Some recent papers (updated  Jan 2014.)

complete list :

Condensed Matter, Ab-initio Quantum Molec Dynamics for cracks, dislocations, kinks.
We predict the mechanical properties (fracture toughness, ductility) of perfect crystals using atomistic quantum mechanical calculations. 
25. "Electronic structure of the unreconstructed 30 partial dislocation in silicon", J. Northrup, M.L. Cohen, J. Chelikowsky, J. Spence and A. Olsen, Phys. Rev. B24, 4623-4628 (1981).
201 "Atomistics and mechanical properties of silicon". J.C.Spence. Acta Mat et Met. (1999). 47, p. 4153.
81. "A Kink Mechanism for Formation of the Si(111)-(2x1) Reconstructed Surface", J. Spence. Phys. Rev. B38, p. 12672-12674 (1988) 
105. "The influence of internal surfaces on the (2x1) shuffle and glide cleavage reconstructions"  Y.M.Huang, J.C.H.Spence, O. Sankey, and G. Adams. Surface Science  (1991) 256, p.344.
146. "Dislocation kink motion in silicon". Y. M. Huang, J.C.H.Spence and O. Sankey. Phys. Rev. Letts. 74, p. 3392 (1995) . 
120.  "Lattice trapping and surface reconstruction for silicon cleavage on (111). Ab- initio quantum molecular dynamics calculations". J. Spence, Y. Huang and O.Sankey. Acta Met. 41, p. 2815 (1993). 
46. "High energy transmission electron diffraction and imaging studies of the silicon surface", J.C.H.Spence, Ultramic., 11, 117 (1983).
139  "The effect of impurities on the ideal tensile strength of silicon" Y. Huang, J. Spence and O. F Sankey, Phil Mag. 1994. 70, p.53. 
120. "Lattice trapping, reconstruction for silicon cleavage on (111).Ab- initio quantum molecular dynamics calculations". J. Spence, Y. Huang  & O.Sankey. Acta Met. 41, 2815 (1993)

Biophysics _Protein structure and dynamics by femtosecond X-ray diffraction from a liquid  jet of hydrated molecules (at the LCLS XFEL).  Jet development.
We form molecular movies (eg of photosynthesis with P. Fromme) by optical  excitation followed by snapshot hard X-ray laser diffraction, outruning damage at room temperature.
439  ""X-ray lasers for structural and dynamic biology". A review. J.C.H.Spence, U. Weierstall and H.N.Chapman. Rep. Prog. Phys. 75,  102601 (2012) .
303  "Single Molecule Diffraction". J.C.H.Spence and B.Doak. Physical Review Letters. 92, 198102
327   "Diffraction and imaging from a beam of laser-aligned proteins". J.C.H.Spence et al.  Acta Cryst A61, p.237. (2005) see also  J. Chem Phys. 123, 244304 (2005).
372 "Gas dynamic virtual nozzle for generation of microscopic droplet beams". D. De Ponte et al. J. Phys. D. Appl Phys. 41, 195505 (2008)
401 "Femtosecond protein nanocrystallography - data analysis methods". R. Kirian et al  Optics Express  18, p.5713 (2010).
408 "Femtosecond protein nanocrystallography".  H. Chapman, P. Fromme...... J.C.H.Spence. Nature 470, p73-77  (2011).
409  "Single mimivirus particles imaged on-the-fly with an X-ray laser" M. Seibert....J. Hajdu. Nature 470, p. 78 (2011)
412  "Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals". J.C.H.Spence et al  Optics Express 19, 2866-2873 (2010)
425  "Signal , noise and resolution  in correlated flucuations from snapshot SAXS" R.Kirian et al. Phys Rev E 84, 011921 (2011).
436  "Time-resolved protein nanocrystallography using an X-ray free-electron laser" A. Aquilla.....J. Spence Optics Express 20, 2706 (2012).
444  "Trypanosoma brucei procathepsin B structure solved to 2.1 A using an X-ray laser".  L. Redecke et al  Science 339, 227 (2013).
Papers in special issue of Phil Trans Roy Soc. from 2013 conference on X-ray lasers for structural biology.

Ordering in Glasses.
" The most important unsolved problem in Condensed Matter Physics" (P. Anderson).
261 "Long range structural fluctuations in a CaO-Al2O3-2SiO2 glass by spatially resolved near-edge spectroscopy. N. Jiang, J. Qiu and J.C.H.Spence. Phys Rev B66, p.054203 (2002).

Organic materials,  Cryo-electronmicroscopy.
288 Three-dimensional diffractive imaging for crystalline monolayers with 1D compact support. J.Spence, U. Weierstall, K. Downing and R. M. Glaeser. J. Struct. Biol. 144, 209. 2003.
262   Kinematic and dynamical CBED for solving thin organic films at low temperature; experimental tests with anthracene. J.S. Wu and J.C.H. Spence. Acta Cryst A58, p.580. (2002)
399  "Design of an electron microscope phase plate using a focussed continuous-wave laser". H. Muller et al. New J Phys. 12, 073011 (2010).

Bonding in solids. Electron Microdiffraction. 
We develop new methods for imaging the chemical bonds which glue atoms together in solids, and test many-electron theoretical approximations for bonding.
177."Charge density of MgO: Implications of precise new measurements for theory". J.M.Zuo, M. O'Keeffe, P. Rez, J. Spence. Phys Rev Letts.  78, p. 4777-4780. (1998)
174 "Direct inversion of dynamical electron diffraction patterns to structure factors".  J. Spence. Acta Cryst. A. 1998. A54  p. 7 - 18.
153 "Effect of Mn doping on chanrge density in g-TiAl by quantitative CBED" R. Holmestad, J. Zuo, J. Spence R Hoier and Z. Horita. Philos. Mag. (1995) 72, p. 579 
28 "A simple method for determining structure factor phases  and crystal polarity using electron diffraction", J. Tafto/ and J. Spence, J. Appl.  Cryst., 15, 60-64 (1982), 
82. "Bonding in GaAs", J.M. Zuo, J. Spence and M. O'Keefe. Phys. Rev.  Letts Vol. 61, p353 (1988) 
90. "Accurate structure-factor phase determination by electron diffraction in acentric crystals", J.M. Zuo, J. Spence and R. Hoier.  Phys.  Rev.  Letts. (1989) 62 p. 547.
103  "Charge ordering in magnetite at low temperatures". J.M.Zuo, J.C.H. Spence and  W.Petusky. Phys. Rev. B.42,  p.8451  (1990). 
218  "On the measurement of dislocation core periods by nanodiffraction". J.C.H.Spence and C. Koch. Phil Mag. B.81, 11,pp.1701-1711(2001). (Bourret Festschrift).
104. Bonding in copper oxide - direct observation of chemical bonds."Direct Observation of d holes and Cu-Cu bonding in Cu2O". J. Zuo, Y.Kim, M. O'Keeffe, J. Spence. Nature Vol 401, p.49, (1999). 226 "On closed shell interactions, polar covalences, d shell holes, and direct images of orbitals: the case of cuprite". J.Zuo, M.O’Keeffe, M.Kim, J.Spence. Angew Chem Int Ed 2000, 39, p. 3791. See For images, click below. Nature99CopperOxideBonds

Solving crystal structures by electron microdiffraction.
The focussed electron beam for microdiffration has diameter less than 1 nm.
387 "The kinematic convergent beam method for solving nanocrystal structures". J. McKeown and J.C.H.Spence. J. Appl Phys. 106, 074309  (2009)

Coherent Bremsstrahlung 
Charged particles buzzing through crystals generate tunable coherent X-ray with the buzz frequency.
68. "Pendellosung Radiation and Coherent Bremsstrahlung", J.C.H. Spence and G.  Reese, Acta Cryst. (P. Ewald Festschrift) 1986 Acta Cryst. A42, p. 577-585, NSF

Electron energy -loss spectroscopy.
Provides similar information to soft-Xray absorption spectra, but with nanometer spatial resolution.
2. "Observation of double plasmon excitation in aluminium", J.C.H. Spence and A.E.C. Spargo, Phys. Rev. Letters 26, 985 (1971). 
70. "The electron energy loss near edge structure of Be2C", M.M. Disko, J.C.H. Spence, O.F. Sankey and D. Saldin. Phys. Rev. B. (1986) B33, p. 5642-51, ARO 83. 
33. "STEM Microanalysis by Transmission Electron Energy Loss Spectroscopy in Crystals", J.C.H. Spence and J. Lynch, Ultramicroscopy, 9, 267 (1982), ARO. 
60. "Determination of the single-scattering energy-loss distibution from multiple-loss data". D.W.Johnson and J.C.H. Spence J. Phys D 7, 771 (1974).

Channeling effects on secondary processes, internal source holography 
Electron standing waves in crystals can be used to locate foreign dopant atoms.
47. "ALCHEMI - a new technique for locating atoms in small crystals", J.C.H Spence and J. Tafto, J. Micros, 130, 147 (1983), NSF 80. 
79. "Adatom site determination using channelling effects in RHEED on X-ray and Auger electron production", J.C.H. Spence and Y. Kim (1988).  in "Reflection High Energy Electron Diffraction and Reflection Electron Imaging of Surfaces"  Eds. P.K. Larsen and P.J. Dobson, p. 117-128 Plenum1988 NSF 85. 
"Atomic String Holography". J. Spence and C. Koch. Phys. Rev. Letts. 86, p. 5510 (2001).

In-situ observation of STM operation in a TEM 
Manipulate atoms by STM and watch simultaneously by TEM
124  Investigation of STM image artifacts by in-situ reflection electron microscopy. W. Lo and J. Spence. Ultramic. (1992). 48, p.433.

Atomic-scale imaging of defects, ordering. High Tc, Dislocation kink dynamics. 
The atomic structure of defects controls many materials properties.
17. "Distinguishing dissociated Shuffle and Glide set dislocations by high resolution electron microscopy", A. Olsen and J.C.H. Spence, Phil. Mag. A43, 945-965 (1980) 
154 "Observation of moving dislocation kinks and pinning". H. Kolar, J. Spence and H. Alexander. Phys. Rev. Letts. 77, p. 4031-4034 (1996) .  KinkImages 
74. "Microstructure, Oxygen Ordering and planar defects in in high Tc superconductor Ba2YCu3O6.9", A. Ourmazd, J.C. Spence, M. et al  Nature (1987) 327, p. 308, NSF 85. 
9. "Lattice imaging in STEM", J.C.H. Spence ,J.M. Cowley, Optik, 50, 129 (1978). 
170 "The enhancement of electron microscope resolution by use of atomic focusers". J. M. Cowley, J. Spence and V.V. Smirnov. Ultramic. 68, p. 135 (1997).  
200. Electron nanodiffraction for dislocation kinks and core reconstruction". C. Koch, J.Spence et al.. J. Phys (Cond. Matter) 12, p. 1-9 (2000).
281 "Oxygen in crystals - seeing is believing". Science. 299, p. 839 (2003) "Perspective".

Field emission nanotips, electron antibunching, low energy electron holography in biology, photofield emission. 
131 "Brightness measurement of nanometer sized field emission electron sources". W. Qian, M. Scheinfein and J. Spence. J. Appl. Phys. 73, 7041 (1993).
138 "Electron source information from Fresnel fringes in field emission point projection electron microscopy" J. Spence= et al.. J. Vac Sci. A12. p.542 (1994)
122 Aberrations of emission cathodes: Nanometer diameter field emission electron sources. M. Scheinfein, W, Qian and J, Spence. J. Appl. Phys. 73 (1993) p.2057
187  "Imaging of Tobacco Mosaic Virus at 40 volts by electron holography". U. Weierstall and J. Spence. Micron 30, p.335  (1999). ARO. 
232 "Electron Holography of field-emitting carbon nanotubes". Cumings, Zettl, McCartney, Spence. Phys Rev Letts. 88, p.056804 (2002)
266  "Spaced out electrons". Electron antibunching. News and Views. Nature 418, p. 377 2002. J.C.H. Spence.
396 "A coherent photofield electron source for fast diffractive and point-projection imaging". J.C.H. Spence, T. Vecchione and U. Weierstall. Phil Mag. Accepted (2010)

New electron detectors.
This facilitated the development of tomography in cryo-electron micoscopy, previously requiring multiple recordings on film.
86. "A large dynamic range parallel detection CCD system for electron diffraction and  imaging", J.C.H. Spence and J.M. Zuo, J. Sci. Instr. 59(9), p. 2102-2105 (1988) 

Cathodolluminescence in STEM 
Atomic-level spatial resolution with the energy resolution of optical spectroscopy.
54. "Cathodoluminescence and polarization studies of dislocations in diamond", N. Yamamoto, J.C.H. Spence and D. Fathy, Phil. Mag B49, p. 609-629 (1984).

Electron holography. Ferroelectrics 
Electron holography allows one to map out electric and magnetic fields in solids.
160 "Theory and principles of electron holography"  J. Cowley, J. Spence. in : Intro to electron holography. Eds Allard et al.  Plenum (NY) 1996 
129  "Electron holographic study of ferroelectric domain walls" J.C.H.Spence, J.M. Cowley and J.M. Zuo. Appl. Phys. Letts. 62, p. 2446 (1993) 
232 "Electron holography of field-emitting carbon nanotubes". Cummings, Zettl, McCartney, Spence. Phys. Rev. Letts. 88, p.056804 (2002).

The Scanning Tunnelling Atom Probe. 
Our machine combines an STM with a time-of-flight atom probe.
189 "Atomic species identification  in STM using an imaging atom-probe technique". U. Weierstall and J. Spence. Surf Sci. 398 p. 267-279. 

Inversion problem of multiple electron or X-ray scattering.
Direct, non-iterative methods for recovering potentials from multiple-scattering data.
174. "Direct inversion of dynamical electron diffraction patterns to structure factors". J. Spence. Acta Cryst. A. 1998. A54 p. 7 - 18.
3. "Determination of single-scattering distribution from multiple scattering data in ELS", D Johnson, and J. Spence, J.Phys. D.7, 771 (1974).
256 "A useful disentanglement of the exponential of the sum of two non-commuting matrices, one of which is diagonal". C. T. Koch and J.C.H.Spence. J. Phys A36, 803 .2003. 
382 "Two-wavelength inversion of multiply-scattered soft X-ray intensities to charge density". J.C.H.Spence. Acta Cryst A65. p.28-38 (2009)

X-ray holography, diffraction-imaging, lensless imaging and powder diffraction by iterative phasing.
Images can now be reconstructed from far-field scattering from non-periodic objects. Applications to femtosecond X-ray diffraction from proteins or single particles.
241  "Workshop on "New approaches to the Phase Problem for non-periodic objects" John C.H.Spence, M. Howells, L.D.Marks and J. Miao. Ultramic. 90, p.1-6 (2001).
237. "Holography of atoms". J.C.H.Spence. Nature. 410, p.1037. (2001).
249  "Phase recovery and lensless imaging by iterative methods in optical and electron diffraction". J..Spence, U. Weierstall ,M. Howells. Phil. Trans. 360, p.875 (2002).
289  " X-ray image reconstruction from a diffraction pattern alone. S. Marchesini,  J.C.H. Spence et al... Phys Rev  B68, 140101(R)
343 "Ab initio phasing of X-ray powder diffraction patterns by charge flipping". J.S.Wu, J.C.H.Spence, M. O'Keeffe, K. Leinenweber.  Nature Materials. 5, 647 2006. 
367  "Dose, exposure time and resolution in serial crystallography". D. Starodub, J. Spence et al.  J. Synch Res. 15,  62-73 (2008)
388  "Triple-beam tomographic femtosecond X-ray diffractive imaging". K. Schmidt, J. Spence et al. .J. Phys Rev Letts. 101, 115507  (2008)
386   "Powder diffraction from a continuous microjet of nanoscale protein crystals". D.A. Shapiro...... J.C.H.Spence.  J. Synch. Rad.  15, 593-599 (2008). (2008).
377  "Ultrafast, ultrabright, X-ray holography using a uniformly redundant array". S.Marchesini J.C. H. Spence et al. (2008) Nature Photonics 2, 560 - 563 (2008).