pp. 254-261
-
-
Gustafsson, M.1
Hörnquist, M.2
Lombardi, A.3
-
57
-
-
63849175334
-
Reverse engineering of gene networks with LASSO and nonlinear basis functions
-
Gustafsson M, Hörnquist M, Lundström J, Björkegren J, Tegnér J.Reverse engineering of gene networks with LASSO and nonlinear basis functions.Ann N Y Acad Sci.2009;1158:265-75.
-
(2009)
Ann N Y Acad Sci.
, vol.1158
, pp. 265-275
-
-
Gustafsson, M.1
Hörnquist, M.2
Lundström, J.3
Björkegren, J.4
Tegnér, J.5
-
58
-
-
17444430052
-
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
-
Guthke R, Möller U, Hoffmann M, Thies F, Töpfer S.Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.Bioinformatics.2005;21:1626-34.
-
(2005)
Bioinformatics.
, vol.21
, pp. 1626-1634
-
-
Guthke, R.1
Möller, U.2
Hoffmann, M.3
Thies, F.4
Töpfer, S.5
-
59
-
-
84880266648
-
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al.De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.Nat Protoc.2013;8:1494-512.
-
(2013)
Nat Protoc.
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
Bowden, J.6
-
60
-
-
34447539654
-
Text mining: Powering the database revolution
-
Hahn U, Wermter J, Blasczyk R, Horn PA.Text mining: powering the database revolution.Nature.2007;448(7150):130.
-
(2007)
Nature.
, vol.448
, Issue.7150
, pp. 130
-
-
Hahn, U.1
Wermter, J.2
Blasczyk, R.3
Horn, P.A.4
-
61
-
-
84862197985
-
Predictive networks: A flexible, open source, web application for integration and analysis of human gene networks
-
Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, et al.Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.Nucleic Acids Res.2012;40(Database issue): D866-D875
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.Database issue
, pp. D866-D875
-
-
Haibe-Kains, B.1
Olsen, C.2
Djebbari, A.3
Bontempi, G.4
Correll, M.5
Bouton, C.6
-
62
-
-
0035221560
-
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
-
Hartemink AJ, Gifford DK, Jaakkola TS, Young RA.Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.Pac Symp Biocomput.2001:422-33.
-
(2001)
Pac Symp Biocomput.
, pp. 422-433
-
-
Hartemink, A.J.1
Gifford, D.K.2
Jaakkola, T.S.3
Young, R.A.4
-
63
-
-
84925334433
-
Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization
-
Hasegawa T, Yamaguchi R, Nagasaki M, Miyano S, Imoto S.Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.PLoS One.2014;9(8):e105942.
-
(2014)
PLoS One.
, vol.9
, Issue.8
, pp. e105942
-
-
Hasegawa, T.1
Yamaguchi, R.2
Nagasaki, M.3
Miyano, S.4
Imoto, S.5
-
65
-
-
61349180117
-
Gene regulatory network inference: Data integration in dynamic models - A review
-
Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R.Gene regulatory network inference: data integration in dynamic models - a review.Biosystems.2009a;96:86-103.
-
(2009)
Biosystems.
, vol.96
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Toepfer, S.3
van Someren, E.4
Guthke, R.5
-
66
-
-
70449434583
-
Integrative modeling of transcriptional regulation in response to antirheumatic therapy
-
Hecker M, Goertsches RH, Engelmann R, Thiesen HJ, Guthke R.Integrative modeling of transcriptional regulation in response to antirheumatic therapy.BMC Bioinformatics.2009b;10:262.
-
(2009)
BMC Bioinformatics.
, vol.10
, pp. 262
-
-
Hecker, M.1
Goertsches, R.H.2
Engelmann, R.3
Thiesen, H.J.4
Guthke, R.5
-
67
-
-
0035852785
-
Dynamic modeling of gene expression data
-
Holter NS, Maritan A, Cieplak M, Fedoroff NV, Banavar JR.Dynamic modeling of gene expression data.Proc Natl Acad Sci U S A.2001;98:1693-8.
-
(2001)
Proc Natl Acad Sci U S A.
, vol.98
, pp. 1693-1698
-
-
Holter, N.S.1
Maritan, A.2
Cieplak, M.3
Fedoroff, N.V.4
Banavar, J.R.5
-
68
-
-
84897740390
-
Interactive exploration of integrated biological datasets using context-sensitive workflows
-
Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R.Interactive exploration of integrated biological datasets using context-sensitive workflows.Front Genet.2014;5:21.
-
(2014)
Front Genet.
, vol.5
, pp. 21
-
-
Horn, F.1
Rittweger, M.2
Taubert, J.3
Lysenko, A.4
Rawlings, C.5
Guthke, R.6
-
69
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang DW, Sherman BT, Lempicki RA.Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.Nucleic Acids Res.2009;37:1-13.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
70
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P.Inferring regulatory networks from expression data using tree-based methods.PLoS One.2010;5(9): e12776.
-
(2010)
PLoS One.
, vol.5
, Issue.9
, pp. e12776
-
-
Huynh-Thu, V.A.1
Irrthum, A.2
Wehenkel, L.3
Geurts, P.4
-
72
-
-
75249096608
-
The Gene Interaction Miner: A new tool for data mining contextual information for protein-protein interaction analysis
-
Ikin A, Riveros C, Moscato P, Mendes A.The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis.Bioinformatics.2010;26:283-4.
-
(2010)
Bioinformatics.
, vol.26
, pp. 283-284
-
-
Ikin, A.1
Riveros, C.2
Moscato, P.3
Mendes, A.4
-
73
-
-
84897891549
-
Bayesian network prior: Network analysis of biological data using external knowledge
-
Isci S, Dogan H, Ozturk C, Otu HH.Bayesian network prior: network analysis of biological data using external knowledge.Bioinformatics.2014;30:860-7.
-
(2014)
Bioinformatics.
, vol.30
, pp. 860-867
-
-
Isci, S.1
Dogan, H.2
Ozturk, C.3
Otu, H.H.4
-
75
-
-
84903513963
-
Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads
-
Jiang H, Lei R, Ding SW, Zhu S.Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.BMC Bioinformatics.2014; 15(1):18.
-
(2014)
BMC Bioinformatics.
, vol.15
, Issue.1
, pp. 18
-
-
Jiang, H.1
Lei, R.2
Ding, S.W.3
Zhu, S.4
-
76
-
-
77955641867
-
Integrative inference of generegulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
-
Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S.Integrative inference of generegulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.BMC Syst Biol.2010;4:116.
-
(2010)
BMC Syst Biol.
, vol.4
, pp. 116
-
-
Kaleta, C.1
Göhler, A.2
Schuster, S.3
Jahreis, K.4
Guthke, R.5
Nikolajewa, S.6
-
77
-
-
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;22:437-67.
-
(1969)
J Theor Biol.
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
78
-
-
77955867869
-
TRANSWESD: Inferring cellular networks with transitive reduction
-
Klamt S, Flassig RJ, Sundmacher K.TRANSWESD: inferring cellular networks with transitive reduction.Bioinformatics.2010;26:2160-8.
-
(2010)
Bioinformatics.
, vol.26
, pp. 2160-2168
-
-
Klamt, S.1
Flassig, R.J.2
Sundmacher, K.3
-
79
-
-
0037155938
-
The seven pillars of life
-
Koshland DE Jr.The seven pillars of life.Science.2002;295(5563):2215-6.
-
(2002)
Science.
, vol.295
, Issue.5563
, pp. 2215-2216
-
-
Koshland Jr, D.E.1
-
80
-
-
84861168271
-
Inferring gene regulatory networks by ANOVA
-
Küffner R, Petri T, Tavakkolkhah P, Windhager L, Zimmer R.Inferring gene regulatory networks by ANOVA.Bioinformatics.2012;28:1376-82.
-
(2012)
Bioinformatics.
, vol.28
, pp. 1376-1382
-
-
Küffner, R.1
Petri, T.2
Tavakkolkhah, P.3
Windhager, L.4
Zimmer, R.5
-
81
-
-
84963940835
-
Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression
-
Küffner R, Zach N, Norel R, Hawe J, Schoenfeld D, Wang L, et al.Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression.Nat Biotechnol.2015;33:51-7.
-
(2015)
Nat Biotechnol.
, vol.33
, pp. 51-57
-
-
Küffner, R.1
Zach, N.2
Norel, R.3
Hawe, J.4
Schoenfeld, D.5
Wang, L.6
-
82
-
-
84871412941
-
Gene regulatory network modeling using literature curated and high throughput data
-
Kulkarni VV, Arastoo R, Bhat A, Subramanian K, Kothare MV, Riedel MC.Gene regulatory network modeling using literature curated and high throughput data.Syst Synth Biol.2012;6(3-4):69-77.
-
(2012)
Syst Synth Biol.
, vol.6
, Issue.3-4
, pp. 69-77
-
-
Kulkarni, V.V.1
Arastoo, R.2
Bhat, A.3
Subramanian, K.4
Kothare, M.V.5
Riedel, M.C.6
-
83
-
-
84911861819
-
IVT-seq reveals extreme bias in RNA sequencing
-
Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, et al.IVT-seq reveals extreme bias in RNA sequencing.Genome Biol.2014;15(6):R86.
-
(2014)
Genome Biol.
, vol.15
, Issue.6
, pp. R86
-
-
Lahens, N.F.1
Kavakli, I.H.2
Zhang, R.3
Hayer, K.4
Black, M.B.5
Dueck, H.6
-
84
-
-
49449086368
-
Survival of the sparsest: Robust gene networks are parsimonious
-
Leclerc RD.Survival of the sparsest: robust gene networks are parsimonious.Mol Syst Biol.2008;4: 213.
-
(2008)
Mol Syst Biol.
, vol.4
, pp. 213
-
-
Leclerc, R.D.1
-
85
-
-
68449103579
-
The systems biology graphical notation
-
Erratum in: Nat Biotechnol.2009;27:864
-
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, et al.The systems biology graphical notation.Nat Biotechnol.2009;27:735-41.Erratum in: Nat Biotechnol.2009;27:864.
-
(2009)
Nat Biotechnol.
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
-
86
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang S, Fuhrman S, Somogyi R.Reveal, a general reverse engineering algorithm for inference of genetic network architectures.Pac Symp Biocomput.1998:18-29.
-
(1998)
Pac Symp Biocomput.
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
87
-
-
84897397058
-
FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
-
Liao Y, Smyth GK, Shi W.featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.Bioinformatics.2013;30:923-30.
-
(2013)
Bioinformatics.
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
88
-
-
78049407924
-
Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells
-
Linde J, Wilson D, Hube B, Guthke R.Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells.BMC Syst Biol.2010;4:148.
-
(2010)
BMC Syst Biol.
, vol.4
, pp. 148
-
-
Linde, J.1
Wilson, D.2
Hube, B.3
Guthke, R.4
-
89
-
-
84984916524
-
Fullgenomic network inference for non-model organism: A case study for the fungal pathogen Candida albicans
-
Heidelberg - Mannheim, Germany, August 28th - September 1st
-
Linde J, Buyko E, Robert A, Hahn U, Guthke R.Fullgenomic network inference for non-model organism: A case study for the fungal pathogen Candida albicans.In: International Conference on Systems Biology (ICSB-2011).Heidelberg - Mannheim, Germany, August 28th - September 1st, 2011.
-
(2011)
International Conference on Systems Biology (ICSB-2011)
-
-
Linde, J.1
Buyko, E.2
Robert, A.3
Hahn, U.4
Guthke, R.5
-
90
-
-
84855871849
-
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach
-
Linde J, Hortschansky P, Fazius E, Brakhage AA, Guthke R, Haas H.Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach.BMC Syst Biol.2012;6:6.
-
(2012)
BMC Syst Biol.
, vol.6
, pp. 6
-
-
Linde, J.1
Hortschansky, P.2
Fazius, E.3
Brakhage, A.A.4
Guthke, R.5
Haas, H.6
-
91
-
-
84893242996
-
RNA-seq differential expression studies: More sequence or more replication?
-
Liu Y, Zhou J, White KP.RNA-seq differential expression studies: more sequence or more replication? Bioinformatics.2013;30:301-4.
-
(2013)
Bioinformatics.
, vol.30
, pp. 301-304
-
-
Liu, Y.1
Zhou, J.2
White, K.P.3
-
92
-
-
84864946487
-
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data
-
Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, et al.Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.BMC Syst Biol.2012;6:101.
-
(2012)
BMC Syst Biol.
, vol.6
, pp. 101
-
-
Lo, K.1
Raftery, A.E.2
Dombek, K.M.3
Zhu, J.4
Schadt, E.E.5
Bumgarner, R.E.6
-
93
-
-
0003422388
-
-
4th ed (section 11.6).New York: W.H.Freeman
-
Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J: Molecular cell biology, 4th ed (section 11.6).New York: W.H.Freeman, 2000.
-
(2000)
Molecular cell biology
-
-
Lodish, H.1
Berk, A.2
Zipursky, S.L.3
Matsudaira, P.4
Baltimore, D.5
Darnell, J.6
-
94
-
-
84555203262
-
Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge
-
Loh PR, Tucker G, Berger B.Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge.PLoS One.2011;6(12):e29095.
-
(2011)
PLoS One.
, vol.6
, Issue.12
, pp. e29095
-
-
Loh, P.R.1
Tucker, G.2
Berger, B.3
-
95
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love MI, Huber W, Anders S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.Genome Biol.2014;15:550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
96
-
-
78149461178
-
DREAM3: Network inference using dynamic context likelihood of relatedness and the inferelator
-
Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R.DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator.PLoS One.2010;5(3):e9803.
-
(2010)
PLoS One.
, vol.5
, Issue.3
, pp. e9803
-
-
Madar, A.1
Greenfield, A.2
Vanden-Eijnden, E.3
Bonneau, R.4
-
97
-
-
79957665988
-
Microarrays, deep sequencing and the true measure of the transcriptome
-
Malone JH, Oliver B.Microarrays, deep sequencing and the true measure of the transcriptome.BMC Biology.2011;9(1):34.
-
(2011)
BMC Biology.
, vol.9
, Issue.1
, pp. 34
-
-
Malone, J.H.1
Oliver, B.2
-
98
-
-
84921293466
-
Comparing bioinformatic gene expression profiling methods: Microarray and RNA-seq
-
Mantione KJ, Kream RM, Kuzelova H, Ptacek R, Raboch J, Samuel JM, et al.Comparing bioinformatic gene expression profiling methods: microarray and RNA-seq.Med Sci Monit Basic Res.2014;20:138-41.
-
(2014)
Med Sci Monit Basic Res.
, vol.20
, pp. 138-141
-
-
Mantione, K.J.1
Kream, R.M.2
Kuzelova, H.3
Ptacek, R.4
Raboch, J.5
Samuel, J.M.6
-
99
-
-
63849258962
-
Combining multiple results of a reverse-engineering algorithm: Application to the DREAM five-gene network challenge
-
Marbach D, Mattiussi C, Floreano D.Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge.Ann N Y Acad Sci.2009a;1158:102-13.
-
(2009)
Ann N Y Acad Sci.
, vol.1158
, pp. 102-113
-
-
Marbach, D.1
Mattiussi, C.2
Floreano, D.3
-
100
-
-
59649096341
-
Replaying the evolutionary tape: Biomimetic reverse engineering of gene networks
-
Marbach D, Mattiussi C, Floreano D.Replaying the evolutionary tape: biomimetic reverse engineering of gene networks.Ann N Y Acad Sci.2009b;1158:234-45.
-
(2009)
Ann N Y Acad Sci.
, vol.1158
, pp. 234-245
-
-
Marbach, D.1
Mattiussi, C.2
Floreano, D.3
-
101
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.Revealing strengths and weaknesses of methods for gene network inference.Proc Natl Acad Sci U S A.2010;107:6286-91.
-
(2010)
Proc Natl Acad Sci U S A.
, vol.107
, pp. 6286-6291
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
Mattiussi, C.4
Floreano, D.5
Stolovitzky, G.6
-
102
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, et al.Wisdom of crowds for robust gene network inference.Nat Methods.2012;9:796-804.
-
(2012)
Nat Methods.
, vol.9
, pp. 796-804
-
-
Marbach, D.1
Costello, J.C.2
Küffner, R.3
Vega, N.M.4
Prill, R.J.5
Camacho, D.M.6
-
103
-
-
84877765675
-
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
-
Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, et al.Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.Sci Transl Med.2013;5(181):181re1.
-
(2013)
Sci Transl Med.
, vol.5
, Issue.181
, pp. 181re1
-
-
Margolin, A.A.1
Bilal, E.2
Huang, E.3
Norman, T.C.4
Ottestad, L.5
Mecham, B.H.6
-
104
-
-
27744489138
-
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
-
Markowetz F, Bloch J, Spang R.Non-transcriptional pathway features reconstructed from secondary effects of RNA interference.Bioinformatics.2005;21: 4026-32.
-
(2005)
Bioinformatics.
, vol.21
, pp. 4026-4032
-
-
Markowetz, F.1
Bloch, J.2
Spang, R.3
-
105
-
-
34248572623
-
Boolean dynamics of genetic regulatory networks inferred from microarray time series data
-
Martin S, Zhang Z, Martino A, Faulon JL.Boolean dynamics of genetic regulatory networks inferred from microarray time series data.Bioinformatics.2007;23:866-74.
-
(2007)
Bioinformatics.
, vol.23
, pp. 866-874
-
-
Martin, S.1
Zhang, Z.2
Martino, A.3
Faulon, J.L.4
-
106
-
-
84891808382
-
JASPAR.2014: An extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier A, Zhao X, Zhang A, Parcy F, Worsley-Hunt R, Arenillas DJ, et al.JASPAR.2014: an extensively expanded and updated open-access database of transcription factor binding profiles.Nucleic Acids Res.2013;42(Database issue):D142-7.
-
(2013)
Nucleic Acids Res.
, vol.42
, Issue.Database issue
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
-
107
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, et al.TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.Nucleic Acids Res.2006;34: D108-10.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D108-D110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
-
108
-
-
78650901444
-
Gene regulatory networks from multifactorial perturbations using Graphical Lasso: Application to the DREAM4 challenge
-
Menéndez P, Kourmpetis YA, ter Braak CJ, van Eeuwijk FA.Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge.PLoS One.2010; 5(12):e14147.
-
(2010)
PLoS One.
, vol.5
, Issue.12
, pp. e14147
-
-
Menéndez, P.1
Kourmpetis, Y.A.2
ter Braak, C.J.3
van Eeuwijk, F.A.4
-
110
-
-
84893710009
-
Network topology and parameter estimation: From experimental design methods to gene regulatory network kinetics using a community based approach
-
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, et al.Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.BMC Syst Biol.2014;8(1):13.
-
(2014)
BMC Syst Biol.
, vol.8
, Issue.1
, pp. 13
-
-
Meyer, P.1
Cokelaer, T.2
Chandran, D.3
Kim, K.H.4
Loh, P.R.5
Tucker, G.6
-
111
-
-
84907952658
-
A first look at the Oxford Nanopore MinION sequencer
-
Mikheyev AS, Tin MM.A first look at the Oxford Nanopore MinION sequencer.Mol Ecol Resour.2014;14:1097-102.
-
(2014)
Mol Ecol Resour.
, vol.14
, pp. 1097-1102
-
-
Mikheyev, A.S.1
Tin, M.M.2
-
113
-
-
34250112778
-
On the concept of attractor
-
Milnor J.On the concept of attractor.Commun Math Phys.1985;99:177-95.
-
(1985)
Commun Math Phys.
, vol.99
, pp. 177-195
-
-
Milnor, J.1
-
114
-
-
84898940253
-
From coexpression to coregulation: An approach to inferring transcriptional regulation among gene classes from large-scale expression data
-
Solla SA, Leen TK, Müller KR (eds), Cambridge, MA: MIT Press
-
Mjolsness E, Mann T, Castaño R, Wold B.From coexpression to coregulation: An approach to inferring transcriptional regulation among gene classes from large-scale expression data.In: Solla SA, Leen TK, Müller KR (eds).Advances in neural information processing systems, Vol.12 (pp 928-34).Cambridge, MA: MIT Press, 2000.
-
(2000)
Advances in neural information processing systems
, vol.12
, pp. 928-934
-
-
Mjolsness, E.1
Mann, T.2
Castaño, R.3
Wold, B.4
-
115
-
-
84908648308
-
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
-
Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.GeneMANIA: Fast gene network construction and function prediction for Cytoscape.F1000Res.2014 1;3:153.
-
(2014)
F1000Res.
, vol.1
, Issue.3
, pp. 153
-
-
Montojo, J.1
Zuberi, K.2
Rodriguez, H.3
Bader, G.D.4
Morris, Q.5
-
116
-
-
47949084846
-
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
-
Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, et al.Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.Biotechniques.2008;45(1):81-94.
-
(2008)
Biotechniques.
, vol.45
, Issue.1
, pp. 81-94
-
-
Morin, R.1
Bainbridge, M.2
Fejes, A.3
Hirst, M.4
Krzywinski, M.5
Pugh, T.6
-
117
-
-
84903886103
-
Improved performance of the PacBio SMRT technology for 16S rDNA sequencing
-
Mosher JJ, Bowman B, Bernberg EL, Shevchenko O, Kan J, Korlach J, et al.Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.J Microbiol Methods.2014;104:59-60.
-
(2014)
J Microbiol Methods.
, vol.104
, pp. 59-60
-
-
Mosher, J.J.1
Bowman, B.2
Bernberg, E.L.3
Shevchenko, O.4
Kan, J.5
Korlach, J.6
-
118
-
-
47549107689
-
GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function
-
Mostafavi S, Debajyoti R, Warde-Farley D, Grouios C, Morris Q.GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function.Genome Biology.2008;9(Suppl 1):S4.
-
(2008)
Genome Biology.
, vol.9
, pp. S4
-
-
Mostafavi, S.1
Debajyoti, R.2
Warde-Farley, D.3
Grouios, C.4
Morris, Q.5
-
121
-
-
84899531301
-
Network completion for static gene expression data
-
Nakajima N, Akutsu T.Network completion for static gene expression data.Adv Bioinformatics.2014;2014:382452.
-
(2014)
Adv Bioinformatics.
, vol.2014
, pp. 382452
-
-
Nakajima, N.1
Akutsu, T.2
-
122
-
-
84870197769
-
Network completion using dynamic programming and least-squares fitting
-
Nakajima N, Tamura T, Yamanishi Y, Horimoto K, Akutsu T.Network completion using dynamic programming and least-squares fitting.Sci World J.2012;2012:957620.
-
(2012)
Sci World J.
, vol.2012
, pp. 957620
-
-
Nakajima, N.1
Tamura, T.2
Yamanishi, Y.3
Horimoto, K.4
Akutsu, T.5
-
123
-
-
51049117937
-
Models from experiments: Combinatorial drug perturbations of cancer cells
-
Nelander S, Wang W, Nilsson B, She QB, Pratilas C, Rosen N, et al.Models from experiments: combinatorial drug perturbations of cancer cells.Mol Syst Biol.2008;4:216.
-
(2008)
Mol Syst Biol.
, vol.4
, pp. 216
-
-
Nelander, S.1
Wang, W.2
Nilsson, B.3
She, Q.B.4
Pratilas, C.5
Rosen, N.6
-
124
-
-
0242559054
-
Pathway studio - The analysis and navigation of molecular networks
-
Nikitin A, Egorov S, Daraselia N, Mazo I.Pathway studio - the analysis and navigation of molecular networks.Bioinformatics.2003;19:2155-215.
-
(2003)
Bioinformatics.
, vol.19
, pp. 2155-2215
-
-
Nikitin, A.1
Egorov, S.2
Daraselia, N.3
Mazo, I.4
-
125
-
-
84906213917
-
Relevance of different prior knowledge sources for inferring gene interaction networks
-
Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B.Relevance of different prior knowledge sources for inferring gene interaction networks.Front Genet.2014;5:177.
-
(2014)
Front Genet.
, vol.5
, pp. 177
-
-
Olsen, C.1
Bontempi, G.2
Emmert-Streib, F.3
Quackenbush, J.4
Haibe-Kains, B.5
-
126
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
Oshlack A, Wakefield MJ.Transcript length bias in RNA-seq data confounds systems biology.Biology Direct.2009;4(1):14-10.
-
(2009)
Biology Direct.
, vol.4
, Issue.1
, pp. 14-110
-
-
Oshlack, A.1
Wakefield, M.J.2
-
127
-
-
77957769655
-
High-throughput sequencing and clinical microbiology: Progress, opportunities and challenges
-
Pallen MJ, Loman NJ, Penn CW.High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.Curr Opin Microbiol.2010;13:625-31.
-
(2010)
Curr Opin Microbiol.
, vol.13
, pp. 625-631
-
-
Pallen, M.J.1
Loman, N.J.2
Penn, C.W.3
-
128
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, d’Alché-Buc F.Gene networks inference using dynamic Bayesian networks.Bioinformatics.2003;19 (Suppl 2):ii138-48.
-
(2003)
Bioinformatics
, vol.19
, pp. ii138-ii148
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
d’Alché-Buc, F.6
-
129
-
-
78149429509
-
From knockouts to networks: Establishing direct cause-effect relationships through graph analysis
-
Pinna A, Soranzo N, de la Fuente A.From knockouts to networks: establishing direct cause-effect relationships through graph analysis.PLoS One.2010;5(10): e12912.
-
(2010)
PLoS One.
, vol.5
, Issue.10
, pp. e12912
-
-
Pinna, A.1
Soranzo, N.2
de la Fuente, A.3
-
130
-
-
84881178444
-
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: Improved methods and their evaluation
-
Pinna A, Heise S, Flassig RJ, de la Fuente A, Klamt S.Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation.BMC Syst Biol.2013;7:73.
-
(2013)
BMC Syst Biol.
, vol.7
, pp. 73
-
-
Pinna, A.1
Heise, S.2
Flassig, R.J.3
de la Fuente, A.4
Klamt, S.5
-
131
-
-
84878568206
-
Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge
-
Plenge RM, Greenberg JD, Mangravite LM, Derry JM, Stahl EA, Coenen MJ, et al.Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge.Nat Genet.2013;45: 468-9.
-
(2013)
Nat Genet.
, vol.45
, pp. 468-469
-
-
Plenge, R.M.1
Greenberg, J.D.2
Mangravite, L.M.3
Derry, J.M.4
Stahl, E.A.5
Coenen, M.J.6
-
132
-
-
0015101072
-
Biological order, structure and instabilities
-
Prigogine I, Nicolis G.Biological order, structure and instabilities.Q Rev Biophys.1971;4:107-48.
-
(1971)
Q Rev Biophys.
, vol.4
, pp. 107-148
-
-
Prigogine, I.1
Nicolis, G.2
-
133
-
-
84906921702
-
Extension of life span by impaired glucose metabolism in Caenorhabditis elegans is accompanied by structural rearrangements of the transcriptomic network
-
Priebe S, Menzel U, Zarse K, Groth M, Platzer M, Ristow M, et al.Extension of life span by impaired glucose metabolism in Caenorhabditis elegans is accompanied by structural rearrangements of the transcriptomic network.PLoS One.2013;8(10):e77776.
-
(2013)
PLoS One.
, vol.8
, Issue.10
, pp. e77776
-
-
Priebe, S.1
Menzel, U.2
Zarse, K.3
Groth, M.4
Platzer, M.5
Ristow, M.6
-
134
-
-
84929141855
-
FungiFun2: A comprehensive online resource for systematic analysis of gene lists from fungal species
-
Priebe S, Kreisel C, Horn F, Guthke R, Linde J.FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.Bioinformatics.2015;31:445-6.
-
(2015)
Bioinformatics.
, vol.31
, pp. 445-446
-
-
Priebe, S.1
Kreisel, C.2
Horn, F.3
Guthke, R.4
Linde, J.5
-
135
-
-
77949644952
-
Towards a rigorous assessment of systems biology models: The DREAM3 challenges
-
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, et al.Towards a rigorous assessment of systems biology models: the DREAM3 challenges.PLoS One.2010;5(2):e9202.
-
(2010)
PLoS One.
, vol.5
, Issue.2
, pp. e9202
-
-
Prill, R.J.1
Marbach, D.2
Saez-Rodriguez, J.3
Sorger, P.K.4
Alexopoulos, L.G.5
Xue, X.6
-
136
-
-
80052592949
-
Crowdsourcing network inference: The DREAM predictive signaling network challenge
-
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.Crowdsourcing network inference: the DREAM predictive signaling network challenge.Sci Signal.2011;4(189):mr7.
-
(2011)
Sci Signal.
, vol.4
, Issue.189
, pp. mr7
-
-
Prill, R.J.1
Saez-Rodriguez, J.2
Alexopoulos, L.G.3
Sorger, P.K.4
Stolovitzky, G.5
-
137
-
-
84923922737
-
Comparative evaluation of gene set analysis approaches for RNA-Seq data
-
Rahmatallah Y, Emmert-Streib F, Glazko G.Comparative evaluation of gene set analysis approaches for RNA-Seq data.BMC Bioinformatics.2014;15(1):397.
-
(2014)
BMC Bioinformatics.
, vol.15
, Issue.1
, pp. 397
-
-
Rahmatallah, Y.1
Emmert-Streib, F.2
Glazko, G.3
-
138
-
-
77649166995
-
An empirical Bayesian method for estimating biological networks from temporal microarray data
-
article 9
-
Rau A, Jaffrézic F, Foulley JL, Doerge RW.An empirical Bayesian method for estimating biological networks from temporal microarray data.Stat Appl Genet Mol Biol.2010;9:article 9.
-
(2010)
Stat Appl Genet Mol Biol.
, vol.9
-
-
Rau, A.1
Jaffrézic, F.2
Foulley, J.L.3
Doerge, R.W.4
-
139
-
-
77649299348
-
An atlas of combinatorial transcriptional regulation in mouse and man
-
Erratum in: Cell.2010;141:369
-
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, et al.An atlas of combinatorial transcriptional regulation in mouse and man.Cell.2010;140:744-52.Erratum in: Cell.2010;141:369.
-
(2010)
Cell.
, vol.140
, pp. 744-752
-
-
Ravasi, T.1
Suzuki, H.2
Cannistraci, C.V.3
Katayama, S.4
Bajic, V.B.5
Tan, K.6
-
140
-
-
77949481863
-
Ruan J
-
Kamburov A, Kaur M, MacPherson CR, Radovanovic A, Schwartz A [added].Ruan J.A top-performing algorithm for the DREAM3 gene expression prediction challenge.PLoS One.2010;5(2):e8944.
-
(2010)
A top-performing algorithm for the DREAM3 gene expression prediction challenge.PLoS One.
, vol.5
, Issue.2
, pp. e8944
-
-
Kamburov, A.1
Kaur, M.2
MacPherson, C.R.3
Radovanovic, A.4
Schwartz, A.5
-
141
-
-
84908190303
-
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
-
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, et al.A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.Biosystems.2014;124:26-38.
-
(2014)
Biosystems.
, vol.124
, pp. 26-38
-
-
Ryll, A.1
Bucher, J.2
Bonin, A.3
Bongard, S.4
Gonçalves, E.5
Saez-Rodriguez, J.6
-
142
-
-
84879452903
-
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks
-
Samaga R, Klamt S.Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks.Cell Commun Signal.2013;11(1):43.
-
(2013)
Cell Commun Signal.
, vol.11
, Issue.1
, pp. 43
-
-
Samaga, R.1
Klamt, S.2
-
143
-
-
34247587012
-
Genetics.Getting closer to the whole picture
-
Sauer U, Heinemann M, Zamboni N.Genetics.Getting closer to the whole picture.Science.2007; 316 (5824):550-1.
-
(2007)
Science
, vol.316
, Issue.5824
, pp. 550-551
-
-
Sauer, U.1
Heinemann, M.2
Zamboni, N.3
-
144
-
-
34848908079
-
Reverse engineering genetic networks using the GeneNet package
-
Schäfer J, Opgen-Rhein R, Strimmer K.Reverse engineering genetic networks using the GeneNet package.R News.2006;5/6:50-3.
-
(2006)
R News.
, vol.5-6
, pp. 50-53
-
-
Schäfer, J.1
Opgen-Rhein, R.2
Strimmer, K.3
-
145
-
-
84927523798
-
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data
-
Schulze S, Henkel SG, Driesch D, Guthke R, Linde J.Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.Front Microbiol.2015;6:65.
-
(2015)
Front Microbiol.
, vol.6
, pp. 65
-
-
Schulze, S.1
Henkel, S.G.2
Driesch, D.3
Guthke, R.4
Linde, J.5
-
146
-
-
0036184629
-
Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty ER, Kim S, Zhang W.Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.Bioinformatics.2002;18:261-74.
-
(2002)
Bioinformatics.
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
147
-
-
84892728434
-
Sequencing depth and coverage: Key considerations in genomic analyses
-
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP.Sequencing depth and coverage: key considerations in genomic analyses.Nat Rev Genetics.2014;15: 121-32.
-
(2014)
Nat Rev Genetics.
, vol.15
, pp. 121-132
-
-
Sims, D.1
Sudbery, I.2
Ilott, N.E.3
Heger, A.4
Ponting, C.P.5
-
148
-
-
84874677498
-
A comparison of methods for differential expression analysis of RNA-seq data
-
Soneson D, Delorenzi M.A comparison of methods for differential expression analysis of RNA-seq data.BMC Bioinformatics.2013;14:91.
-
(2013)
BMC Bioinformatics.
, vol.14
, pp. 91
-
-
Soneson, D.1
Delorenzi, M.2
-
149
-
-
12344296457
-
A reductionist’s systems biology
-
Sorger PK.A reductionist’s systems biology.Curr Opin Cell Biol.2005;17:9-11.
-
(2005)
Curr Opin Cell Biol.
, vol.17
, pp. 9-11
-
-
Sorger, P.K.1
-
150
-
-
33747828539
-
Jcell - A Java-based framework for inferring regulatory networks from time series data
-
Spieth C, Supper J, Streichert F, Speer N, Zell A.Jcell - a Java-based framework for inferring regulatory networks from time series data.Bioinformatics.2006;22:2051-2.
-
(2006)
Bioinformatics.
, vol.22
, pp. 2051-2052
-
-
Spieth, C.1
Supper, J.2
Streichert, F.3
Speer, N.4
Zell, A.5
-
151
-
-
36249019789
-
Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference
-
Stolovitzky G, Monroe D, Califano A.Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference.Ann N Y Acad Sci.2007;1115:1-22.
-
(2007)
Ann N Y Acad Sci.
, vol.1115
, pp. 1-22
-
-
Stolovitzky, G.1
Monroe, D.2
Califano, A.3
-
153
-
-
84941051170
-
STRING v10: Protein-protein interaction networks, integrated over the tree of life
-
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al.STRING v10: protein-protein interaction networks, integrated over the tree of life.Nucleic Acids Res.2015;43(Database issue):D447-52.
-
(2015)
Nucleic Acids Res.
, vol.43
, Issue.Database issue
, pp. D447-D452
-
-
Szklarczyk, D.1
Franceschini, A.2
Wyder, S.3
Forslund, K.4
Heller, D.5
Huerta-Cepas, J.6
-
154
-
-
84887433583
-
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
-
‘t Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, et al.Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.Nat Biotechnol.2013;31:1015-22.
-
(2013)
Nat Biotechnol.
, vol.31
, pp. 1015-1022
-
-
‘t Hoen, P.A.1
Friedländer, M.R.2
Almlöf, J.3
Sammeth, M.4
Pulyakhina, I.5
Anvar, S.Y.6
-
155
-
-
84877953144
-
PHISTO: Pathogen-host interaction search tool
-
Tekir SD, Cakır T, Ardıç E, Sayılırbaş AS, Konuk G, Konuk M, et al.PHISTO: pathogen-host interaction search tool.Bioinformatics.2013;29:1357-8.
-
(2013)
Bioinformatics.
, vol.29
, pp. 1357-1358
-
-
Tekir, S.D.1
Cakır, T.2
Ardıç, E.3
Sayılırbaş, A.S.4
Konuk, G.5
Konuk, M.6
-
156
-
-
85194972808
-
Regression shrinkage and selection via the Lasso
-
Tibshirani R.Regression shrinkage and selection via the Lasso.J Roy Stat Soc Ser B.1996;58:267-88.
-
(1996)
J Roy Stat Soc Ser B.
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
157
-
-
84865175959
-
An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells
-
Tierney L, Linde J, Müller S, Brunke S, Molina JC, Hube B, et al.An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells.Front Microbiol.2012;3:85.
-
(2012)
Front Microbiol.
, vol.3
, pp. 85
-
-
Tierney, L.1
Linde, J.2
Müller, S.3
Brunke, S.4
Molina, J.C.5
Hube, B.6
-
158
-
-
84859885816
-
Differential gene and transcript expressionanalysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al.Differential gene and transcript expressionanalysis of RNA-seq experiments with TopHat and Cufflinks.Nat Protoc.2012;7:562-78.
-
(2012)
Nat Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
-
159
-
-
83855165105
-
Repetitive DNA and nextgeneration sequencing: Computational challenges and solutions
-
Treangen TJ, Salzberg SL.Repetitive DNA and nextgeneration sequencing: computational challenges and solutions.Nat Rev Genet.2011;13:146.
-
(2011)
Nat Rev Genet.
, vol.13
, pp. 146
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
160
-
-
84905640975
-
Ensemble inference and inferability of gene regulatory networks
-
Ud-Dean SM, Gunawan R.Ensemble inference and inferability of gene regulatory networks.PLoS One.2014;9(8):e103812.
-
(2014)
PLoS One.
, vol.9
, Issue.8
, pp. e103812
-
-
Ud-Dean, S.M.1
Gunawan, R.2
-
162
-
-
32544457104
-
Least absolute regression network analysis of the murine osteoblast differentiation network
-
van Someren EP, Vaes BL, Steegenga WT, Sijbers AM, Dechering KJ, Reinders MJ.Least absolute regression network analysis of the murine osteoblast differentiation network.Bioinformatics.2006;22:477-84.
-
(2006)
Bioinformatics.
, vol.22
, pp. 477-484
-
-
van Someren, E.P.1
Vaes, B.L.2
Steegenga, W.T.3
Sijbers, A.M.4
Dechering, K.J.5
Reinders, M.J.6
-
163
-
-
84455173311
-
Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis
-
Vignes M, Vandel J, Allouche D, Ramadan-Alban N, Cierco-Ayrolles C, Schiex T, et al.Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis.PLoS One.2011;6(12):e29165.
-
(2011)
PLoS One.
, vol.6
, Issue.12
, pp. e29165
-
-
Vignes, M.1
Vandel, J.2
Allouche, D.3
Ramadan-Alban, N.4
Cierco-Ayrolles, C.5
Schiex, T.6
-
164
-
-
84870053474
-
The extended TILAR approach: A novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes
-
Vlaic S, Schmidt-Heck W, Matz-Soja M, Marbach E, Linde J, Meyer-Baese A, et al.The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes.BMC Syst Biol.2012;6:147.
-
(2012)
BMC Syst Biol.
, vol.6
, pp. 147
-
-
Vlaic, S.1
Schmidt-Heck, W.2
Matz-Soja, M.3
Marbach, E.4
Linde, J.5
Meyer-Baese, A.6
-
165
-
-
0034104824
-
Coarse-grained reverse engineering of genetic regulatory networks
-
Wahde M, Hertz J.Coarse-grained reverse engineering of genetic regulatory networks.Biosystems.2000;55(1-3):129-36.
-
(2000)
Biosystems
, vol.55
, Issue.1-3
, pp. 129-136
-
-
Wahde, M.1
Hertz, J.2
-
166
-
-
33750016109
-
Inferring gene regulatory networks from multiple microarray datasets
-
Wang Y, Joshi T, Zhang XS, Xu D, Chen L.Inferring gene regulatory networks from multiple microarray datasets.Bioinformatics.2006;22:2413-20.
-
(2006)
Bioinformatics.
, vol.22
, pp. 2413-2420
-
-
Wang, Y.1
Joshi, T.2
Zhang, X.S.3
Xu, D.4
Chen, L.5
-
167
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M.RNA-Seq: a revolutionary tool for transcriptomics.Nat Rev Genet.2009;10:57-63.
-
(2009)
Nat Rev Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
168
-
-
84865079833
-
Identification of aberrant pathways and network activities from high-throughput data
-
Wang J, Zhang Y, Marian C, Ressom HW.Identification of aberrant pathways and network activities from high-throughput data.Brief Bioinform.2012;13:406-19.
-
(2012)
Brief Bioinform.
, vol.13
, pp. 406-419
-
-
Wang, J.1
Zhang, Y.2
Marian, C.3
Ressom, H.W.4
-
169
-
-
84871681271
-
Inference of dynamical generegulatory networks based on time-resolved multistimuli multi-experiment data applying NetGenerator V2.0
-
Weber M, Henkel SG, Vlaic S, Guthke R, van Zoelen EJ, Driesch D.Inference of dynamical generegulatory networks based on time-resolved multistimuli multi-experiment data applying NetGenerator V2.0.BMC Syst Biol.2013;7:1.
-
(2013)
BMC Syst Biol.
, vol.7
, pp. 1
-
-
Weber, M.1
Henkel, S.G.2
Vlaic, S.3
Guthke, R.4
van Zoelen, E.J.5
Driesch, D.6
-
170
-
-
84873594686
-
Evaluation of methods for modelling transcription factor sequence specificity
-
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, et al.Evaluation of methods for modelling transcription factor sequence specificity.Nat Biotechnol.2013;31:126-34.
-
(2013)
Nat Biotechnol.
, vol.31
, pp. 126-134
-
-
Weirauch, M.T.1
Cote, A.2
Norel, R.3
Annala, M.4
Zhao, Y.5
Riley, T.R.6
-
173
-
-
84858266638
-
Learning transcriptional regulation on a genome scale: A theoretical analysis based on gene expression data
-
Wu M, Chan C.Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data.Brief Bioinform.2012;13:150-61.
-
(2012)
Brief Bioinform.
, vol.13
, pp. 150-161
-
-
Wu, M.1
Chan, C.2
-
174
-
-
79959986975
-
KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases
-
Web Server issue
-
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, et al.KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.Nucleic Acids Res.2011;39(Web Server issue):W316-22.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W316-W322
-
-
Xie, C.1
Mao, X.2
Huang, J.3
Ding, Y.4
Wu, J.5
Dong, S.6
-
175
-
-
33745553265
-
Multi-scale methodology: A key to deciphering systems biology
-
Ye X, Chu J, Zhuang Y, Zhang S.Multi-scale methodology: a key to deciphering systems biology.Front Biosci.2005;10:961-5.
-
(2005)
Front Biosci.
, vol.10
, pp. 961-965
-
-
Ye, X.1
Chu, J.2
Zhuang, Y.3
Zhang, S.4
-
176
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
Yeung MK, Tegnér J, Collins JJ.Reverse engineering gene networks using singular value decomposition and robust regression.Proc Natl Acad Sci U S A.2002;99:6163-8.
-
(2002)
Proc Natl Acad Sci U S A.
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegnér, J.2
Collins, J.J.3
-
177
-
-
82755198509
-
Construction of regulatory networks using expression time-series data of a genotyped population
-
Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, et al.Construction of regulatory networks using expression time-series data of a genotyped population.Proc Natl Acad Sci U S A.2011;108:19436-41.
-
(2011)
Proc Natl Acad Sci U S A.
, vol.108
, pp. 19436-19441
-
-
Yeung, K.Y.1
Dombek, K.M.2
Lo, K.3
Mittler, J.E.4
Zhu, J.5
Schadt, E.E.6
-
178
-
-
77749264188
-
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data
-
Yip KY, Alexander RP, Yan KK, Gerstein M.Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.PLoS One.2010;5(1):e8121.
-
(2010)
PLoS One.
, vol.5
, Issue.1
, pp. e8121
-
-
Yip, K.Y.1
Alexander, R.P.2
Yan, K.K.3
Gerstein, M.4
-
179
-
-
77953212372
-
Gene ontology analysis for RNA-seq: Accounting for selection bias
-
Young MD, Wakefield MJ, Smyth GK, Oshlack A.Gene ontology analysis for RNA-seq: accounting for selection bias.Genome Biol.2010;11(2):R14.
-
(2010)
Genome Biol.
, vol.11
, Issue.2
, pp. R14
-
-
Young, M.D.1
Wakefield, M.J.2
Smyth, G.K.3
Oshlack, A.4
-
180
-
-
84899971737
-
Fast Bayesian inference for gene regulatory networks using ScanBMA
-
Young WC, Raftery AE, Yeung KY.Fast Bayesian inference for gene regulatory networks using ScanBMA.BMC Syst Biol.2014;8:47.
-
(2014)
BMC Syst Biol.
, vol.8
, pp. 47
-
-
Young, W.C.1
Raftery, A.E.2
Yeung, K.Y.3
-
181
-
-
84905912949
-
A comparative study of techniques for differential expression analysis on RNA-seq data
-
Zhang ZH, Jhaveri DJ, Marshall VM, Bauer DC, Edson J, et al.A comparative study of techniques for differential expression analysis on RNA-seq data.Plos One.2014;9(8):e103207.
-
(2014)
Plos One.
, vol.9
, Issue.8
, pp. e103207
-
-
Zhang, Z.H.1
Jhaveri, D.J.2
Marshall, V.M.3
Bauer, D.C.4
Edson, J.5
-
182
-
-
16244401458
-
Regularization and variable selection via the elastic net
-
Zou H, Hastie T.Regularization and variable selection via the elastic net.J Roy Stat Soc Ser B.2005;67:301-20.
-
(2005)
J Roy Stat Soc Ser B.
, vol.67
, pp. 301-320
-
-
Zou, H.1
Hastie, T.2
-
183
-
-
77952663448
-
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
-
Zoppoli P, Morganella S, Ceccarelli M.TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.BMC Bioinformatics.2010;11:154.
-
(2010)
BMC Bioinformatics.
, vol.11
, pp. 154
-
-
Zoppoli, P.1
Morganella, S.2
Ceccarelli, M.3
|