Publications - 2012

2012

1. Dazard J-E., RAO J.S. MARKOWITZ S. Local Sparse Bump Hunting Reveals Molecular Heterogeneity of Colon Tumors. Statistics in Medicine (2012) 31(11-12), 1203-1220. PMCID: PMC3668571.

2. Dazard J-E., Rao J.S. Joint Adaptive Mean-Variance Regularization and Variance Stabilization of High Dimensional Data. Comput. Statist. Data Anal. (2012) 56(7): 2317-2333. PMCID: PMC3375876.

3. Erten S, Chowdhury SA, Guan X, Nibbe RK, Barnholtz-Sloan JS, Chance MR, Koyutürk M. Identifying stage-specific protein subnetworks for colorectal cancer. BMC Proc. 2012 Nov 13;6 Suppl 7:S1. doi: 10.1186/1753-6561-6-S7-S1. Epub 2012 Nov 13. PubMed PMID: 23173715; PubMed Central PMCID: PMC3504924.

4. Sun X, Vengoechea J, Elston R, Chen Y, Amos CI, Armstrong G, Bernstein JL, Claus E, Davis F, Houlston RS, Il'yasova D, Jenkins RB, Johansen C, Lai R, Lau CC, Liu Y, McCarthy BJ, Olson SH, Sadetzki S, Schildkraut J, Shete S, Yu R, Vick NA, Merrell R, Wrensch M, Yang P, Melin B, Bondy ML, Barnholtz-Sloan JS; Gliogene Consortium. A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma. Cancer Epidemiol Biomarkers Prev. 2012 Dec;21(12):2242-51. doi: 10.1158/1055-9965.EPI-12-0703. Epub 2012 Sep 7. PubMed PMID: 22962404; PubMed Central PMCID: PMC3518573.

5. Guan X, Chance MR, Barnholtz-Sloan JS. Splitting random forest (SRF) for determining compact sets of genes that distinguish between cancer subtypes. J Clin Bioinforma. 2012 May 22;2(1):13. doi: 10.1186/2043-9113-2-13. PubMed PMID: 22616791; PubMed Central PMCID: PMC3444418.

6. Nickel GC, Barnholtz-Sloan J, Gould MP, McMahon S, Cohen A, Adams MD, Guda K, Cohen M, Sloan AE, LaFramboise T. Characterizing mutational heterogeneity in a glioblastoma patient with double recurrence. PLoS One. 2012;7(4):e35262. doi:10.1371/journal.pone.0035262. Epub 2012 Apr 20. PubMed PMID: 22536362; PubMed Central PMCID: PMC3335059.

7. Leidner RS, Ravi L, Leahy P, Chen Y, Bednarchik B, Streppel M, Canto M, Wang JS, Maitra A, Willis J, Markowitz SD, Barnholtz-Sloan J, Adams MD, Chak A, Guda K. The microRNAs, MiR-31 and MiR-375, as candidate markers in Barrett's esophageal carcinogenesis. Genes Chromosomes Cancer. 2012 May;51(5):473-9. doi: 10.1002/gcc.21934. Epub 2012 Feb 3. PubMed PMID: 22302717; PubMed Central PMCID: PMC3547654.

8. Moinova H, Leidner RS, Ravi L, Lutterbaugh J, Barnholtz-Sloan JS, Chen Y, Chak A, Markowitz SD, Willis JE. Aberrant vimentin methylation is characteristic of upper gastrointestinal pathologies. Cancer Epidemiol Biomarkers Prev. 2012 Apr;21(4):594-600. doi: 10.1158/1055-9965.EPI-11-1060. Epub 2012 Feb 7. PubMed PMID: 22315367; PubMed Central PMCID: PMC3454489.

9. Chak A, Chen Y, Vengoechea J, Canto MI, Elston R, Falk GW, Grady WM, Guda K, Kinnard M, Markowitz S, Mittal S, Prasad G, Shaheen N, Willis JE, Barnholtz-Sloan JS. Variation in age at cancer diagnosis in familial versus nonfamilial Barrett's esophagus. Cancer Epidemiol Biomarkers Prev. 2012 Feb;21(2):376-83. doi: 10.1158/1055-9965.EPI-11-0927. Epub 2011 Dec 16. PubMed PMID: 22178570; PubMed Central PMCID: PMC3275661.

10. Valence band effective-mass Hamiltonians for the group-III nitrides from quasiparticle self-consistent GW band structures, Atchara Punya and Walter R. L. Lambrecht, Phys. Rev. B 85, 195147 (2012) - Published 29 May 2012

11. Jayapandian CP, Chen CH, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS.

12. Electrophysiological Signal Analysis and Visualization using Cloudwave for Epilepsy Clinical Research. Studies in health technology and informatics 192 (2012): 817-821. [PMID: 23920671]

13. Yang, Y. “Two-Center Two-Electron Covalent Bonds with Deficient Bonding Densities” J. Phys. Chem. A 2012, 116, 10150–10159.

14. S. Gajurel and R. Bielefeld, "A Fast Near Optimal Vertex Cover Algorithm (NOVCA)", IJEA, vol. 3, issue 1, 2012. Link to article

15. Haibo Wang, Mirabela Rusu, Thea Golden, Andrew Gow and Anant Madabhushi, Mouse Lung Volume Reconstruction from Efficient Groupwise Registration of Individual Histological Slices with Natural Gradient, SPIE Medical Imaging (oral), 2012.

16. Haleema Asiri and A. B. Anderson,"Cyclic Voltammograms for Hupd on Pt(111) Calculated from Total Gibbs Energies", 222 ECS Fall Meeting, October 7-12, 2012.  Poster presentation by Haleema Asiri.  A conference proceedings abstract was published by the Electrochemical Society.

17. Heckler, J. E.; Zeller, M.; Hunter, A. D.; Gray, T. G. Angewandte Chemie (International ed. in English) 2012, 51, 5924–8.

18. Flatt JW, Fox TL, Makarova N, Blackwell JL, Dmitriev IP, Kashentseva EA, Curiel DT, Stewart PL. (2012) CryoEM visualization of an adenovirus capsid-incorporated HIV antigen. PLoS One, 7(11): e49607. BPoD Biomedical Picture of the Day, bpod.mrc.ac.uk, December 14, 2012.

19. Doronin K*, Flatt JF*, Di Paolo NC*, Khare R, Kalyuzhniy O, Acchione M, Sumida JP, Ohto U, Shimizu T, Akashi-Takamura S, Miyake K, MacDonald JW, Bammler TK, Beyer RP, Farin FM, Stewart PL, Shayakhmetov DM. (2012) Coagulation factor X activates innate immunity to human species C adenovirus. Science, 338:795-798 (*Equal contribution authors)

20. Guo, H.; Zehavi, I.; Zheng, Z., "A New Method to Correct for Fiber Collisions in Galaxy Two-point Statistics", The Astrophysical Journal 2012, 756, 127-139

21. Yang, Y.; Kennedy, V. O.; Updegraph, J. B.; Samas, B.; Macikenas, D.; Chaloux, B.; Miller, J. A.; Van Goethem, E. M.; Kenney, M. E., "Long Directional Interactions (LDIs) in Oligomeric Cofacial Silicon Phthalocyanines and Other Oligomeric and Polymeric Cofacial Phthalocyanines," The Journal of Physical Chemistry A 2012, 116, 8718-8730. Link to article

22. Yang, Y. "Metal–ligand coordination in subphthalocyanines and phthalocyanines: DFT, AIM and ELF analyses," Polyhedron 2012, 33, 310-318. Link to article

23. Yang, Y. "Pyrrolic macrocycles with stabilized triplet states: Metal-centered and ligand-centered separation of unpaired electrons," Polyhedron 2012, 42, 249-257. Link to Article

24. Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S., " How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?," BioData Min. 2012 Jun 18;5(1):6. Link to Article

25. Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J., "Global mutational profiling of formalin-fixed human colon cancers from a pathology archive," Mod Pathol. 2012 Aug 10. doi: 10.1038/modpathol.2012.121. Link to Article

26. Sanjaya Gajurel and Roger Bielefeld, A Simple NOVCA: Near Optimal Vertex Cover Algorithm, ICCS 2012, vol 9, pp. 747-753. Link to article

27. Krishnakumar M. Ravikumar, Wei Huang, and Sichun Yang*, Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective. Biophysical Journal Volume 103 August 2012 837–845. Link to article

28. Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Quasiparticle band structure calculation of monolayer, bilayer, and bulk MoS_{2}. Phys. Rev. B 85, 205302 (2012). Link to article

29. Zuber, M. T., D. E. Smith, R. J. Phillips, S. C. Solomon, G. A. Neumann, S. A. Hauck, II, S. J. Peale, O. S. Barnouin, J. W. Head, C. L. Johnson, F. G. Lemoine, E. Mazarico, X. Sun, M. H. Torrence, A. M. Freed, C. Klimczak, J.-L. Margot, J. Oberst, M. E. Perry, R. L. McNutt, Jr., J. A. Balcerski, N. Michel, M. J., Talpe, D. Yang, Topography of the northern hemisphere of Mercury from MESSENGER laser altimetry, Science, 336, 217-220, doi: 10.1126/science.1218805, 2012. Link to article.

30. Smith, D. E., M. T. Zuber, R. J. Phillips, S. C. Solomon, S. A. Hauck, II, F. G. Lemoine, E. Mazarico, G. A. Neumann, S. J. Peale, J.-L. Margot, C. L. Johnson, M. H. Torrence, M. E. Perry, D. D. Rowlands, S. Goossens, J. W. Head, A. H. Taylor, Gravity field and internal structure of Mercury from MESSENGER, Science, 336, 214-217, 2012. Link to article.

31. Alfred  B. Anderson, “Insights Into Electrocatalysis,” Phys. Chem. Chem. Phys. 2012, 14, 1330-1338. Link to article

32. Alfred B. Anderson, “Volcano Plots and Effective Reversible Potentials for Oxygen Electroreduction,” Electrocatalysis 9 March 2012. Online First, and open access DOI: 10.1007/s12678-012-0088-z.

33. Gao, L.; Tang, S.; Zhu, L.; Sauvé, G. “Synthesis and characterization of azadipyrromethene- alt- p-phenylene ethynylene conjugated polymers and their chelates” Macromolecules 2012, 45, 7404-7412.

34. Fernando, R.; Sauve, G. "Naphthalene Diimide-based Macromolecules for Opto-electronic Applications" International Conference on Science and Technology of Synthetic Metals, Atlanta, GA, United States, July 08-13, 2012; Submitted poster.

35. Fernando, R.; Sauve, G. "Design and Synthesis of Naphthalene Diimide-based Copolymers" 6th Annual Cleveland State Interdisciplinary Research Conference, Cleveland State University, Cleveland, OH, United States, November 3, 2012; Submitted poster. 

36. P. R. H. French, “Immersion Lithography Materials,” in Encyclopedia of Nanotechnology, P. B. Bhushan, Ed. Springer Netherlands, 2012, pp. 1063–1069

37. P. R. H. French, “Immersion Lithography,” in Encyclopedia of Nanotechnology, P. B. Bhushan, Ed. Springer Netherlands, 2012, pp. 1056–1063

38. Yang Hu, J. Karas, Roger H. French, Dave Hollingshead, Scott A Brown, and M. A. Schuetz, “An Introduction to the SunFarm Outdoor Test Facilities at the Solar Durability and Lifetime Extension Center in Case Western Reserve University,” presented at the PV Module Reliability Workshop, NREl, Golden CO, 01-Mar-2012

39. Yang Hu, Donald Huckle, Roger Harquail French, Dave Hollingshead, and Mark Schuetz, “Introduction to the SunFarm Outdoor Test Facilities at the Solar Durability and Lifetime Extension Center in Case Western Reserve University,” presented at the IEEE EnergyTech, Cleveland, OH, 30-May-2012

40. L.S. Bruckman and RH French, “PMMA Acrylic in a Stress-Response Framework for PV Materials,” presented at the CPV-8, Toledo, Spain, 22-Apr-2012.

41. L.S. Bruckman and R. H, French, “Lifetime and Degradation of Acrylic for PV,” presented at the Solar Durability Workshop: Photovoltaics, LEDs, and other Outdoor Exposed Technologies, Cleveland, OH, 09-Apr-2012.

42. L.S. Bruckman, M.P. Murray, Samuel Richardson, S.A. Brown, M. A. Schuetz, and RH FRENCH, “Degradation of Back Surface Mirrors: Implications for Low Concentration and Mirror Augmented Photovoltaics,” presented at the IEEE EnergyTech, Clevel, 30-May-2012

43. Wei-Chun Lin, Dave Hollingshead, Roger H. French, Kara A. Shell, Mark Schuetz, and Joseph Karas, “Non-tracked  mirror-augmented photovoltaic design and performance Proceedings,” in 2012 38th IEEE Photovoltaic Specialists Conference (PVSC), 2012, pp. 002076–002081.

44. Wei-Chun Lin et al., “Mirror-augmented photovoltaic designs and performance,” in 2012 IEEE Energytech, 2012, pp. 1–5

45. Myles P. Murray et al., “Degradation of back surface acrylic mirrors for low concentration and mirror-augmented photovoltaics,” in Proc. of SPIE, 2012, vol. 8472, p. 847205.

46. M. P. Murray, L. S. Bruckman, and R. H. French, “Durability of Materials in a Stress-Response Framework: Acrylic Materials for Photovoltaic Systems,” in MRS Online Proceedings Library, 2012, vol. 1391 

47. M.P. Murray, L.S. Bruckman, and R.H. French, “Durability of acrylic: Stress and response characterization of materials for photovoltaics,” in 2012 IEEE Energytech, 2012, pp. 1–6

48. M. P. Murray, L. S. Bruckman, and R. H. French, “Photodegradation in a stress and response framework: poly(methyl methacrylate) for solar mirrors and lens,” J. Photon. Energy, vol. 2, no. 1, pp. 022004–022004, Nov. 2012

49. Mark A Schuetz, Kara A Shell, Scott A Brown, Gregory S Reinbolt, Roger H French, and Robert J Davis, “Design and construction of a 7X low-concentration photovoltaic system based on compound parabolic concentrators,” Photovoltaics, IEEE Journal of, vol. 2, no. 3, pp. 382–386, 2012