-
1
-
-
84873801934
-
High-throughput sequencing for biology and medicine
-
PMID: 23340846
-
Soon WW, Hariharan M, Snyder M.P. (2013) High-throughput sequencing for biology and medicine. Mol Syst Biol 9: 640. doi: 10.1038/msb.2012.61 PMID: 23340846
-
(2013)
Mol Syst Biol
, vol.9
, pp. 640
-
-
Soon, W.W.1
Hariharan, M.2
Snyder, M.P.3
-
2
-
-
79952674000
-
Interactome networks and human disease
-
PMID: 21414488
-
Vidal M, Cusick ME, Barabási AL (2011) Interactome networks and human disease. Cell 144(6): 986-998. doi: 10.1016/j.cell.2011.02.016 PMID: 21414488
-
(2011)
Cell
, vol.144
, Issue.6
, pp. 986-998
-
-
Vidal, M.1
Cusick, M.E.2
Barabási, A.L.3
-
3
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
PMID: 14735121
-
Barabási A-L, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nature Reviews Genetics 5(2): 101-113. PMID: 14735121
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
4
-
-
33749335282
-
The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease
-
PMID: 17008526
-
Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, et al. (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313 (5795): 1929-1935. PMID: 17008526
-
(2006)
Science
, vol.313
, Issue.5795
, pp. 1929-1935
-
-
Lamb, J.1
Crawford, E.D.2
Peck, D.3
Modell, J.W.4
Blat, I.C.5
Wrobel, M.J.6
-
5
-
-
84864256761
-
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes
-
PMID: 22838965
-
Wu C, Zhu J, Zhang X. (2012) Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. BMC Bioinformatics, 13:182. PMID: 22838965
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 182
-
-
Wu, C.1
Zhu, J.2
Zhang, X.3
-
6
-
-
0034660224
-
Nature insight
-
Genomics Functional. In: Nature insight. Nature 2000; 405:819-85.
-
(2000)
Nature
, vol.405
, pp. 819-885
-
-
-
7
-
-
19344365567
-
Submission of microarray data to public repositories
-
PMID: 15340489
-
Ball CA, Brazma A, Causton H., Chervitz S, Edgar R, Hingamp P., et al. (2004) Submission of microarray data to public repositories. PLoS Biol 2(9): E317. PMID: 15340489
-
(2004)
PLoS Biol
, vol.2
, Issue.9
, pp. E317
-
-
Ball, C.A.1
Brazma, A.2
Causton, H.3
Chervitz, S.4
Edgar, R.5
Hingamp, P.6
-
8
-
-
72849144434
-
Sequencingtechnologies - The next generation
-
PMID: 19997069
-
Metzker ML (2010) Sequencingtechnologies - the next generation. Nat Rev Genet 11(1): 31-46. doi: 10.1038/nrg2626 PMID: 19997069
-
(2010)
Nat Rev Genet
, vol.11
, Issue.1
, pp. 31-46
-
-
Metzker, M.L.1
-
10
-
-
67749113808
-
Transcriptional regulatory circuits: Predicting numbers from alphabets
-
PMID: 19628860
-
Kim HD, Shay T, O'Shea EK, Regev A (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325 (5939): 429-432. doi: 10.1126/science.1171347 PMID: 19628860
-
(2009)
Science
, vol.325
, Issue.5939
, pp. 429-432
-
-
Kim, H.D.1
Shay, T.2
O'Shea, E.K.3
Regev, A.4
-
11
-
-
22344449669
-
Constructing transcriptional regulatory networks
-
PMID: 15998805
-
Blais A, Dynlacht BD (2005) Constructing transcriptional regulatory networks. Genes Dev. 19(13): 1499-1511. PMID: 15998805
-
(2005)
Genes Dev.
, vol.19
, Issue.13
, pp. 1499-1511
-
-
Blais, A.1
Dynlacht, B.D.2
-
12
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
PMID: 17571346
-
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146): 799-816. PMID: 17571346
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigó, R.4
Gingeras, T.R.5
-
13
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
PMID: 19443739
-
Badis G, Berger MF, Philippakis A.A., Talukder S, Gehrke AR, Jaeger SA, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324 (5935): 1720-1723. doi: 10.1126/science.1162327 PMID: 19443739
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
-
14
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
PMID: 10812473
-
Stormo GD (2000). "DNA binding sites: representation and discovery". Bioinformatics 16(1): 16-23. PMID: 10812473
-
(2000)
Bioinformatics
, vol.16
, Issue.1
, pp. 16-23
-
-
Stormo, G.D.1
-
15
-
-
33747064917
-
How does DNA sequence motif discovery work?
-
PMID: 16900144
-
D'haeseleer P (2006) How does DNA sequence motif discovery work? Nat Biotechnol 24(8): 959-961. PMID: 16900144
-
(2006)
Nat Biotechnol
, vol.24
, Issue.8
, pp. 959-961
-
-
D'Haeseleer, P.1
-
16
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotechnol 26(12): 1351-1359.
-
(2008)
Nature Biotechnol
, vol.26
, Issue.12
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
17
-
-
84855170482
-
MotifMap: Integrative genome-wide maps of regulatory motif sites for model species
-
PMID: 22208852
-
Daily K, Patel VR, Rigor P, Xie X., Baldi P. (2011) MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinformatics 12: 495. doi: 10.1186/1471-2105-12-495 PMID: 22208852
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 495
-
-
Daily, K.1
Patel, V.R.2
Rigor, P.3
Xie, X.4
Baldi, P.5
-
18
-
-
0037174671
-
Transcriptional regulatory networks in saccharomyces cerevisiae
-
PMID: 12399584
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298 (5594): 799-804. PMID: 12399584
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
-
19
-
-
33644873683
-
The YEASTRACT database: A tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae
-
PMID: 16381908
-
Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, et al. (2006)The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 34(Database issue): D446-D451. PMID: 16381908
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
, pp. D446-D451
-
-
Teixeira, M.C.1
Monteiro, P.2
Jain, P.3
Tenreiro, S.4
Fernandes, A.R.5
Mira, N.P.6
-
20
-
-
78651343711
-
DroID 2011: A comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for drosophila
-
PMID: 21036869
-
Murali T, Pacifico S, Yu J, Guest S, Roberts GG, Finley RL (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res 39(Database issue): D736-D743. doi: 10.1093/nar/gkq1092 PMID: 21036869
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
, pp. D736-D743
-
-
Murali, T.1
Pacifico, S.2
Yu, J.3
Guest, S.4
Roberts, G.G.5
Finley, R.L.6
-
21
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
PMID: 22955616
-
ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489 (7414): 57-74. doi: 10.1038/nature11247 PMID: 22955616
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
Collins, P.J.4
Davis, C.A.5
-
22
-
-
84865121188
-
An encyclopedia of mouse DNA elements (Mouse ENCODE)
-
PMID: 22889292
-
Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13(8): 418. doi: 10.1186/gb-2012-13-8-418 PMID: 22889292
-
(2012)
Genome Biol
, vol.13
, Issue.8
, pp. 418
-
-
Stamatoyannopoulos, J.A.1
Snyder, M.2
Hardison, R.3
Ren, B.4
Gingeras, T.5
-
23
-
-
84865852567
-
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
-
PMID: 22955990
-
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, et al. (2012) Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 22(9): 1798-1812. doi: 10.1101/gr.139105.112 PMID: 22955990
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1798-1812
-
-
Wang, J.1
Zhuang, J.2
Iyer, S.3
Lin, X.4
Whitfield, T.W.5
Greven, M.C.6
-
24
-
-
84865049521
-
HTRIdb: An open-access database for experimentally verified human transcriptional regulation interactions
-
PMID: 22900683
-
Bovolenta LA, Acencio ML, Lemke N. (2012) HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics 13: 405. doi: 10.1186/1471-2164-13-405 PMID: 22900683
-
(2012)
BMC Genomics
, vol.13
, pp. 405
-
-
Bovolenta, L.A.1
Acencio, M.L.2
Lemke, N.3
-
25
-
-
79958135926
-
Molecular signatures database (MSigDB) 3.0
-
PMID: 21546393
-
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdottir H, Tamayo P, Mesirov JP(2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics 27(12): 1739-1740. doi: 10.1093/bioinformatics/btr260 PMID: 21546393
-
(2011)
Bioinformatics
, vol.27
, Issue.12
, pp. 1739-1740
-
-
Liberzon, A.1
Subramanian, A.2
Pinchback, R.3
Thorvaldsdottir, H.4
Tamayo, P.5
Mesirov, J.P.6
-
26
-
-
84876543942
-
Regulon DB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, crossvalidated gold standards and more
-
PMID: 23203884
-
Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, Garcia-Sotelo JS, et al. (2013) Regulon DB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, crossvalidated gold standards and more. Nucleic Acids Res 41(Database issue): D203-D213. doi: 10.1093/nar/gks1201 PMID: 23203884
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D203-D213
-
-
Salgado, H.1
Peralta-Gil, M.2
Gama-Castro, S.3
Santos-Zavaleta, A.4
Muñiz-Rascado, L.5
Garcia-Sotelo, J.S.6
-
27
-
-
0033976586
-
TRANSFAC: An integrated system for gene expression regulation
-
PMID: 10592259
-
Wingender E, Chen X, Hehl R., Karas H, Liebich I, Matys V., et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28(1): 316-319. PMID: 10592259
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 316-319
-
-
Wingender, E.1
Chen, X.2
Hehl, R.3
Karas, H.4
Liebich, I.5
Matys, V.6
-
28
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
PMID: 16381825
-
Matys V, Kel-Margoulis OV, Fricke E., Liebich I, Land S, Barre-Dirrie A, et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34(Database issue): D108-D110. PMID: 16381825
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
, pp. D108-D110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
-
29
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open access database of transcription factor binding profiles
-
PMID: 24194598
-
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas D.J., et al. (2014) JASPAR 2014: an extensively expanded and updated open access database of transcription factor binding profiles. Nucleic Acids Res 42 (Database issue): D142-D147. doi: 10.1093/nar/gkt997 PMID: 24194598
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.DATABASE ISSUE
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
-
30
-
-
84874809425
-
HOCO-MOCO: A comprehensive collection of human transcription factor binding sites models
-
PMID: 23175603
-
Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, et al. (2013) HOCO-MOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res 41(Database issue): D195-D202. doi: 10.1093/nar/gks1089 PMID: 23175603
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D195-D202
-
-
Kulakovskiy, I.V.1
Medvedeva, Y.A.2
Schaefer, U.3
Kasianov, A.S.4
Vorontsov, I.E.5
Bajic, V.B.6
-
31
-
-
84946068207
-
UniPROBE, update2015: Newtools and content for the online database of protein-binding microarray data on protein-DNA interactions
-
PMID: 25378322
-
Hume MA, Barrera LA, Gisselbrecht S.S., Bulyk ML (2014) UniPROBE, update2015: newtools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res; doi: 10.1093/nar/gku1045 PMID: 25378322
-
(2014)
Nucleic Acids Res
-
-
Hume, M.A.1
Barrera, L.A.2
Gisselbrecht, S.S.3
Bulyk, M.L.4
-
32
-
-
77957243164
-
ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
-
PMID: 20709693
-
Lachmann A, Xu H, Krishnan J., Berger SI, Mazloom AR, Ma'ayan A (2010) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26(19): 2438-44. doi: 10.1093/bioinformatics/btq466 PMID: 20709693
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2438-2444
-
-
Lachmann, A.1
Xu, H.2
Krishnan, J.3
Berger, S.I.4
Mazloom, A.R.5
Ma'Ayan, A.6
-
33
-
-
84885827147
-
ChEA2: Gene-set libraries from ChIP-X experiments to decode the transcription regulome
-
CD-ARES 2013. Lecture Notes in Computer Science 8127
-
Kou Y, Chen EY, Clark N.R., Tan CM, Ma'ayan A (2013) ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. Multidisciplinary Research and Practice for Information Systems. CD-ARES 2013. Lecture Notes in Computer Science 8127: 416-430.
-
(2013)
Multidisciplinary Research and Practice for Information Systems
, pp. 416-430
-
-
Kou, Y.1
Chen, E.Y.2
Clark, N.R.3
Tan, C.M.4
Ma'Ayan, A.5
-
34
-
-
61449203001
-
KEA: Kinase enrichment analysis
-
PMID: 19176546
-
Lachmann A, Ma'ayan A (2009) KEA: Kinase Enrichment Analysis. Bioinformatics 25(5): 684-6. doi: 10.1093/bioinformatics/btp026 PMID: 19176546
-
(2009)
Bioinformatics
, vol.25
, Issue.5
, pp. 684-686
-
-
Lachmann, A.1
Ma'Ayan, A.2
-
35
-
-
84855171722
-
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers
-
PMID: 22080467
-
Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma'ayan A (2012) Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers. Bioinformatics 28(1): 105-111. doi: 10.1093/bioinformatics/btr625 PMID: 22080467
-
(2012)
Bioinformatics
, vol.28
, Issue.1
, pp. 105-111
-
-
Chen, E.Y.1
Xu, H.2
Gordonov, S.3
Lim, M.P.4
Perkins, M.H.5
Ma'Ayan, A.6
-
36
-
-
84880569366
-
Relating genes to function: Identifying enriched transcription factors using the ENCODE ChIP-seq significance tool
-
PMID: 23732275
-
Auerbach RK, Chen B, Butte A.J. (2013) Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics 29(15): 1922-1924. doi: 10.1093/bioinformatics/btt316 PMID: 23732275
-
(2013)
Bioinformatics
, vol.29
, Issue.15
, pp. 1922-1924
-
-
Auerbach, R.K.1
Chen, B.2
Butte, A.J.3
-
37
-
-
84864446871
-
Inferring the regulatory network behind a gene expression experiment
-
PMID: 22693210
-
Bleda M, Medina I, Alonso R., De Maria A, Salavert F, Dopazo J. (2012) Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res 40(Web Server issue): W168-W172. doi: 10.1093/nar/gks573 PMID: 22693210
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.WEB SERVER ISSUE
, pp. W168-W172
-
-
Bleda, M.1
Medina, I.2
Alonso, R.3
De Maria, A.4
Salavert, F.5
Dopazo, J.6
-
38
-
-
23144464901
-
WebGestalt: An integrated system for exploring gene sets in various biological contexts
-
PMID: 15980575
-
Zhang B, Kirov SA, Snoddy J.R. (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 33(Web Server issue): W741-748. PMID: 15980575
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.WEB SERVER ISSUE
, pp. W741-748
-
-
Zhang, B.1
Kirov, S.A.2
Snoddy, J.R.3
-
39
-
-
84880993473
-
Whole-genome rVISTA: A tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomicdata
-
PMID: 23736530
-
Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, et al. (2013) Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomicdata. Bioinformatics 29(16): 2059-61. doi: 10.1093/bioinformatics/btt318 PMID: 23736530
-
(2013)
Bioinformatics
, vol.29
, Issue.16
, pp. 2059-2061
-
-
Dubchak, I.1
Munoz, M.2
Poliakov, A.3
Salomonis, N.4
Minovitsky, S.5
Bodmer, R.6
-
40
-
-
0036105591
-
RVista for comparative sequencebased discovery of functional transcription factor binding sites
-
PMID: 11997350
-
Loots GG, Ovcharenko I, Pachter L., Dubchak I, Rubin E.M. (2002) rVista for comparative sequencebased discovery of functional transcription factor binding sites. Genome Res 12(5): 832-839. PMID: 11997350
-
(2002)
Genome Res
, vol.12
, Issue.5
, pp. 832-839
-
-
Loots, G.G.1
Ovcharenko, I.2
Pachter, L.3
Dubchak, I.4
Rubin, E.M.5
-
41
-
-
0038444122
-
Genome-wide in-silico identification of transcriptional regulators controlling cell cycle in human cells
-
PMID: 12727897
-
Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y (2003) Genome-wide In-silico Identification of Transcriptional Regulators Controlling Cell Cycle in Human Cells. Genome Res 13(5): 773-780. PMID: 12727897
-
(2003)
Genome Res
, vol.13
, Issue.5
, pp. 773-780
-
-
Elkon, R.1
Linhart, C.2
Sharan, R.3
Shamir, R.4
Shiloh, Y.5
-
42
-
-
2542584654
-
Detection of functional DNA motifs via statistical over-representation
-
PMID: 14988425
-
Frith MC, Fu Y, Yu L., Chen J-F, Hansen U, Weng Z (2004) Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res 32(4): 1372-81. PMID: 14988425
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.4
, pp. 1372-1381
-
-
Frith, M.C.1
Fu, Y.2
Yu, L.3
Chen, J.-F.4
Hansen, U.5
Weng, Z.6
-
43
-
-
1242342957
-
Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification
-
PMID: 14704355
-
Haverty PM, Hansen U, Weng Z. (2004) Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 32(1): 179-188. PMID: 14704355
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.1
, pp. 179-188
-
-
Haverty, P.M.1
Hansen, U.2
Weng, Z.3
-
44
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth G (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: 3.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, pp. 3
-
-
Smyth, G.1
-
45
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
PMID: 11309499
-
Tusher VG, Tibshirani R, Chu G (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U SA 98(9): 5116-5121. PMID: 11309499
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
46
-
-
33747344944
-
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
-
PMID: 16872483
-
Jeffery IB, Higgins DG, Culhane A.C. (2006) Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7: 359. PMID: 16872483
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 359
-
-
Jeffery, I.B.1
Higgins, D.G.2
Culhane, A.C.3
-
47
-
-
84864044868
-
Linking the transcriptional profiles and the physiological states of mycobacterium tuberculosis during an extended intracellular infection
-
PMID: 22737072
-
Rohde KH, Veiga DF, Caldwell S, Balázsi G, Russell D.G. (2012) Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis during an Extended Intracellular Infection. PLoS Pathog 8(6): e1002769. doi: 10.1371/journal.ppat.1002769 PMID: 22737072
-
(2012)
PLoS Pathog
, vol.8
, Issue.6
-
-
Rohde, K.H.1
Veiga, D.F.2
Caldwell, S.3
Balázsi, G.4
Russell, D.G.5
-
48
-
-
79960444757
-
The transcriptional regulatory network of mycobacterium tuberculosis
-
PMID: 21818301
-
Sanz J, Navarro J, Arbués A, Martín C, Marijuán PC, Moreno Y. (2011) The Transcriptional Regulatory Network of Mycobacterium tuberculosis. PLoS ONE 6(7): e22178. doi: 10.1371/journal.pone.0022178 PMID: 21818301
-
(2011)
PLoS ONE
, vol.6
, Issue.7
-
-
Sanz, J.1
Navarro, J.2
Arbués, A.3
Martín, C.4
Marijuán, P.C.5
Moreno, Y.6
-
49
-
-
70449370314
-
The transcription unit architecture of the Escherichia coli genome
-
Cho BK, Zengler K, Qiu Y., Park YS, Knight EM, Barrett CL, et al. (2009) The transcription unit architecture of the Escherichia coli genome. Nucleic Acids Res 27(11): 1043-1049.
-
(2009)
Nucleic Acids Res
, vol.27
, Issue.11
, pp. 1043-1049
-
-
Cho, B.K.1
Zengler, K.2
Qiu, Y.3
Park, Y.S.4
Knight, E.M.5
Barrett, C.L.6
-
50
-
-
11144263144
-
PH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12
-
PMID: 15601715
-
Maurer LM, Yohannes E, Bondurant SS, Radmacher M, Slonczewski JL(2005) pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J Bacteriol 187(1): 304-319. PMID: 15601715
-
(2005)
J Bacteriol
, vol.187
, Issue.1
, pp. 304-319
-
-
Maurer, L.M.1
Yohannes, E.2
Bondurant, S.S.3
Radmacher, M.4
Slonczewski, J.L.5
-
51
-
-
58149265291
-
Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non-ionic osmotica
-
PMID: 18793315
-
Shabala L, Bowman J, Brown J., Ross T, McMeekin T, Shabala S. (2009) Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non-ionic osmotica. Environ Microbiol 11(1): 137-148. doi: 10.1111/j.1462-2920.2008.01748.x PMID: 18793315
-
(2009)
Environ Microbiol
, vol.11
, Issue.1
, pp. 137-148
-
-
Shabala, L.1
Bowman, J.2
Brown, J.3
Ross, T.4
McMeekin, T.5
Shabala, S.6
-
52
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
PMID: 17214507
-
Faith JJ, Hayete B, Thaden J.T., Mogno I., Wierzbowski J, Cottarel G, et al (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5(1): e8. PMID: 17214507
-
(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
-
53
-
-
38549134505
-
Many microbe microarrays database: Uniformly normalized affymetrix compendia with structured experimental metadata
-
PMID: 17932051
-
Faith JJ, Driscoll ME, Fusaro V.A., Cosgrove EJ, Hayete B, Juhn FS, et al (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 36(Database issue): D866-70. PMID: 17932051
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.DATABASE ISSUE
, pp. D866-D870
-
-
Faith, J.J.1
Driscoll, M.E.2
Fusaro, V.A.3
Cosgrove, E.J.4
Hayete, B.5
Juhn, F.S.6
-
54
-
-
84859257158
-
Exploring the complexity of the HIV-1 fitness landscape
-
PMID: 22412384
-
Kouyos RD, Leventhal GE, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, et al. (2012) Exploring the Complexity of the HIV-1 Fitness Landscape. PLoS Genet 8(3): e1002551. doi: 10.1371/journal.pgen.1002551 PMID: 22412384
-
(2012)
PLoS Genet
, vol.8
, Issue.3
-
-
Kouyos, R.D.1
Leventhal, G.E.2
Hinkley, T.3
Haddad, M.4
Whitcomb, J.M.5
Petropoulos, C.J.6
-
55
-
-
0003712305
-
-
Santa-Fe Institute Studies in the Sciences of Complexity, Addison-Wesley, Redwood City, CA, USA
-
Weisbuch G (1990) Complex Systems Dynamics. Santa-Fe Institute Studies in the Sciences of Complexity, Addison-Wesley, Redwood City, CA, USA.
-
(1990)
Complex Systems Dynamics
-
-
Weisbuch, G.1
-
56
-
-
84902775598
-
Empirical fitness landscapes and the predictability of evolution
-
PMID: 24913663
-
Arjan J, de Visser GM, Krug J. (2014) Empirical fitness landscapes and the predictability of evolution. Nature Rev Genet 15(7): 480-490. doi: 10.1038/nrg3744 PMID: 24913663
-
(2014)
Nature Rev Genet
, vol.15
, Issue.7
, pp. 480-490
-
-
Arjan, J.1
De Visser, G.M.2
Krug, J.3
-
57
-
-
0023647382
-
Towards a general theory of adaptive walks on rugged landscapes
-
PMID: 3431131
-
Kauffman S, Levin S. (1987) Towards a general theory of adaptive walks on rugged landscapes. J TheorBiol 128(1): 11-45. PMID: 3431131
-
(1987)
J TheorBiol
, vol.128
, Issue.1
, pp. 11-45
-
-
Kauffman, S.1
Levin, S.2
-
59
-
-
0023266407
-
New optimization methods: From physics and biology
-
1987
-
Bounds DG (1987) New Optimization Methods: from Physics and Biology. Nature 329: 215-218, 1987.
-
(1987)
Nature
, vol.329
, pp. 215-218
-
-
Bounds, D.G.1
-
60
-
-
0343136966
-
Optimization by simulated annealing: Quantitative studies
-
Kirkpatrick S (1984) Optimization by Simulated Annealing: Quantitative Studies. J Stat Phys 34(5-6): 975-986.
-
(1984)
J Stat Phys
, vol.34
, Issue.5-6
, pp. 975-986
-
-
Kirkpatrick, S.1
-
61
-
-
26444479778
-
Optimization by simulated annealing
-
PMID: 17813860
-
Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by Simulated Annealing. Science 220 (4598): 671-680. PMID: 17813860
-
(1983)
Science
, vol.220
, Issue.4598
, pp. 671-680
-
-
Kirkpatrick, S.1
Gelatt, C.D.2
Vecchi, M.P.3
-
62
-
-
84941871856
-
The kolmogorov-smirnov test for goodness of fit
-
Massey FJ (1951) The Kolmogorov-Smirnov Test for Goodness of Fit. J American Stat Assoc 46, 253: 68-78.
-
(1951)
J American Stat Assoc 46
, vol.253
, pp. 68-78
-
-
Massey, F.J.1
-
63
-
-
84965191948
-
Mapping and manipulating the mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
-
PMID: 25380655
-
Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, et al. (2014) Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol 15(11): 502. PMID: 25380655
-
(2014)
Genome Biol
, vol.15
, Issue.11
, pp. 502
-
-
Rustad, T.R.1
Minch, K.J.2
Ma, S.3
Winkler, J.K.4
Hobbs, S.5
Hickey, M.6
-
64
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
PMID: 19033363
-
Huang da W., Sherman BT, Lempicki R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1): 1-13. doi: 10.1093/nar/gkn923 PMID: 19033363
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.1
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
65
-
-
0038005018
-
DAVID: Database for annotation, visualization, and integrated discovery
-
PMID: 12734009
-
Dennis G Jr, Sherman B.T., Hosack DA, Yang J, Gao W, Lane H.C., et al. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4(5): P3. PMID: 12734009
-
(2003)
Genome Biol
, vol.4
, Issue.5
, pp. P3
-
-
Dennis, G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
-
66
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
PMID: 10802651
-
Ashburner M, Ball CA, Blake J.A., Botstein D., Butler H, Cherry JM, et al (2000) Gene Ontology: tool for the unification of biology. Nature Genet 25(1): 25-29. PMID: 10802651
-
(2000)
Nature Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
-
67
-
-
34547571030
-
G: Profiler - A web-based toolset for functional profiling of gene lists from large-scale experiments
-
PMID: 17478515
-
Reimand J, Kull M, Peterson H., Hansen J, Vilo J. (2007) g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 35(Web Server issue): W193-W200. PMID: 17478515
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.WEB SERVER ISSUE
, pp. W193-W200
-
-
Reimand, J.1
Kull, M.2
Peterson, H.3
Hansen, J.4
Vilo, J.5
-
68
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
PMID: 16199517
-
Subramanian A, Tamayo P, Mootha V.K., Mukherjee S., Ebert BL, Gillette MA, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102(43): 15545-15550. PMID: 16199517
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
-
69
-
-
73449134439
-
Gene set enrichment analysis made simple
-
PMID: 20048385
-
Irizarry RA, Wang C, Zhou Y, Speed TP (2009) Gene Set Enrichment Analysis Made Simple. Stat Methods: Med Res 18(6): 565-575. doi: 10.1177/0962280209351908 PMID: 20048385
-
(2009)
Stat Methods: Med Res
, vol.18
, Issue.6
, pp. 565-575
-
-
Irizarry, R.A.1
Wang, C.2
Zhou, Y.3
Speed, T.P.4
-
70
-
-
27944474776
-
ErmineJ: Tool for functional analysis of gene expression datasets
-
PMID: 16280084
-
Lee HK, Braynen W, Keshav K., Pavlidis P. (2005) ErmineJ: tool for functional analysis of gene expression datasets. BMC Bioinformatics 6: 269. PMID: 16280084
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 269
-
-
Lee, H.K.1
Braynen, W.2
Keshav, K.3
Pavlidis, P.4
-
71
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
PMID: 17940530
-
Chuang HY, Lee E, Liu Y.T., Lee D., Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3:140. PMID: 17940530
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
72
-
-
0000301097
-
Greedy heuristic for the set-covering problem
-
Chvatal VA (1979) Greedy Heuristic for the Set-Covering Problem. Mathematics of Operations Research 4(3): 233-235.
-
(1979)
Mathematics of Operations Research
, vol.4
, Issue.3
, pp. 233-235
-
-
Chvatal, V.A.1
-
73
-
-
84859748911
-
Causal reasoning on biological networks: Interpreting transcriptional changes
-
PMID: 22355083
-
Chindelevitch L, Ziemek D, Enayetellah A., Randhawa R, Sidders B, Brockel C., et al. (2012) Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics 28(8): 1114-1121. doi: 10.1093/bioinformatics/bts090 PMID: 22355083
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1114-1121
-
-
Chindelevitch, L.1
Ziemek, D.2
Enayetellah, A.3
Randhawa, R.4
Sidders, B.5
Brockel, C.6
-
74
-
-
84864470208
-
SteinerNet: A web server for integrating 'omic' data to discover hidden components of response pathways
-
PMID: 22638579
-
Tuncbag N, McCallum S, Huang S.S., Fraenkel E. (2012) SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res 40(Web Server issue): W505-9. doi: 10.1093/nar/gks445 PMID: 22638579
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.WEB SERVER ISSUE
, pp. W505-W509
-
-
Tuncbag, N.1
McCallum, S.2
Huang, S.S.3
Fraenkel, E.4
-
75
-
-
84876073379
-
A steiner tree-based method for biomarker discovery and classification in breast cancer metastasis
-
PMID: 23134806
-
Jahid MJ, Ruan J (2012) A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. BMC Genomics 13(Suppl 6): S8. doi: 10.1186/1471-2164-13-S6-S8 PMID: 23134806
-
(2012)
BMC Genomics
, vol.13
, pp. S8
-
-
Jahid, M.J.1
Ruan, J.2
-
77
-
-
33745449162
-
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
-
PMID: 16762362
-
Balaji S, Babu MM, Iyer L.M., Luscombe NM, Aravind L. (2006) Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol 360(1): 213-227. PMID: 16762362
-
(2006)
J Mol Biol
, vol.360
, Issue.1
, pp. 213-227
-
-
Balaji, S.1
Babu, M.M.2
Iyer, L.M.3
Luscombe, N.M.4
Aravind, L.5
-
78
-
-
84867524223
-
The co-regulation mechanism of transcription factors in the human gene regulatory network
-
PMID: 22798495
-
Kim J, Choi M, Kim J-R, Jin H, Kim V.N., Cho K-H (2012) The co-regulation mechanism of transcription factors in the human gene regulatory network. Nucleic Acids Res 40(18): 8849-8861. doi: 10.1093/nar/gks664 PMID: 22798495
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.18
, pp. 8849-8861
-
-
Kim, J.1
Choi, M.2
Kim, J.-R.3
Jin, H.4
Kim, V.N.5
Cho, K.-H.6
-
79
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
PMID: 20363979
-
Gotea V, Visel A, Westlund J.M., Nobrega MA, Pennacchio LA, Ovcharenko I (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20(5): 565-577. doi: 10.1101/gr.104471.109 PMID: 20363979
-
(2010)
Genome Res
, vol.20
, Issue.5
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
Ovcharenko, I.6
-
80
-
-
84881430615
-
Statistical significance of combinatorial regulations
-
PMID: 23882073
-
Terada A, Okada-Hatakeyama M, Tsuda K, Sese J (2013) Statistical significance of combinatorial regulations. Proc Natl Acad Sci USA 110(32): 12996-13001. doi: 10.1073/pnas.1302233110 PMID: 23882073
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.32
, pp. 12996-13001
-
-
Terada, A.1
Okada-Hatakeyama, M.2
Tsuda, K.3
Sese, J.4
-
81
-
-
0002386913
-
On the interpretation of %2 from contingency tables, and the calculation of P
-
Fisher RA (1922) On the interpretation of %2 from contingency tables, and the calculation of P. J Royal Stat Soc 85(1): 87-94.
-
(1922)
J Royal Stat Soc
, vol.85
, Issue.1
, pp. 87-94
-
-
Fisher, R.A.1
-
82
-
-
0028931857
-
Multiple significance tests: The bonferroni method
-
PMID: 7833759
-
Bland JM, Altman D.G. (1995) Multiple significance tests: The Bonferroni method. BMJ 310 (6973): 170. PMID: 7833759
-
(1995)
BMJ
, vol.310
, Issue.6973
, pp. 170
-
-
Bland, J.M.1
Altman, D.G.2
-
83
-
-
84872256757
-
Machine learning and its applications to biology
-
PMID: 17604446
-
Tarca AL, Carey VJ, Chen XW, Romero R, Dràghici S (2007) Machine Learning and Its Applications to Biology. PLoS Comput Biol 3(6): e116. PMID: 17604446
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.6
, pp. e116
-
-
Tarca, A.L.1
Carey, V.J.2
Chen, X.W.3
Romero, R.4
Dràghici, S.5
-
84
-
-
0036081355
-
Gene expression omnibus: Ncbi gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30(10): 207-210.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.10
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
85
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets - Update
-
PMID: 23193258
-
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. (2013) NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res 41(Database issue): D991-D995. doi: 10.1093/nar/gks1193 PMID: 23193258
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
Evangelista, C.4
Kim, I.F.5
Tomashevsky, M.6
-
86
-
-
0001884644
-
Individual comparisons by ranking methods
-
Wilcoxon F (1945) Individual comparisons by ranking methods. Biometrics Bulletin 1(6): 80-83.
-
(1945)
Biometrics Bulletin
, vol.1
, Issue.6
, pp. 80-83
-
-
Wilcoxon, F.1
-
87
-
-
84955491942
-
-
MTB Portal Data Center. Available: http://networks.systemsbiology.net/mtb/data-center.
-
MTB Portal Data Center
-
-
|