Publications

TABLE OF CONTENTS

  • Peer reviewed
  • Conferences
  • Patents & patent applications
  • Unpublished manuscripts & technical reports
  • citation analysis

PEER REVIEWED

  1. Timothy R. Julian, Joseph D. Baugher, Christine Rippinger, Rebecca Pinekenstein, Abimbola O. Kolawole, Thomas Mehoke, Christiane E. Wobus, Andrew Feldman, Fernando J. Pineda, Kellogg J. Schwab, Murine norovirus (MNV-1) exposure in vitro to the purine nucleoside analog Ribavirin increases quasispecies diversity. Virus Research, accepted Oct. 2015.
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  2. Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ and Hardwick JM, Genome-wide Consequences of Deleting Any Single Gene.Mol Cell. 2013 Nov 6. pii: S1097-2765(13)00748-X. doi: 10.1016/j.molcel.2013.09.026.
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    Media Coverage: The ScientistScience DailyHealth News Digest, e!Science News
  3. Teng, X., Cheng, W.C., Qi, B., Yu, T.X., Ramachandran, K., Boersma, M.D., Hattier, T., Lehmann, P.V., Pineda, F.J., and Hardwick, J.M., Gene-dependent cell death in yeast. Cell Death Dis, 2011. 2: p. e188.
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  4. Leek, J.T., Taub, M.A., and Pineda, F.J., Cooperation between Referees and Authors Increases Peer Review Accuracy. PLoS ONE, 2011. 6(11): p. e26895.
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    Media Coverage: BioTechniques
  5. Chen, Y.B., Aon, M.A., Hsu, Y.T., Soane, L., Teng, X., McCaffery, J.M., Cheng, W.C., Qi, B., Li, H., Alavian, K.N., Dayhoff-Brannigan, M., Zou, S., Pineda, F.J., O’Rourke, B., Ko, Y.H., Pedersen, P.L., Kaczmarek, L.K., Jonas, E.A., and Hardwick, J.M., Bcl-xL regulates mitochondrial energetics by stabilizing the inner membrane potential. J Cell Biol, 2011. 195(2): p. 263-76.
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  6. Norris, L.C., Fornadel, C.M., Hung, W.C., Pineda, F.J., and Norris, D.E., Frequency of multiple blood meals taken in a single gonotrophic cycle by Anopheles arabiensis mosquitoes in Macha, Zambia. Am J Trop Med Hyg, 2010. 83(1): p. 33-7.
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  7. Berman, S.B., Chen, Y.B., Qi, B., McCaffery, J.M., Rucker, E.B., 3rd, Goebbels, S., Nave, K.A., Arnold, B.A., Jonas, E.A., Pineda, F.J., and Hardwick, J.M., Bcl-x L increases mitochondrial fission, fusion, and biomass in neurons. J Cell Biol, 2009. 184(5): p. 707-19.
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  8. Syversen, E., Pineda, F.J., and Watson, J., Temperature variations recorded during interinstitutional air shipments of laboratory mice. J Am Assoc Lab Anim Sci, 2008. 47(1): p. 31-6.
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  9. Berman, S.B., Pineda, F.J., and Hardwick, J.M., Mitochondrial fission and fusion dynamics: the long and short of it. Cell Death Differ, 2008. 15(7): p. 1147-52.
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  10. Kafsack, B.F., Carruthers, V.B., and Pineda, F.J., Kinetic modeling of Toxoplasma gondii invasion. J Theor Biol, 2007. 249(4): p. 817-25.
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  11. Cheng, W.C., Berman, S.B., Ivanovska, I., Jonas, E.A., Lee, S.J., Chen, Y., Kaczmarek, L.K., Pineda, F., and Hardwick, J.M., Mitochondrial factors with dual roles in death and survival. Oncogene, 2006. 25(34): p. 4697-705.
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  12. Kumar, N., Cha, G., Pineda, F., Maciel, J., Haddad, D., Bhattacharyya, M., and Nagayasu, E., Molecular complexity of sexual development and gene regulation in Plasmodium falciparum. Int J Parasitol, 2004. 34(13-14): p. 1451-8.
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  13. Wang, I.-J., Diehl, C., and Pineda, F., A Statistical Model of Proteolytic Digestion, in Computational Systems Bioinformatics, 2003 2003. Stanford University: IEEE Computer Society.
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  14. Pineda, F.J., Antoine, M.D., Demirev, P.A., Feldman, A.B., Jackman, J., Longenecker, M., and Lin, J.S., Microorganism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers. Anal Chem, 2003. 75(15): p. 3817-22.
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  15. Pineda, F., A Database for MALDI-TOF-MS Rapid Microorganism Identification, in AMS Biodefense Conference. 2003. Baltimore, MD.
  16. Pineda, F., Antoine, M., Demirev, P., Feldman, A., Jackman, J., and Lin, J., Towards Model-based Microorganism Identification for MALDI-TOF-MS, in 50th Annual ASMS conference. 2002. Orlando, FL.
  17. Lin, J.S., Bryden, W.A., Pineda, F.J., Resch, C.L., Saksena, A., and Feldman, A.B., A fully-automated peak extraction and baseline estimation method for high-throughput MALDI-TOF-MS-based detection of biological agents, in 50th ASMS Conference. 2002.
  18. Pineda, F.J., Antoine, M., Amy Karlson, J.L., Scholl, P., Woods, N., Fenselau, C., and Demirev, P., Model-based methods for microorganism identification and protein identification, in 13th Sanibel Conference on Mass Spectrometry. 2001. Sanibel Island, FL.
  19. Demirev, P.A., Lin, J.S., Pineda, F.J., and Fenselaut, C., Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori. Anal Chem, 2001. 73(19): p. 4566-73.
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  20. Pineda, F.J., Lin, J.S., Fenselau, C., and Demirev, P.A., Testing the significance of microorganism identification by mass spectrometry and proteome database search. Anal Chem, 2000. 72(16): p. 3739-44.
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  21. Resch, C.L., Pineda, F.J., and Wang, I.-J., Automatic Recognition and Assignment of Missile Pieces in Clutter, in IJCNN ’99. International Joint Conference on Neural Networks. 1999. Washington, DC.
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  22. Hayek, C.S., Pineda, F.J., Doss, O.W., and Lin, J.S., Computer-Assisted Interpretation of Mass Spectra. Johns Hopkins APL Technical Digest, 1999. 20(3): p. 7-15.
  23. Pineda, F.J., Cauwenberghs, G., Edwards, T., Ryals, K., and Steigerwald, D., Bang, Click, Thud, or Whack?. Johns Hopkins University APL Technical Digest, 1997. 18.
  24. Pineda, F.J., Mean-Field Theory for Batched TD(λ). Neural Computation, 1997. 9(7): p. 1403-1419.
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  25. Edwards, R.T., Cauwenberghs, G., and Pineda, F.J., A Mixed-Signal Correlator for Acoustic Transient Classification, in IEEE International Symposium on Circuits and Systems 1997. 1997.
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  26. Pineda, F.J., Edwards, T., and Cauwenberghs, G., Bangs, Clicks, Snaps, Thuds and Whacks: an Architecture for Acoustic Transient Processing, in Neural Information Processing Systems 1996. 1996. Cambridge MA: MIT Press.
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  27. Pineda, F.J. and Sommerer, J.C., A Fast Algorithm for Estimating Generalized Dimensions and Choosing Time Delays, in Time series Prediction: Forecasting the Future and Understanding the Past, NATO Advanced Research Workshop on Comparative Time Series Analysis. 1994. Santa Fe, New Mexico: Addison-Wesley.
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  28. Pineda, F.J. and Andreou, A.G., An Analog Neural Network Inspired by Fractal Block Coding, in Neural Information Processing Systems 1994. 1994. Denver, CO: MIT Press.
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  29. Baldi, P. and Pineda, F., Contrastive Learning and Neural Oscillations. Neural Computation, 1991. 3(4): p. 526-545.
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  30. Pineda, F.J., Time-Dependent Adaptive Neural Networks, in Neural Information Processing Systems 1989. 1990. Denver, CO: Morgan-Kaufman.
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  31. Pineda, F.J., Recurrent Backpropagation and the Dynamical Approach to Adaptive Neural Computation. Neural Computation, 1989. 1(2): p. 161-172.
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  32. Pineda, F.J., Generalization of Back-propagation to Recurrent and higher order Neural Networks, in IEEE Conference on Neural Information Processing Systems 1987. Denver, CO: American Institute of Physics.
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  33. Pineda, F.J., Generalization of back-propagation to recurrent neural networks. Physical Review Letters, 1987. 59(19): p. 2229-2232.
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  34. Pineda, F.J. and Gross, D.H.E., On the tunneling through a time dependent barrier. Zeitschrift für Physik A Hadrons and Nuclei, 1983. 312: p. 73-80.
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  35. Pineda, F.J., Delvaille, J.P., Schnopper, H.W., and Grindlay, J.E., X-ray and optical observations of MCG-6-30-15. Astrophysical Journal, 1980. 237: p. 414-417.
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  36. Harris, D.E., Pineda, F.J., Delvaille, J.P., Schnopper, H.W., Costain, C.H., and Strom, R.G., Radio and X-ray observations of Abell 754. Astronomy and Astrophysics, 1980. 90: p. 283-289.
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SELECTED CONFERENCES

  1. Pineda, F.J. and Wu, G., Improving SVR predition of RNA minimum free-energy z-score (Poster H06). in Intelligent Systems for Molecular Biology. 2008 of Conference. Toronto, CA.
  2. Pineda, F.J., Wu, G., Maciel, J.E., and Kumar, N., Detecting and validating novel non-coding RNA candidates in Plasmodium falciparum. in Molecular Parasiteology Meeting XVIII. 2007 of Conference. Woods Hole, MA.
  3. Wang, I.J., Diehl, C.D., and Pineda, F.J., A Statistical Model of Proteolytic DIgestions. in 38th Annual Conference on Information Sciences and Systems. 2004 of Conference. Princeton, NJ.
  4. Kafsack, B., Pineda, F.J., and Carruthers, V.B., Use of Kinetic Modeling to Analyze Host Cell Invasion by Toxoplasma gondii. in The American Society for Cell Biology 43rd Annual Meeting. 2003 of Conference. San Francisco, CA.
  5. Pineda, F.J., Lin, J., Demirev, P., and Fenselau, C., Factors Affecting Microorganism Identification by Mass-based Searching of Proteome Databases. in 48th Annual ASMS Conference. 2000 of Conference. Long Beach, CA.
  6. Fenselau, B., Demirev, Carson, Wagner, Lin and Pineda, Proteomics and biocapture surfaces for mass spectrometric analysis of microorganisms. in 15th Intl. Mass Spectrometry Conf. 2000 of Conference. Paris, France.
  7. Pineda, F.J. and Wang, I.-J., Perturbative field theory for sigmoid belief networks. in Snowbird Learning Workshop. 1999 of Conference. Snowbird, UT.