Recent Publications in the College of Science

Publications 2019

Department of Biological Sciences

  • S. Lambrecht: Cheptou P-O and SC Lambrecht (forthcoming 2019) Sidewalk plants as a model for studying plant adaptation to urban fragmentation. Book chapter in Urban Evolutionary Biology. Oxford University Press
  • B.K. Grillo-Hill and K.A. White. “Oncogenic Beta-catenin mutations evade pH-regulated degradation.” 2019. Molecular and Cellular Oncology 11(6):1-3.
  • K.A. White, B. K. Grillo-Hill, M. Esquivel2, J. Peralta3, V.N. Bui3, I. Chire3, D. L. Barber1. “β-catenin is a pH sensor with decreased stability at higher intracellular pH”. 2018. Journal of Cell Biology 217(11):3965-3976.
  • Castillo Vardaro, J.A., Epps CW*, Frable BW, and Ray C*. 2018. Identification of a contact zone and hybridization for two subspecies of the American pika (Ochotona princeps) within a single protected area. PLOS ONE 13(7): e0199032. Rodhouse, T.J., M.R. Jeffress, K.R. Sherrill, S.R. Mohren, N.J. Nordensten, M.L. Magnuson, D. Schwalm*, J.A. Castillo, M. Shinderman, and C.W. Epps*. 2018. Geographical variation in the influence of habitat and climate on site occupancy turnover in American pika (Ochotona princeps). Diversity and Distributions. DOI: 10.1111/ddi.12791 *indicates faculty members at other institutions.
  • Ali HR, Assiri MA, Harris PS, Michel CR, Yun Y, Marentette JO, Huynh FK, Orlicky DJ, Shearn CT, Saba LM, Reisdorph R, Reisdorph N, Hirschey MD, and Fritz KS (2019) Quantifying competition among mitochondrial protein acylation events induced by ethanol metabolism. Journal of Proteome Research, Epub January 2019.

Department of Chemistry

  • Herrington, D.;Sweeder, R.;Daubenmire, P.; Bauer, C.; Bretz, S.; Bunce, D.; Carmel, J.; Cole, R.; DeKorver, B.; Kelly, R.; Lewis, S.; Hoyo, M.; Ryan, S.; Stains, M.; Towns, M.; Yezierski, E. (2019). Supporting the growth and impact of the chemistry-education-research community. Journal of Chemical Education. DOI: 10.1021/acs.jchemed.8b00823..
  • Jun Isoe+, Lauren E. Koch, Yurika E. Isoe, Alberto A. Rascón Jr., Heidi E. Brown, Brooke B. Massani, Roger L. Miesfeld#. (2019) Identification and characterization of a mosquito-specific eggshell organizing factor in Aedes aegypti mosquitoes. PLoS Biology 17(1): e3000068. +Lead Research Scientist. #Chair, Chemistry Department, University of Arizona..

Department of Computer Science

  • Feature analysis of encrypted malicious traffic, with A. S. Shekhawat (grad student) and F. Di Troia, Expert Systems with Applications, 125:130–141, July 2019.
  • An analysis of Android adware, with S. Suresh (grad student), F. Di Troia, and K. Potika (SJSU CS faculty), to appear in Journal of Computer Virology and Hacking Techniques.
  • Hidden Markov models with random restarts vs boosting for malware detection, with A. Raghavan (grad student) and F. Di Troia, to appear in Journal of Computer Virology and Hacking Techniques.
  • R. Raju*, M. Moh, and T.-S. Moh#, Compression of Wearable and Implantable Body Sensor Network (WIBN) Data, chapter in Smart Data: State-of-the-Art Perspectives in Computing and Applications, 1st ed., edited by K. Li, B. Ei Martino, L. T. Yang, and Q. Zhang, published by Chapman and Hall/CRC, Mar. 2019, pp. 215-242..
  • M. Moh, Online Learning and Heuristic Algorithms for 5G Cloud-RAN Load Balance, chapter in Next-Generation Wireless Networks Meet Advanced Machine Learning Applications, edited by I-S Comsa and R. Trestian, published by IGI Global, Jan. 2019, pp. 199-234.
  • R. Raju* and M. Moh, Using Machine Learning for Protecting the Security and Privacy of Internet-of-Things (IoT) Systems, chapter in Fog and Edge Computing: Principles and Paradigms, edited by R. Buyya and S. N. Srirama, published by Wiley, Jan. 2019, pp. 223-253.

Department of Mathematics

  • A paper "Characterization of an Isosceles Tetrahedron", no co-authors, accepted for publication on February 2019, to be published in Journal For Geometry and Graphics of Vienna University of Technology.
  • Sidney, P., Thompson, C., & Rivera, F. (accepted). Number lines, not area models, support children’s accuracy and conceptual models of fraction division. Contemporary Educational Psychology. (Impact factor of 3.356)
  • Unicyclic graphs with second largest and second smallest permanental sums (with Tinzeng Wu), Applied Mathematics and Computation 351 (2019) 168--175..
  • P. Koev. Accurate eigenvalues and exact zero Jordan blocks of totally nonnegative matrices. Numerische Mathematik, 141: pp 693-713, 2019.
  • Matthew D. Johnston and Evan Burton***. Computing weakly reversible deficiency zero network translations using elementary flux modes. Accepted in Bull. Math. Biol., 2019.
  • Matthew D. Johnston, Stefan Muller, and Casian Pantea. A deficiency-based approach to parametrizing positive equilibria of biochemical reaction systems. Bull. Math. Biol. 81(4):1143-1172, 2019.
  • Georgy Szlobodnyik, Gabor Szederkény, Matthew D. Johnston, Reachability analysis of subconservative discrete chemical reaction networks, MATCH Commun. Math. Comput. Chem., 81(3), pp. 705-736., 2019.
  • Jordan Schettler, Wendy Carlos's Xenharmonic Keyboard, Mathematics Magazine, 2019.
  • C. Tortora, B. C. Franczak (Faculty), R. P. Browne (Faculty), and P. D. McNicholas (Faculty). A Mixture of Coalesced Generalized Hyperbolic Distributions Journal of Classification 2019.
  • C. Rainey, (Master student at SJSU), Tortora and F.Palumbo (Faculty). A parametric version of probabilistic distance clustering. In Studies in Classification, Data Analysis, and Knowledge Organization.
  • F. Liu (Master student at SJSU) , S. Gupta (Master student at SJSU), and C.Tortora Cluster Correspondence Analysis and Reduced K-means; a two-step approach to Cluster Low Back Pain Patients, 2019, The Archives of Data Science series B. Accept.
  • L. Phan (Master student at SJSU), H. Liu (Master student at SJSU), and C.Tortora K-means clustering on Multiple Correspondence Analysis coordinates, 2019, The Archives of Data Science series B, 1(1).
  • J. Fitch (Master student at SJSU), N. Khan (Master student at SJSU), and C.Tortora Medical Back Pain: A Spectral Clustering Approach, 2019, The Archives of Data Science series B.
  • R. Fraser, K. Hambrook, Explicit Salem sets, Fourier restriction, and metric Diophantine approximation in the p-adic numbers, Proceedings of the Royal Society of Edinburgh, Section A: Mathematics, (2019).
  • K. Hambrook, Explicit Salem sets and applications to metrical Diophantine approximation, Transactions of the American Mathematical Society, 371 (2019), no. 6, 4353-4376..
  • Maciejewski, W., and Star, J. (2019). Justifications for Choices Made in Procedures. Educational Studies in Mathematics, DOI: 10.1007/s10649-019-09886-7.
  • Maciejewski, W. (2019). Future-oriented Thinking and Activity in Mathematical Problem Solving. In (Liljedahl, P. & Santos-Trigo, M., Eds.) Mathematical Problem Solving: Current Themes, Trends, and Research. Springer..
  • Author: Yan X Zhang Paper Title: A unified enumeration of 1-dimension Garden Algebras and Valise Adinkras Journal Name: Annales de L'Institut Henri Poincare D.

Department of Meteorology and Climate Science

  • D’Alessandro, J., M. Diao, C. Wu,, X. Liu, B. Stephens, and J.B. Jensen, “Cloud phase and relative humidity distribution over the Southern Ocean based on in-situ observations and global climate model simulations”, Journal of Climate, doi:10.1175/JCLI-D-18-0232.1, 2019
  • Camacho, C.P., C.B. Clements, N.P. Lareau, 2019: Mobile Doppler Lidar Observations of the Convective Boundary Layer, Atmosphere
  • Clements, C. B., A. K. Kochanski, D. Seto*, B. Davis*, C. Camacho*, N. P. Lareau, J. Contezac, W. E. Heilman, S K. Krueger, B. Butler, J. Restaino, R. D. Ottmar, R. Vihnanek, J. Flynn, Jean-Baptiste Filippi, T. Barboni, D. E. Hall*, J. Mandel, M. A. Jenkins, and J. O’Brien, B. Hornsby, and C. Teske: The FireFlux II Experiment (FF2): A model-guided field experiment to understand fire-atmosphere interactions and fire spread. International Journal of Wildland Fire
  • Prichard SJ, Larkin NK, Ottmar RD, French NHF, Brown T, Baker K, Clements CB, Dickinson M, Hudak A, Kochanski A, Linn R, Liu Y, Potter B, Mell WE, Tanzer D, Urbanski S, Watts A, 2019: The Fire and Smoke Model Evaluation Experiment – a plan for integrated, large fire-atmosphere field campaigns. Atmosphere. 10(2), 66.
  • Walsh, E.M. (leader) & Cordero, E. (faculty member) (2019 -- currently online; will be in 29:1) Climate action filmmaking to support youth science expertise and environmental identities. Environmental Education Research. doi: 10.1080/13504622.2019.1569206
  • Walsh, E. and E. Cordero, 2019: Youth science expertise, environmental identity, engagement, and agency in climate action filmmaking, Environmental Education Research. Accepted for publication. (E. Walsh - SJSU Faculty).
  • Behringer, D. and S. Chiao, 2019: Numerical Investigations of Atmospheric Rivers and the Rain Shadow over the Santa Clara Valley, Atmosphere, 10, 114,

Department of Physics and Astronomy

  • Ken Wharton, "Fundamental is Non-Random": chapter in book "What is Fundamental?", A. Aguirre, B. Foster, Z. Merali (Eds.); Springer (2019).
  • Harrer, B. W., Paul, C. A., (forthcoming). “Modeling Energy Dynamics with the Energy-Interaction Diagram”. Accepted in November 2018 for The Physics Teacher (to be published in Fall 2019).
  • Harrer, B. W. (forthcoming). “Energy-Interaction Diagrams: Fostering Resources for Productive Disciplinary Engagement with Energy”. Accepted (pending final editorial treatment) in March 2019 for the American Journal of Physics (to be published in AJP Special Issue on "Novel Research in Energy Topics and Transformative Methods for Teaching Energy" in June 2019).
  • "Fluctuating Hydrodynamics and Debye-Hückel-Onsager Theory for Electrolytes", A. Donev, A. L. Garcia, J.-P. Péraud, A. J. Nonaka, and J. B. Bell, Current Opinion in Electrochemistry, Vol. 13 1 (2019).
  • "Fluctuating hydrodynamics of electrolytes at electroneutral scales", A. Donev, A. J. Nonaka, C. Kim, A. L. Garcia, and J. B. Bell, accepted and to appear in Physical Review Fluids, (2019).
  • "On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration", D. Ladiges, A. Nonaka, J.B. Bell, and A.L. Garcia, invited paper; submitted to Physics of Fluids (2019).
  • Madsen, A., Mckagan, S. B., Sayre, E. C., & Paul, C. A. (2018). Resource Letter RBAI-2: Research-based assessment instruments: Beyond physics topics. ArXiv, 1–62. (Accepted Spring 2019, American Journal of Physics).
  • Webb, D., Paul, C. A., Chessey, M.K., Relative impacts of different grade-scales on student success in introductory physics (Submitted to Physical Review – Physics Education Research Spring 2019).
  • Damineli, A.; Fernandez-Lajus, E.; Almeida, L.A.; Corcoran, M.F.; Damineli, D.S.C.; Gull, T.R., Hamaguchi, K.; Hillier, D.J.; Jablonski, F.J.; Madura, T.I.; Moffat, A.F.J.; Navarete, F.; Richardson, N.D.; Ruiz, G.F.; Salerno, N.E.; Scalia, M.C.; Weigelt, G. “Distinguishing Circumstellar from Stellar Photometric Variability in Eta Carinae,” Monthly Notices of the Royal Astronomical Society, 2019, Volume 484, Issue 1, p. 1325 – 1346.

Moss Landing Marine Labs

  • Hooper, A.W.^, R.W. Burger, L. S. Rubin^, B.I. McDonald*, and D.E. Crocker*. Maternal age influences offspring behavior and growth efficiency during provisioning in northern elephant seals (Mirounga angustirostris). Animal Behavior.
  • Ropert-Coubert, Y., A. Van de Putte, R. Reisinger, H. Bornemann, J-B. Charrassin, D. Costa, …B.I. McDonald, …, M. Hindell (80 authors). The Retrospective Analysis of Antarctic Tracking Data Project. Scientific Data.
  • Connolly, T. P. and A. R. Kirincich. High-resolution observations of subsurface fronts and alongshore bottom temperature variability over the inner shelf, Journal of Geophysical Research: Oceans. 2019. 124, 593–614.
  • Aiello, I.W, Beaufort, L., Goldhammer, T., Heuer, V., Hinrichs, K-U and Zabel, M., 2019. Anatomy of a ‘suspended’ seafloor over a mud volcano in the hypersaline Urania Basin. In: Revisiting the Eastern Mediterranean: Recent knowledge on the physical, biogeochemical and ecosystem states and trends “: Deep-Sea Research II (accepted for publication). Kender, S., Ravelo, A.C., Worne, S., Swann, G.E., Leng, M.J., Asahi, H., Becker, J., Detlef, H., Aiello, I.W., Andreasen, D. and Hall, I.R., 2018. Closure of the Bering Strait caused Mid-Pleistocene Transition cooling. Nature communications, 9..