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Items: 1 to 50 of 135

1.

Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal.

Wu P, Heins ZJ, Muller J, Katsnelson L, de Bruijn I, Abeshouse AA, Schultz N, Fenyö D, Gao J.

Mol Cell Proteomics. 2019 Jul 15. pii: mcp.TIR119.001673. doi: 10.1074/mcp.TIR119.001673. [Epub ahead of print]

2.

Extracting Pathway-level Signatures from Proteogenomic Data in Breast Cancer Using Independent Component Analysis.

Liu W, Payne SH, Ma S, Fenyö D.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S169-S182. doi: 10.1074/mcp.TIR119.001442. Epub 2019 Jun 18.

3.

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.

Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyö D, Li S, Liu T, Carr SA, Ding L.

Mol Cell Proteomics. 2019 Aug;18(8):1630-1650. doi: 10.1074/mcp.RA118.001243. Epub 2019 Jun 13.

PMID:
31196969
4.

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.

Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH.

Mob DNA. 2019 Mar 8;10:8. doi: 10.1186/s13100-019-0148-5. eCollection 2019.

5.

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V.

Zhang X, Nguyen KD, Rudnick PA, Roper N, Kawaler E, Maity TK, Awasthi S, Gao S, Biswas R, Venugopalan A, Cultraro CM, Fenyö D, Guha U.

Mol Cell Proteomics. 2019 Apr;18(4):622-641. doi: 10.1074/mcp.RA118.001266. Epub 2019 Jan 7.

PMID:
30617155
6.

Transcription shapes DNA replication initiation and termination in human cells.

Chen YH, Keegan S, Kahli M, Tonzi P, Fenyö D, Huang TT, Smith DJ.

Nat Struct Mol Biol. 2019 Jan;26(1):67-77. doi: 10.1038/s41594-018-0171-0. Epub 2018 Dec 31.

7.

The ULK1-FBXW5-SEC23B nexus controls autophagy.

Jeong YT, Simoneschi D, Keegan S, Melville D, Adler NS, Saraf A, Florens L, Washburn MP, Cavasotto CN, Fenyö D, Cuervo AM, Rossi M, Pagano M.

Elife. 2018 Dec 31;7. pii: e42253. doi: 10.7554/eLife.42253.

8.

Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells.

Hadi T, Boytard L, Silvestro M, Alebrahim D, Jacob S, Feinstein J, Barone K, Spiro W, Hutchison S, Simon R, Rateri D, Pinet F, Fenyo D, Adelman M, Moore KJ, Eltzschig HK, Daugherty A, Ramkhelawon B.

Nat Commun. 2018 Nov 27;9(1):5022. doi: 10.1038/s41467-018-07495-1.

9.

Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks.

Whelan DR, Lee WTC, Yin Y, Ofri DM, Bermudez-Hernandez K, Keegan S, Fenyo D, Rothenberg E.

Nat Commun. 2018 Sep 24;9(1):3882. doi: 10.1038/s41467-018-06435-3.

10.

Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.

Coudray N, Ocampo PS, Sakellaropoulos T, Narula N, Snuderl M, Fenyö D, Moreira AL, Razavian N, Tsirigos A.

Nat Med. 2018 Oct;24(10):1559-1567. doi: 10.1038/s41591-018-0177-5. Epub 2018 Sep 17.

PMID:
30224757
11.

Integrative omics analyses broaden treatment targets in human cancer.

Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F, Ding L.

Genome Med. 2018 Jul 27;10(1):60. doi: 10.1186/s13073-018-0564-z.

12.

Diaphanous 1 (DIAPH1) is Highly Expressed in the Aged Human Medial Temporal Cortex and Upregulated in Myeloid Cells During Alzheimer's Disease.

Derk J, Bermudez Hernandez K, Rodriguez M, He M, Koh H, Abedini A, Li H, Fenyö D, Schmidt AM.

J Alzheimers Dis. 2018;64(3):995-1007. doi: 10.3233/JAD-180088.

13.

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression.

Sun X, Wang X, Tang Z, Grivainis M, Kahler D, Yun C, Mita P, Fenyö D, Boeke JD.

Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5526-E5535. doi: 10.1073/pnas.1722565115. Epub 2018 May 25.

14.

UXT is required for spermatogenesis in mice.

Schafler ED, Thomas PA, Ha S, Wang Y, Bermudez-Hernandez K, Tang Z, Fenyö D, Vigodner M, Logan SK.

PLoS One. 2018 Apr 12;13(4):e0195747. doi: 10.1371/journal.pone.0195747. eCollection 2018.

15.

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors.

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S.

Nat Methods. 2018 May;15(5):330-338. doi: 10.1038/nmeth.4632. Epub 2018 Mar 19.

16.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

17.

Human Memory B Cells Targeting Staphylococcus aureus Exotoxins Are Prevalent with Skin and Soft Tissue Infection.

Pelzek AJ, Shopsin B, Radke EE, Tam K, Ueberheide BM, Fenyö D, Brown SM, Li Q, Rubin A, Fulmer Y, Chiang WK, Hernandez DN, El Bannoudi H, Sause WE, Sommerfield A, Thomsen IP, Miller AO, Torres VJ, Silverman GJ.

MBio. 2018 Mar 13;9(2). pii: e02125-17. doi: 10.1128/mBio.02125-17.

18.

Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers.

Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.

Cancer Res. 2018 May 15;78(10):2732-2746. doi: 10.1158/0008-5472.CAN-17-1990. Epub 2018 Feb 22.

19.

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA.

Genome Biol. 2018 Jan 31;19(1):12. doi: 10.1186/s13059-017-1377-x.

20.

LINE-1 protein localization and functional dynamics during the cell cycle.

Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD.

Elife. 2018 Jan 8;7. pii: e30058. doi: 10.7554/eLife.30058.

21.

Dissection of affinity captured LINE-1 macromolecular complexes.

Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J.

Elife. 2018 Jan 8;7. pii: e30094. doi: 10.7554/eLife.30094.

22.

Large Scale Identification of Variant Proteins in Glioma Stem Cells.

Mostovenko E, Végvári Á, Rezeli M, Lichti CF, Fenyö D, Wang Q, Lang FF, Sulman EP, Sahlin KB, Marko-Varga G, Nilsson CL.

ACS Chem Neurosci. 2018 Jan 17;9(1):73-79. doi: 10.1021/acschemneuro.7b00362. Epub 2017 Dec 21.

23.

A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy.

Bermudez-Hernandez K, Keegan S, Whelan DR, Reid DA, Zagelbaum J, Yin Y, Ma S, Rothenberg E, Fenyö D.

Sci Rep. 2017 Nov 1;7(1):14882. doi: 10.1038/s41598-017-14922-8.

24.

Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data.

Ray B, Liu W, Fenyö D.

Cancer Inform. 2017 Aug 18;16:1176935117725727. doi: 10.1177/1176935117725727. eCollection 2017.

25.

Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner.

Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM.

Sci Signal. 2017 Aug 8;10(491). pii: eaam8065. doi: 10.1126/scisignal.aam8065.

26.

A Systems Biology Approach Identifies FUT8 as a Driver of Melanoma Metastasis.

Agrawal P, Fontanals-Cirera B, Sokolova E, Jacob S, Vaiana CA, Argibay D, Davalos V, McDermott M, Nayak S, Darvishian F, Castillo M, Ueberheide B, Osman I, Fenyö D, Mahal LK, Hernando E.

Cancer Cell. 2017 Jun 12;31(6):804-819.e7. doi: 10.1016/j.ccell.2017.05.007.

27.

Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas.

Snuderl M, Zhang G, Wu P, Jennings TS, Shroff S, Ortenzi V, Jain R, Cohen B, Reidy JJ, Dushay MS, Wisoff JH, Harter DH, Karajannis MA, Fenyo D, Neubert TA, Zagzag D.

Am J Pathol. 2017 Aug;187(8):1867-1878. doi: 10.1016/j.ajpath.2017.04.004. Epub 2017 Jun 9.

28.

GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael BJ, Wendl MC, Ding L.

Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18.

29.

Methods, Tools and Current Perspectives in Proteogenomics.

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR.

Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29. Review.

30.

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Apr 25;8:15479. doi: 10.1038/ncomms15479. No abstract available.

31.

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Mar 28;8:14864. doi: 10.1038/ncomms14864.

32.

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.

Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD.

Science. 2017 Mar 10;355(6329). pii: eaaf4831. doi: 10.1126/science.aaf4831.

PMID:
28280154
33.

A First Step towards a Clinical Decision Support System for Post-traumatic Stress Disorders.

Ma S, Galatzer-Levy IR, Wang X, Fenyö D, Shalev AY.

AMIA Annu Symp Proc. 2017 Feb 10;2016:837-843. eCollection 2016.

34.

Single Molecule Localization Microscopy of DNA Damage Response Pathways in Cancer.

Whelan DR, Yin Y, Bermudez-Hernandez K, Keegan S, Fenyö D, Rothenberg E.

Microsc Microanal. 2016 Jul;22(Suppl 3):1016-1017. doi: 10.1017/S1431927616005924. Epub 2016 Jul 25. No abstract available.

35.

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae.

Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, Bader JS, Boeke JD.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1470-E1479. doi: 10.1073/pnas.1621250114. Epub 2017 Feb 7.

36.

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer.

Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E733-E740. doi: 10.1073/pnas.1619797114. Epub 2017 Jan 17.

37.

Somatic retrotransposition is infrequent in glioblastomas.

Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH.

Mob DNA. 2016 Nov 11;7:22. doi: 10.1186/s13100-016-0077-5. eCollection 2016.

38.

Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2.

Dankert JF, Rona G, Clijsters L, Geter P, Skaar JR, Bermudez-Hernandez K, Sassani E, Fenyö D, Ueberheide B, Schneider R, Pagano M.

Mol Cell. 2016 Nov 3;64(3):507-519. doi: 10.1016/j.molcel.2016.09.010. Epub 2016 Oct 20.

39.

Next Generation Sequencing Data and Proteogenomics.

Ruggles KV, Fenyö D.

Adv Exp Med Biol. 2016;926:11-19. Review.

PMID:
27686803
40.

Breast Cancer Prognostics Using Multi-Omics Data.

Ma S, Ren J, Fenyö D.

AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:52-9. eCollection 2016.

41.

Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP.

Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyo D, Boeke JD.

Biol Proced Online. 2016 Aug 15;18:16. doi: 10.1186/s12575-016-0046-x. eCollection 2016.

42.

OpenSlice: Quantitative data sharing from HyperPeaks to global ion chromatograms (GICs).

Askenazi M, Fenyö D.

Proteomics. 2016 Sep;16(18):2495-501. doi: 10.1002/pmic.201600096.

PMID:
27436706
43.

HIV-host interactome revealed directly from infected cells.

Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA.

Nat Microbiol. 2016 Jul;1(7):16068. Epub 2016 May 23.

44.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.

45.

Proteogenomics connects somatic mutations to signalling in breast cancer.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.

Nature. 2016 Jun 2;534(7605):55-62. doi: 10.1038/nature18003. Epub 2016 May 25.

46.

A Complex Systems Approach to Causal Discovery in Psychiatry.

Saxe GN, Statnikov A, Fenyo D, Ren J, Li Z, Prasad M, Wall D, Bergman N, Briggs EC, Aliferis C.

PLoS One. 2016 Mar 30;11(3):e0151174. doi: 10.1371/journal.pone.0151174. eCollection 2016.

47.

Erratum: Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc.

Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng-Xia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Delmar M.

Nat Commun. 2016 Feb 22;7:10919. doi: 10.1038/ncomms10919. No abstract available.

48.

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG.

Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13.

49.

g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.

Keegan S, Cortens JP, Beavis RC, Fenyö D.

J Proteome Res. 2016 Mar 4;15(3):983-90. doi: 10.1021/acs.jproteome.5b01018. Epub 2016 Feb 18.

PMID:
26842767
50.

Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc.

Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng-Xia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Rothenberg E, Delmar M.

Nat Commun. 2016 Jan 20;7:10342. doi: 10.1038/ncomms10342. Erratum in: Nat Commun. 2016;7:10919. Rothenberg, Eli [Added].

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