-
1
-
-
84874232489
-
The coming age of complete, accurate, and ubiquitous proteomes
-
Mann, M., Kulak, N. A., Nagaraj, N. et al. (2013) The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell, 49, 583-590.
-
(2013)
Mol. Cell
, vol.49
, pp. 583-590
-
-
Mann, M.1
Kulak, N.A.2
Nagaraj, N.3
-
2
-
-
79960179572
-
The human proteome project: Current state and future direction
-
Legrain, P., Aebersold, R., Archakov, A. et al. (2011) The human proteome project: current state and future direction. Mol. Cell Proteomics, 10, M111 009993.
-
(2011)
Mol. Cell Proteomics
, vol.10
, pp. M111009993
-
-
Legrain, P.1
Aebersold, R.2
Archakov, A.3
-
3
-
-
84863229647
-
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome
-
Paik, Y. K., Jeong, S. K., Omenn, G. S. et al. (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat. Biotechnol., 30, 221-223.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 221-223
-
-
Paik, Y.K.1
Jeong, S.K.2
Omenn, G.S.3
-
4
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M. S., Pinto, S. M., Getnet, D. et al. (2014) A draft map of the human proteome. Nature, 509, 575-581.
-
(2014)
Nature
, vol.509
, pp. 575-581
-
-
Kim, M.S.1
Pinto, S.M.2
Getnet, D.3
-
5
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
Wilhelm, M., Schlegl, J., Hahne, H. et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509, 582-587.
-
(2014)
Nature
, vol.509
, pp. 582-587
-
-
Wilhelm, M.1
Schlegl, J.2
Hahne, H.3
-
6
-
-
84907958189
-
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive resources for discovery and targeted proteomics
-
Kusebauch, U., Deutsch, E. W., Campbell, D. S. et al. (2014) Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr. Protoc. Bioinformatics, 46, 13 25 1-13 25 28.
-
(2014)
Curr. Protoc. Bioinformatics
, vol.46
, pp. 13251-132528
-
-
Kusebauch, U.1
Deutsch, E.W.2
Campbell, D.S.3
-
7
-
-
84874762979
-
The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
-
Vizcaino, J. A., Cote, R. G., Csordas, A. et al. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res., 41, D1063-D1069.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1063-D1069
-
-
Vizcaino, J.A.1
Cote, R.G.2
Csordas, A.3
-
8
-
-
84941042092
-
Beyond protein expression, MOPED goes multi-omics
-
Montague, E., Janko, I., Stanberry, L. et al. (2015) Beyond protein expression, MOPED goes multi-omics. Nucleic Acids Res., 43, D1145-D1151.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D1145-D1151
-
-
Montague, E.1
Janko, I.2
Stanberry, L.3
-
9
-
-
84864817904
-
PaxDb, a database of protein abundance averages across all three domains of life
-
Wang, M., Weiss, M., Simonovic, M. et al. (2012) PaxDb, a database of protein abundance averages across all three domains of life. Mol. Cell Proteomics, 11, 492-500.
-
(2012)
Mol. Cell Proteomics
, vol.11
, pp. 492-500
-
-
Wang, M.1
Weiss, M.2
Simonovic, M.3
-
10
-
-
84857980282
-
Analysis of high accuracy, quantitative proteomics data in the MaxQB database
-
Schaab, C., Geiger, T., Stoehr, G. et al. (2012) Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell Proteomics, 11, M111 014068.
-
(2012)
Mol. Cell Proteomics
, vol.11
, pp. M111014068
-
-
Schaab, C.1
Geiger, T.2
Stoehr, G.3
-
11
-
-
78049480691
-
GeneCards Version 3: The human gene integrator
-
Safran, M., Dalah, I., Alexander, J. et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford), 2010, baq020.
-
(2010)
Database (Oxford)
, vol.2010
, pp. baq020
-
-
Safran, M.1
Dalah, I.2
Alexander, J.3
-
12
-
-
84985000589
-
PathCards: Multisource consolidation of human biological pathways
-
2015
-
Belinky, F., Nativ, N., Stelzer, G. et al. (2015) PathCards: multisource consolidation of human biological pathways. Database (Oxford), 2015
-
(2015)
Database (Oxford)
-
-
Belinky, F.1
Nativ, N.2
Stelzer, G.3
-
13
-
-
84876569934
-
The TissueNet database of human tissue protein-protein interactions
-
Barshir, R., Basha, O., Eluk, A. et al. (2013) The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res., 41, D841-D844.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D841-D844
-
-
Barshir, R.1
Basha, O.2
Eluk, A.3
-
14
-
-
84941028211
-
COXPRESdb in 2015: Coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
-
Okamura, Y., Aoki, Y., Obayashi, T. et al. (2015) COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic Acids Res., 43, D82-D86.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D82-D86
-
-
Okamura, Y.1
Aoki, Y.2
Obayashi, T.3
-
15
-
-
84920269464
-
Proteomics. Tissue-based map of the human proteome
-
Uhlen, M., Fagerberg, L., Hallstrom, B. M. et al. (2015) Proteomics. Tissue-based map of the human proteome. Science, 347, 1260419.
-
(2015)
Science
, vol.347
, pp. 1260419
-
-
Uhlen, M.1
Fagerberg, L.2
Hallstrom, B.M.3
-
16
-
-
84884416048
-
Human housekeeping genes, revisited
-
Eisenberg, E. and Levanon, E. Y. (2013) Human housekeeping genes, revisited. Trends Genet., 29, 569-574.
-
(2013)
Trends Genet.
, vol.29
, pp. 569-574
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
17
-
-
79960819723
-
Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis
-
Chang, C. W., Cheng, W. C., Chen, C. R. et al. (2011) Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS One, 6, e22859.
-
(2011)
PLoS One
, vol.6
, pp. e22859
-
-
Chang, C.W.1
Cheng, W.C.2
Chen, C.R.3
-
18
-
-
84941051170
-
STRING v10: Protein-protein interaction networks, integrated over the tree of life
-
Szklarczyk, D., Franceschini, A., Wyder, S. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D447-D452
-
-
Szklarczyk, D.1
Franceschini, A.2
Wyder, S.3
-
19
-
-
72949089708
-
Global signatures of protein and mRNA expression levels
-
de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M. et al. (2009) Global signatures of protein and mRNA expression levels. Mol. Biosyst., 5, 1512-1526.
-
(2009)
Mol. Biosyst.
, vol.5
, pp. 1512-1526
-
-
De Sousa Abreu, R.1
Penalva, L.O.2
Marcotte, E.M.3
-
20
-
-
84858439862
-
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
-
Vogel, C. and Marcotte, E. M. (2012) Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet., 13, 227-232.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 227-232
-
-
Vogel, C.1
Marcotte, E.M.2
-
21
-
-
84941799987
-
Next-generation analysis of gene expression regulation - Comparing the roles of synthesis and degradation
-
McManus, J., Cheng, Z. and Vogel, C. (2015) Next-generation analysis of gene expression regulation - comparing the roles of synthesis and degradation. Mol. Biosyst., 11, 2680-2689.
-
(2015)
Mol. Biosyst.
, vol.11
, pp. 2680-2689
-
-
McManus, J.1
Cheng, Z.2
Vogel, C.3
-
22
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhausser, B., Busse, D., Li, N. et al. (2011) Global quantification of mammalian gene expression control. Nature, 473, 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhausser, B.1
Busse, D.2
Li, N.3
-
23
-
-
84874541273
-
In silico estimation of translation efficiency in human cell lines: Potential evidence for widespread translational control
-
Stevens, S. G. and Brown, C. M. (2013) In silico estimation of translation efficiency in human cell lines: potential evidence for widespread translational control. PLoS One, 8, e57625.
-
(2013)
PLoS One
, vol.8
, pp. e57625
-
-
Stevens, S.G.1
Brown, C.M.2
-
24
-
-
84946037477
-
Ensembl 2015
-
Cunningham, F., Amode, M. R., Barrell, D. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D662-D669
-
-
Cunningham, F.1
Amode, M.R.2
Barrell, D.3
-
25
-
-
84891783174
-
Activities at the universal protein resource (UniProt)
-
UniProt, C. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D191-D198
-
-
UniProt, C.1
-
26
-
-
84878682420
-
The genotype-tissue expression (GTEx) project
-
GTEx Consortium. (2013) The Genotype-Tissue Expression (GTEx) project. Nat. Genet., 45, 580-585.
-
(2013)
Nat. Genet.
, vol.45
, pp. 580-585
-
-
GTEx Consortium1
-
27
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
28
-
-
84929015296
-
Human genomics. The human transcriptome across tissues and individuals
-
Mele, M., Ferreira, P. G., Reverter, F. et al. (2015) Human genomics. The human transcriptome across tissues and individuals. Science, 348, 660-665.
-
(2015)
Science
, vol.348
, pp. 660-665
-
-
Mele, M.1
Ferreira, P.G.2
Reverter, F.3
-
29
-
-
84887620404
-
What is the total number of protein molecules per cell volume? A call to rethink some published values
-
Milo, R. (2013) What is the total number of protein molecules per cell volume? A call to rethink some published values. Bioessays, 35, 1050-1055.
-
(2013)
Bioessays
, vol.35
, pp. 1050-1055
-
-
Milo, R.1
-
30
-
-
84899633396
-
Defining functional DNA elements in the human genome
-
Kellis, M., Wold, B., Snyder, M. P. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. U S A., 111, 6131-6138.
-
(2014)
Proc. Natl. Acad. Sci. U S A.
, vol.111
, pp. 6131-6138
-
-
Kellis, M.1
Wold, B.2
Snyder, M.P.3
-
31
-
-
84901788541
-
COMPARTMENTS: Unification and visualization of protein subcellular localization evidence
-
Binder, J. X., Pletscher-Frankild, S., Tsafou, K. et al. (2014) COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database (Oxford), 2014, bau012.
-
(2014)
Database (Oxford)
, vol.2014
, pp. bau012
-
-
Binder, J.X.1
Pletscher-Frankild, S.2
Tsafou, K.3
-
32
-
-
84937919422
-
MalaCards: A comprehensive automatically-mined database of human diseases
-
Rappaport, N., Twik, M., Nativ, N. et al. (2014) MalaCards: a comprehensive automatically-mined database of human diseases. Curr. Protoc. Bioinformatics, 47, 1 24 1-1 24 19.
-
(2014)
Curr. Protoc. Bioinformatics
, vol.47
, pp. 1241-12419
-
-
Rappaport, N.1
Twik, M.2
Nativ, N.3
-
33
-
-
71849119227
-
GeneDecks: Paralog hunting and gene-set distillation with GeneCards annotation
-
Stelzer, G., Inger, A., Olender, T. et al. (2009) GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. Omics, 13, 477-487.
-
(2009)
Omics
, vol.13
, pp. 477-487
-
-
Stelzer, G.1
Inger, A.2
Olender, T.3
-
34
-
-
84964907479
-
GeneAnalytics: An integrative gene set analysis tool
-
in press
-
Ben-Ari, Fuchs S, Lieder, I, Stelzer, G. et al. (2016) GeneAnalytics: An integrative gene set analysis tool, OMICS, in press.
-
(2016)
OMICS
-
-
Ben-Ari, F.S.1
Lieder, I.2
Stelzer, G.3
-
35
-
-
0037255084
-
Human gene-centric databases at the weizmann institute of science: GeneCards, UDB, CroW 21 and HORDE
-
Safran, M., Chalifa-Caspi, V., Shmueli, O. et al. (2003) Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res., 31, 142-146.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 142-146
-
-
Safran, M.1
Chalifa-Caspi, V.2
Shmueli, O.3
-
36
-
-
71849092560
-
GIFtS: Annotation landscape analysis with GeneCards
-
Harel, A., Inger, A., Stelzer, G. et al. (2009) GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics, 10, 348.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 348
-
-
Harel, A.1
Inger, A.2
Stelzer, G.3
-
37
-
-
78651317908
-
Entrez Gene: Gene-centered information at NCBI
-
Maglott, D., Ostell, J., Pruitt, K. D. et al. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D52-D57
-
-
Maglott, D.1
Ostell, J.2
Pruitt, K.D.3
-
38
-
-
84930603726
-
Can "normal" protein expression ranges be estimated with high-throughput proteomics?
-
Higdon, R. and Kolker, E. (2015) Can "normal" protein expression ranges be estimated with high-throughput proteomics? J. Proteome Res., 14, 2398-407.
-
(2015)
J. Proteome Res.
, vol.14
, pp. 2398-2407
-
-
Higdon, R.1
Kolker, E.2
-
39
-
-
84905372152
-
Analyzing the first drafts of the human proteome
-
Ezkurdia, I., Vazquez, J., Valencia, A. et al. (2014) Analyzing the first drafts of the human proteome. J. Proteome Res., 13, 3854-3855.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 3854-3855
-
-
Ezkurdia, I.1
Vazquez, J.2
Valencia, A.3
-
40
-
-
33746092533
-
Widespread ectopic expression of olfactory receptor genes
-
Feldmesser, E., Olender, T., Khen, M. et al. (2006) Widespread ectopic expression of olfactory receptor genes. BMC Genomics, 7, 121.
-
(2006)
BMC Genomics
, vol.7
, pp. 121
-
-
Feldmesser, E.1
Olender, T.2
Khen, M.3
-
41
-
-
84920070787
-
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
-
Perez-Riverol, Y., Alpi, E., Wang, R. et al. (2015) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics, 15, 930-949.
-
(2015)
Proteomics
, vol.15
, pp. 930-949
-
-
Perez-Riverol, Y.1
Alpi, E.2
Wang, R.3
-
42
-
-
84941089280
-
Recent advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light
-
Paik, Y. K., Omenn, G. S., Overall, C. M. et al. (2015) Recent advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J. Proteome Res., 14, 3409-3414.
-
(2015)
J. Proteome Res.
, vol.14
, pp. 3409-3414
-
-
Paik, Y.K.1
Omenn, G.S.2
Overall, C.M.3
-
43
-
-
84940547273
-
A scalable approach for protein false discovery rate estimation in large proteomic data sets
-
Savitski, M. M., Wilhelm, M., Hahne, H. et al. (2015) A scalable approach for protein false discovery rate estimation in large proteomic data sets. Mol. Cell Proteomics, 14, 2394-2404.
-
(2015)
Mol. Cell Proteomics
, vol.14
, pp. 2394-2404
-
-
Savitski, M.M.1
Wilhelm, M.2
Hahne, H.3
-
44
-
-
84941749221
-
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines
-
Wang, M., Herrmann, C. J., Simonovic, M. et al. (2015) Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15, 3163-3168.
-
(2015)
Proteomics
, vol.15
, pp. 3163-3168
-
-
Wang, M.1
Herrmann, C.J.2
Simonovic, M.3
-
45
-
-
84941717906
-
Comprehensive comparison of large-scale tissue expression datasets
-
Santos, A., Tsafou, K., Stolte, C. et al. (2015) Comprehensive comparison of large-scale tissue expression datasets. PeerJ, 3, e1054.
-
(2015)
PeerJ
, vol.3
, pp. e1054
-
-
Santos, A.1
Tsafou, K.2
Stolte, C.3
-
46
-
-
76249090489
-
BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources
-
Wu, C., Orozco, C., Boyer, J. et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130.
-
(2009)
Genome Biol.
, vol.10
, pp. R130
-
-
Wu, C.1
Orozco, C.2
Boyer, J.3
-
47
-
-
84930607351
-
Sharing and Specificity of Co-expression Networks across 35 Human Tissues
-
Pierson, E., Consortium, G. T., Koller, D. et al. (2015) Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLoS Comput. Biol., 11, e1004220.
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004220
-
-
Pierson, E.1
Consortium, G.T.2
Koller, D.3
-
48
-
-
84901269108
-
High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation
-
Levy, E. D., Kowarzyk, J. and Michnick, S. W. (2014) High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation. Cell Rep., 7, 1333-1340.
-
(2014)
Cell Rep.
, vol.7
, pp. 1333-1340
-
-
Levy, E.D.1
Kowarzyk, J.2
Michnick, S.W.3
-
49
-
-
84884518215
-
Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data
-
Lopez-Kleine, L., Leal, L. and Lopez, C. (2013) Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data. Brief Funct. Genomics, 12, 457-467.
-
(2013)
Brief Funct. Genomics
, vol.12
, pp. 457-467
-
-
Lopez-Kleine, L.1
Leal, L.2
Lopez, C.3
-
50
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai, I., Benjamin, H., Shmoish, M. et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics, 21, 650-659.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
-
51
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj, N., Wisniewski, J. R., Geiger, T. et al. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol., 7, 548.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
-
52
-
-
13844254513
-
LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression
-
Higdon, R., Kolker, N., Picone, A. et al. (2004) LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression. OMICS: JIB, 8, 357-369.
-
(2004)
OMICS: JIB
, vol.8
, pp. 357-369
-
-
Higdon, R.1
Kolker, N.2
Picone, A.3
-
53
-
-
84902265781
-
MOPED 2.5-An integrated multi-omics resource: Multi-omics profiling expression database now includes transcriptomics data
-
Montague, E., Stenberry, L., Higdon, R. et al. (2014) MOPED 2.5-An integrated multi-omics resource: Multi-omics profiling expression database now includes transcriptomics data. OMICS: JIB., 18, 335-343.
-
(2014)
OMICS: JIB.
, vol.18
, pp. 335-343
-
-
Montague, E.1
Stenberry, L.2
Higdon, R.3
|