-
1
-
-
34250788809
-
AKT/PKB signaling: Navigating downstream
-
Manning BD, Cantley LC. AKT/PKB signaling: navigating downstream. Cell 2007;129:1261-74.
-
(2007)
Cell
, vol.129
, pp. 1261-1274
-
-
Manning, B.D.1
Cantley, L.C.2
-
2
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007;4:207-14.
-
(2007)
Nat Methods
, vol.4
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
3
-
-
78650466243
-
A tissue-specific atlas of mouse protein phosphorylation and expression
-
Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 2010;143:1174-89.
-
(2010)
Cell
, vol.143
, pp. 1174-1189
-
-
Huttlin, E.L.1
Jedrychowski, M.P.2
Elias, J.E.3
Goswami, T.4
Rad, R.5
Beausoleil, S.A.6
-
4
-
-
52449092107
-
Breast tumor cells with PI3K mutation or HER2 amplification are selectively addicted to Akt signaling
-
She QB, Chandarlapaty S, Ye Q, Lobo J, Haskell KM, Leander KR, et al. Breast tumor cells with PI3K mutation or HER2 amplification are selectively addicted to Akt signaling. PLoS One 2008;3:e3065.
-
(2008)
PLoS One
, vol.3
-
-
She, Q.B.1
Chandarlapaty, S.2
Ye, Q.3
Lobo, J.4
Haskell, K.M.5
Leander, K.R.6
-
5
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013;14:R36.
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
6
-
-
84864483625
-
RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics
-
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 2012;40:W622-7.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W622-W627
-
-
Lohse, M.1
Bolger, A.M.2
Nagel, A.3
Fernie, A.R.4
Lunn, J.E.5
Stitt, M.6
-
7
-
-
84928987900
-
HTSeq - A Python framework to work with high-throughput sequencing data
-
Anders S, Pyl PT, Huber W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166-9.
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
8
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008;322: 1845-8.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
9
-
-
84923935202
-
A mechanism for asymmetric cell division resulting in proliferative asynchronicity
-
Dey-Guha I, Alves CP, Yeh AC, Salony, Sole X, Darp R, et al. A mechanism for asymmetric cell division resulting in proliferative asynchronicity. Mol Cancer Res 2015;13:223-30.
-
(2015)
Mol Cancer Res
, vol.13
, pp. 223-230
-
-
Dey-Guha, I.1
Alves, C.P.2
Yeh, A.C.3
Salony4
Sole, X.5
Darp, R.6
-
10
-
-
79961218347
-
Asymmetric cancer cell division regulated by AKT
-
Dey-Guha I, Wolfer A, Yeh AC, J GA, Darp R, Leon E, et al. Asymmetric cancer cell division regulated by AKT. Proc Natl Acad Sci U S A 2011;108: 12845-50.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 12845-12850
-
-
Dey-Guha, I.1
Wolfer, A.2
Yeh, A.C.3
Ga, J.4
Darp, R.5
Leon, E.6
-
11
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25: 2078-9.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
12
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010;7:709-15.
-
(2010)
Nat Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
-
13
-
-
84924415145
-
Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis
-
Van Rechem C, Black JC, Boukhali M, Aryee MJ, Graslund S, Haas W, et al. Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Cancer Discov 2015;5:255-63.
-
(2015)
Cancer Discov
, vol.5
, pp. 255-263
-
-
Van Rechem, C.1
Black, J.C.2
Boukhali, M.3
Aryee, M.J.4
Graslund, S.5
Haas, W.6
-
14
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 2011;17:10-2.
-
(2011)
EMBnetjournal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
15
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
16
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-2.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
17
-
-
80051941094
-
Identification of novel transcripts in annotated genomes using RNA-Seq
-
Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011;27: 2325-9.
-
(2011)
Bioinformatics
, vol.27
, pp. 2325-2329
-
-
Roberts, A.1
Pimentel, H.2
Trapnell, C.3
Pachter, L.4
-
18
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha VK,Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-50.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
-
19
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002;30:207-10.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
20
-
-
0037204948
-
TNF-R1 signaling: A beautiful pathway
-
Chen G, Goeddel DV. TNF-R1 signaling: a beautiful pathway. Science 2002;296:1634-5.
-
(2002)
Science
, vol.296
, pp. 1634-1635
-
-
Chen, G.1
Goeddel, D.V.2
-
21
-
-
84929278824
-
EVpedia: A community web resource for prokaryotic and eukaryotic extracellular vesicles research
-
Kim DK, Lee J, Simpson RJ, Lotvall J, Gho YS. EVpedia: a community web resource for prokaryotic and eukaryotic extracellular vesicles research. Semin Cell Dev Biol 2015;40:4-7.
-
(2015)
Semin Cell Dev Biol
, vol.40
, pp. 4-7
-
-
Kim, D.K.1
Lee, J.2
Simpson, R.J.3
Lotvall, J.4
Gho, Y.S.5
-
22
-
-
84929293007
-
Extracellular vesicles as modulators of the cancer microenvironment
-
Webber J, Yeung V, Clayton A. Extracellular vesicles as modulators of the cancer microenvironment. Semin Cell Dev Biol 2015;40:27-34.
-
(2015)
Semin Cell Dev Biol
, vol.40
, pp. 27-34
-
-
Webber, J.1
Yeung, V.2
Clayton, A.3
-
23
-
-
77249179196
-
Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation
-
Ericson K,Gan C, Cheong I, Rago C, Samuels Y, Velculescu VE, et al. Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation. Proc Natl Acad Sci U S A 2010;107:2598-603.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 2598-2603
-
-
Ericson, K.1
Gan, C.2
Cheong, I.3
Rago, C.4
Samuels, Y.5
Velculescu, V.E.6
-
24
-
-
84862998910
-
Small molecule-induced cytosolic activation of protein kinase Akt rescues ischemia-elicited neuronal death
-
Jo H, Mondal S, Tan D, Nagata E, Takizawa S, Sharma AK, et al. Small molecule-induced cytosolic activation of protein kinase Akt rescues ischemia-elicited neuronal death. Proc Natl Acad Sci U S A 2012;109: 10581-6.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 10581-10586
-
-
Jo, H.1
Mondal, S.2
Tan, D.3
Nagata, E.4
Takizawa, S.5
Sharma, A.K.6
-
25
-
-
77952111459
-
MIR-210 - Micromanager of the hypoxia pathway
-
Huang X, Le QT, Giaccia AJ. MiR-210 - micromanager of the hypoxia pathway. Trends Mol Med 2010;16:230-7.
-
(2010)
Trends Mol Med
, vol.16
, pp. 230-237
-
-
Huang, X.1
Le, Q.T.2
Giaccia, A.J.3
-
26
-
-
84876947528
-
Reactive oxygen speciesresponsive MIR-210 regulates proliferation and migration of adiposederived stem cells via PTPN2
-
Kim JH, Park SG, Song SY, Kim JK, Sung JH. Reactive oxygen speciesresponsive miR-210 regulates proliferation and migration of adiposederived stem cells via PTPN2. Cell Death Dis 2013;4:e588.
-
(2013)
Cell Death Dis
, vol.4
, pp. e588
-
-
Kim, J.H.1
Park, S.G.2
Song, S.Y.3
Kim, J.K.4
Sung, J.H.5
-
27
-
-
66349123063
-
MicroRNA-320 is involved in the regulation of cardiac ischemia/reperfusion injury by targeting heat-shock protein 20
-
Ren XP, Wu J, Wang X, Sartor MA, Qian J, Jones K, et al. MicroRNA-320 is involved in the regulation of cardiac ischemia/reperfusion injury by targeting heat-shock protein 20. Circulation 2009;119:2357-66.
-
(2009)
Circulation
, vol.119
, pp. 2357-2366
-
-
Ren, X.P.1
Wu, J.2
Wang, X.3
Sartor, M.A.4
Qian, J.5
Jones, K.6
-
28
-
-
84894240235
-
A genotoxic stress-responsive MIRNA, MIR-574-3p, delays cell growth by suppressing the enhancer of rudimentary homolog gene in vitro
-
Ishikawa K, Ishikawa A, Shoji Y, Imai T. A genotoxic stress-responsive miRNA, miR-574-3p, delays cell growth by suppressing the enhancer of rudimentary homolog gene in vitro. Int J Mol Sci 2014;15:2971-90.
-
(2014)
Int J Mol Sci
, vol.15
, pp. 2971-2990
-
-
Ishikawa, K.1
Ishikawa, A.2
Shoji, Y.3
Imai, T.4
-
29
-
-
84887110965
-
MIR-92b regulates the cell growth, cisplatin chemosensitivity of A549 non small cell lung cancer cell line and target PTEN
-
Li Y, Li L, Guan Y, Liu X, Meng Q, Guo Q. MiR-92b regulates the cell growth, cisplatin chemosensitivity of A549 non small cell lung cancer cell line and target PTEN. Biochem Biophys Res Commun 2013;440:604-10.
-
(2013)
Biochem Biophys Res Commun
, vol.440
, pp. 604-610
-
-
Li, Y.1
Li, L.2
Guan, Y.3
Liu, X.4
Meng, Q.5
Guo, Q.6
-
30
-
-
84880288028
-
MIR-375 is upregulated in acquired paclitaxel resistance in cervical cancer
-
Shen Y,Wang P, Li Y, Ye F,Wang F,Wan X, et al. miR-375 is upregulated in acquired paclitaxel resistance in cervical cancer. Br J Cancer 2013;109: 92-9.
-
(2013)
Br J Cancer
, vol.109
, pp. 92-99
-
-
Shen, Y.1
Wang, P.2
Li, Y.3
Ye, F.4
Wang, F.5
Wan, X.6
-
31
-
-
84908052464
-
MIR-375 mediated acquired chemo-resistance in cervical cancer by facilitating EMT
-
Shen Y, Zhou J, Li Y, Ye F, Wan X, Lu W, et al. miR-375 mediated acquired chemo-resistance in cervical cancer by facilitating EMT. PLoS One 2014;9: e109299.
-
(2014)
PLoS One
, vol.9
-
-
Shen, Y.1
Zhou, J.2
Li, Y.3
Ye, F.4
Wan, X.5
Lu, W.6
-
32
-
-
84903289147
-
MIR-345 in metastatic colorectal cancer: A non-invasive biomarker for clinical outcome in non-KRAS mutant patients treated with 3rd line cetuximab and irinotecan
-
Schou JV, Rossi S, Jensen BV, Nielsen DL, Pfeiffer P, Hogdall E, et al. miR-345 in metastatic colorectal cancer: a non-invasive biomarker for clinical outcome in non-KRAS mutant patients treated with 3rd line cetuximab and irinotecan. PLoS One 2014;9:e99886.
-
(2014)
PLoS One
, vol.9
-
-
Schou, J.V.1
Rossi, S.2
Jensen, B.V.3
Nielsen, D.L.4
Pfeiffer, P.5
Hogdall, E.6
-
33
-
-
84927005034
-
The clinical relevance of the MIR-197/CKS1B/STAT3-mediated PD-L1 network in chemoresistant non-small-cell lung cancer
-
Fujita Y, Yagishita S, Hagiwara K, Yoshioka Y, Kosaka N, Takeshita F, et al. The clinical relevance of the miR-197/CKS1B/STAT3-mediated PD-L1 network in chemoresistant non-small-cell lung cancer. Mol Ther 2015;23: 717-27.
-
(2015)
Mol Ther
, vol.23
, pp. 717-727
-
-
Fujita, Y.1
Yagishita, S.2
Hagiwara, K.3
Yoshioka, Y.4
Kosaka, N.5
Takeshita, F.6
-
34
-
-
84947128253
-
MIR-197 induces Taxol resistance in human ovarian cancer cells by regulating NLK
-
Zou D, Wang D, Li R, Tang Y, Yuan L, Long X, et al. MiR-197 induces Taxol resistance in human ovarian cancer cells by regulating NLK. Tumour Biol 2015;36:6725-32.
-
(2015)
Tumour Biol
, vol.36
, pp. 6725-6732
-
-
Zou, D.1
Wang, D.2
Li, R.3
Tang, Y.4
Yuan, L.5
Long, X.6
-
35
-
-
70450237022
-
Mechanism of chemoresistance mediated by MIR-140 in human osteosarcoma and colon cancer cells
-
Song B, Wang Y, Xi Y, Kudo K, Bruheim S, Botchkina GI, et al. Mechanism of chemoresistance mediated by miR-140 in human osteosarcoma and colon cancer cells. Oncogene 2009;28:4065-74.
-
(2009)
Oncogene
, vol.28
, pp. 4065-4074
-
-
Song, B.1
Wang, Y.2
Xi, Y.3
Kudo, K.4
Bruheim, S.5
Botchkina, G.I.6
-
38
-
-
84905726946
-
Drug resistance via feedback activation of Stat3 in oncogene-addicted cancer cells
-
Lee HJ, Zhuang G, Cao Y, Du P, Kim HJ, Settleman J. Drug resistance via feedback activation of Stat3 in oncogene-addicted cancer cells. Cancer Cell 2014;26:207-21.
-
(2014)
Cancer Cell
, vol.26
, pp. 207-221
-
-
Lee, H.J.1
Zhuang, G.2
Cao, Y.3
Du, P.4
Kim, H.J.5
Settleman, J.6
-
39
-
-
84928174677
-
Therapyinduced tumour secretomes promote resistance and tumour progression
-
Obenauf AC, Zou Y, Ji AL, Vanharanta S, Shu W, Shi H, et al. Therapyinduced tumour secretomes promote resistance and tumour progression. Nature 2015;520:368-72.
-
(2015)
Nature
, vol.520
, pp. 368-372
-
-
Obenauf, A.C.1
Zou, Y.2
Ji, A.L.3
Vanharanta, S.4
Shu, W.5
Shi, H.6
-
40
-
-
77949881221
-
The senescence-associated secretory phenotype: The dark side of tumor suppression
-
Coppe JP, Desprez PY, Krtolica A, Campisi J. The senescence-associated secretory phenotype: the dark side of tumor suppression. Annu Rev Pathol 2010;5:99-118.
-
(2010)
Annu Rev Pathol
, vol.5
, pp. 99-118
-
-
Coppe, J.P.1
Desprez, P.Y.2
Krtolica, A.3
Campisi, J.4
-
41
-
-
84865718193
-
Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses
-
www
-
McAlister GC, Huttlin EL, Haas W, Ting L, Jedrychowski MP, Rogers JC, et al. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal Chem 2012; 84:7469-78. www.
-
(2012)
Anal Chem
, vol.84
, pp. 7469-7478
-
-
McAlister, G.C.1
Huttlin, E.L.2
Haas, W.3
Ting, L.4
Jedrychowski, M.P.5
Rogers, J.C.6
|