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Items: 1 to 50 of 58

1.

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms.

Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F.

Nucleic Acids Res. 2018 Nov 16. doi: 10.1093/nar/gky1159. [Epub ahead of print]

PMID:
30445427
2.

iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.

Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N.

G3 (Bethesda). 2018 Nov 5. pii: g3.200637.2018. doi: 10.1534/g3.118.200637. [Epub ahead of print]

3.

Kras mutant genetically engineered mouse models of human cancers are genomically heterogeneous.

Chung WJ, Daemen A, Cheng JH, Long JE, Cooper JE, Wang BE, Tran C, Singh M, Gnad F, Modrusan Z, Foreman O, Junttila MR.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10947-E10955. doi: 10.1073/pnas.1708391114. Epub 2017 Dec 4.

4.

USP7 small-molecule inhibitors interfere with ubiquitin binding.

Kategaya L, Di Lello P, Rougé L, Pastor R, Clark KR, Drummond J, Kleinheinz T, Lin E, Upton JP, Prakash S, Heideker J, McCleland M, Ritorto MS, Alessi DR, Trost M, Bainbridge TW, Kwok MCM, Ma TP, Stiffler Z, Brasher B, Tang Y, Jaishankar P, Hearn BR, Renslo AR, Arkin MR, Cohen F, Yu K, Peale F, Gnad F, Chang MT, Klijn C, Blackwood E, Martin SE, Forrest WF, Ernst JA, Ndubaku C, Wang X, Beresini MH, Tsui V, Schwerdtfeger C, Blake RA, Murray J, Maurer T, Wertz IE.

Nature. 2017 Oct 26;550(7677):534-538. doi: 10.1038/nature24006. Epub 2017 Oct 18.

PMID:
29045385
5.

Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle.

Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G.

J Biol Chem. 2017 Sep 1;292(35):14311-14324. doi: 10.1074/jbc.M117.792754. Epub 2017 Jun 27.

6.

Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers.

Goldstein LD, Lee J, Gnad F, Klijn C, Schaub A, Reeder J, Daemen A, Bakalarski CE, Holcomb T, Shames DS, Hartmaier RJ, Chmielecki J, Seshagiri S, Gentleman R, Stokoe D.

Cell Rep. 2016 Sep 6;16(10):2605-2617. doi: 10.1016/j.celrep.2016.08.010. Epub 2016 Aug 25.

7.

Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.

Estrada J, Andrew N, Gibson D, Chang F, Gnad F, Gunawardena J.

PLoS Comput Biol. 2016 Jul 1;12(7):e1004995. doi: 10.1371/journal.pcbi.1004995. eCollection 2016 Jul.

8.

Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network.

Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M.

Proteomics. 2016 Jul;16(14):1992-7. doi: 10.1002/pmic.201600118. Epub 2016 Jul 8.

PMID:
27282143
9.

Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms.

Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M.

Proteomics. 2016 Jul;16(14):1998-2004. doi: 10.1002/pmic.201600119.

PMID:
27273156
10.

Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death.

Anania VG, Yu K, Gnad F, Pferdehirt RR, Li H, Ma TP, Jeon D, Fortelny N, Forrest W, Ashkenazi A, Overall CM, Lill JR.

Mol Cell Proteomics. 2016 Jul;15(7):2293-307. doi: 10.1074/mcp.M115.055376. Epub 2016 Apr 28.

11.

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.

Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S.

Nat Genet. 2016 Apr;48(4):407-16. doi: 10.1038/ng.3520. Epub 2016 Feb 29.

PMID:
26928227
12.

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer.

McCleland ML, Mesh K, Lorenzana E, Chopra VS, Segal E, Watanabe C, Haley B, Mayba O, Yaylaoglu M, Gnad F, Firestein R.

J Clin Invest. 2016 Feb;126(2):639-52. doi: 10.1172/JCI83265. Epub 2016 Jan 11.

13.

Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer.

Gnad F, Doll S, Manning G, Arnott D, Zhang Z.

BMC Genomics. 2015;16 Suppl 8:S5. doi: 10.1186/1471-2164-16-S8-S5. Epub 2015 Jun 18.

14.

A comprehensive transcriptional portrait of human cancer cell lines.

Klijn C, Durinck S, Stawiski EW, Haverty PM, Jiang Z, Liu H, Degenhardt J, Mayba O, Gnad F, Liu J, Pau G, Reeder J, Cao Y, Mukhyala K, Selvaraj SK, Yu M, Zynda GJ, Brauer MJ, Wu TD, Gentleman RC, Manning G, Yauch RL, Bourgon R, Stokoe D, Modrusan Z, Neve RM, de Sauvage FJ, Settleman J, Seshagiri S, Zhang Z.

Nat Biotechnol. 2015 Mar;33(3):306-12. doi: 10.1038/nbt.3080. Epub 2014 Dec 8.

PMID:
25485619
15.

Diverse modes of genomic alteration in hepatocellular carcinoma.

Jhunjhunwala S, Jiang Z, Stawiski EW, Gnad F, Liu J, Mayba O, Du P, Diao J, Johnson S, Wong KF, Gao Z, Li Y, Wu TD, Kapadia SB, Modrusan Z, French DM, Luk JM, Seshagiri S, Zhang Z.

Genome Biol. 2014 Aug 26;15(8):436. doi: 10.1186/s13059-014-0436-9.

16.

PAK1 mediates pancreatic cancer cell migration and resistance to MET inhibition.

Zhou W, Jubb AM, Lyle K, Xiao Q, Ong CC, Desai R, Fu L, Gnad F, Song Q, Haverty PM, Aust D, Grützmann R, Romero M, Totpal K, Neve RM, Yan Y, Forrest WF, Wang Y, Raja R, Pilarsky C, de Jesus-Acosta A, Belvin M, Friedman LS, Merchant M, Jaffee EM, Zheng L, Koeppen H, Hoeflich KP.

J Pathol. 2014 Dec;234(4):502-13. doi: 10.1002/path.4412. Epub 2014 Oct 6.

17.

Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer.

Liu J, McCleland M, Stawiski EW, Gnad F, Mayba O, Haverty PM, Durinck S, Chen YJ, Klijn C, Jhunjhunwala S, Lawrence M, Liu H, Wan Y, Chopra V, Yaylaoglu MB, Yuan W, Ha C, Gilbert HN, Reeder J, Pau G, Stinson J, Stern HM, Manning G, Wu TD, Neve RM, de Sauvage FJ, Modrusan Z, Seshagiri S, Firestein R, Zhang Z.

Nat Commun. 2014 May 8;5:3830. doi: 10.1038/ncomms4830.

18.

Integrative analysis of two cell lines derived from a non-small-lung cancer patient--a panomics approach.

Mayba O, Gnad F, Peyton M, Zhang F, Walter K, Du P, Huntley MA, Jiang Z, Liu J, Haverty PM, Gentleman RC, Li R, Minna JD, Li Y, Shames DS, Zhang Z.

Pac Symp Biocomput. 2014:75-86.

19.

Assessment of computational methods for predicting the effects of missense mutations in human cancers.

Gnad F, Baucom A, Mukhyala K, Manning G, Zhang Z.

BMC Genomics. 2013;14 Suppl 3:S7. doi: 10.1186/1471-2164-14-S3-S7. Epub 2013 May 28.

20.

Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics.

Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich KP.

Mol Cell Proteomics. 2013 Aug;12(8):2070-80. doi: 10.1074/mcp.M112.027052. Epub 2013 Apr 22.

21.

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events.

Liu J, Lee W, Jiang Z, Chen Z, Jhunjhunwala S, Haverty PM, Gnad F, Guan Y, Gilbert HN, Stinson J, Klijn C, Guillory J, Bhatt D, Vartanian S, Walter K, Chan J, Holcomb T, Dijkgraaf P, Johnson S, Koeman J, Minna JD, Gazdar AF, Stern HM, Hoeflich KP, Wu TD, Settleman J, de Sauvage FJ, Gentleman RC, Neve RM, Stokoe D, Modrusan Z, Seshagiri S, Shames DS, Zhang Z.

Genome Res. 2012 Dec;22(12):2315-27. doi: 10.1101/gr.140988.112. Epub 2012 Oct 2.

22.

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma.

Wiśniewski JR, Ostasiewicz P, Duś K, Zielińska DF, Gnad F, Mann M.

Mol Syst Biol. 2012;8:611. doi: 10.1038/msb.2012.44.

23.

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer.

Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S.

Nat Genet. 2012 Oct;44(10):1111-6. doi: 10.1038/ng.2405. Epub 2012 Sep 2.

24.

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models.

Borchert N, Krug K, Gnad F, Sinha A, Sommer RJ, Macek B.

Mol Cell Proteomics. 2012 Dec;11(12):1631-9. doi: 10.1074/mcp.M112.022103. Epub 2012 Aug 25.

25.

Recurrent R-spondin fusions in colon cancer.

Seshagiri S, Stawiski EW, Durinck S, Modrusan Z, Storm EE, Conboy CB, Chaudhuri S, Guan Y, Janakiraman V, Jaiswal BS, Guillory J, Ha C, Dijkgraaf GJ, Stinson J, Gnad F, Huntley MA, Degenhardt JD, Haverty PM, Bourgon R, Wang W, Koeppen H, Gentleman R, Starr TK, Zhang Z, Largaespada DA, Wu TD, de Sauvage FJ.

Nature. 2012 Aug 30;488(7413):660-4. doi: 10.1038/nature11282.

26.

Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery.

Zielinska DF, Gnad F, Schropp K, Wiśniewski JR, Mann M.

Mol Cell. 2012 May 25;46(4):542-8. doi: 10.1016/j.molcel.2012.04.031.

27.

Proteus: a web-based, context-specific modelling tool for molecular networks.

Gnad F, Estrada J, Gunawardena J.

Bioinformatics. 2012 May 1;28(9):1284-6. doi: 10.1093/bioinformatics/bts126. Epub 2012 Mar 15.

28.

Conditional activation of Pik3ca(H1047R) in a knock-in mouse model promotes mammary tumorigenesis and emergence of mutations.

Yuan W, Stawiski E, Janakiraman V, Chan E, Durinck S, Edgar KA, Kljavin NM, Rivers CS, Gnad F, Roose-Girma M, Haverty PM, Fedorowicz G, Heldens S, Soriano RH, Zhang Z, Wallin JJ, Johnson L, Merchant M, Modrusan Z, Stern HM, Seshagiri S.

Oncogene. 2013 Jan 17;32(3):318-26. doi: 10.1038/onc.2012.53. Epub 2012 Feb 27.

29.

Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover.

Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Krüger M, Mann M.

J Proteome Res. 2011 Dec 2;10(12):5275-84. doi: 10.1021/pr101183k. Epub 2011 Nov 3.

PMID:
22050367
30.

Profiling the Trypanosoma cruzi phosphoproteome.

Marchini FK, de Godoy LM, Rampazzo RC, Pavoni DP, Probst CM, Gnad F, Mann M, Krieger MA.

PLoS One. 2011;6(9):e25381. doi: 10.1371/journal.pone.0025381. Epub 2011 Sep 22.

31.

C2 domain-containing phosphoprotein CDP138 regulates GLUT4 insertion into the plasma membrane.

Xie X, Gong Z, Mansuy-Aubert V, Zhou QL, Tatulian SA, Sehrt D, Gnad F, Brill LM, Motamedchaboki K, Chen Y, Czech MP, Mann M, Krüger M, Jiang ZY.

Cell Metab. 2011 Sep 7;14(3):378-89. doi: 10.1016/j.cmet.2011.06.015.

32.

PHOSIDA 2011: the posttranslational modification database.

Gnad F, Gunawardena J, Mann M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D253-60. doi: 10.1093/nar/gkq1159. Epub 2010 Nov 16.

33.

Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif.

Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC.

Mol Cell. 2010 Aug 27;39(4):641-52. doi: 10.1016/j.molcel.2010.07.026.

34.

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.

Mol Cell Proteomics. 2010 Dec;9(12):2642-53. doi: 10.1074/mcp.M110.001594. Epub 2010 Aug 5.

35.

Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints.

Zielinska DF, Gnad F, Wiśniewski JR, Mann M.

Cell. 2010 May 28;141(5):897-907. doi: 10.1016/j.cell.2010.04.012.

36.

Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis.

Soufi B, Kumar C, Gnad F, Mann M, Mijakovic I, Macek B.

J Proteome Res. 2010 Jul 2;9(7):3638-46. doi: 10.1021/pr100150w.

PMID:
20509597
37.

Predicting post-translational lysine acetylation using support vector machines.

Gnad F, Ren S, Choudhary C, Cox J, Mann M.

Bioinformatics. 2010 Jul 1;26(13):1666-8. doi: 10.1093/bioinformatics/btq260. Epub 2010 May 26.

38.

Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology.

Wiśniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M.

J Proteome Res. 2010 Jun 4;9(6):3280-9. doi: 10.1021/pr1002214.

PMID:
20415495
39.

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M.

Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.

40.

High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.

Gnad F, de Godoy LM, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M.

Proteomics. 2009 Oct;9(20):4642-52. doi: 10.1002/pmic.200900144.

PMID:
19795423
41.

Lysine acetylation targets protein complexes and co-regulates major cellular functions.

Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.

Science. 2009 Aug 14;325(5942):834-40. doi: 10.1126/science.1175371. Epub 2009 Jul 16.

42.

Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins.

Zielinska DF, Gnad F, Jedrusik-Bode M, Wiśniewski JR, Mann M.

J Proteome Res. 2009 Aug;8(8):4039-49. doi: 10.1021/pr900384k.

PMID:
19530675
43.

Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics.

Hilger M, Bonaldi T, Gnad F, Mann M.

Mol Cell Proteomics. 2009 Aug;8(8):1908-20. doi: 10.1074/mcp.M800559-MCP200. Epub 2009 May 9.

44.

Large-scale proteomics analysis of the human kinome.

Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Kéri G, Mann M, Daub H.

Mol Cell Proteomics. 2009 Jul;8(7):1751-64. doi: 10.1074/mcp.M800588-MCP200. Epub 2009 Apr 15.

45.

Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry.

Zanivan S, Gnad F, Wickström SA, Geiger T, Macek B, Cox J, Fässler R, Mann M.

J Proteome Res. 2008 Dec;7(12):5314-26.

PMID:
19367708
46.

Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life.

Aivaliotis M, Macek B, Gnad F, Reichelt P, Mann M, Oesterhelt D.

PLoS One. 2009;4(3):e4777. doi: 10.1371/journal.pone.0004777. Epub 2009 Mar 10.

47.

MAPU 2.0: high-accuracy proteomes mapped to genomes.

Gnad F, Oroshi M, Birney E, Mann M.

Nucleic Acids Res. 2009 Jan;37(Database issue):D902-6. doi: 10.1093/nar/gkn773. Epub 2008 Oct 23.

48.

Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors.

Pan C, Gnad F, Olsen JV, Mann M.

Proteomics. 2008 Nov;8(21):4534-46. doi: 10.1002/pmic.200800105.

PMID:
18846507
49.

Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.

Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Körner R, Greff Z, Kéri G, Stemmann O, Mann M.

Mol Cell. 2008 Aug 8;31(3):438-48. doi: 10.1016/j.molcel.2008.07.007.

50.

The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins.

Soufi B, Gnad F, Jensen PR, Petranovic D, Mann M, Mijakovic I, Macek B.

Proteomics. 2008 Sep;8(17):3486-93. doi: 10.1002/pmic.200800069.

PMID:
18668697

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