Laboratory of Computational Proteomics
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Center for Health Informatics and Bioinformatics
 
High Performance Computing Facility
NYU Langone Medical Center
NIH
NCI
NIGMS
NIST

2017

  • Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D*, Zhang B*, Mani DR*: "Methods, tools and current perspectives in proteogenomics", Mol Cell Proteomics. 2017

  • 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: "Proteogenomic integration reveals therapeutic targets in breast cancer xenografts", Nat Commun. 8 (2017) 14864.

  • 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: "Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond", Science 355 (2017) 6329.

  • 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, Fenyö D, Bader JS, Boeke JD: "Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae", Proc Natl Acad Sci U S A. 2017 Feb 7. pii: 201621250.

  • Tang Z, Steranka JP, Ma S, Grivainis M, Rodic N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH: "Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer", Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201619797.

  • 2016

  • Achanta P, Steranka JP, Tang Z, Rodic N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CR, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH: "Somatic retrotransposition is infrequent in glioblastomas", Mob DNA. 2016.

  • Dankert JF, Rona G, Geter P, Clijsters L, Skaar JR, Bermudez-Hernandez K, Fenyö D, Ueberheide B, Schneider R, Pagano M: "Cyclin F-mediated degradation of SLBP limits H2A.X accumulation and apoptosis upon genotoxic stress in G2", Molecular Cell 2016.

  • Ruggles KV, Fenyö D: "Next Generation Sequencing Data and Proteogenomics", Adv. Exp. Med. Biol. 926 (2016) 11-19.

  • Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyö D, Boeke JD: "Fluorescence ImmunoPrecipitation (FLIP): a novel assay for high-throughput IP", Biological Procedures Online (2016) 18:16.

  • Askenazi M & Fenyö D: "OpenSlice: Quantitative Data Sharing from HyperPeaks to Global Ion Chromatograms (GICs)", Proteomics 2016 July 19.

  • Whelan DR, Yin Y, Bermudez-Hernandez K, Keegan S, Fenyö D, Rothenberg E: "Single Molecule Localization Microscopy of DNA Damage Response Pathways in Cancer", Microsc Microanal. 22 (2016) 1016-1017.

  • Zhang H, Liu T, Zhang Z, Payne S, Zhang B, McDermott J, Zhou JY, Petyuk V, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha S, Aiyetan P, Woo S, Tian Y, Gritsenko M, Choi C, Monroe M, Thomas S, Moore R, Yu KH, Tabb D, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja E, Hiltke T, Rivers R, Sokoll L, Zhu H, Shih IM, Pandey A, Zhang B, Snyder M, Levine D, Smith R, Chan D, Rodland K: "Deep proteogenomic characterization of human ovarian cancer", Cell 2016.

  • 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 K-l, 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 & the NCI CPTAC: "Proteogenomics connects somatic mutations to signaling in breast cancer", Nature 534 (2016) 55-62.

  • Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA: "Probing the HIV-Host Interactome in Infected Cells", Nature Microbiology 2016 May 23.

  • Ma S, Ren J, Fenyö D, "Breast Cancer Prognostics Using Multi-Omics Data", AMIA Jt Summits Transl Sci Proc. 2016.

  • Saxe G, Statnikov A, Fenyö D, Ren J, Li Z, Prasad M, Wall D, Bergman N, Briggs E, Aliferis C, "A Complex Systems Approach to Causal Discovery in Psychiatry", PLOS ONE 2016 March 30.

  • 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. "Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays". Methods Mol Biol. 1410 (2016) 223-236.

  • Keegan S, Cortens JP, Beavis RC, Fenyo D, "g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates", J Proteome Res. 2016 Feb 4.

  • Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Fengxia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Delmar M, "Nanoscale Visualization of a Functional Adhesion/Excitability Node at the Cardiac Intercalated Disc", Nature Communications 2016 Jan 20.

  • Thompson MK, Fridy PC, Sarah Keegan S, Chait BT, Fenyö D, Rout MP, "Optimizing Selection of Large Animals for Antibody Production by Screening Immune Response to Standard Vaccines", Journal of Immunological Methods 2016 Jan 9.

  • Tufariello JM, Chapman JR, Kerantzas CA, Wong KW, Vilcheze C, Jones CM, Cole LE, Tinaztepe E, Thompson V, Fenyö D, Niederweis M, Ueberheide B, Philips JA, Jacobs WR Jr. "Separable Roles for Mycobacterium tuberculosis ESX-3 Effectors in Iron Acquisition and Virulence", PNAS 2016.

  • 2015

  • Fenyo D, Beavis RC, "Selenocysteine: Wherefore art thou?", J Proteome Res. 2015. PMID: 26680273.

  • Menschaert G, Fenyo D, "Proteogenomics from a bioinformatics angle: A growing field", Mass Spectrometry Reviews 2015.

  • Askenazi M, Ruggles K, Fenyo D, "PGx: Putting Peptides to BED", J Proteome Res. 2015.

  • Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D, "An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer", Mol Cell Proteomics. 2015

  • Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyo D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL., "Integrated Bottom-up and Top-down Proteomics of Patient-derived Breast Tumor Xenografts", Mol Cell Proteomics. 2015 Oct 26.

  • Boeke JD, Fenyo D, "Much Ado about Zero", Cell. 163 (2015) 534-5.

  • Ruggles K, Fenyö D, "Proteogenomics" in Next-generation DNA sequencing Informatics, 2nd Edition, Ed. Stuart Brown, Cold Spring Harbor Laboratory Press 2015, Cold Spring Harbor, New York.

  • Hakhverdyan Z, Domanski M, Hough L, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy K, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J, "Rapid Optimized Interactomic Screening", Nature Methods 2015 May 4. PMID 25938370.

  • Fenyö D, Beavis R, "The GPMDB REST Interface", Bioinformatics 2015. PMID: 25697819.

  • Reid D, Keegan S, Leo-Macias A, Watanabe G, Strande NT, Oksuz BA, Fenyö D, Lieber MR, Ramsden DA, Rothenberg E, "Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair", PNAS 2015 May 4 PMID 25941401.

  • 2014

  • P.C. Fridy, Y. Li, S. Keegan, M.K. Thompson, I. Nudelman, J.F. Scheid, M. Oeffinger, M.C. Nussenzweig, D. Fenyö, B.T. Chait, M.P. Rout, "A robust pipeline for rapid production of versatile nanobody repertoires", Nature Methods 11 (2014) 1253-1260.

  • Sun J, Zhang G, Li S, Ivanov AR, Fenyö D, Lisacek F, Murthy SK, Karger BL, Brusic V, "Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study", BMC Genomics 2014.

  • Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári A, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G., "Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome", J Proteome Res. 2014

  • Agullo-Pascual E, Lin X, Leo-Macias A, Zhang M, Liang FX, Li Z, Pfenniger A, Lübkemeier I, Keegan S, Fenyö D, Willecke K, Rothenberg E, Delmar M., "Super-resolution imaging reveals that loss of the C-terminus of Connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc", Cardiovasc Res. 2014 Aug 18. pii: cvu195.

  • Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC), "Proteogenomic characterization of human colon and rectal cancer", Nature 2014 Jul 20.

  • Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SA, Ruggles KV, Fenyö D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA, "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels", Mol Cell Proteomics. 2014

  • Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG., "CPTAC Assay Portal: a repository of targeted proteomic assays", Nat Methods 11 (2014) 703-4.

  • 2013

  • Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes R, Moskal JR, Fenyö D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Végvári A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL, "Integrated Chromosome 19 Transcriptomic and Proteomic Datasets Derived from Glioma Cancer Stem Cell Lines", J Proteome Res. 2013

  • Agullo-Pascual E, Reid DA, Keegan S, Sidhu M, Fenyö D, Rothenberg E, Delmar M. "Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque", Cardiovasc Res. 2013

  • J. Malm, T.E. Fehniger, P. Danmyr, A. Végvári, C. Welinder, H. Lindberg, R. Appelqvist, K. Sjödin, E. Wieslander, T. Laurell, S. Hober, F. Berven, D. Fenyö D, X. Wang, P.E. Andrén, G. Edula, E. Carlsohn, M. Fuentes, C. Nilsson C, M. Dahlbäck, M. Rezeli, D. Erlinge, G. Marko-Varga, "Developments in biobanking workflow standardization providing sample integrity and stability" J Proteomics 2013

  • Y. Bao, S. Waldemarson, G. Zhang, A. Wahlander, B. Ueberheide, S. Myung, B. Reed, K. Molloy, J.C. Padovan, J. Eriksson, T.A. Neubert, B.T. Chait, D. Fenyö "Detection and Correction of Interference in SRM Analysis" Methods 61(2013) 299-303

  • M.F. Muellenbeck, B. Ueberheide, B. Amulic, A. Epp, D Fenyö, C.E. Busse, M. Esen, M. Theisen, B. Mordmüller, H. Wardemann "Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies" J Exp Med. 210 (2013) 389-99

  • S. Liu, H. Im, A. Bairoch, M. Cristofanilli, R. Chen, E.W. Deutsch, S. Dalton, D. Fenyö, S. Fanayan, C. Gates, P. Gaudet, M. Hincapie, S. Hanash, H. Kim, S.-K. Jeong, E. Lundberg, G. Mias, R. Menon, Z. Mu, E. Nice, Y.-K. Paik, M. Uhlen, L. Wells, S.-L. Wu, F.Yan, F.Zhang, Y.Zhang, M.Snyder, G.S. Omenn, R.C. Beavis, W.S. Hancock "A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17" J. Proteome Res. 12 (2013) 45-57

  • C.L. Nilsson, F. Berven, F. Selheim, H. Liu, J.R. Moskal, R.A. Kroes, E.P. Sulman, C.A. Conrad, F.F. Lang, P.E. Andrén, A. Nilsson, E. Carlsohn, H. Lilja, J. Malm, D. Fenyö, D. Subramaniyam, X. Wang, M. Gonzales-Gonzales, N. Dasilva, P. Diez, M. Fuentes, Á. Végvári, K. Sjödin, C. Welinder, T. Laurell, T.E. Fehniger, H. Lindberg, M. Rezeli, G. Edula, S. Hober, G. Marko-Varga "Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium" J. Proteome Res. 12 (2013) 135-150

  • E. Kefaloyianni, J.S. Lyssand, C. Moreno, D. Delaroche, M. Hong, D. Fenyö, C.V. Mobbs, T.A. Neubert, W.A. Coetzee "A comparative proteomic analysis of the KATP channel complex in different tissue types" Proteomics 13 (2013) 368-78

  • 2012

  • L. Bozzacco, H. Yu, J. Dengjel, C. Trumpfheller, H.A. Zebroski III, N. Zhang, V. Küttner, B.M. Ueberheide, H. Deng, B.T. Chait, R.M. Steinman, S. Mojsov, D. Fenyö "Strategy for Identifying Dendritic Cell-Processed CD4(+) T Cell Epitopes from the HIV Gag p24 Protein", PLoS One 7 (2012):e41897.

  • 2011

  • J.F. Scheid, H. Mouquet, B. Ueberheide, R. Diskin, F. Klein, T.Y.K. Olivera, J. Pietzsch, D. Fenyö, A. Abadir, K. Velinzon, A. Hurley, S. Myung, F. Boulad, P. Poignard, D. Burton, F. Pereyra, D.D. Ho, B.D. Walker, M.S. Seaman, P.J. Bjorkman, B.T. Chait, M.C. Nussenzweig. "Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding", Science 6049 (2011) 1633-7.

  • C.F. Aliferis, A.V. Alekseyenko, Y. Aphinyanaphongs, S. Brown, D. Fenyö, L. Fu, S. Shen, A. Statnikov, J. Wang, "Trends and Developments in Bioinformatics in 2010: Prospects and Perspectives" IMIA Yearbook of Medical Informatics 6 (2011) 146-155.

  • S. Myung, H. Cohen, D. Fenyö, J.C. Padovan, A.N. Krutchinsky, B.T. Chait, "High-capacity ion trap coupled to a time-of-flight mass spectrometer for comprehensive linked scans with no scanning losses", International Journal of Mass Spectrometry 301 (2011) 211-219.

  • J. Eriksson, D. Fenyö, "Modeling mass spectrometry-based protein analysis", Methods Mol Biol. 694 (2011) 109-17.

  • 2010

    D. Fenyö,(Ed.) "Computational Biology", Methods Mol Biol 673 (2010).

  • J. Eriksson, D. Fenyö, "Modeling experimental design for proteomics", Methods Mol Biol 673 (2010) 223-30.

  • G. Zhang, B.M. Ueberheide, S. Waldemarson, S. Myung, K. Molloy, J. Eriksson, B.T. Chait, T.A. Neubert, D. Fenyö, "Protein quantitation using mass spectrometry", Methods Mol Biol 673 (2010) 211-22.

  • D. Fenyö, J. Eriksson, R. Beavis, "Mass spectrometric protein identification using the global proteome machine", Methods Mol Biol 673 (2010) 189-202.

  • L. Peng, E.A. Kapp, D. Fenyö, M.S. Kwon, P. Jiang, S. Wu, Y. Jiang, M.I. Aguilar, N. Ahmed, M.S. Baker, Z. Cai, Y.J. Chen, P. Van Chi, M.C. Chung, F. He, A.C. Len, P.C. Liao, K. Nakamura, S.M. Ngai, Y.K. Paik, T.L. Pan, T.C. Poon, G. Hosseini Salekdeh, R.J. Simpson, R. Sirdeshmukh, C. Srisomsap, J. Svasti, Y.C. Tyan, F.S. Dreyer, D. McLauchlan, P. Rawson, T.W. Jordan, "The asia oceania human proteome organisation membrane proteomics initiative. preparation and characterization of the carbonate-washed membrane standard", Proteomics 2010 May 18.

  • A.G. Paulovich, D. Billheimer, A.J. Ham, L. Vega-Montoto, P.A. Rudnick, D.L. Tabb, P. Wang, R.K. Blackman, D.M. Bunk, H.L. Cardasis, K.R. Clauser, C.R. Kinsinger, B. Schilling, T.J. Tegeler, A.M. Variyath, M. Wang, J.R. Whiteaker, L.J. Zimmerman, D. Fenyo, S.A. Carr, S.J. Fisher, B.W. Gibson, M. Mesri, T.A. Neubert, F.E. Regnier, H. Rodriguez, C. Spiegelman, S.E. Stein, P. Tempst, D.C. Liebler, "Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance", Mol Cell Proteomics, 9 (2010) 242-254.

  • M.D. Sekedat, D. Fenyö, R.S. Rogers, A.J. Tackett, J.D. Aitchison, B.T. Chait, "GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome", Mol Syst Biol. 6 (2010) 353.

  • 2009

  • B.M. Ueberheide, D. Fenyö, P.F. Alewood, B.T. Chait, "Rapid sensitive analysis of cysteine rich peptide venom components", Proc Natl Acad Sci 106 (2009) 6910-6915.

  • T.N. Siegel, D.R. Hekstra, L.E. Kemp, L.M. Figueiredo, J.E. Lowell, D. Fenyö, X. Wang, S. Dewell, G.A. Cross, "Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei", Genes Dev. 23 (2009) 1063-1076.

  • G. Zhang, D. Fenyö, T.A. Neubert, "Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell Culture", J Proteome Res 8 (2009) 1285-1292.

  • 2008

  • J. Eriksson and D. Fenyö, "Optimizing Sensitivity and Specificity in Mass Spectrometric Proteome Analysis", pp. 211-222 in: Mass Spectrometry: Instrumentation, Interpretation, and Applications, Eds. R. Ekman, J. Silberring, A.M. Brinkmalm, D.M. Desiderio, N.M. Nibbering, Wiley 2008.

  • G. Zhang, D. Fenyö, T.A. Neubert, "Use of DNA Ladders for Reproducible Protein Fractionation by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) for Quantitative Proteomics", J Proteome Res 7 (2008) 678-686.

  • G. Zhang, D. Fenyö, T.A. Neubert, "Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer", J Proteome Res 7 (2008) 4715-4726.

  • M. Falth, M. Svensson, A. Nilsson, K. Skold, D. Fenyö, P.E. Andren, "Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra", J Proteome Res 7 (2008) 3049-3053.

  • E.M. Woo, D. Fenyö, B.H. Kwok, H. Funabiki, B.T. Chait BT, "Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting", Anal Chem 80 (2008) 2419-2425.

  • L.F. Westblade, L. Minakhin, K. Kuznedelov, A.J. Tackett, E.J. Chang, R.A. Mooney, I. Vvedenskaya, Q.J. Wang, D. Fenyö, M.P. Rout, R. Landick, B.T. Chait, K. Severinov, S.A. Darst, "Rapid Isolation and Identification of Bacteriophage T4-Encoded Modifications of Escherichia coli RNA Polymerase: A Generic Method to Study Bacteriophage/Host Interactions", J Proteome Res 7 (2008) 1244-1250.

  • C.C. Darie, V. Shetty, D.S. Spellman, G. Zhang, C. Xu, H.L. Cardasis, S. Blais, D. Fenyö, and T.A. Neubert, Blue Native PAGE and Mass Spectrometry Analysis of Ephrin Stimulation-Dependent Protein-Protein Interactions in NG108-EPHB2 Cells", in Applications of Mass Spectrometry in Life Safety, C. Popescu et al. (eds.), Springer 2008.

  • D. Fenyö, R.C. Beavis, "Informatics development: Challenges and solutions for MALDI mass spectrometry", Mass Spectrom Rev 27 (2008) 1-19.

  • 2007

  • J. Eriksson, D. Fenyö, "Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs". Nature Biotechnology 25 (2007) 651-655.

  • D. Fenyö, Q.J. Wang, J.A. DeGrasse, J.C. Padovan, M. Cadene, B.T. Chait, "MALDI sample preparation: the ultra thin layer method". Journal of Visualized Experiments Issue 3 (2007).

  • D. Fenyö, B.S.Phinney, R.C. Beavis, "Determining the Overall Merit of Protein Identification Data Sets: rho-Diagrams and rho-Scores". J Proteome Res 6 (2007) 1997-2004.

  • M. Falth, K. Sköld, M. Svensson, A. Nilsson, D. Fenyö, P.E. Andren, "Neuropeptidomics: Strategies for specific and sensitive identification of endogenous peptides". Mol Cell Proteomics 6 (2007) 1188-1197.

  • A. Kaplan, M. Söderström, D. Fenyö, H. Pettersen, S. Lindqvist, K. Sköld, M. Svensson, P. Svenningsson, P.E. Andren & L. Björkesten, "An automated method for scanning LC-MS data sets for significant peptides and proteins, including quantitative profiling and interactive confirmation", Journal of Proteome Research 6 (2007) 28880-2895.

  • 2006

  • R. Craig, J.C. Cortens, D. Fenyö, R.C. Beavis, "Using Annotated Peptide Mass Spectrum Libraries for Protein Identification" Journal of Proteome Research, 5 (2006) 1843-1849.

  • M. Fälth, K. Sköld, M. Norrman, M. Svensson, D. Fenyö, P.E. Andren, "SwePep – A Database Designed for Endogenous Peptides and Mass Spectrometry" Molecular and Cellular Proteomics 5 (2006) 998-1005.

  • E. Ossipova, D. Fenyö, J. Eriksson, "Optimizing Search Conditions for the Mass-Fingerprint-Based Identification of Proteins" Proteomics 6 (2006) 2079-85.

  • M. Berg, A. Parbel, H. Pettersen, D. Fenyö, & L. Björkesten, "Detection of Artifacts and Peptide Modifications in LC-MS data Using Two-Dimensional Signal Intensity Map Data Visualization", Rapid Communications in Mass Spectrometry 20 (2006) 1558-62.

  • M. Berg, A. Parbel, H. Pettersen, D. Fenyö, & L. Björkesten, "Reproducibility of LC-MS-based protein identification", Journal of Experimental Botany, 57 (2006) 1509-14.

  • 2005

  • J. Eriksson, D. Fenyö "Protein Identification in Complex Mixtures", J Proteome Research 4 (2005) 387-93.

  • E. A. Kapp, F. Schutz, L. M. Connolly, J. A. Chakel, J. E. Meza, C. A. Miller, D. Fenyö, J. K. Eng, J.N. Adkins, G.S. Omenn & R.J. Simpson, "An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis", Proteomics, 5 (2005) 3475-90.

  • J. Eriksson & D. Fenyö, "Simulation as a Tool for Optimizing Proteome Analysis", pp. 521-532 in: Comprehensive Analytical Chemistry vol. 46, Ed. G. Marko-Varga, Elsevier 2005.

  • A. Thelemann, F. Petti, G. Griffin, K. Iwata, T. Hunt, T. Settinari, D. Fenyö, N. Gibson and J. D. Haley, "Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells", Molecular and Cellular Proteomics, 4 (2005) 356-76.

  • D. Fenyö, "Protein fingerprinting", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Ed. M. Dunn, John Wiley & Sons, 2005.

  • D. Fenyö, J. Eriksson & R.C. Beavis, "Protein Identification by Searching Collections of Sequences with Mass Spectrometric Information", pp. 267-276 in: Informatics in Proteomics Research, Ed. S. Srivastava, CRC Press 2005.

  • 2004

  • J. Eriksson, D. Fenyö"The Statistical Significance of Protein Identification Results as a Function of the Number of Protein Sequences Searched", J. Proteome Research 3 (2004) 979-82.

  • J. Eriksson, D. Fenyö "Probity: A Protein Identification Algorithm with Accurate Assignment of the Significance of the Results", J Proteome Research 3 (2004) 32-36.

  • H. Nordvarg, J. Flensburg, O. Rönn, J. Öhman, R. Marouga, B. Lundgren, D. Haid, E. Malmport, J. Goscinski, L. Hörnsten, M. Scigelova, S. Bourin, P. Garberg, G. Woffendin, D. Fenyö, H. Bergling & E. Forsberg "A Proteomics Approach to the Study of Absorption, Distribution, Metabolism, Excretion and Toxicity", Journal of Biomolecular Techniques, 15 (2004) 265-75.

  • R.C. Beavis & D. Fenyö, "Finding protein sequences using PROWL", Current Protocols in Bioinformatics, Ed. D. Davidson, John Wiley & Sons, 2004.

  • 2003

  • D. Fenyö, R.C. Beavis, "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes", Analytical Chemistry 75 (2003) 768-74.

  • M. Trester-Zedlitz, K. Kamada, S.K. Burley, D. Fenyö, B.T. Chait, T.W. Muir, "A Modular Cross-Linking Approach for Exploring Protein Interactions" J Am Chem Soc 125 (2003) 2416-2425.

  • 2002

  • D. Fenyö, R.C. Beavis "Informatics and data management in proteomics", Trends Biotechnol 20 (2002) S35-8.

  • J. Eriksson, D. Fenyö "A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis", Proteomics. 2 (2002) 262-70. Erratum in: Proteomics 2 (2002) 603.

  • H.I. Field, D. Fenyö, R.C. Beavis "RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database", Proteomics 2 (2002) 36-47.

  • 2000

  • J. Eriksson, B.T. Chait, D. Fenyö "A statistical basis for testing the significance of mass spectrometric protein identification results" Anal Chem 72 (2000) 999-1005.

  • D. Fenyö"Identifying the proteome: software tools" Current Opinion in Biotechnology, 11 (2000) 391-395.

  • R.C. Beavis & D. Fenyö, "Database searching with mass spectrometric information", In Proteomics: A Trends Guide, Eds. M. Mann and W. Blackstock, pp 23-27, Elsevier 2000.

  • 1999

  • D. Fenyö "The Biopolymer Markup Language" Bioinformatics 15 (1999) 339-340.

  • 1998

  • D. Fenyö and R.C. Beavis, "Network-Based Bioinformatics in Protein Mass Spectrometry", in Mass spectrometry of Biological Materials, Eds. B. Larsen & C. McEwen, Marcel Dekker, 1998.

  • D. Fenyö, J. Qin, B.T. Chait "Protein Identification using Mass Spectrometric Information" Electrophoresis 19 (1998) 998-1005.

  • 1997

  • Y. Wang, K. Severinov, N. Loizos, D. Fenyö, E. Heyduk, T. Heyduk, B. T. Chait, S.A. Darst "Determinants for Escherichia coli RNA Polymerase Assembly within the β Subunit" J Mol Biol (1997) 648-662.

  • J. Qin, D. Fenyö, Y. Zhao, W.W. Hall, D.M. Chao, C.J. Wilson, R.A. Young and B.T. Chait "A Strategy for Rapid, High Confidence Protein Identification" Anal Chem 69 (1997) 3995-4001.

  • D. Fenyö, B.T. Chait, T.E. Johnson, J.S. Lindsey "Laser desorption Mass Spectrometry of Large Synthetic Porphyrin Arrays" J Por and Phthalocy 1 (1997) 93-99.

  • D. Fenyö "A Software Tool for Analysis of Mass Spectrometric Disulfide Mapping Experiments" Computer Applications in the Biosciences (CABIOS) 13 (1997) 617-8.

  • 1996

  • E. Severinova, K. Severinov, D. Fenyö, M. Marr, E.N. Brody, J.W. Roberts, B.T. Chait, S.A. Darst "Organization of the Escherichia coli RNA polymerase σ70 subunit" J Mol Biol, 263 (1996) 637-647.

  • D. Fenyö, W. Zhang, B.T. Chait, R.C. Beavis "Internet-based Analytical Chemistry Resources. A Model Project" Anal Chem 68 (1996) 721A-726A.

  • A.A. Stewart, J.D. Haley, G.-Y. Qu, K. Stam, D. Fenyö, B.T. Chait, D.R. Marshak, A.Y.-K. Ng, G. Marley, K.K. Iwata "Unbilical Cord Transforming Growth Factor-β3. Isolation, Comparison with Recombinant TGF-β3 and Cellular Localization" Growth Factors, 13 (1996) 87-98.

  • 1995

  • K. Stam, A.A. Stewart, G.Y. Qu, K.K. Iwata, D. Fenyö, B.T. Chait, D.R. Marshak, J.D. Haley "Physical and Biologial Characterization of a Growth-Inhibitors Activity Purified from the Neuroepithelioma cell-line A673" Biochem J 305 (1995) 87.

  • 1994

  • K. Severinov, D. Fenyö, E. Severinov, B.T. Chait, A. Goldfarb, S. Darst, "The σ-Subunit Conserved Region 3 is Part of the "5’-Face" of the active Center of E. coli RNA Polymerase", J Biol Chem 269 (1994) 20826-8.

  • H. Tang, K. Severinov, A. Goldfarb, D. Fenyö, B.T. Chait, R. Ebright "Location, Structure, and Function of the Target of a Transcription Activator Protein", Gene Dev 8 (1994) 3058-67.

  • P. Sinnis, P. Clavijo, D. Fenyö, B.T. Chait, C. Cerami, V. Nussenzweig, "Structural and Functional Properties of Region II-Plus of the Malaria Circumsporozoite Protein", J Exp Med 180 (1994) 297-306.

  • T.S.R. Krishna, D. Fenyö, X–P. Kong, S. Gary, B.T. Chait, P. Burgers, J. Kuriyan "Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces cerevisiae", J Mol Biol 241 (1994) 265-268.

  • G. Brinkmalm, P. Demirev, J. Eriksson, D. Fenyö, P. Håkansson & B. U. R. Sundqvist, "Electronic Sputtering of Fullerenes and the Influence of Primary Ion Charge-State", Nuclear Instuments and Methods in Physics Research B84 (1994) 37-42.

  • R.M. Papaleo, G. Brinkmalm, D. Fenyö, J. Eriksson, H.-F. Kammer, P. Demirev, P. Håkansson & B. U. R. Sundqvist, "MeV ion sputtering of polymers: correlation between secondary ion radial velocity distributions and heavy ion track structure", Nuclear Instuments and Methods in Physics Research B91 (1994) 667-671.

  • D. Fenyö, P. Håkansson & B. U. R. Sundqvist, "On the Ejection of Hydrogen Ions from Organic Solids Impacted by MeV Ions", Nuclear Instruments and Methods B84 (1994) 31.

  • 1993

  • G. Brinkmalm, P. Demirev, D. Fenyö, P. Håkansson, J. Kopniczky & B. U. R. Sundqvist, "Formation of Fullerenes in MeV-ion Sputtering from Organic Solids", Physical Review B47 (1993) 7560-7567.

  • P. Demirev, D. D. N. B. Daya, G. Brinkmalm, D. Fenyö, P. Håkansson & B. U. R. Sundqvist, "On Molecular Ion Formation by Hydride Abstraction in Plasma Desorption Mass Spectrometry", International Journal of Mass Spectrometry and Ion Processes 123 (1993) 69.

  • D. Fenyö, "Sputtering by a Sum of Impulses: The Effect of Finite Track Width", Physical Review B47 (1993) 8263.

  • 1992

  • D. Fenyö & R. E. Johnson, "Computer Experiments on Molecular Ejection from an Amorphous Solid: Comparison to an Analytic Continuum Mechanical Model", Physical Review B46 (1992) 5090.

  • G. Brinkmalm, D. Barofsky, P. Demirev, D. Fenyö, P. Håkansson, R. E. Johnson, C.T. Reimann & B. U. R. Sundqvist, "Formation of Fullerenes in MeV Ion Track Plasmas", Chemical Physics Letters 191 (1992) 345-350.

  • 1991

  • P. Demirev, G. Brinkmalm, D. Fenyö, P. Håkansson & B. U. R. Sundqvist, "Radial velocities of ejected ions: implications for the mechanism of molecular ion formation in plasma desorption mass spectrometry of biomolecules", International Journal of Mass Spectrometry and Ion Processes 111 (1991) 41.

  • A. Hallen, D. Fenyö, B.U.R. Sundqvist , R.E. Johnson & B.G. Svensson, Dose-Rate, "Dependence on the Defect Production in MeV Proton-Irradiated Silicon", Journal of Applied Physics 70 (1991) 3025.

  • D. Fenyö, "Electronic Sputtering of Organic Solids", ACTA UNIVERSITATIS UPSALIENSIS, Almqvist & Wiksell Int., Stockholm, 1991.

  • B. U. R. Sundqvist, P. Håkansson, A. Hedin, D. Fenyö, G. Brinkmalm, P. Roepstorff & R.E. Johnson, "Plasma Desorption Mass Spectrometry - Achievements and Frontiers, Methods and Mechanisms for Producing Ions from Large Molecules", NATO-ASI series, Eds. W. Ens & K.G. Standing, Plenum Publ. Corp., New York, 1991, p. 7.

  • R. E. Johnson, S. Banarjee, A. Hedin, D. Fenyö & B. U. R. Sundqvist, "Heavy-Ion and Laser Pulse-Induced Ejection of Large Organic Molecules", Methods and Mechanisms for Producing Ions from Large Molecules", NATO-ASI series, Eds. W. Ens & K.G. Standing, Plenum Publ. Corp., New York, 1991, p. 89.

  • P. Demirev, D. Fenyö, P. Håkansson & B. U. R. Sundqvist, "On the Mechanism of Formation of Alkali Cation Adducts in Plasma Desorption Mass Spectrometry of Biomolecules", Organic Mass Spectrometry 26 (1991), 471.

  • 1990

  • D. Fenyö, A. Hedin, P. Håkansson & B. U. R. Sundqvist, "Radial Velocity Distribution of Ions Ejected from Organic Solids by Fast Heavy Ion Bombardment", International Journal of Mass Spectrometry and Ion Processes 100 (1990) 63.

  • D. Fenyö, B. U. R. Sundqvist, B. Karlsson & R. E. Johnson, "A Molecular Dynamics Study of Sputtering of Large Molecules", Physical Review B42 (1990) 1895.

  • D. Fenyö, A. Hedin, P. Håkansson & B. U. R. Sundqvist, "Electronic Sputtering of Large Organic Molecules", Proceedings from the 3rd International Wangerooge Workshop on the Physics of Small Systems, Ed. E.R. Hilf, W. Tuszynski, World Scientific, Singapore 1990.

  • D. Fenyö, A. Hedin, P. Håkansson, R. E. Johnson & B. U. R. Sundqvist, "Radial Velocity Distributions in Electronic Sputtering of Large Organic Molecules", Proceedings from the 5th International Workshop on Ion Formation from Organic Solids, John Wiley & Sons 1990 England.

  • 1989

  • R. E. Johnson, B. U. R. Sundqvist, A. Hedin & D. Fenyö, "Sputtering by Fast Ions Using a Sum of Impulses", Physical Review B40 (1989) 49.

  • A. Hedin, D. Fenyö, P. Håkansson, G. Jonsson & B. U. R. Sundqvist, "Electronic Sputtering of Biomolecules", Nuclear Instruments and Methods B40/41 (1989) 275.

  • B. U. R Sundqvist, D. Fenyö, A. Hedin, P. Håkansson, G. Jonsson, W. Ens & R. E. Johnson, "Directional Correlations Between Incident Particle and Secondary Ions in Electronic Sputtering of Large Organic Molecules", Radiation Effects and Defects in Solids 109 (1989) 169.

  • W. Ens, B. U. R Sundqvist, P. Håkansson, D. Fenyö, A. Hedin & G. Jonsson, "Radial velocity Measurements of Secondary Molecular Ions in keV and MeV bombardement", Journal de Physique 50 (1989) C2-9.

  • D. Fenyö, B. U. R. Sundqvist, B. Karlsson & R. E. Johnson, "A Molecular Dynamics Study of Electronic Sputtering of Large Organic Molecules", Journal de Physique 50 (1989) C2-33.

  • 1988

  • B. U. R Sundqvist, A. Ariyaratne, W. Ens, D. Fenyö, A. Hedin, P. Håkansson, G. Jonsson, "On the Upper Limit of Secondary Ions Ejected In Electronic Sputtering from Organic Solids", Proceedings from the 4th International Workshop on Ion Formation from Organic Solids, 1988.

  • B. U. R Sundqvist, D. Fenyö, P. Håkansson, G. Säve, S.-E. Lindqvist, E. Söderström & J. Berg, "Fast Ion Induced Desorption of Secondary Ions from Langmuir - Blodgett Films of Fatty Acids", Secondary Ion Mass Spectrometry SIMS VI, John Wiley & Sons 1988, p 615-618.

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