-
1
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei, I.A., Schmidt, S., Peshkin, L., Ramensky, V.E., Gerasimova, A., Bork, P., et al. A method and server for predicting damaging missense mutations. Nature Methods 7:4 (2010), 248–249.
-
(2010)
Nature Methods
, vol.7
, Issue.4
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool. Journal of Molecular Biology 215:3 (1990), 403–410.
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
84894380391
-
Emerging evidence for functional peptides encoded by short open reading frames
-
Andrews, S.J., Rothnagel, J.A., Emerging evidence for functional peptides encoded by short open reading frames. Nature Reviews. Genetics 15:3 (2014), 193–204.
-
(2014)
Nature Reviews. Genetics
, vol.15
, Issue.3
, pp. 193-204
-
-
Andrews, S.J.1
Rothnagel, J.A.2
-
4
-
-
84960413025
-
PGx: Putting peptides to BED
-
Askenazi, M., Ruggles, K.V., Fenyö, D., PGx: Putting peptides to BED. Journal of Proteome Research 15:3 (2016), 795–799.
-
(2016)
Journal of Proteome Research
, vol.15
, Issue.3
, pp. 795-799
-
-
Askenazi, M.1
Ruggles, K.V.2
Fenyö, D.3
-
5
-
-
33847234661
-
Lookup peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry
-
Bern, M., Cai, Y., Goldberg, D., Lookup peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Analytical Chemistry 79:4 (2007), 1393–1400.
-
(2007)
Analytical Chemistry
, vol.79
, Issue.4
, pp. 1393-1400
-
-
Bern, M.1
Cai, Y.2
Goldberg, D.3
-
6
-
-
34547782215
-
How does eukaryotic gene prediction work?
-
Brent, M.R., How does eukaryotic gene prediction work?. Nature Biotechnology, 25(8), 2007, 883.
-
(2007)
Nature Biotechnology
, vol.25
, Issue.8
, pp. 883
-
-
Brent, M.R.1
-
7
-
-
37249005195
-
Steady progress and recent breakthroughs in the accuracy of automated genome annotation
-
Brent, M.R., Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nature Reviews. Genetics 9:1 (2008), 62–73.
-
(2008)
Nature Reviews. Genetics
, vol.9
, Issue.1
, pp. 62-73
-
-
Brent, M.R.1
-
8
-
-
79955555530
-
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
-
Brosch, M., Saunders, G.I., Frankish, A., Collins, M.O., Yu, L., Wright, J., et al. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Research 21:5 (2011), 756–767, 10.1101/gr.114272.110.
-
(2011)
Genome Research
, vol.21
, Issue.5
, pp. 756-767
-
-
Brosch, M.1
Saunders, G.I.2
Frankish, A.3
Collins, M.O.4
Yu, L.5
Wright, J.6
-
9
-
-
34249717879
-
A high-quality catalog of the Drosophila melanogaster proteome
-
Brunner, E., Ahrens, C.H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., et al. A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology 25:5 (2007), 576–583, 10.1038/nbt1300.
-
(2007)
Nature Biotechnology
, vol.25
, Issue.5
, pp. 576-583
-
-
Brunner, E.1
Ahrens, C.H.2
Mohanty, S.3
Baetschmann, H.4
Loevenich, S.5
Potthast, F.6
-
10
-
-
58549101102
-
Discovery and revision of Arabidopsis genes by proteogenomics
-
Castellana, N.E., Payne, S.H., Shen, Z., Stanke, M., Bafna, V., Briggs, S.P., Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences of the United States of America 105:52 (2008), 21034–21038, 10.1073/pnas.0811066106.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.52
, pp. 21034-21038
-
-
Castellana, N.E.1
Payne, S.H.2
Shen, Z.3
Stanke, M.4
Bafna, V.5
Briggs, S.P.6
-
11
-
-
84891760451
-
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays
-
Castellana, N.E., Shen, Z., He, Y., Walley, J.W., Cassidy, C.J., Briggs, S.P., et al. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Molecular & Cellular Proteomics 13:1 (2014), 157–167, 10.1074/mcp.M113.031260.
-
(2014)
Molecular & Cellular Proteomics
, vol.13
, Issue.1
, pp. 157-167
-
-
Castellana, N.E.1
Shen, Z.2
He, Y.3
Walley, J.W.4
Cassidy, C.J.5
Briggs, S.P.6
-
12
-
-
84867345063
-
A cross-platform toolkit for mass spectrometry and proteomics
-
Chambers, M.C., Maclean, B., Burke, R., Amodei, D., Ruderman, D.L., Neumann, S., et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology 30:10 (2012), 918–920, 10.1038/nbt.2377.
-
(2012)
Nature Biotechnology
, vol.30
, Issue.10
, pp. 918-920
-
-
Chambers, M.C.1
Maclean, B.2
Burke, R.3
Amodei, D.4
Ruderman, D.L.5
Neumann, S.6
-
13
-
-
79957845610
-
A honey bee (Apis mellifera L.) peptide atlas crossing castes and tissues
-
Chan, Q.W.T., Parker, R., Sun, Z., Deutsch, E.W., Foster, L.J., A honey bee (Apis mellifera L.) peptide atlas crossing castes and tissues. BMC Genomics, 12(290), 2011, 1, 10.1186/1471-2164-12-290.
-
(2011)
BMC Genomics
, vol.12
, Issue.290
, pp. 1
-
-
Chan, Q.W.T.1
Parker, R.2
Sun, Z.3
Deutsch, E.W.4
Foster, L.J.5
-
14
-
-
84941266080
-
A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
-
Chick, J.M., Kolippakkam, D., Nusinow, D.P., Zhai, B., Rad, R., Huttlin, E.L., et al. A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nature Biotechnology 33:7 (2015), 743–749.
-
(2015)
Nature Biotechnology
, vol.33
, Issue.7
, pp. 743-749
-
-
Chick, J.M.1
Kolippakkam, D.2
Nusinow, D.P.3
Zhai, B.4
Rad, R.5
Huttlin, E.L.6
-
15
-
-
84907472562
-
High-resolution transcriptome analysis with long-read RNA sequencing
-
Cho, H., Davis, J., Li, X., Smith, K.S., Battle, A., Montgomery, S.B., High-resolution transcriptome analysis with long-read RNA sequencing. PloS One, 9(9), 2014, e108095.
-
(2014)
PloS One
, vol.9
, Issue.9
, pp. e108095
-
-
Cho, H.1
Davis, J.2
Li, X.3
Smith, K.S.4
Battle, A.5
Montgomery, S.B.6
-
16
-
-
43949138227
-
Blast2GO: A comprehensive suite for functional analysis in plant genomics
-
Conesa, A., Gotz, S., Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 2008, 619832, 10.1155/2008/619832.
-
(2008)
International Journal of Plant Genomics
, vol.2008
, pp. 619832
-
-
Conesa, A.1
Gotz, S.2
-
17
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
-
Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 26:12 (2008), 1367–1372.
-
(2008)
Nature Biotechnology
, vol.26
, Issue.12
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
18
-
-
67649400942
-
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
-
Cox, J., Matic, I., Hilger, M., Nagaraj, N., Selbach, M., Olsen, J.V., et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nature Protocols 4:5 (2009), 698–705.
-
(2009)
Nature Protocols
, vol.4
, Issue.5
, pp. 698-705
-
-
Cox, J.1
Matic, I.2
Hilger, M.3
Nagaraj, N.4
Selbach, M.5
Olsen, J.V.6
-
19
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig, R., Beavis, R.C., TANDEM: Matching proteins with tandem mass spectra. Bioinformatics (Oxford, England) 20:9 (2004), 1466–1467, 10.1093/bioinformatics/bth092.
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
, Issue.9
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
20
-
-
84896690037
-
Finding the missing honey bee genes: Lessons learned from a genome upgrade
-
Elsik, C.G., Worley, K.C., Bennett, A.K., Beye, M., Camara, F., Childers, C.P., et al. Finding the missing honey bee genes: Lessons learned from a genome upgrade. BMC Genomics, 15(1), 2014, 1.
-
(2014)
BMC Genomics
, vol.15
, Issue.1
, pp. 1
-
-
Elsik, C.G.1
Worley, K.C.2
Bennett, A.K.3
Beye, M.4
Camara, F.5
Childers, C.P.6
-
21
-
-
84872371907
-
Comet: An open-source MS/MS sequence database search tool
-
Eng, J.K., Jahan, T.A., Hoopmann, M.R., Comet: An open-source MS/MS sequence database search tool. Proteomics 13:1 (2013), 22–24.
-
(2013)
Proteomics
, vol.13
, Issue.1
, pp. 22-24
-
-
Eng, J.K.1
Jahan, T.A.2
Hoopmann, M.R.3
-
22
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.K., McCormack, A.L., Yates, J.R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5:11 (1994), 976–989.
-
(1994)
Journal of the American Society for Mass Spectrometry
, vol.5
, Issue.11
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
23
-
-
84893276590
-
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
-
Fagerberg, L., Hallstrom, B.M., Oksvold, P., Kampf, C., Djureinovic, D., Odeberg, J., et al. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular & Cellular Proteomics 13:2 (2014), 397–406, 10.1074/mcp.M113.035600.
-
(2014)
Molecular & Cellular Proteomics
, vol.13
, Issue.2
, pp. 397-406
-
-
Fagerberg, L.1
Hallstrom, B.M.2
Oksvold, P.3
Kampf, C.4
Djureinovic, D.5
Odeberg, J.6
-
24
-
-
13844319908
-
PepNovo: De novo peptide sequencing via probabilistic network modeling
-
Frank, A., Pevzner, P., PepNovo: De novo peptide sequencing via probabilistic network modeling. Analytical Chemistry 77:4 (2005), 964–973.
-
(2005)
Analytical Chemistry
, vol.77
, Issue.4
, pp. 964-973
-
-
Frank, A.1
Pevzner, P.2
-
25
-
-
84913534612
-
ProteoAnnotator–open source proteogenomics annotation software supporting PSI standards
-
Ghali, F., Krishna, R., Perkins, S., Collins, A., Xia, D., Wastling, J., et al. ProteoAnnotator–open source proteogenomics annotation software supporting PSI standards. Proteomics 14:23-24 (2014), 2731–2741.
-
(2014)
Proteomics
, vol.14
, Issue.23-24
, pp. 2731-2741
-
-
Ghali, F.1
Krishna, R.2
Perkins, S.3
Collins, A.4
Xia, D.5
Wastling, J.6
-
26
-
-
84870596055
-
Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques
-
Goodswen, S.J., Kennedy, P.J., Ellis, J.T., Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PloS One, 7(11), 2012, e50609.
-
(2012)
PloS One
, vol.7
, Issue.11
, pp. e50609
-
-
Goodswen, S.J.1
Kennedy, P.J.2
Ellis, J.T.3
-
27
-
-
26844526643
-
AUDENS: A tool for automated peptide de novo sequencing
-
Grossmann, J., Roos, F.F., Cieliebak, M., Lipták, Z., Mathis, L.K., Müller, M., et al. AUDENS: A tool for automated peptide de novo sequencing. Journal of Proteome Research 4:5 (2005), 1768–1774.
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.5
, pp. 1768-1774
-
-
Grossmann, J.1
Roos, F.F.2
Cieliebak, M.3
Lipták, Z.4
Mathis, L.K.5
Müller, M.6
-
28
-
-
35448952134
-
Exon size distribution and the origin of introns
-
Gudlaugsdottir, S., Boswell, D.R., Wood, G.R., Ma, J., Exon size distribution and the origin of introns. Genetica 131:3 (2007), 299–306.
-
(2007)
Genetica
, vol.131
, Issue.3
, pp. 299-306
-
-
Gudlaugsdottir, S.1
Boswell, D.R.2
Wood, G.R.3
Ma, J.4
-
29
-
-
70349912263
-
False discovery rates of protein identifications: A strike against the two-peptide rule
-
Gupta, N., Pevzner, P.A., False discovery rates of protein identifications: A strike against the two-peptide rule. Journal of Proteome Research 8:9 (2009), 4173–4181.
-
(2009)
Journal of Proteome Research
, vol.8
, Issue.9
, pp. 4173-4181
-
-
Gupta, N.1
Pevzner, P.A.2
-
30
-
-
84958093420
-
Tissue restricted splice junctions originate not only from tissue-specific gene loci, but gene loci with a broad pattern of expression
-
Hestand, M.S., Zeng, Z., Coleman, S.J., Liu, J., MacLeod, J.N., Tissue restricted splice junctions originate not only from tissue-specific gene loci, but gene loci with a broad pattern of expression. PloS One, 10(12), 2015, e0144302, 10.1371/journal.pone.0144302.
-
(2015)
PloS One
, vol.10
, Issue.12
, pp. e0144302
-
-
Hestand, M.S.1
Zeng, Z.2
Coleman, S.J.3
Liu, J.4
MacLeod, J.N.5
-
31
-
-
84926334587
-
A cost-effective RNA sequencing protocol for large-scale gene expression studies
-
Hou, Z., Jiang, P., Swanson, S.A., Elwell, A.L., Nguyen, B.K.S., Bolin, J.M., et al. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Scientific Reports, 5, 2015, 10.1038/srep09570.
-
(2015)
Scientific Reports
, vol.5
-
-
Hou, Z.1
Jiang, P.2
Swanson, S.A.3
Elwell, A.L.4
Nguyen, B.K.S.5
Bolin, J.M.6
-
32
-
-
84925027070
-
LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification
-
Huesgen, P.F., Lange, P.F., Rogers, L.D., Solis, N., Eckhard, U., Kleifeld, O., et al. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nature Methods 12:1 (2015), 55–58.
-
(2015)
Nature Methods
, vol.12
, Issue.1
, pp. 55-58
-
-
Huesgen, P.F.1
Lange, P.F.2
Rogers, L.D.3
Solis, N.4
Eckhard, U.5
Kleifeld, O.6
-
33
-
-
84915751047
-
Flexible and accessible workflows for improved proteogenomic analysis using the galaxy framework
-
Jagtap, P.D., Johnson, J.E., Onsongo, G., Sadler, F.W., Murray, K., Wang, Y., et al. Flexible and accessible workflows for improved proteogenomic analysis using the galaxy framework. Journal of Proteome Research 13:12 (2014), 5898–5908.
-
(2014)
Journal of Proteome Research
, vol.13
, Issue.12
, pp. 5898-5908
-
-
Jagtap, P.D.1
Johnson, J.E.2
Onsongo, G.3
Sadler, F.W.4
Murray, K.5
Wang, Y.6
-
34
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., et al. InterProScan 5: Genome-scale protein function classification. Bioinformatics (Oxford, England) 30:9 (2014), 1236–1240, 10.1093/bioinformatics/btu031.
-
(2014)
Bioinformatics (Oxford, England)
, vol.30
, Issue.9
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
-
35
-
-
84936763159
-
Social evolution: Genomic signatures of evolutionary transitions from solitary to group living
-
Kapheim, K.M., Pan, H., Li, C., Salzberg, S.L., Puiu, D., Magoc, T., et al. Social evolution: Genomic signatures of evolutionary transitions from solitary to group living. Science 348:6239 (2015), 1139–1143, 10.1126/science.aaa4788.
-
(2015)
Science
, vol.348
, Issue.6239
, pp. 1139-1143
-
-
Kapheim, K.M.1
Pan, H.2
Li, C.3
Salzberg, S.L.4
Puiu, D.5
Magoc, T.6
-
36
-
-
67650064592
-
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
-
Keightley, P.D., Trivedi, U., Thomson, M., Oliver, F., Kumar, S., Blaxter, M.L., Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Research 19:7 (2009), 1195–1201, 10.1101/gr.091231.109.
-
(2009)
Genome Research
, vol.19
, Issue.7
, pp. 1195-1201
-
-
Keightley, P.D.1
Trivedi, U.2
Thomson, M.3
Oliver, F.4
Kumar, S.5
Blaxter, M.L.6
-
37
-
-
84947217723
-
NextSearch: A search engine for mass spectrometry data against a compact nucleotide exon graph
-
Kim, H., Park, H., Paek, E., NextSearch: A search engine for mass spectrometry data against a compact nucleotide exon graph. Journal of Proteome Research 14:7 (2015), 2784–2791.
-
(2015)
Journal of Proteome Research
, vol.14
, Issue.7
, pp. 2784-2791
-
-
Kim, H.1
Park, H.2
Paek, E.3
-
38
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., et al. A draft map of the human proteome. Nature 509:7502 (2014), 575–581.
-
(2014)
Nature
, vol.509
, Issue.7502
, pp. 575-581
-
-
Kim, M.1
Pinto, S.M.2
Getnet, D.3
Nirujogi, R.S.4
Manda, S.S.5
Chaerkady, R.6
-
39
-
-
84953258062
-
SpectroGene: A tool for proteogenomic annotations using top-down spectra
-
Kolmogorov, M., Liu, X., Pevzner, P.A., SpectroGene: A tool for proteogenomic annotations using top-down spectra. Journal of Proteome Research 15:1 (2015), 144–151.
-
(2015)
Journal of Proteome Research
, vol.15
, Issue.1
, pp. 144-151
-
-
Kolmogorov, M.1
Liu, X.2
Pevzner, P.A.3
-
40
-
-
2942544417
-
Gene finding in novel genomes
-
Korf, I., Gene finding in novel genomes. BMC Bioinformatics, 5(1), 2004, 1.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 1
-
-
Korf, I.1
-
41
-
-
84941129045
-
PPLine: An automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics
-
Krasnov, G.S., Dmitriev, A.A., Kudryavtseva, A.V., Shargunov, A.V., Karpov, D.S., Uroshlev, L.A., et al. PPLine: An automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics. Journal of Proteome Research 14:9 (2015), 3729–3737.
-
(2015)
Journal of Proteome Research
, vol.14
, Issue.9
, pp. 3729-3737
-
-
Krasnov, G.S.1
Dmitriev, A.A.2
Kudryavtseva, A.V.3
Shargunov, A.V.4
Karpov, D.S.5
Uroshlev, L.A.6
-
42
-
-
84887111113
-
Deep coverage of the escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments
-
Krug, K., Carpy, A., Behrends, G., Matic, K., Soares, N.C., Macek, B., Deep coverage of the escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments. Molecular & Cellular Proteomics 12:11 (2013), 3420–3430, 10.1074/mcp.M113.029165.
-
(2013)
Molecular & Cellular Proteomics
, vol.12
, Issue.11
, pp. 3420-3430
-
-
Krug, K.1
Carpy, A.2
Behrends, G.3
Matic, K.4
Soares, N.C.5
Macek, B.6
-
43
-
-
0035851192
-
Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase
-
Law, G.L., Raney, A., Heusner, C., Morris, D.R., Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase. Journal of Biological Chemistry 276:41 (2001), 38036–38043.
-
(2001)
Journal of Biological Chemistry
, vol.276
, Issue.41
, pp. 38036-38043
-
-
Law, G.L.1
Raney, A.2
Heusner, C.3
Morris, D.R.4
-
44
-
-
80055116048
-
RNA-seq improves annotation of protein-coding genes in the cucumber genome
-
Li, Z., Zhang, Z., Yan, P., Huang, S., Fei, Z., Lin, K., RNA-seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 12(1), 2011, 1.
-
(2011)
BMC Genomics
, vol.12
, Issue.1
, pp. 1
-
-
Li, Z.1
Zhang, Z.2
Yan, P.3
Huang, S.4
Fei, Z.5
Lin, K.6
-
45
-
-
84952937024
-
A call for biological data mining approaches in epidemiology
-
Lynch, S.M., Moore, J.H., A call for biological data mining approaches in epidemiology. BioData Mining, 9(1), 2016, 1.
-
(2016)
BioData Mining
, vol.9
, Issue.1
, pp. 1
-
-
Lynch, S.M.1
Moore, J.H.2
-
46
-
-
0141989734
-
PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry
-
Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty-Kirby, A., et al. PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Communications in Mass Spectrometry 17:20 (2003), 2337–2342.
-
(2003)
Rapid Communications in Mass Spectrometry
, vol.17
, Issue.20
, pp. 2337-2342
-
-
Ma, B.1
Zhang, K.2
Hendrie, C.3
Liang, C.4
Li, M.5
Doherty-Kirby, A.6
-
47
-
-
84957631938
-
Toward an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics
-
McAfee, A., Harpur, B.A., Michaud, S., Beavis, R., Kent, C.F., Zayed, A., et al. Toward an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics. Journal of Proteome Research 15:2 (2016), 411–421.
-
(2016)
Journal of Proteome Research
, vol.15
, Issue.2
, pp. 411-421
-
-
McAfee, A.1
Harpur, B.A.2
Michaud, S.3
Beavis, R.4
Kent, C.F.5
Zayed, A.6
-
48
-
-
45549108577
-
Cross-kingdom patterns of alternative splicing and splice recognition
-
McGuire, A.M., Pearson, M.D., Neafsey, D.E., Galagan, J.E., Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biology, 9(3), 2008, R50.
-
(2008)
Genome Biology
, vol.9
, Issue.3
, pp. R50
-
-
McGuire, A.M.1
Pearson, M.D.2
Neafsey, D.E.3
Galagan, J.E.4
-
49
-
-
53549100731
-
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
-
Merrihew, G.E., Davis, C., Ewing, B., Williams, G., Kall, L., Frewen, B.E., et al. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Research 18:10 (2008), 1660–1669, 10.1101/gr.077644.108.
-
(2008)
Genome Research
, vol.18
, Issue.10
, pp. 1660-1669
-
-
Merrihew, G.E.1
Davis, C.2
Ewing, B.3
Williams, G.4
Kall, L.5
Frewen, B.E.6
-
50
-
-
84942570636
-
A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases
-
Miller, N.A., Farrow, E.G., Gibson, M., Willig, L.K., Twist, G., Yoo, B., et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine, 7(100), 2015, 10.1038/srep09570.
-
(2015)
Genome Medicine
, vol.7
, Issue.100
-
-
Miller, N.A.1
Farrow, E.G.2
Gibson, M.3
Willig, L.K.4
Twist, G.5
Yoo, B.6
-
51
-
-
84929657446
-
PGTools: A software suite for proteogenomic data analysis and visualization
-
Nagaraj, S.H., Waddell, N., Madugundu, A.K., Wood, S., Jones, A., Mandyam, R.A., et al. PGTools: A software suite for proteogenomic data analysis and visualization. Journal of Proteome Research 14:5 (2015), 2255–2266.
-
(2015)
Journal of Proteome Research
, vol.14
, Issue.5
, pp. 2255-2266
-
-
Nagaraj, S.H.1
Waddell, N.2
Madugundu, A.K.3
Wood, S.4
Jones, A.5
Mandyam, R.A.6
-
52
-
-
84908540871
-
Proteogenomics: Concepts, applications and computational strategies
-
Nesvizhskii, A.I., Proteogenomics: Concepts, applications and computational strategies. Nature Methods 11:11 (2014), 1114–1125.
-
(2014)
Nature Methods
, vol.11
, Issue.11
, pp. 1114-1125
-
-
Nesvizhskii, A.I.1
-
53
-
-
78751570979
-
RNA sequencing: Advances, challenges and opportunities
-
Ozsolak, F., Milos, P.M., RNA sequencing: Advances, challenges and opportunities. Nature Reviews. Genetics 12:2 (2011), 87–98.
-
(2011)
Nature Reviews. Genetics
, vol.12
, Issue.2
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
54
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D.N., Pappin, D.J., Creasy, D.M., Cottrell, J.S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:18 (1999), 3551–3567, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2.
-
(1999)
Electrophoresis
, vol.20
, Issue.18
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
55
-
-
84879330970
-
Peppy: Proteogenomic search software
-
Risk, B.A., Spitzer, W.J., Giddings, M.C., Peppy: Proteogenomic search software. Journal of Proteome Research 12:6 (2013), 3019–3025.
-
(2013)
Journal of Proteome Research
, vol.12
, Issue.6
, pp. 3019-3025
-
-
Risk, B.A.1
Spitzer, W.J.2
Giddings, M.C.3
-
56
-
-
34447646955
-
Manual superscaffolding of honey bee (Apis mellifera) chromosomes 12-16: Implications for the draft genome assembly version 4, gene annotation, and chromosome structure
-
Robertson, H.M., Reese, J.T., Milshina, N.V., Agarwala, R., Solignac, M., Walden, K.K., et al. Manual superscaffolding of honey bee (Apis mellifera) chromosomes 12-16: Implications for the draft genome assembly version 4, gene annotation, and chromosome structure. Insect Molecular Biology 16:4 (2007), 401–410.
-
(2007)
Insect Molecular Biology
, vol.16
, Issue.4
, pp. 401-410
-
-
Robertson, H.M.1
Reese, J.T.2
Milshina, N.V.3
Agarwala, R.4
Solignac, M.5
Walden, K.K.6
-
57
-
-
34249807325
-
A mass spectrometry-friendly database for cSNP identification
-
Schandorff, S., Olsen, J.V., Bunkenborg, J., Blagoev, B., Zhang, Y., Andersen, J.S., et al. A mass spectrometry-friendly database for cSNP identification. Nature Methods 4:6 (2007), 465–466.
-
(2007)
Nature Methods
, vol.4
, Issue.6
, pp. 465-466
-
-
Schandorff, S.1
Olsen, J.V.2
Bunkenborg, J.3
Blagoev, B.4
Zhang, Y.5
Andersen, J.S.6
-
58
-
-
84903477229
-
Translation of small open reading frames within unannotated RNA transcripts in saccharomyces cerevisiae
-
Smith, J.E., Alvarez-Dominguez, J.R., Kline, N., Huynh, N.J., Geisler, S., Hu, W., et al. Translation of small open reading frames within unannotated RNA transcripts in saccharomyces cerevisiae. Cell Reports 7:6 (2014), 1858–1866.
-
(2014)
Cell Reports
, vol.7
, Issue.6
, pp. 1858-1866
-
-
Smith, J.E.1
Alvarez-Dominguez, J.R.2
Kline, N.3
Huynh, N.J.4
Geisler, S.5
Hu, W.6
-
59
-
-
84873801934
-
High-throughput sequencing for biology and medicine
-
Soon, W.W., Hariharan, M., Snyder, M.P., High-throughput sequencing for biology and medicine. Molecular Systems Biology, 9(1), 2013, 640, 10.1038/msb.2012.61.
-
(2013)
Molecular Systems Biology
, vol.9
, Issue.1
, pp. 640
-
-
Soon, W.W.1
Hariharan, M.2
Snyder, M.P.3
-
60
-
-
84888871954
-
Assessment of transcript reconstruction methods for RNA-seq
-
Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., Hubbard, T.J., Guigó, R., et al. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods 10:12 (2013), 1177–1184.
-
(2013)
Nature Methods
, vol.10
, Issue.12
, pp. 1177-1184
-
-
Steijger, T.1
Abril, J.F.2
Engström, P.G.3
Kokocinski, F.4
Hubbard, T.J.5
Guigó, R.6
-
61
-
-
33846884410
-
Improving gene annotation using peptide mass spectrometry
-
Tanner, S., Shen, Z., Ng, J., Florea, L., Guigo, R., Briggs, S.P., et al. Improving gene annotation using peptide mass spectrometry. Genome Research 17:2 (2007), 231–239, 10.1101/gr.5646507.
-
(2007)
Genome Research
, vol.17
, Issue.2
, pp. 231-239
-
-
Tanner, S.1
Shen, Z.2
Ng, J.3
Florea, L.4
Guigo, R.5
Briggs, S.P.6
-
62
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks
-
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nature Protocols 7:3 (2012), 562–578.
-
(2012)
Nature Protocols
, vol.7
, Issue.3
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
-
63
-
-
0035895505
-
The sequence of the human genome
-
Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., et al. The sequence of the human genome. Science (New York, N.Y.) 291:5507 (2001), 1304–1351, 10.1126/science.1058040.
-
(2001)
Science (New York, N.Y.)
, vol.291
, Issue.5507
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
-
64
-
-
77955876447
-
Mass spectrometry-based proteomics in cell biology
-
Walther, T.C., Mann, M., Mass spectrometry-based proteomics in cell biology. The Journal of Cell Biology 190:4 (2010), 491–500, 10.1083/jcb.201004052.
-
(2010)
The Journal of Cell Biology
, vol.190
, Issue.4
, pp. 491-500
-
-
Walther, T.C.1
Mann, M.2
-
65
-
-
84904215863
-
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: How much do we miss?
-
Ward, N., Moreno-Hagelsieb, G., Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: How much do we miss?. PloS One, 9(7), 2014, e101850.
-
(2014)
PloS One
, vol.9
, Issue.7
, pp. e101850
-
-
Ward, N.1
Moreno-Hagelsieb, G.2
-
66
-
-
33750460281
-
Insights into social insects from the genome of the honeybee Apis mellifera
-
Weinstock, G.M., Robinson, G.E., Gibbs, R.A., Worley, K.C., Evans, J.D., Maleszka, R., et al. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:7114 (2006), 931–949.
-
(2006)
Nature
, vol.443
, Issue.7114
, pp. 931-949
-
-
Weinstock, G.M.1
Robinson, G.E.2
Gibbs, R.A.3
Worley, K.C.4
Evans, J.D.5
Maleszka, R.6
-
67
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A.M., Lieberenz, M., Savitski, M.M., et al. Mass-spectrometry-based draft of the human proteome. Nature 509:7502 (2014), 582–587.
-
(2014)
Nature
, vol.509
, Issue.7502
, pp. 582-587
-
-
Wilhelm, M.1
Schlegl, J.2
Hahne, H.3
Gholami, A.M.4
Lieberenz, M.5
Savitski, M.M.6
-
68
-
-
84900918962
-
Gene annotation methods
-
Springer New York
-
Wilming, L., Harrow, J., Gene annotation methods. Bioinformatics, 2009, Springer, New York, 121–136.
-
(2009)
Bioinformatics
, pp. 121-136
-
-
Wilming, L.1
Harrow, J.2
-
69
-
-
84891801883
-
Proteogenomic database construction driven from large scale RNA-seq data
-
Woo, S., Cha, S.W., Merrihew, G., He, Y., Castellana, N., Guest, C., et al. Proteogenomic database construction driven from large scale RNA-seq data. Journal of Proteome Research 13:1 (2013), 21–28.
-
(2013)
Journal of Proteome Research
, vol.13
, Issue.1
, pp. 21-28
-
-
Woo, S.1
Cha, S.W.2
Merrihew, G.3
He, Y.4
Castellana, N.5
Guest, C.6
-
70
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell, M., Ence, D., A beginner's guide to eukaryotic genome annotation. Nature Reviews. Genetics 13:5 (2012), 329–342, 10.1038/nrg3174.
-
(2012)
Nature Reviews. Genetics
, vol.13
, Issue.5
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
71
-
-
0029645432
-
Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
-
Yates, J.R. III, Eng, J.K., McCormack, A.L., Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Analytical Chemistry 67:18 (1995), 3202–3210.
-
(1995)
Analytical Chemistry
, vol.67
, Issue.18
, pp. 3202-3210
-
-
Yates, J.R.1
Eng, J.K.2
McCormack, A.L.3
-
72
-
-
84876148755
-
Protein analysis by shotgun/bottom-up proteomics
-
Zhang, Y., Fonslow, B.R., Shan, B., Baek, M., Yates, J.R. III, Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews 113:4 (2013), 2343–2394.
-
(2013)
Chemical Reviews
, vol.113
, Issue.4
, pp. 2343-2394
-
-
Zhang, Y.1
Fonslow, B.R.2
Shan, B.3
Baek, M.4
Yates, J.R.5
-
73
-
-
84928752639
-
IPred—Integrating ab initio and evidence based gene predictions to improve prediction accuracy
-
Zickmann, F., Renard, B.Y., IPred—Integrating ab initio and evidence based gene predictions to improve prediction accuracy. BMC Genomics, 16(1), 2015, 1.
-
(2015)
BMC Genomics
, vol.16
, Issue.1
, pp. 1
-
-
Zickmann, F.1
Renard, B.Y.2
|