Publications - Bioanalytical Measurement
On this page:
2017
McCampbell AS, Raghunathan V, Tom-Moy M, Workman RK, Haven R, Ben-Dor A, Rasmussen OF, Jacobsen L, Lindberg M, Yamada NA, Schembri C “Tissue Thickness Effects on Immunohistochemical Staining Intensity of Markers of Cancer” Appl Immunohistochem Mol Morphol 2017 Oct 27. doi: 10.1097/PAI.0000000000000593. Epub 2017 Oct 27.
2016
Kraiczek KG,2, Mannion J, Post S, Tsupryk A, Raghunathan V, Brennen R, Zengerle R. “Micromachined Fused Silica Liquid Core Waveguide Capillary Flow Cell. ” Anal Chem. 2016 Jan 19;88(2):1100-5. doi: 10.1021/acs.analchem.5b03219. Epub 2015 Dec 30.
2015
Hendel A; Bak RO; Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn L, Porteus MH. “Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. ” Nature Biotechnology, 2015 Sep;33(9):985-9. doi: 10.1038/nbt.3290. Epub 2015 Jun 29.
Haakensen VD; Steinfeld I; Saldova R; Shehni AA; Kifer I; Naume B; Rudd PM; Borresen-Dale AL; Yakhini Z. “ Serum N-glycan analysis in breast cancer patients - Relation to tumour biology and clinical outcome.” Molecular Oncology, 2015 Aug 19. pii: S1574-7891(15)00148-9. doi: 10.1016/j.molonc.2015.08.002.
Shalem O; Sharon E; Lubliner S; Regev I; Lotan-Pompan M; Yakhini Z; Segal E. “Systematic dissection of the sequence determinants of gene 3' end mediated expression control.” PLoS Genetics, 2015 Apr 15;11(4):e1005147. doi:10.1371/journal.pgen.1005147.
Drory Retwitzer M; Kifer I; Sengupta S; Yakhini Z; Barash D. “ An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.” PLoS One, 2015 Jul 31;10(7):e0134262. doi:10.1371/journal.pone.0134262.
Drory Retwitzer M; Polishchuk M; Churkin E; Kifer I; Yakhini Z; Barash D. “RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.” Nucleic Acids Research, 2015 Jul 1;43(W1):W507-12. doi: 10.1093/nar/gkv435.
Levo M, Zalckvar E, Sharon E, Dantas Machado AC, Kalma Y, Lotam-Pompan M, Weinberger A, Yakhini Z, Rohs R, Segal E. “Unraveling determinants of transcription factor binding outside the core binding site. ” Genome Research, 2015 Jul;25(7):1018-29. doi: 10.1101/gr.185033.114.
Steinfeld I; Navon R; Creech ML; Yakhini Z; Tsalenko A. “ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types.” Bioinformatics, 2015 May 15;31(10):1683-5. doi:10.1093/bioinformatics/btu853.
2014
Shaer O; Valdes C; Liu S; Lu K; Chang K; Xu W; Haddock T; Bhatia S; Densmore D; Kincaid R. “ Designing reality-based interfaces for experiential bio-design.” Personal and Ubiquitous Computing, 2014; 18(6): 1515-1532.
Vitkin E; Ben-Dor A; Shmoish M; Hartmann MF; Yakhini Z; Wudy SA; Hochberg Z. “ Peer group normalization and urine to blood context in steroid metabolomics: The case of CAH and obesity.” Steroids, Jul 17, 2014;88C:83-89. DOI: 10.1016/j.steroids.2014.07.003.
Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. “Probing the effect of promoters on noise in gene expression using thousands of designed sequences.” Genome Research, Jul 16, 2014. PII: gr.168773.113.
Saldova R; Asadi Shehni A; Haakensen VD; Steinfeld I; Hilliard M; Kifer I; Helland A; Yakhini Z; Borresen-Dale AL; Rudd PM. “ Association of N-Glycosylation with Breast Carcinoma and Systemic Features Using High-Resolution Quantitative UPLC.” J Proteome Research, Apr 11, 2014
Leibovich L; Yakhini Z. “Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs.” Algorithms Mol Biol. 2014 Apr 5; 9(1):11. DOI: 10.1186/1748-7188-9-11.
Nejman D; Straussman R; Steinfeld I; Ruvolo M; Roberts D; Yakhini Z; Cedar H. “Molecular rules governing de novo methylation in cancer.” Cancer Res. 2014 Mar 1;74(5):1475-83. DOI: 10.1158/0008-5472.CAN-13-3042.
Tahiri A; Leivonen SK; Luders T; Steinfeld I; Ragle Aure M; Geisler J; Makela R; Nord S; Riis ML; Yakhini Z; Kleivi Sahlberg K; Borresen-Dale AL; Perala M; Bukholm IR; Kristensen VN. “Deregulation of cancer-related miRNAs is a common event in both benign and malignant human breast tumors. ” Carcinogenesis. 2014 Jan;35(1):76-85.DOI: 10.1093/carcin/bgt333.
2013
Aure, MR; Steinfeld, I; Baumbusch, LO; Liestol, K; Lipson, D; Nyberg, S; Naume, B; Sahlberg, KK; Kristensen, VN; Borresen-Dale, AL; Lingjaerde, OC; Yakhini, Z. “Identifying In-Trans Process Associated Genes in Breast Cancer by Integrated Analysis of Copy Number and Expression Data.” PLoS One 8 (1), Jan. 30, 2013. DOI:10.1371/journal.pone.0053014.
Ben-Elazar, S; Yakhini, Z; and Yanai, I. “Spatial Localization of Co-regulated Genes Exceeds Genomic Gene Clustering in the Saccharomyces Cerevisiae Genome.” Nucleic Acids Research 41 (4), Feb. 1, 2013: 2191-2201. DOI 10.1093/nar/gks1360.
Herrmann, A; Sieben, C; Kappel, C; Zhu, R; Rankl, C; Wozniak, A; Hinterdorfer, P; and Grubmuller, H. “Influenza Virus Binds its Host Cell using Multiple Dynamic Interactions Revealed by Single Virus Force Spectroscopy and Force Probe Molecular Dynamics.” Biophysical Journal 104 (2), Jan. 29, 2013: 415A-415A.
Johansson, HJ; Sanchez, BC; Mundt, F; Forshed, J; Kovacs, A; Panizza, E; Hultin-Rosenberg, L; Lundgren, B; Martens, U; Mathe, G; Yakhini, Z; Helou, K; Krawiec, K; Kanter, L; Hjerpe, A; Stal, O; Linderholm, BK; and Lehtio, J. “Retinoic Acid Receptor Alpha is Associated with Tamoxifen Resistance in Breast Cancer.” Nat Commun 4 (2175), July 19, 2013. DOI:10.1038/ncomms3175.
Lee, HY; Haurwitz, RE; Apffel, A; Zhoua, K; Smart, B; Wenger, CD; Laderman, S; Bruhn, L; and Doudna, JA. “RNA–Protein Analysis Using a Conditional CRISPR Nuclease.” PNAS 110 (14), April 2, 2013: 5416-5421. DOI:10.1073/pnas.1302807110.
Lopez-Avila, V; and Zorio, M. "Identification of Methylhexaneamine by GC High-resolution TOFMS and Soft Ionization." Forensic Science International 231, April, 2013: 113–119.
Powell, WT; Coulson, RL; Crary, FK; Wong, SS; Ach, RA; Tsang, P; Yamada, NA; Yasui, DH; and LaSalle, JM. “A Prader–Willi Locus lncRNA Cloud Modulates Diurnal Genes and Energy Expenditure.” Hum. Mol. Genet., June 13, 2013:1-11. DOI:10.1093/hmg/ddt281.
Powell, WT; Coulson, RL; Gonzales, ML; Crary, FK; Wong, SS; Adams, S; Ach, RA; Tsang, P; Yamada, NA; Yasui, DH; Chédin, F; and LaSalle; JM. “R-loop Formation at Snord116 Mediates Topotecan Inhibition of Ube3a-antisense and Allele-specific Chromatin Decondensation.” PNAS 110 (34), Aug. 5, 2013: 13938-13943. DOI:10.1073/pnas.1305426110.
Shay Ben-Elazar, S; Yakhini, Z; and Yanai, I. "Spatial Localization of Co-regulated Genes Exceeds Genomic Gene Clustering in the Saccharomyces Cerevisiae Genome." Nucl. Acids Res. 2013, Jan. 8. 2013: 1-11. DOI: 10.1093/nar/gks1360.
Souza-Silva, ÉA; Lopez-Avila, V; Pawliszyn, J. “Fast and Robust Direct Immersion Solid Phase Microextraction Coupled with Gas Chromatography–time-of-flight Mass Spectrometry Method Employing a Matrix Compatible Fiber for Determination of Triazole Fungicides in Fruits.” J. Chromatogr., A, 1313, July 2013: 139-146.
Steinfeld, I; Navon, R; Ach, R; and Yakhini, Z. “miRNA Target Enrichment Analysis Reveals Directly Active miRNAs in Health and Disease.” Nucleic Acids Res. 41(3) Feb 1, 2013. DOI: 10.1093/nar/gks1142.
Wenger, CD; and Coon, JJ. "A Proteomics Search Algorithm Specifically Designed for High- Resolution Tandem Mass Spectra." J. Proteome Res. 12 (3), March 1, 2013: 1377−1386. DOI: 10.1021/ pr301024c.
2012
Aumann, Y; Lewenstein, M; Melamud, O; Pinter, R; Yakhini, Z. “Dotted Interval Graphs.” ACM Transactions on Algorithms 8 (2), April 2012: Article No. 9. DOI: 10.1145/2151171.2151172.
Chen, K; Mackie, JC: Kennedy, EM; Dlugogorski, BZ. “Determination of Toxic Products Released in Combustion of Pesticides.” Progress in Energy and Combustion Science 38 (3), Feb. 20, 2012: 400-418. DOI: 10.1016/j.pecs.2012.01.002.
Draz, MS; Fang, BA; Li, L; Chen, Z; Wang, Y; Xu, Y; Yang, J; Killeen, K; and Chen, FQ. “Hybrid Nanocluster Plasmonic Resonator for Immunological Detection of Hepatitis B Virus.” ACS Nano, Article ASAP, Aug. 31, 2012. DOI: 10.1021/nn3034056.
Farkash-Amar, S; David, Y; Polten, A; Hezroni, H; Eldar, YC; Meshorer, E; Yakhini, Z; and Simon, I. "Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization." PLoS One 7 (11), Nov. 7, 2012. DOI: 10.1371/journal.pone.0048986.
Haschemi, A; Kosma, P; Gille, L; Evans, CR; Burant, CF; Starkl, P; Knapp, B; Haas, R; Schmid, JA; Jandl, C; Amir, S; Lubec, G; Park, J; Esterbauer, H; Bilban, M; Brizuela, L; Pospisilik, JA; Otterbein, LE; and Wagner, O. “The Sedoheptulose Kinase CARKL Directs Macrophage Polarization through Control of Glucose Metabolism.” Cell Metab. 15 (6), Jun 6, 2012: 813-26.
Leibovich, L; and Yakhini, Z. "Efficient Motif Search in Ranked Lists and Applications to Variable Gap Motifs." Nucleic Acids Res. (40) 13, March 13, 2012: 5832-47. DOI: 10.1093/nar/gks206.
Lopez-Avila, V; Cooley, J; Urdahl, R; and Thevis, M. “Determination of Stimulants Using Gas Chromatography/High-Resolution Time-of-Flight Mass Spectrometry and a Soft Ionization Source.” Rapid Commun Mass Spectrom. 26 (23), Oct. 15, 2012: 2714-2724. DOI: 10.1002/rcm.6398.
Lopez-Avila, V; Gao, W; and Urdahl, R. "Mass Spectral Fragmentation of Cathinones by High-Resolution TOFMS Using a Soft Iionization Source." J Pharm Sci Innov 1(6), Nov-Dec 2012: 44-53.
Manzenreiter, R; Kienberger, F; Marcos, V; Schilcher, K; Krautgartner, WD; Obermayer, A; Huml, M; Stoiber, W; Hector, A; Griese, M; Hannig, M; Studnicka, M; Vitkov, L; and Hart, D. “Ultrastructural Characterization of Cystic Fibrosis Sputum Using Atomic Force and Scanning Electron Microscopy.” J Cyst Fibros 11 (2), March 2012:84-92. DOI: 10.1016/j.jcf.2011.09.008.
Pareja, F; Ferraro, DA; Rubin, C; Cohen-Dvashi, H; Zhang, F; Aulmann, S; Ben-Chetrit, N; Pines, G; Navon, R; Crosetto, N; Kostler, W; Carvalho, S; Lavi, S; Schmitt, F; Dikic, I; Yakhini, Z; Sinn, P; Mills, GB; Yarden, Y. "Deubiquitination of EGFR by Cezanne-1 Contributes to Cancer Progression." Oncogene 31 (43), Oct. 25, 2012: 4599-4608: DOI: 10.1038/onc.2011.587 OCT 2012.
Rabinovich, EI; Kapetanaki, MG; Steinfeld, I; Gibson, KF; Pandit, KV; Yu, GY; Yakhini, Z; and Kaminski, N. “Global Methylation Patterns in Idiopathic Pulmonary Fibrosis.” PLoS One 7 (4), April 10, 2012: e33770.
Sharon, E; Kalma, Y; Sharp, A; Raveh-Sadka, T; Levo, M; Zeevi, D; Keren, L; Yakhini, Z; Weinberger, A; and Segal, E. “Inferring Gene Regulatory Logic From High-Throughput Measurements of Thousands of Systematically Designed Promoters.” Nature Biotechnology 30 (6), June 2012: 521-530. DOI: 10.1038/nbt.2205.
Sieben, C; Kappel, C; Zhu, R; Wozniak, A; Rankl, C; Hinterdorfer, P; Grubmuller, H; and Herrmann, A. “Influenza Virus Binds Its Host Cell Using Multiple Dynamic Interactions.” PNAS 109 (34), Aug. 21, 2012: 13626-13631. DOI: 10.1073/pnas.1120265109.
Steinfeld, I; Navon, R; Ach, R; and Yakhini, Z. "miRNA Target Enrichment Analysis Reveals Directly Active miRNAs in Health and Disease." Nucleic Acids Res. 41 (3), Dec. 2012: e45. DOI: 10.1093/nar/gks1142.
Tomoda, K; Takahashi, K; Leung, K; Okada, A; Narita, M; Yamada, NA; Eilertson, KE; Tsang, P; Baba, S; White, MP; Sarni, S; Srivastava, D; Conklin, BR; Panning, B; and Yamanaka, S. "Derivation Conditions Impact X-Inactivation Status in Female Human Induced Pluripotent Stem Cells." Cell Stem Cell 11 (1), July 6, 2012: 91-99. DOI: 10.1016/j.stem.2012.05.019.
Xue, J; Urdahl, RS; and Cooley, JE. “Plasma Resonances in a Microwave-Driven Microdischarge.” Appl. Phys. Lett. 100 (6) Feb. 6, 2012: 064102. DOI:10.1063/1.3681146.
Xue, J; Cooley, JE; and Urdahl, RS. “Density of Metastable Atoms in the Plume of a Low-Pressure Argon Microplasma.” J. Phys. D: Appl. Phys. 45 (36), Aug. 21, 2012: 365201 (8pp). DOI:10.1088/0022-3727/45/36/365201.
Zehavi, L; Avraham, R; Barzilai, A; Bar-Ilan, D; Navon, R; Sidi, Y; Avni, D; and Leibowitz-Amit. R. “Silencing of a Large micro-RNA Cluster on Human Chromosome 14q32 in Melanoma: Biological Effects of mir-376a and mir-376c on Insulin Growth Factor 1 Receptor.” Molecular Cancer 11 (44), July 2, 2012. DOI:10.1186/1476-4598-11-44.
Zhang, C; Hanspers, K; Kuchinsky, A; Salomonis, N; Xu, D; Pico, AR. “Mosaic: Making Biological Sense of Complex Networks.” Bioinformatics 28 (14), July 15, 2012: 1943-1944. DOI: 10.1093/bioinformatics/bts278.
2011
Borgan, E; Navon, R; Vollan, HKM; Schlichting, E; Sauer, T; Yakhini, Z; Lingjærde, OC; Sørlie, T; and Børresen-Dale, AL. “Ischemia Caused by Time to Freezing Induces Systematic microRNA and mRNA Responses in Cancer Tissue.” Molecular Oncology 5(6), Dec. 2011: 564-576. DOI: 10.1016/j.molonc.2011.08.004.
Bozna, BL; Polzella, P; Rankl, C; Zhu, R; Salio, M; Shepherd, D; Duman, M; Cerundolo, V; and Hinterdorfer, P. “Binding Strength and Dynamics of Invariant Natural Killer Cell T Cell Receptor/CD1d-Glycosphingolipid Interaction on Living Cells by Single Molecule Force Spectroscopy.” Journal of Biological Chemistry 286 (18), May 6, 2011: 15973-15979. DOI: 10.1074/jbc.M110.192674.
Dellinger, DJ; Timár, Z; Myerson, J; Sierzchala, AB; Turner, J; Ferreira, F; Kupihár, Z; Dellinger, G; Hill, KW; Powell, JA; Sampson, JR; and Caruthers, MH. “Streamlined Process for the Chemical Synthesis of RNA Using 2′-O-Thionocarbamate-Protected Nucleoside Phosphoramidites in the Solid Phase.” J. Am. Chem. Soc. 133 (30), June 20, 2011: 11540–11556. DOI: 10.1021/ja201561z.
Huang, Y; Shi, XF; Yu, X; Leymarie, N; Staples, GO; Yin, HF; Killeen, K; and Zaia, J. “Improved Liquid Chromatography-MS/MS of Heparan Sulfate Oligosaccharides via Chip-Based Pulsed Makeup Flow.” Anal. Chem. 83 (21), Sept. 16, 2011: 8222-8229.
DOI: 10.1021/ac201964n.
Kastner, M; Rankl, C; Ebner, A; Pollheimer, PD; Howorka, S; Gruber, HJ; Blaas, D; and Hinterdorfer, P. Bhushan, B. (Ed.) “Nanoimaging, Molecular Interaction, and Nanotemplating of Human Rhinovirus: Scanning Probe Microscopy.” Nanoscience and Nanotechnology, Springer Berlin Heidelberg, 2011, 589-643.
Kinsinger, CR; Apffel, J; Baker, M; Bian, XP; Borchers, CH; Bradshaw, R; Brusniak, MY; Chan, DW; Deutsch, EW; Domon, B; Gorman, J; Grimm, R; Hancock, W; Hermjakob, H; Horn, D; Hunter, C; Kolar, P; Kraus, HJ; Langen, H; Linding, R; Moritz, RL; Omenn, GS; Orlando, R; Pandey, A; Ping, PP; Rahbar, A; Rivers, R; Seymour, SL; Simpson, RJ; Slotta, D; Smith, RD; Stein, SE; Tabb, DL; Tagle, D; Yates, JR; and Rodriguez, H. “Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles).” J Proteome Res. 11 (2), Nov. 4, 2011: 1412-1419. DOI: 10.1021/pr201071t.
Kinsinger, CR; Apffel, J; Baker, M; Bian, XP; Borchers, CH; Bradshaw, R; Brusniak, MY; Chan, DW; Deutsch, EW; Domon, B; Gorman, J; Grimm, R; Hancock, W; Hermjakob, H; Horn, D; Hunter, C; Kolar, P; Kraus, HJ; Langen, H; Linding, R; Moritz, RL; Omenn, GS; Orlando, R; Pandey, A; Ping, PP; Rahbar, A; Rivers, R; Seymour, SL; Simpson, RJ; Slotta, D; Smith, RD; Stein, SE; Tabb, DL; Tagle, D; Yates, JR; and Rodriguez, H. “Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles).” Molecular & Cellular Proteomics 10 (12), Dec. 2011: 1-9. DOI: 10.1074/mcp.O111.015446-1.
Kinsinger, CR; Apffel, J; Baker, M; Bian, XP; Borchers, CH; Bradshaw, R; Brusniak, MY; Chan, DW; Deutsch, EW; Domon, B; Gorman, J; Grimm, R; Hancock, W; Hermjakob, H; Horn, D; Hunter, C; Kolar, P; Kraus, HJ; Langen, H; Linding, R; Moritz, RL; Omenn, GS; Orlando, R; Pandey, A; Ping, PP; Rahbar, A; Rivers, R; Seymour, SL; Simpson, RJ; Slotta, D; Smith, RD; Stein, SE; Tabb, DL; Tagle, D; Yates, JR; and Rodriguez, H. “Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles).” Proteomics 12 (1), Dec. 14, 2011: 11-20. DOI: 10.1002/pmic.201100562.
Kinsinger, CR; Apffel, J; Baker, M; Bian, XP; Borchers, CH; Bradshaw, R; Brusniak, MY; Chan, DW; Deutsch, EW; Domon, B; Gorman, J; Grimm, R; Hancock, W; Hermjakob, H; Horn, D; Hunter, C; Kolar, P; Kraus, HJ; Langen, H; Linding, R; Moritz, RL; Omenn, GS; Orlando, R; Pandey, A; Ping, PP; Rahbar, A; Rivers, R; Seymour, SL; Simpson, RJ; Slotta, D; Smith, RD; Stein, SE; Tabb, DL; Tagle, D; Yates, JR; and Rodriguez, H. ”Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam principles).” Proteomics Clinical Applications 5 (11-12), Dec. 2011: 580-589. DOI: 10.1002/prca.201100097.
Lopez-Avila, V; and Yefchak, G. "Mass Spectral Fragmentation Studies of Coumarin-Type Compounds Using GC High-Resolution MS." The Open Analytical Chemistry Journal (5), August 31, 2011: 27-36.
Manzenreiter, R; Kienberger, F; Marcos, V; Schilcher, K; Krautgartner, WD; Obermayer, A; Huml, M; Stoiber, W; Hector, A; Griese, M; Hannig, M; Studnicka, M; Vitkov, L; Hartl, D. “Ultrastructural Characterization of Cystic Fibrosis Sputum Using Atomic Force and Scanning Electron Microscopy.”J Cyst Fibros. 11(2), March 11, 2012: 84-92.
Mueller, S; Ravi, H; Novoradovskaya, N; Kincaid, R; and Chee, YL. “Enhanced Fish Species Identification By PCR-RFLP Using the 2100 Bioanalyzer System.” International Food Research Journal 18 (3), 2011: 1154-1158.
Neundlinger, I; Poturnayova, A; Karpisova, I; Rankl, C; Hinterdorfer, P; Snejdarkova, M; Hianik, T; and Ebner, A. “Characterization of Enhanced Monovalent and Bivalent Thrombin DNA Aptamer Binding Using Single Molecule Force Spectroscopy.” Biophysical Journal 101 (7), Oct. 5, 2011: 1781-1787.
Oh, YJ; Huber, HP; Hochleitner, M; Duman, M; Bozna, B; Kastner, M; Kienberger, F; and Hinterdorfer, P. “High-frequency Electromagnetic Dynamics Properties of THP1 Cells Using Scanning Microwave Microscopy.” Ultramicroscopy 111 (11), Nov. 2011: 1625-1629. 10.1016/j.ultramic.2011.09.005.
Pareja, F; Ferraro, DA; Rubin, C; Cohen-Dvashi, H; Zhang, F; Aulmann, S; Ben-Chetrit, N; Pines, G; Navon, R; Crosetto, N; Köstler, W; Carvalho, S; Lavi, S; Schmitt, F; Dikic, I; Yakhini, Z; Sinn, P; Mills, GB; and Yarden, Y. “Deubiquitination of EGFR by Cezanne-1 Contributes to Cancer Progression.” Oncogene, Dec 19, 2011. doi: 10.1038/onc.2011.587.
Rankl, C; Wildling, L: Neundlinger, I; Kienberger, F; Gruber, H; Blaas, D; Hinterdorfer. P. “Determination of the Kinetic On- and Off-Rate of Single Virus–Cell Interactions.” Braga, P; and Ricci, D. ed. “Atomic Force Microscopy in Biomedical Research,” Humana Press, New York. Methods in Molecular Biology 736, 2011: 197-210.
Richmond, GS; Khine, H; Zhou, TT; Ryan, DE; Brand, T; McBride, MT; and Killeen, K. "MassCode Liquid Arrays as a Tool for Multiplexed High-Throughput Genetic Profiling." PLoS ONE 6 (4), April 6, 2011: e18967. http://dx.doi.org/10.1371%2Fjournal.pone.0018967.
Singh, A; Bradel, L; Endert, A; Kincaid, R; Andrews, C; and North, C. “Supporting the Cyber Analytic Process Using Visual History on Large Displays.” VizSec '11 Proceedings of the 8th International Symposium on Visualization for Cyber Security, July 20, 2011: Article No. 3. DOI:10.1145/2016904.2016907.
Wildling, L; Unterauer, B; Zhu, R; Rupprecht, A; Haselgrubler, T; Rankl, C; Ebner, A; Vater, D; Pollheimer, P; Pohl, EE; Hinterdorfer, P; and Gruber, HJ. “Linking of Sensor Molecules with Amino Groups to Amino-Functionalized AFM Tips” Bioconjugate Chemistry 22 (6), 2011: 1239-1248. DOI: 10.1021/bc200099t.
Yamada, NA; Rector, LS; Tsang, P; Carr, E; Scheffer, A; Sederberg, MC; Aston, ME; Ach, RA; Tsalenko, A; Sampas, N; Peter, B; Bruhn, L; Brothman, AR. “Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH.” Cytogenet Genome Res 132 (4), Feb. 2011:248-254. DOI: 10.1159/000322717
2010
Avraham, R; Sas-Chen, A; Manor, O; Steinfeld, I; Shalgi, R; Tarcic, G; Bossel, N; Zeisel, A; Amit, I; Zwang, Y; Enerly, E; Russnes, HG; Biagioni, F; Mottolese, M; Strano, S; Blandino, G; Børresen-Dale, AL; Pilpel, Y; Yakhini, Z; Segal, E; and Yarden, Y. “EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors.” Science Signaling 3 (124), June 1, 2010: ra43. DOI: 10.1126/scisignal.2000876.
Butterworth, J; Pao, L; and Abramovitch, D. "Adaptive-Delay Combined Feedforward/Feedback Control for Raster Tracking with Applications to AFMs." Proceedings of the 2010 American Control Conference, June 2010: 5738 – 5744.
Duman, M; Peger, M; Zhu, R; Rankl, C; Chtcheglova, LA; Neundlinger, I; Bozna, BL; Mayer, B; Salio, M; Shepherd, D. et al. "Improved Localization of Cellular Membrane Receptors Using Combined Fluorescence Microscopy and Simultaneous Topography and Recognition Imaging." Nanotechnolgy 21(11), March 19, 2010:115504.
Edvardsen, H; Brunsvig, PF; Solvang, H; Tsalenko, A; Andersen, A; Syvanen, AC; Yakhini, Z; Børresen-Dale, AL; Olsen, H; Aamdal, S; and Kristensen, VN. "SNPs in Genes Coding for ROS Metabolism and Signalling in Association with Docetaxel Clearance." Pharmacogenomics J. 10 (6), Dec. 2010: 513-23. DOI:10.1038/tpj.2010.6.
Flórez, A; Park, D; Bhak, J; Kim, BC; Kuchinsky, A; Morris, JH; and Espinosa, J.” Protein Network Prediction and Topological Analysis in Leishmania Major as a Tool for Drug Target Selection.” BMC Bioinformatics 2010 11:484. DOI:10.1186/1471-2105-11-484.
Formosa, R; Ravi, H; Happe, S; Huffman, D; Novoradovskaya, N; Kincaid, R. and Garrett, S. “DNA-based Fish Species Identification Protocol.” Journal of Visualized Experiments 38, 2010. DOI: 10.3791/1871
Hofer, M; Adamsmaier, S; van Zanten, TS; Chtcheglova, LA; Manzo, C; Duman, M; Mayer, B; Ebner, A; Moertelmaier, M; Kada, G; Garcia-Parajob, MF; Hinterdorfer, P; and Kienberger, F. "Molecular Recognition Imaging Using Tuning Fork-Based Transverse Dynamic Force Microscopy." Ultramicroscopy 110 (6), May 2010: 605 - 611.
Huppa, JB; Axmann, M; Mortelmaier, MA; Lillemeier, BF; Newell, EW; Brameshuber, M; Klein, LO; Schutz, GJ; and Davis, MM. "TCR–Peptide–MHC Interactions In Situ Show Accelerated Kinetics and Increased Affinity." Nature, 463 (7283), Feb. 2010: 963 – 967.
Katletz, S; Stroh, C; Rankl, C; Titulaer, UM; and Hinterdorfer, P. "Force-Induced Lysozyme—HyHEL5 Antibody Dissociation and Its Analysis by Means of a Cooperative Binding Model." Biophysical Journal 99 (7), July 2010: 323-332. DOI:10.1016/j.bpj.2010.03.060
Kienberger, F; Zhu, R; Rankl, C; Gruber, HJ; Blaas, D; and Hinterdorfer, P. "Atomic Force Microscopy Studies of Human Rhinovirus: Topology and Molecular Forces. Methods Enzymol 475, 2010: 515-39.
Kidd, JM; Sampas, N; Antonacci, F; Graves, T; Fulton, R; Hayden, HS; Alkan, C; Malig, M; Ventura, M; Giannuzzi, G; Kallicki, J; Anderson, P; Tsalenko, A; Yamada, NA; Tsang, P; Kaul, R; Wilson, RK; Bruhn, L.; Eichler, E.E. "Characterization of Missing Human Genome Sequences and Copy-Number Polymorphic Insertions." Nature Methods 7, May 2010: 365 - 371.
LeProust, EM; Peck, BJ; Spirin, K; McCuen, HB; Moore, B; Namsaraev, E; Caruthers, MH."Synthesis of High-Quality Libraries of Long (150mer) Oligonucleotides by a Novel Depurination Controlled Process." Nucleic Acids Res. 38 (8), May 1, 2010:2522-40.
Ling, XB; Lau, K; Deshpande, C; Park, JL; Milojevic, D; Macaubas, C; Xiao, C; Lopez-Avila, V; Kanegaye, J; Burns, JC; Cohen, H; Schilling, J; and Mellins, ED. "Urine Peptidomic and Targeted Plasma Protein Analyses in the Diagnosis and Monitoring of Systemic Juvenile Idiopathic Arthritis." Clin Proteomics 6 (4), Dec. 2010: 175-193. DOI 10.1007/s12014-010-9058-8.
Rankl, C; Zhu, R; Luengo, GS; Donovan, M; Baghdadli, N; and Hinterdorfer, P. "Detection of Corneodesmosin on the Surface of Stratum Corneum Using Atomic Force Microscopy." Experimental Dermatology 19 (11), 2010:1014 -1019.
Sudmant, PH; Kitzman, JO; Antonacci, F; Alkan, C; Malig, M; Tsalenko, A; Sampas, N; Bruhn, L; Shendure, J; 1000 Genomes Project; Eichler, EE. "Diversity of Human Copy Number Variation and Multicopy Genes." Science 330 (6004), Oct. 29, 2010: 641 - 646. DOI: 10.1126/science.1197005
Zhu,R; Howorka, S; Pröll, J; Kienberger, F; Preiner, J; Hesse, J; Ebner, A; Pastushenko, VP; Gruber, HJ; and Hinterdorfer, P. "Nanomechanical Recognition Measurements of Individual DNA Molecules Reveal Epigenetic Methylation Patterns." Nature Nanotechnology 5 (11), 2010: 788 - 791. DOI:10.1038/nnano.2010.212
2009
Abramovitch, D. "A Tale of Three Actuators: How Mechanics, Business Models and Position Sensing Affect Different Mechatronic Servo Problems." Proceedings of the American Control Conference, June 2009: 3358 – 3371.
Abramovitch, DY; and Franklin, GF. "Fifty-Five Years in Control: The Story of the CSS.” Proceedings of IEEE Conference on the History of Technical Societies , 2009: 1 – 17.
Abramovitch, DY; Hoen, S; and Workman, R. "Semi-automatic Tuning of PID Gains for Atomic Force Microscopes." Asian Journal of Control 11 (2) March 2009: 188–195.
Bassik, MC; Lebbink, RJ; Churchman, LS; Ingolia, NT; Patena, W; LeProust, EM; Schuldiner, M; Weissman, JS; McManus, MT. “ Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries.” Nat Methods. 6(6), Jun 2009: 443-5.
Butterworth, JA; Pao, LY; and Abramovitch, DY. "A Comparison of Control Architectures for Atomic Force Microscopes." Asian Journal of Control 11 (2), March 2009: 175 - 181.
Dulebo, A; Preiner, J; Kienberger, F; Kada, G; Rankl, C; Chtcheglova, L; Lamprecht, C; Kaftan, D; and Hinterdorfer, P. “Second Harmonic Atomic Force Microscopy Imaging of Live and Fixed Mammalian Cells.” Ultramicroscopy 109 (8), July 2009: 1056-1060. DOI:10.1016/j.ultramic.2009.03.020
Ebner, A; Nevo, R; Rankl, C; Preiner, J; Gruber, H; Kapon, R; Reich, Z; and Hinterdorfer,P. “Probing the Energy Landscape of Protein-Binding Reactions by Dynamic Force Spectroscopy.” Handbook of Single-Molecule Biophysics. Peter Hinterdorfer and Antoine van Oijen, editors. New York: Springer, 2009. 407 - 447.
Gnirke, A; Melnikov, A; Maguire, J; Rogov, P; LeProust, EM; Brockman, W; Fennell, T; Giannoukos, G; Fisher, S; Russ, C; Gabriel, S; Jaffe, DB; Lander, ES; Nusbaum, C. “Solution Hybrid Selection with Ultra-Long Oligonucleotides for Massively Parallel Targeted Sequencing.” Nat Biotechnol. 27 (2), Feb 2009:182-9.
Kincaid, R; and Dejgaard, K. “MassVis: Visual Analysis of Protein Complexes Using Mass Spectrometry.” IEEE Symposium on Visual Analytics Science and Technology (VAST ‘09), October 2009. DOI: 10.1109/VAST.2009.5333895
Lamprecht, C; Danzberger, J; Lukanov, P; Tîlmaciu, CM; Galibert, AM; Soula, B; Flahaut, E; Gruber, HJ; Hinterdorfer, P; Ebner, A; Kienberger, F. “AFM Imaging of Functionalized Double-Walled Carbon Nanotubes.” Ultramicroscopy, 109 (8), July 2009: 899 - 906. DOI:10.1016/j.ultramic.2009.03.034
Lamprecht, C; Liashkovich, I; Neves, V; Danzberger, J; Heister, E; Rangl, M; Coley, HM; McFadden, J; Flahaut, E; Gruber, HJ; Hinterdorfer, P; Kienberger, F; and Ebner, A. “AFM Imaging of Functionalized Carbon Nanotubes on Biological Membranes.” Nanotechnology 20 (43), October 28, 2009: 434001. DOI: 10.1088/0957-4484/20/43/434001
Li, JB; Gao, Y; Aach, J; Zhang, K; Kryukov, GV; Xie, B; Ahlford, A; Yoon, JK; Rosenbaum, AM; Zaranek, AW; LeProust, E; Sunyaev, SR; Church, G.M. “Multiplex Padlock Targeted Sequencing Reveals Human Hypermutable CpG Variations.” Genome Res. 19(9), Sep 2009:1606-15.
Li, JB; Levanon, EY; Yoon, JK; Aach, J; Xie, B; Leproust, E; Zhang, K; Gao, Y; Church, GM. “ Genome-Wide Identification of Human RNA Editing Sites By Parallel DNA Capturing and Sequencing.” Science 324 (5931), May 29, 2009:1210-3.
Lopez-Avila, V; Robinson, WH; and Lokits, K. “Ceruloplasmin Levels in Human Sera from Various Diseases and Their Correlation with Patient’s Age and Gender.“ Health 1 (2), Sept. 2009: 104-110. DOI:10.4236/health.2009.12017.
Lopez-Avila, V; and Yefchak, G. "Identification of Compounds in Commercial Kava Extracts by Gas Chromatography with Electron Ionization High-Resolution Mass Spectrometry." The Open Analytical Chemistry Journal 3, 2009: 22-31. DOI:10.2174/1874065000903010022
Mahringer, C; Fureder, M; Kastner, M; Ebner, A; Hinterdorfer, P; Vitkov, L; Hannig, M; Kienberger, F; Schilcher, K. “Examination of Native and Carbamide Peroxide-Bleached Human Tooth Enamel by Atomic Force Microscopy.” Ultrastruct Pathol. 33 (5), Oct. 2009: 189-96.
Spindler, V; Heupel, WM; Efthymiadis, A; Schmidt, E; Eming, R; Rankl, C; Hinterdorfer, P; Müller, T; Drenckhahn, D; and Waschke, J. “Desmocollin 3-Mediated Binding is Crucial for Keratinocyte Cohesion and is Impaired in Pemphigus.” Journal of Biological Chemistry, 284 (44), Oct. 2009: 30556 -30564.
2008
Abramovitch, DY. “ Efficient and Flexible Simulation of Phase Locked Loops, Part I: Simulator Design.'' Proceedings of the American Control Conference, June 2008: 4672 – 4677.
Abramovitch, DY. “ Efficient and Flexible Simulation of Phase Locked Loops, Part II: Post Processing and a Design Example.” Proceedings of the American Control Conference, June 2008. 4678 – 4683.
Abramovitch, DY; Hoen, S; and Workman, R. "Semi-automatic Tuning of PID Gains for Atomic Force Microscopes." Proceedings of 2008 American Control Conference, June 2008: 2684 – 2689.
Artelsmair, H; Kienberger, F; Tinazli, A; Schlapak, R; Zhu, R; Preiner, J; Wruss, J; Kastner, M; Saucedo-Zeni, N; Hoelzl, M; Rankl, C; Baumgartner, W; Howorka, S; Blaas, D; Gruber, HJ; Tampé, R; Hinterdorfer, P. “Atomic Force Microscopy-Derived Nanoscale Chip for the Detection of Human Pathogenic Viruses.” Small 4 (6), June 2008: 847–854. DOI: 10.1002/smll.200700691
Ashcroft, BA; Spadola, Q; Qamar, S; Zhang, P; Kada, G; Bension, R; and Lindsay, S. “An AFM/Rotaxane Molecular Reading Head for Sequence-Dependent DNA Structures.” Small 4 (9), Sept. 2008: 1468-1475. DOI: 10.1002/smll.200800233
Barsky, A; Munzner, T; Gardy, J; and Kincaid, R. “Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context.” IEEE Transactions on Visualization and Computer Graphics (InfoVis ’08) 14 (6), Nov.- Dec. 2008: 1253 - 1260. DOI:10.1109/TVCG.2008.117
Butterworth, J; Pao, L; and Abramovitch, D. “The Effect of Nonminimum-Phase Zero Locations on the Performance of Feedforward Model-Inverse Control Techniques in Discrete-Time Systems.” Proceedings of the American Control Conference, June 2008: 2696 – 2702.
Ebner, A; Marek, M; Kaiser, K; Kada, G; Hahn, CD; Lackner, B; and Gruber, H J. “Application of Biotin-4-Fluorescein in Homogeneous Fluorescence Assays for Avidin, Streptavidin and Biotin or Biotin Derivatives." Methods in Molecular Biology. Volume 418: Avidin-Biotin Interactions. Methods and Applications (McMahon, R.J., Ed.) pp 73-88, Chapter 7, Humana Press, Totowa, NJ. (2008).
Kada, G; Kienberger, F; and Hinterdorfer, P. “Atomic Force Microscopy in Bionanotechnology.” Nano Today 3 (1-2), Feb. - April 2008: 12-19. DOI:10.1016/S1748-0132(08)70011-2
Kidd, JM; Cooper, GM; Donahue, WF; Hayden, HS; Sampas, N; Graves, T; Hansen, N; Teague, B; Alkan, C; Antonacci, F; Haugen, E; Zerr, T; Yamada, NA; Tsang, P; Newman, TL; Tüzün, E; Cheng, Z; Ebling, HM; Tusneem, N; David, R; Gillett, W; Phelps, KA; Weaver, M; Saranga, D; Brand, A; Tao, W; Gustafson, E; McKernan, K; Chen, L; Malig, M; Smith, JD; Korn, JM; McCarroll, SA; Altshuler, DA; Peiffer, DA; Dorschner, M; Stamatoyannopoulos, J; Schwartz, D; Nickerson, DA; Mullikin, JC; Wilson, RK; Bruhn, L; Olson, MV; Kaul, R; Smith DR; and Eichler, EE. “Mapping and Sequencing of Structural Variation from Eight Human Genomes.” Nature 453, May 1, 2008: 56-64. DOI:10.1038/nature06862.
Kincaid, R. Kuchinsky, A; and Creech, M. “VistaClara: An Expression Browser Plug-in for Cytoscape.” Bioinformatics 24 (18), Sept. 15, 2008: 2112–2114. DOI:10.1093/bioinformatics/btn368
Lopez-Avila, V; and Spencer, JV. “Methods for Detection of Matrix Metalloproteinases as Biomarkers in Cardiovascular Disease.” Clinical Medicine: Cardiology 2, 2008:1–14.
Lu, J; Yuan, D; Liu, J; Leng, W; and Kopley, TE. “Three Dimensional Single-Walled Carbon Nanotubes.” ASAP Nano Lett., Sept. 5, 2008. DOI: 10.1021/nl801744z.
Perry, GH; Ben-Dor, A; Tsalenko, A; Sampas, N; Rodriguez-Revenga, L; Tran, CW; Scheffer, A; Steinfeld, I.; Tsang, P; Yamada, NA; Park, HS; Kim, JI; Seo, JS; Yakhini, Z; Laderman, S; Bruhn, L; and Lee, C. "The Fine-Scale and Complex Architecture of Human Copy-Number Variation." The Journal of Human Genetics 82, March 2008: 1-11. DOI:10.1016/j.ajhg.2007.12.010.
Rankl, C; Kienberger, F; Wildling, L; Wruss, J; Gruber, HJ; Blaas, D; Hinterdorfer, P. “Multiple Receptors Involved in Human Rhinovirus Attachment to Live Cells.” Proceedings of the National Academy of Sciences 105 (46), Nov. 2008: 17778-17783. DOI: 10.1073/pnas.0806451105
Sun, H; Chua, MS; Yang, D; Tsalenko, A; Peter BJ; and So, S. "Antibody Arrays Identify Potential Diagnostic Markers of Hepatocellular Carcinoma." Biomarker Insights 2008:3 1-18.
Valenta, J; Fucikova, A; Pelant, I; Kůsová, K; Dohnalová, K; Aleknavičius, A; Cibulka, O; Fojtík, A; and Kada, G. “On the Origin of the Fast Photoluminescence Band in Small Silicon Nanoparticles." New Journal of Physics 10, July 11, 2008: 073022. DOI:10.1088/1367-2630/10/7/073022.
Vitkov, L; Kastner, M; Kienberger, F; Hinterdorfer, P; Schilcher, K; Grunert, I; Dumfahrt, H; and Krautgartner, WD. “Correlations between AFM and SEM Imaging of Acid-Etched Tooth Enamel.”  Ultrastructural Pathology 32 (1), Jan-Feb. 2008:1 – 4.DOI: 10.1080/01913120701808065
Zhang, M; Liu, M; Prest, H; Fischer, S. “Nanoparticles Secreted from Ivy Rootlets for Surface Climbing.” Nano Lett. 2008; ASAP Article; DOI: 10.1021/nl0725704.
2007
Abramovitch, DY; Andersson, SB; Pao, LY; and Schitter, G. “A Tutorial on the Mechanisms, Dynamics, and Control of Atomic Force Microscopes.'' Proceedings of the American Control Conference, July 2007: 3488 – 3502.
Ach, RA; Floore, A; Curry, B; Lazar, V; Glas, AM; Pover, R; Tsalenko, A; Ripoche, H; Cardoso, F; Saghatchian d’Assignies, M; Bruhn, L; and Van’t Veer, LJ. “Robust Interlaboratory Reproducibility of a Gene Expression Signature Measurement Consistent with the Needs of a New Generation of Diagnostic Tools.” BMC Genomics 8, 2007: 148.
Andersson, SB; and Abramovitch, DY. “A Survey of Non-Raster Scan Methods with Application to Atomic Force Microscopy.'' Proceedings of the American Control Conference, July 2007: 3516 – 3521.
Ben-Dor, A; Lipson, D; Tsalenko, A; Reimers, M; Baumbusch, LO; Barrett, MT; Weinstein, JN; Børresen-Dale, AL; and Yakhini, Z. “Framework for Identifying Common Aberrations in DNA Copy Number Data.” RECOMB 2007: 122-136.
Bynum, MA; VanWiggeren, GD; Thrush, E; Jefferson, S; Robotti, K; Baney, DM; and Killeen, K. "Novel Sensor Architecture for High-throughput and High-sensitivity Biomolecular Interaction Analysis."
LEOS Summer Topical Meetings, 2007 Digest of the IEEE,
July 23-25, 2007: 131 - 132. DOI 10.1109/LEOSST.2007.4288367.
Davies-Tuck, M; Lee, TH; Apffel, A; and Aguilar, MI. "Hydrophobic and Electrostatic Forces Control the Retention of Membrane Peptides and Proteins With an Immobilised Phosphatidic Acid Column." Journal of Chromatography A, 1156, 2007: 167-173.
de Smith, AJ; Tsalenko, A; Sampas, N; Scheffer, A; Yamada, NA; Tsang, P; Ben-Dor, A; Yakhini, Z; Ellis, RJ; Bruhn, L; Laderman, S; Froguel, P; and Blakemore, AIF. “Array CGH Analysis of Copy Number Variation Identifies 1284 New Genes Variant in Healthy White Males: Implications for Association Studies of Complex Diseases.” Human Molecular Genetics, Advance Access, July 31, 2007: DOI:10.1093/hmg/ddm208.
Keats, JJ; Fonseca, R; Chesi, M; Schop, R; Baker, A; Chng, WJ; Wier, SV; Tiedemann, R; Chi, CX; Sebag, M; Braggio, E; Henry, T; Zhu, YX; Fogle, H; Price-Torska, T; Ahmann, G; Mancini, C; Brents, LA; Kumar, S; Greipp, P; Dispenzieri, A; Bryant, B; Mulligan, G; Bruhn, L; Barrett, M; Valdez, R; Trent, J; Stewart, AK; Carpten, J; and Bergsagel, PL. “Promiscuous Mutations Activate the Noncanonical NF-kB Pathway in Multiple Myeloma.” Cancer Cell 12, Aug. 2007: 131-144.
Kienberger,F;Â Costa, LT;Â Zhu, R; Kada, G; Reithmayer, M; Chtcheglova, L; Rankl, C; Pacheco, ABF; Thalhammer, S; Pastushenko, V; Heckl, WM; Blaas, D; and Hinterdorfer, P. “Dynamic Force Microscopy Imaging of Plasmid DNA and Viral RNA.” Biomaterials 28 (15), May 2007:2403 - 2411.
Lam, H; Munzner, T; and Kincaid, R. “Overview Use in Multiple Visual Information Resolution Interfaces.” Transactions on Visualization and Computer Graphics 13(6), Nov.-Dec. 2007: 1278-1285.
Middleton, F; Rosenow, C; Vailaya, A; Kuchinsky, A; Pato, C; and Pato, M. “Integrating Genetic, Functional Genomic, and Bioinformatics Data in a Systems Biology Approach to Complex Diseases: Application to Schizophrenia.” in Methods in Molecular Biology, Neuroinformatics, Humana Press, ISBN13: 978-1-58829-720-4, July 2007.
Pao, LY; Butterworth, JA; and Abramovit ch, DY. “Combined Feedforward/Feedback Control of Atomic Force Microscopes.'' Proceedings of the American Control Conference, July 2007: 3509—3515.
Paris, PL; Sridharan, S; Scheffer, A; Tsalenko, A; Bruhn, L; and Collins, C. “High Resolution Oligonucleotide CGH Using DNA From Archived Prostate Tissue.” Prostate 67(13), Jul 24, 2007:1447-1455.
Perkins, J; Clavijo, A; Ortiz, JI; Salo, TJ; Holland, H; Hindson, BJ; and McBride, MT. “Toward a Multiplexed Serotyping Immunoassay for Foot-and-mouth Disease Virus.” Journal of Veterinary Diagnostic Investigation 19, 2007: 180-184.
Svensson, AM; Curry, CJ; South, ST; Whitby, H; Maxwell, TM; Aston, E; Fisher, J; Carmack, C.E; Scheffer, A; Abu-Shamsieh, A; and Brothman, A.R. “Detection of a De Novo Interstitial 2q Microdeletion by CGH Microarray Analysis in a Patient with Limb Malformations, Microcephaly and Mental Retardation.” American Journal of Medical Genetics. Part A, 143(12), Jun 15, 2007:1348-1353.
VanWiggeren, GD; Bynum, MA; Ertel, JP; Jefferson, S; Robotti, KM; Thrush, EP; Baney, DM; Killeen, KP. "A Novel Optical Method Providing for High-sensitivity and High-throughput Biomolecular Interaction Analysis." Sensors and Actuators B: Chemical 127 (2), Nov. 15, 2007: 341-349.
Wang, H; Ach, RA; and Curry, B. “Direct and Sensitive miRNA Profiling from Low-Input Total RNA.”RNA 13 2007: 151-159.
Yin, H; and Killeen, K. “The Fundamental Aspects and Applications of Agilent HPLC-Chip.” Journal of Separation Science 30, 2007: 1427-1434.
Yosef, N; Yakhini, Z; Tsalenko, A; Kristensen, V; Børresen-Dale, AL; Ruppin, E; and Sharan, R. “A Supervised Approach for Identifying Discriminating Genotype Patterns and Its Application to Breast Cancer Data.” Bioinformatics 23(2), 2007: 91-98.
2006
Ashley, E; Ferrara, R; King, JY; Vailaya, A; Kuchinsky, A; He, X; Byers, B; Gerckens, U; Oblin, S; Tsalenko, A; Soito, A; Spin, JM; Tabibiazar, R; Connolly, AJ; Simpson, JB; Grube, E; and Quertermos, T. “Network Analysis of Human In-Stent Restenosis”, Circulation, Dec. 4, 2006: 2644-2654.
Carter, JC; Alvis, RM; Brown, SB; Langry KC; Wilson. TS; McBride, MT; Myrick. ML; Cox, WR; Grove, ME; and Colston, BW. “Fabricating Optical Fiber Imaging Sensors Using Inkjet Printing Technology: A pH Sensor Proof-of-concept.” Biosensors and Bioelectronics 21, 2006, 1359-1364.
Deng, DXF; Tsalenko, A; Vailaya, A; Ben-Dor, A; Kundu, R; Estay, I; Tabibiazar, R; Kincaid, R; Yakhini, Z; Bruhn, L; and Quertermous, T. "Differences in Vascular Bed Disease Susceptibility Reflect Differences in Gene Expression Response to Atherogenic Stimuli," Circulation Research 98, 2006: 200-208.
Deng, DXF; Spin, JM; Tsalenko, A; Vailaya, A; Ben-Dor, A; Yakhini, Z; Tsao, P; Bruhn, L; and Quertermous, T. “Molecular Signatures Determining Coronary Artery and Saphenous Vein Smooth Muscle Cell Phenotypes: Distinct Responses to Stimuli.” Arteriosclerosis, Thrombosis, and Vascular Biology 26, 2006: 1058 - 1065.
Ghitun, M; Bonneil, E; Fortier, M; Yin, H; Killeen, K; and Thibault, P. “Integrated Microfluidic Devices with Enhanced Separation Performance: Application to Phosphoproteome Analyses of Differentiated Cell Model Systems.” Journal of Separation Science 29, 2006: 1539-1549.
Hindson, BJ; McBride. MT; Makarewicz, AJ; Henderer, BD; Setlur, US; Smith, SM; Guitierrez, DM; Metz, TR; Nasarabadi, SL; Venkateswaran, KS; Farrow, SW; Colston, BW; and Dzenitis, JM. “Autonomous detection of Aerosolized Agents by Multiplexed Immunoassays with PCR Confirmation.” Analytical Chemistry 77, 2005: 284-289.
Kincaid R; and Lam, H. "Line Graph Explorer: Scalable Display of Line Graphs Using Focus+Context," in Proceedings of the Working Conference on Advanced Visual Interfaces. Venezia, Italy: ACM Press, 2006: 404-411.
Kristensen, VN; Edvardsen, H; Tsalenko, A; Nordgard, SH; Sorlie, T; Sharan, R; Vailaya, A; Ben-Dor, A; Lonning, PE; Lien, S; Omholt, S; Syvanen, AC; Yakhini, Z; Borresen-Dale, AL. “Genetic variation in putative regulatory loci controlling gene expression in breast cancer.” Proc Natl Acad Sci. 20, May 16, 2006:7735-40.
Lopez-Avila, V; Sharpe, O; and Robinson, W. “Determination of Ceruloplasmin in Human Serum by SEC-ICPMS.” Analytical and Bioanalytical Chemistry 386 (1), Sept. 2006: 180-188. DOI 10.1007/s00216-006-0528-9.
Lu, J; Kopley, T; Button, D; Liu, J; Qian, C; Son, H; Dresselhaus, M; and Kong, J. “Generating Suspended Single-walled Carbon Nanotubes Across a Large Surface Area Via Patterning Self-assembled Catalyst-containing Block Copolymer Thin Flms Source.” Journal of Physical Chemistry B 110 (22), Jun 8, 2006: 10585-10589.
Lu, J; Yi, SS; Kopley, T; Qian, C; Liu, J; and Gulari, E. “Fabrication of Ordered Catalytically Active Nanoparticles Derived from Block Copolymer Micelle Templates for Controllable Synthesis of Single-walled Carbon Nanotubes.” Journal of Physical Chemistry B 110 (13), May 6, 2006: 6655-6660.
McBride, MT. “Diagnosing Flu Fast.“ Science & Technology Review, Dec. 2006: 4-9.
Ninonuevo, M; Park, Y; Yin, H; Zhang, J; Ward, RE; Clowers, BH; German, JB; Freeman, SL; Killeen, K; Grimm, R; and Lebrilla, CB. “A Strategy for Annotating the Human Milk Glycome.” Journal of Agricultural and Food Chemistry 54, 2006: 7471.
Papalia, GA; Leavitt, S; Bynum, MA; Katsamba, PS; Wilton, R; Qiu, H; Steukers, M; Wang, S; Bindu, L; Phogat, S; et al. “Comparative Analysis of Ten Small Molecules Binding to Carbonic Anhydrase II by Different Investigators using Biacore Technology.” Analytical Biochemistry 359, 2006: 94-105.
Perkins, J; Clavijo, A; Hindson, BJ; Lenhoff, RJ; and McBride. MT. “Multiplexed Detection of Antibodies to Non-structural Proteins of Foot-and-Mouth Disease Virus.” Analytical Chemistry 78, 2006: 5462-5468.
Kristensen, VN; Edvardsen, H; Tsalenko, A; Nordgard, S; Sørlie, T; Sharan, R; Vailaya, A; Ben-Dor, A; Lønning, PE; Lien, S; Omholt, S; Syvanen, AC; Yakhini, Z; and Børresen-Dale, A.L. ”SNPs in Putative Regulatory Loci Controlling Gene Expression in Cancer,” Proceedings of the National Academy of Sciences of the United States of America 103, May 16, 2006: 7735-7740.
2005
Hindson, BJ; Makarewicz, AJ; Setlur, US; Henderer, BD; McBride. MT; and Dzenitis, JM APDS: “The Autonomous Pathogen Detection System.” Biosensors and Bioelectronics 20, 2005: 1925 1931.
Hindson, BJ; McBride, MT; Makarewicz, AJ; Henderer, BD; Setlur, US; Smith, SM; Guitierrez, DM; Metz, TR; Nasarabadi, SL; Venkateswaran, KS; Farrow, SW; Colston, BW; and Dzenitis, JM. “Autonomous detection of Aerosolized Agents by Multiplexed Immunoassays with PCR Confirmation.” Analytical Chemistry 77, 2005: 284-289.
Kincaid, R; Ben-Dor, A; and Yakhini, Z. "Exploratory Visualization of Array-based Comparative Genomic Hybridization," Information Visualization 4, 2005: 176-190.
King, JY; Ferrara, R; Tabibiazar, R; Spin, JM; Chen, MM; Kuchinsky, A; Vailaya, A; Kincaid, R; Tsalenko, A; Deng, DXF; Connolly, A; Zhang, P; Yang, E; Watt, C; Yakhini, Z; Ben-Dor, A; Adler, A; Bruhn, L; Tsao, P; Quertermous, T; and Ashley, EA. "Pathway Analysis of Coronary Atherosclerosis," Physiological Genomics 23, 2005: 103-118.
Lu, J; Kopley, TE; Hueschen, M; Moll, N; Bai, J; Yang, D; Fu, Q; Liu, J; Rider, D; Manners, I; and Winnik, MA. “Single-walled Carbon Nanotubes with Small Diameter, Controlled Density and Defined Locations Produced from Catalyst-containing Polymer Films.” 2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005 Technical Proceedings, 2005: 132-135.
Lu, JQ; Kopley, TE; Moll, N; Roitman, D; Chamberlin, D; Fu, Q; Liu, J; Russell, TP; Rider, DA; Manners, I; and Winnik, MA. “High-quality Single-walled Carbon Nanotubes with Small Diameter, Controlled Density, and Ordered Locations Using a Polyferrocenylsilane Block Copolymer Catalyst Precursor.” Chemistry of Materials 17(9), May 3, 2005: 2227-2231.
McBride, MT; Messenger, SM; Slezak,TR; and Imbro, PM. "Tailored Assays for Detection of Foreign Animal Disease Pathogens: Toward Enhanced Agro Terrorism Security." In Vitro Diagnostics Technology 11, 2005: 49-52.
Niñonuevo, M; An, H; Yin, H; Killeen, K; Grimm, R; German, B; and Lebrilla, C. “Nanoliquid Chromatography-Mass Spectrometry of Oligosaccharides Employing Graphitized Carbon Chromatography on Microchip with High Accuracy Mass Analyzer.” Electrophoresis 26, 2005: 3641.
Vailaya, A; Bluvas, P; Kincaid, R; Kuchinsky, A; Creech, M; and Adler, A. "An Architecture for Biological Information Extraction and Representation," Bioinformatics 21, 2005: 430-438.
Yin, H; Killeen, K; Brennen, R; Sobek, D; Werlich, M; and van de Goor, T. “Microfluidic Chip for Peptide Analysis with an Integrated HPLC Column, Sample Enrichment Column, and Nanoelectrospray Tip.” Analytical Chemistry 77, 2005: 527.
Rosenow, C; Vailaya, A; Kuchinsky, A; and Middleton, FA. "Combining Expression and Genotyping Analysis in Neuropsychiatric Research.” Ed. B. Alysun. Agilent GeneSpring Platform Application Note, Dec. 19, 2005.
2004
Abramovitch, DY, and Franklin, GF. "Fifty Years in Control: The Story of the IEEE Control Systems Society." IEEE Control Systems Magazine, 24 (6), Dec. 2004: 19-36.
Barrett, MT; Scheffer, A; Ben-Dor, A; Sampas, N; Lipson, D; Kincaid, R; Tsang, P; Curry, B; Baird, K; Meltzer, PS; Yakhini, Z; Bruhn, L; andLaderman, S. "Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA," Proceedings of the National Academy of Sciences of the United States of America 101, Dec. 10, 2004: 17765-17770.
Bynum, MA; and Gordon, G.B. “Hybridization Enhancement Using Microfluidic Planetary Centrifugal Mixing.” Analytical Chemistry 76, 2004: 7039-7044.
Cannon MJ; Papalia GA; Navratilova I; Fisher RJ; Roberts LR; Worthy KM; Stephen AG; Marchesini GR; Collins EJ; Casper D; Qiu H; Satpaev D; Liparoto SF; Rice DA; Gorshkova II; Darling RJ; Bennett DB; Sekar M; Hommema E; Liang AM; Day ES; Inman J; Karlicek SM; Ullrich SJ; Hodges D; Chu T; Sullivan E; Simpson J; Rafique A; Luginbuhl B; Westin SN; Bynum M; Cachia P; Li YJ; Kao D; Neurauter A; Wong M; Swanson M; Myszka DG. “Comparative Analyses of a Small Molecule/enzyme Interaction by Multiple Users of Biacore Technology.” Analytical Biochemistry 330, 2004: 98-113.
Hindson, BJ; Brown, SB; Marshall, GD; McBride, MT; Makarewicz, AJ; Gutierrez, DM; Wolcott, DW; Metz, TR; Madabhushi, R; Dzenitis, JM; and Colston, BW. “Development of an Automated Sample Preparation Module for Environmental Monitoring of Biowarfare Agents.” Analytical Chemistry 76, 2004: 3492-3497.
Kincaid, R. "VistaClara: an Interactive Visualization for Exploratory Analysis of DNA Microarrays," in Proceedings of the 2004 ACM Symposium on Applied Computing. Nicosia, Cyprus: ACM Press, 2004: 167-174.
Rao, RS; Visuri, SR; McBride, MT; Albala, JS; Matthews, DL; and Coleman, MA. “A Comparison of Multiplexed Techniques for Detection of Bacterial and Viral Proteins.” Journal of Proteome Research 3(4), 2004: 736-742.
Rozing, GG; van de Goor, T; Yin, H; Killeen, K; Glatz, B; Kraiczek, K; and Lauer, H. “An Experimental Study of Chromatographic Dynamics in Open and Packed non-Cylindrical Conduits,” Journal of Separation Science 27, 2004: 1391.
Vailaya, A; Bluvas, P; Kincaid, R; Kuchinsky, A; Creech, M; and Adler, A. "An Architecture for Biological Information Extraction and Representation," in Proceedings of the 2004 ACM Symposium on Applied Computing. Nicosia, Cyprus: ACM Press, 2004: 103-110.
2003
Chen, MM; Ashley, EA; Deng, DX; Tsalenko, A; Deng, A; Tabibiazar, R; Ben-Dor, A; Fenster, B; Yang E; King, J.Y; Fowler, M; Robbins, R; Johnson, FL; Bruhn, L; McDonagh, T; Dargie, H; Yakhini, Z; Tsao, PS; and Quertermous, T. “Novel Role for the Potent Endogenous Inotrope Apelin in Human Cardiac Dysfunction.” Circulation 108 (12), Sep. 23, 2003:1432-1439.
Ho. M; Yang, E; Matcuk, G; Deng, D; Sampas, N; Tsalenko, A; Tabibiazar, R; Zhang, Y; Chen, M; Talbi, S; Ho, Y.D; Wang, J; Tsao, P.S; Ben-Dor, A; Yakhini, Z; Bruhn, L; and Quertermous, T. “Identification of Endothelial Cell Genes by Combined Database Mining and Microarray Analysis.” Physiol Genomics 13(3), May 13, 2003: 249-262.
McBride, MT; Masquelier, DA; Hindson, BJ; Makarewicz, AJ; Brown, SB; Burris, K; Metz, T; Langlois, RG; Tsang, KT; Bryan, R; Anderson, DO; Venkateswaran, KS; Milanovich, FP; and Colston, B.W. “Autonomous Detection of Aerosolized Bacillus anthracis and Yersinia pestis.” Analytical Chemistry 75, 2003: 5293-529.
McBride, MT; Gammon, S; Pitesky, M; O’Brien, TW; Smith, T; Aldrich, J; Langlois, R; and Venkateswaran, KS. “Multiplexed Liquid Arrays for Simultaneous Detection of Simulants of Biological-Warfare Agents.” Analytical Chemistry 75, 2003: 1924-1930.
2002
Kuchinsky, A; Graham, K; Moh, D; Creech, M; Babaria, K; and Adler, A. “Biological Storytelling: A Software Tool for Biological Information Organization Based on Narrative Structure,” ACM SIGGROUP Bulletin 23 (2), August 2002: 4-5.
Kuchinsky, A; Graham, K; Moh, D; Creech, M; Babaria, K; and Adler, A. “Biological Storytelling: A Software Tool for Biological Information Organization Based on Narrative Structure, “ Proceedings of AVI: International Working Conference on Advanced Visual Interfaces Trento, Italy, May 22-24, 2002.
2001
Delenstarr, G; Cattell, H; Chen, C; Dorsel, AN; Kincaid, RH; Nguyen, K; Sampas, NM; Schidel, S; Shannon, KW; Tu, A; and Wolber, PK. "Estimation of the Confidence Limits of Oligonucleotide-array-based Measurements of Differential Expression" in Proceedings of SPIE 4266, 2001: 120-131.
O’Day, V; Adler, A; Kuchinsky, A; and Bouch, A. “When Worlds Collide: Molecular Biology as Interdisciplinary Collaboration,” Proceedings of European Computer Supported Collaborative Work, Bonn, Germany. September 2001: 399 – 418.
Ito, M; O’Day, V; Adler, A; Linde, C; and Mynatt, E. “Making a Place for Seniors on the Net: SeniorNet, Senior Identity and the Digital Divide,” ACM SIGCAS Computers and Society 31(3), September 2001: 15-21.
2000
Ben-Dor A; Bruhn, L; Friedman, N; Nachman, I; Schummer, M; and Yakhini, Z. “Tissue Classification with Gene Expression Profiles.” J Comput Biol. 7(3-4), 2000:559-83.